/* FILE: topology_global.h */ /* VERSION: 1.600 */ /* DATE: 2/3/2005 */ /* Comments and Questions to: sw-help@rcsb.rutgers.edu */ /* COPYRIGHT 1999-2005 Rutgers - The State University of New Jersey This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT. The user of this software shall indemnify, hold harmless and defend Rutgers, its governors, trustees, officers, employees, students, agents and the authors against any and all claims, suits, losses, liabilities, damages, costs, fees, and expenses including reasonable attorneys' fees resulting from or arising out of the use of this software. This indemnification shall include, but is not limited to, any and all claims alleging products liability. */ /* PDB SOFTWARE LICENSE AGREEMENT BY CLICKING THE ACCEPTANCE BUTTON OR INSTALLING OR USING THIS "SOFTWARE, THE INDIVIDUAL OR ENTITY LICENSING THE SOFTWARE ("LICENSEE") IS CONSENTING TO BE BOUND BY AND IS BECOMING A PARTY TO THIS AGREEMENT. IF LICENSEE DOES NOT AGREE TO ALL OF THE TERMS OF THIS AGREEMENT THE LICENSEE MUST NOT INSTALL OR USE THE SOFTWARE. 1. LICENSE AGREEMENT This is a license between you ("Licensee") and the Protein Data Bank (PDB) at Rutgers, The State University of New Jersey (hereafter referred to as "RUTGERS"). The software is owned by RUTGERS and protected by copyright laws, and some elements are protected by laws governing trademarks, trade dress and trade secrets, and may be protected by patent laws. 2. LICENSE GRANT RUTGERS grants you, and you hereby accept, non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, and distribute in binary and source code format, or any derivative work thereof, together with any associated media, printed materials, and on-line or electronic documentation (if any) provided by RUTGERS (collectively, the "SOFTWARE"), subject to the following terms and conditions: (i) any distribution of the SOFTWARE shall bind the receiver to the terms and conditions of this Agreement; (ii) any distribution of the SOFTWARE in modified form shall clearly state that the SOFTWARE has been modified from the version originally obtained from RUTGERS. 2. COPYRIGHT; RETENTION OF RIGHTS. The above license grant is conditioned on the following: (i) you must reproduce all copyright notices and other proprietary notices on any copies of the SOFTWARE and you must not remove such notices; (ii) in the event you compile the SOFTWARE, you will include the copyright notice with the binary in such a manner as to allow it to be easily viewable; (iii) if you incorporate the SOFTWARE into other code, you must provide notice that the code contains the SOFTWARE and include a copy of the copyright notices and other proprietary notices. All copies of the SOFTWARE shall be subject to the terms of this Agreement. 3. NO MAINTENANCE OR SUPPORT; TREATMENT OF ENHANCEMENTS RUTGERS is under no obligation whatsoever to: (i) provide maintenance or support for the SOFTWARE; or (ii) to notify you of bug fixes, patches, or upgrades to the features, functionality or performance of the SOFTWARE ("Enhancements") (if any), whether developed by RUTGERS or third parties. If, in its sole discretion, RUTGERS makes an Enhancement available to you and RUTGERS does not separately enter into a written license agreement with you relating to such bug fix, patch or upgrade, then it shall be deemed incorporated into the SOFTWARE and subject to this Agreement. You are under no obligation whatsoever to provide any Enhancements to RUTGERS or the public that you may develop over time; however, if you choose to provide your Enhancements to RUTGERS, or if you choose to otherwise publish or distribute your Enhancements, in source code form without contemporaneously requiring end users or RUTGERS to enter into a separate written license agreement for such Enhancements, then you hereby grant RUTGERS a non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into the SOFTWARE or other computer software, distribute, and sublicense your Enhancements or derivative works thereof, in binary and source code form. 4. FEES. There is no license fee for the SOFTWARE. If Licensee wishes to receive the SOFTWARE on media, there may be a small charge for the media and for shipping and handling. Licensee is responsible for any and all taxes. 5. TERMINATION. Without prejudice to any other rights, Licensor may terminate this Agreement if Licensee breaches any of its terms and conditions. Upon termination, Licensee shall destroy all copies of the SOFTWARE. 6. PROPRIETARY RIGHTS. Title, ownership rights, and intellectual property rights in the Product shall remain with RUTGERS. Licensee acknowledges such ownership and intellectual property rights and will not take any action to jeopardize, limit or interfere in any manner with RUTGERS' ownership of or rights with respect to the SOFTWARE. The SOFTWARE is protected by copyright and other intellectual property laws and by international treaties. Title and related rights in the content accessed through the SOFTWARE is the property of the applicable content owner and is protected by applicable law. The license granted under this Agreement gives Licensee no rights to such content. 7. DISCLAIMER OF WARRANTY. THE SOFTWARE IS PROVIDED FREE OF CHARGE, AND, THEREFORE, ON AN "AS IS" BASIS, WITHOUT WARRANTY OF ANY KIND, INCLUDING WITHOUT LIMITATION THE WARRANTIES THAT IT IS FREE OF DEFECTS, MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR NON-INFRINGING. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS BORNE BY LICENSEE. SHOULD THE SOFTWARE PROVE DEFECTIVE IN ANY RESPECT, THE LICENSEE AND NOT LICENSOR ASSUMES THE ENTIRE COST OF ANY SERVICE AND REPAIR. THIS DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF THIS AGREEMENT. NO USE OF THE PRODUCT IS AUTHORIZED HEREUNDER EXCEPT UNDER THIS DISCLAIMER. 8. LIMITATION OF LIABILITY. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE FOR ANY INDIRECT, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF OR INABILITY TO USE THE SOFTWARE, INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL, WORK STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL OTHER COMMERCIAL DAMAGES OR LOSSES, EVEN IF ADVISED OF THE POSSIBILITY THEREOF. */ #ifndef _TOPOLOGY_GLOBAL_ #define _TOPOLOGY_GLOBAL_ #include "TblIndexObj.h" #define NDB_MAX_PARAM_BONDS 25 #define NDB_MAX_PARAM_ANGLES 37 #define MAX_MONOMER 30 typedef struct { float val, std; const char *type; } _MEAN_STD; typedef struct _param_bond { const char *Rep_Name; const char *type; const char *at1; const char *at2; int num; _MEAN_STD mean_std[4]; } MONOMER_BOND; typedef struct _param_angle { const char *Rep_Name; const char *type; const char *at1; const char *at2; const char *at3; int num; _MEAN_STD mean_std[4]; } MONOMER_ANGLE; typedef struct _param_monomer { const char *name; int nbond,nangle; MONOMER_BOND bond[NDB_MAX_PARAM_BONDS]; MONOMER_ANGLE angle[NDB_MAX_PARAM_ANGLES]; } MONOMER; typedef struct _param_db { char resname[4]; int type; MONOMER *mon; } MONOMER_DB; typedef struct { const char *Rep_Name; const char *type; const char *at1; const char *at2; const char *at3; const char *at4; } MONOMER_TORSION; MONOMER_TORSION ALPHA = { "ALPHA", "O3*-P-O5*-C5*", "O3*", "P", "O5*", "C5*" }; /* MONOMER_TORSION BETA = { "BETA", "P-O5*-C5*-C4*", "P", "O5*", "C5*", "C4*" }; MONOMER_TORSION GAMMA = { "GAMMA", "O5*-C5*-C4*-C3*", "O5*", "C5*", "C4*", "C3*" }; MONOMER_TORSION DELTA = { "DELTA", "C5*-C4*-C3*-O3*", "C5*", "C4*", "C3*", "O3*" }; */ MONOMER_TORSION EPSILON = { "EPSILON", "C4*-C3*-O3*-P", "C4*", "C3*", "O3*", "P" }; MONOMER_TORSION ZETA = { "ZATA", "C3*-O3*-P-O5*", "C3*", "O3*", "P", "O5*" }; /* MONOMER_TORSION CHI[2] = { "CHI", "O4*-C1*-N9-C4", "O4*", "C1*", "N9", "C4", "CHI", "O4*-C1*-N1-C2", "O4*", "C1*", "N1", "C2" }; MONOMER_TORSION CHI1[2] = { "CHI1", "O4*-C1*-N9-C8", "O4*", "C1*", "N9", "C8", "CHI1", "O4*-C1*-N1-C6", "O4*", "C1*", "N1", "C6" }; MONOMER_TORSION NU0 = { "NU0", "C4*-O4*-C1*-C2*", "C4*", "O4*", "C1*", "C2*" }; MONOMER_TORSION NU1 = { "NU1", "O4*-C1*-C2*-C3*", "O4*", "C1*", "C2*", "C3*" }; MONOMER_TORSION NU2 = { "NU2", "C1*-C2*-C3*-C4*", "C1*", "C2*", "C3*", "C4*" }; MONOMER_TORSION NU3 = { "NU3", "C2*-C3*-C4*-O4*", "C2*", "C3*", "C4*", "O4*" }; MONOMER_TORSION NU4 = { "NU4", "C3*-C4*-O4*-C1*", "C3*", "C4*", "O4*", "C1*" }; MONOMER_TORSION NU5 = { "NU5", "C5*-C4*-C3*-C2*", "C5*", "C4*", "C3*", "C2*" }; MONOMER_TORSION NU6 = { "NU6", "O4*-C4*-C3*-O3*", "O4*", "C4*", "C3*", "O3*" }; MONOMER_TORSION NU7 = { "NU7", "O3*-C3*-C2*-O2*", "O3*", "C3*", "C2*", "O2*" }; MONOMER_TORSION NU8 = { "NU8", "O5*-C5*-C4*-O4*", "O5*", "C5*", "C4*", "O4*" }; */ #define NUM_TOR_NA 5 MONOMER_TORSION tor_na[NUM_TOR_NA] = { { "BETA", "P-O5*-C5*-C4*", "P", "O5*", "C5*", "C4*" }, { "GAMMA", "O5*-C5*-C4*-C3*", "O5*", "C5*", "C4*", "C3*" }, { "DELTA", "C5*-C4*-C3*-O3*", "C5*", "C4*", "C3*", "O3*" }, { "CHI", "O4*-C1*-N9-C4", "O4*", "C1*", "N9", "C4" }, { "CHI", "O4*-C1*-N1-C2", "O4*", "C1*", "N1", "C2" } }; MONOMER_TORSION PHI = { "PHI", "C-N-CA-C", "C", "N", "CA", "C" }; MONOMER_TORSION PSI = { "PSI", "N-CA-C-N", "N", "CA", "C", "N" }; MONOMER_TORSION OMEGA = { "OMEGA", "CA-C-N-CA", "CA", "C", "N", "CA" }; #if 0 MONOMER_TORSION tor_na[8] = { "Alpha", "O3*-P-O5*-C5*", "O3*", "P", "O5*", "C5*", "Beta", "P-O5*-C5*-C4*", "P", "O5*", "C5*", "C4*", "Gamma", "O5*-C5*-C4*-C3*", "O5*", "C5*", "C4*", "C3*", "Delta", "C5*-C4*-C3*-O3*", "C5*", "C4*", "C3*", "O3*", "Epsilon", "C4*-C3*-O3*-P", "C4*", "C3*", "O3*", "P", "Zeta", "C3*-O3*-P-O5*", "C3*", "O3*", "P", "O5*", "Chi", "O4*-C1*-N9-C4", "O4*", "C1*", "N9", "C4", "Chi", "O4*-C1*-N1-C2", "O4*", "C1*", "N1", "C2" }; MONOMER_TORSION tor_aa[3] = { "Phi", "N-CA-C", "C", "N", "CA", "C", /* 0 */ "Psi", "N-CA-C-N", "N", "CA", "C", "N", /* 1 */ "Omega", "CA-C-N-CA", "CA", "C", "N", "CA", /* 2 */ "Chi-1", "N-CA-CB-CG", "N", "CA", "CB", "CG", /* 3 */ "Chi-1", "N-CA-CB-CG1", "N", "CA", "CB", "CG1", /* 4 */ "Chi-1", "N-CA-CB-OG", "N", "CA", "CB", "OG", /* 5 */ "Chi-1", "N-CA-CB-OG1", "N", "CA", "CB", "OG1", /* 6 */ "Chi-1", "N-CA-CB-SG", "N", "CA", "CB", "SG", /* 7 */ "Chi-2", "CA-CB-CG-CD", "CA", "CB", "CG", "CD", /* 8 */ "Chi-2", "CA-CB-CG-CD1", "CA", "CB", "CG", "CD1", /* 9 */ "Chi-2", "CA-CB-CG-ND1", "CA", "CB", "CG", "ND1", /* 10 */ "Chi-2", "CA-CB-CG-OD1", "CA", "CB", "CG", "OD1", /* 11 */ "Chi-2", "CA-CB-CG-SD", "CA", "CB", "CG", "SD", /* 12 */ "Chi-2", "CA-CB-CG1-CD1", "CA", "CB", "CG1", "CD1", /* 13 */ "Chi-3", "CB-CG-CD-CE", "CB", "CG", "CD", "CE", /* 14 */ "Chi-3", "CB-CG-CD-NE", "CB", "CG", "CD", "NE", /* 15 */ "Chi-3", "CB-CG-CD-OE1", "CB", "CG", "CD", "OE1", /* 16 */ "Chi-3", "CB-CG-SD-CE", "CB", "CG", "SD", "CE", /* 17 */ "Chi-4", "CG-CD-CE-NZ", "CG", "CD", "CE", "NZ", /* 18 */ "Chi-4", "CG-CD-NE-CZ", "CG", "CD", "NE", "CZ", /* 19 */ "Chi-5", "CD-NE-CZ-NH1", "CD", "NE", "CZ", "NH1" /* 20 */ }; #endif MONOMER DA = { "A", 23, 33, // 24, 37, { { "P-O1P/O2P", "O1P-P", "P", "O1P", 1, { { 1.485, 0.017, "s" } } }, { "P-O1P/O2P", "O2P-P", "P", "O2P", 1, { { 1.485, 0.017, "s" } } }, { "P-O5'", "O5*-P", "P", "O5*", 1, { { 1.593, 0.010, "s" } } }, // { "P-O3'", "O3*-P", "P", "O3*", 1, { { 1.607, 0.012, "s" } } }, { "O5'-C5'", "C5*-O5*", "O5*", "C5*", 3, {{ 1.440, 0.016, "(P)O5'-C5'" }, { 1.418, 0.025, "(H)C2'-endo" }, { 1.423, 0.011, "(H)C3'-endo" }} }, { "C5'-C4'", "C4*-C5*", "C5*", "C4*", 2, {{ 1.512, 0.007, "C2'-endo" }, { 1.509, 0.011, "C3'-endo" }} }, { "C3'-C4'", "C3*-C4*", "C4*", "C3*", 2, {{ 1.529, 0.010, "C2'-endo" }, { 1.521, 0.010, "C3'-endo" }} }, { "C2'-C3'", "C2*-C3*", "C3*", "C2*", 2, {{ 1.516, 0.008, "C2'-endo" }, { 1.518, 0.012, "C3'-endo" }} }, { "C1'-C2'", "C1*-C2*", "C2*", "C1*", 2, {{ 1.518, 0.010, "C2'-endo" }, { 1.519, 0.010, "C3'-endo" }} }, { "O4'-C1'", "C1*-O4*", "O4*", "C1*", 2, {{ 1.420, 0.011, "C2'-endo" }, { 1.418, 0.012, "C3'-endo" }} }, { "C4'-O4'", "C4*-O4*", "O4*", "C4*", 2, {{ 1.446, 0.010, "C2'-endo" }, { 1.449, 0.009, "C3'-endo" }} }, { "C3'-O3'", "C3*-O3*", "O3*", "C3*", 2, {{ 1.435, 0.013, "C2'-endo" }, { 1.419, 0.006, "C3'-endo" }} }, { "C1'-N1/N9", "C1*-N9", "C1*", "N9", 2, {{ 1.468, 0.014, "C2'-endo" }, { 1.488, 0.013, "C3'-endo" }} }, { "N1-C2", "C2-N1", "N1", "C2", 1, { { 1.339, 0.009, "s" } } }, { "C2-N3", "C2-N3", "C2", "N3", 1, { { 1.331, 0.009, "s" } } }, { "N3-C4", "C4-N3", "N3", "C4", 1, { { 1.344, 0.006, "s" } } }, { "C4-C5", "C4-C5", "C4", "C5", 1, { { 1.383, 0.007, "s" } } }, { "C5-C6", "C5-C6", "C5", "C6", 1, { { 1.406, 0.009, "s" } } }, { "C6-N1", "C6-N1", "C6", "N1", 1, { { 1.351, 0.007, "s" } } }, { "C5-N7", "C5-N7", "C5", "N7", 1, { { 1.388, 0.006, "s" } } }, { "N7-C8", "C8-N7", "N7", "C8", 1, { { 1.311, 0.007, "s" } } }, { "C8-N9", "C8-N9", "C8", "N9", 1, { { 1.373, 0.008, "s" } } }, { "N9-C4", "C4-N9", "N9", "C4", 1, { { 1.374, 0.006, "s" } } }, { "C6-N6", "C6-N6", "C6", "N6", 1, { { 1.335, 0.008, "s" } } } }, { { "O1P-P-O2P", "O1P-P-O2P", "O1P", "P", "O2P", 1, { { 119.600, 1.5, "s" } } }, { "O5'-P-O1P/O2P", "O1P-P-O5*", "O5*", "P", "O1P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, { "O5'-P-O1P/O2P", "O2P-P-O5*", "O5*", "P", "O2P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, /* { "O3'-P-O5'", "O3*-P-O5*", "O3*", "P", "O5*", 1, { { 104.000, 1.9, "s" } } }, { "O3'-P-O2P/O2P", "O2P-P-O3*", "O2P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, { "O3'-P-O1P/O2P", "O1P-P-O3*", "O1P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, */ { "O5'-C5'-C4'", "C4*-C5*-O5*", "O5*", "C5*", "C4*", 3, {{ 109.400, 0.8, "(P)O5'-C5'-C4'" }, { 110.900, 1.7, "C2'-endo" }, { 111.000, 2.5, "C3'-endo" }} }, { "P-O5'-C5'", "C5*-O5*-P", "P", "O5*", "C5*", 1, { { 120.900, 1.6, "s" } } }, /* { "C3'-O3'-P", "C3*-O3*-P", "P", "O3*", "C3*", 1, { { 119.700, 1.2, "s" } } }, */ { "C3'-C4'-O4'", "C3*-C4*-O4*", "O4*", "C4*", "C3*", 2, {{ 106.000, 0.6, "C2'-endo" }, { 104.500, 0.4, "C3'-endo" }} }, { "C5'-C4'-C3'", "C3*-C4*-C5*", "C5*", "C4*", "C3*", 2, {{ 114.100, 1.8, "C2'-endo" }, { 115.700, 1.2, "C3'-endo" }} }, { "C5'-C4'-O4'", "C5*-C4*-O4*", "C5*", "C4*", "O4*", 2, {{ 109.300, 1.9, "C2'-endo" }, { 109.800, 1.1, "C3'-endo" }} }, { "C4'-O4'-C1'", "C1*-O4*-C4*", "C1*", "O4*", "C4*", 2, {{ 110.100, 1.0, "C2'-endo" }, { 110.300, 0.7, "C3'-endo" }} }, { "C4'-C3'-O3'", "C4*-C3*-O3*", "C4*", "C3*", "O3*", 2, {{ 109.700, 2.5, "C2'-endo" }, { 112.300, 2.0, "C3'-endo" }} }, { "C2'-C3'-O3'", "C2*-C3*-O3*", "C2*", "C3*", "O3*", 2, {{ 109.400, 2.5, "C2'-endo" }, { 112.600, 3.3, "C3'-endo" }} }, { "C2'-C3'-C4'", "C2*-C3*-C4*", "C4*", "C3*", "C2*", 2, {{ 103.100, 0.9, "C2'-endo" }, { 102.200, 0.7, "C3'-endo" }} }, { "C1'-C2'-C3'", "C1*-C2*-C3*", "C3*", "C2*", "C1*", 2, {{ 102.500, 1.2, "C2'-endo" }, { 102.400, 0.8, "C3'-endo" }} }, { "O4'-C1'-C2'", "C2*-C1*-O4*", "O4*", "C1*", "C2*", 2, {{ 105.900, 0.8, "C2'-endo" }, { 106.800, 0.5, "C3'-endo" }} }, { "C2'-C1'-N1/N9", "C2*-C1*-N9", "N9", "C1*", "C2*", 2, {{ 114.300, 1.4, "C2'-endo" }, { 112.600, 1.9, "C3'-endo" }} }, { "O4'-C1'-N1/N9", "N9-C1*-O4*", "O4*", "C1*", "N9", 2, {{ 108.000, 0.7, "C2'-endo" }, { 108.300, 0.3, "C3'-endo" }} }, { "C6-N1-C2", "C2-N1-C6", "C6", "N1", "C2", 1, { { 118.600, 0.6, "s" } } }, { "N1-C2-N3", "N1-C2-N3", "N1", "C2", "N3", 1, { { 129.300, 0.5, "s" } } }, { "C2-N3-C4", "C2-N3-C4", "C2", "N3", "C4", 1, { { 110.600, 0.5, "s" } } }, { "N3-C4-C5", "C5-C4-N3", "N3", "C4", "C5", 1, { { 126.800, 0.7, "s" } } }, { "C4-C5-C6", "C4-C5-C6", "C4", "C5", "C6", 1, { { 117.000, 0.5, "s" } } }, { "C5-C6-N1", "C5-C6-N1", "C5", "C6", "N1", 1, { { 117.700, 0.5, "s" } } }, { "C4-C5-N7", "C4-C5-N7", "C4", "C5", "N7", 1, { { 110.700, 0.5, "s" } } }, { "C5-N7-C8", "C5-N7-C8", "C5", "N7", "C8", 1, { { 103.900, 0.5, "s" } } }, { "N7-C8-N9", "N7-C8-N9", "N7", "C8", "N9", 1, { { 113.800, 0.5, "s" } } }, { "C8-N9-C4", "C4-N9-C8", "C8", "N9", "C4", 1, { { 105.800, 0.4, "s" } } }, { "N9-C4-C5", "C5-C4-N9", "N9", "C4", "C5", 1, { { 105.800, 0.4, "s" } } }, { "N3-C4-N9", "N3-C4-N9", "N3", "C4", "N9", 1, { { 127.400, 0.8, "s" } } }, { "C6-C5-N7", "C6-C5-N7", "C6", "C5", "N7", 1, { { 132.300, 0.7, "s" } } }, { "N1-C6-N6", "N1-C6-N6", "N1", "C6", "N6", 1, { { 118.600, 0.6, "s" } } }, { "C5-C6-N6", "C5-C6-N6", "C5", "C6", "N6", 1, { { 123.700, 0.8, "s" } } }, { "C8-N9-C1'", "C1*-N9-C8", "C8", "N9", "C1*", 1, { { 127.700, 1.8, "s" } } }, { "C4-N9-C1'", "C1*-N9-C4", "C4", "N9", "C1*", 1, { { 126.300, 1.8, "s" } } } } }; MONOMER RA = { "A", 24, 35, // 25, 39, { { "P-O1P/O2P", "O1P-P", "P", "O1P", 1, { { 1.485, 0.017, "s" } } }, { "P-O1P/O2P", "O2P-P", "P", "O2P", 1, { { 1.485, 0.017, "s" } } }, { "P-O5'", "O5*-P", "P", "O5*", 1, { { 1.593, 0.010, "s" } } }, // { "P-O3'", "O3*-P", "P", "O3*", 1, { { 1.607, 0.012, "s" } } }, { "O5'-C5'", "C5*-O5*", "O5*", "C5*", 3, {{ 1.440, 0.016, "(P)O5'-C5'" }, { 1.424, 0.016, "(H)C2'-endo" }, { 1.420, 0.009, "(H)C3'-endo" }} }, { "C5'-C4'", "C4*-C5*", "C5*", "C4*", 2, {{ 1.509, 0.012, "C2'-endo" }, { 1.508, 0.007, "C3'-endo" }} }, { "C3'-C4'", "C3*-C4*", "C4*", "C3*", 2, {{ 1.527, 0.011, "C2'-endo" }, { 1.521, 0.010, "C3'-endo" }} }, { "C2'-C3'", "C2*-C3*", "C3*", "C2*", 2, {{ 1.525, 0.011, "C2'-endo" }, { 1.523, 0.011, "C3'-endo" }} }, { "C1'-C2'", "C1*-C2*", "C2*", "C1*", 2, {{ 1.526, 0.008, "C2'-endo" }, { 1.529, 0.011, "C3'-endo" }} }, { "O4'-C1'", "C1*-O4*", "O4*", "C1*", 2, {{ 1.415, 0.012, "C2'-endo" }, { 1.412, 0.013, "C3'-endo" }} }, { "C4'-O4'", "C4*-O4*", "O4*", "C4*", 2, {{ 1.454, 0.010, "C2'-endo" }, { 1.451, 0.013, "C3'-endo" }} }, { "C3'-O3'", "C3*-O3*", "O3*", "C3*", 2, {{ 1.427, 0.012, "C2'-endo" }, { 1.417, 0.014, "C3'-endo" }} }, { "C1'-N1/N9", "C1*-N9", "C1*", "N9", 2, {{ 1.464, 0.014, "C2'-endo" }, { 1.483, 0.015, "C3'-endo" }} }, { "C2'-O2'", "C2*-O2*", "C2*", "O2*", 2, {{ 1.412, 0.013, "C2'-endo" }, { 1.420, 0.010, "C3'-endo" }} }, { "N1-C2", "C2-N1", "N1", "C2", 1, { { 1.339, 0.009, "s" } } }, { "C2-N3", "C2-N3", "C2", "N3", 1, { { 1.331, 0.009, "s" } } }, { "N3-C4", "C4-N3", "N3", "C4", 1, { { 1.344, 0.006, "s" } } }, { "C4-C5", "C4-C5", "C4", "C5", 1, { { 1.383, 0.007, "s" } } }, { "C5-C6", "C5-C6", "C5", "C6", 1, { { 1.406, 0.009, "s" } } }, { "C6-N1", "C6-N1", "C6", "N1", 1, { { 1.351, 0.007, "s" } } }, { "C5-N7", "C5-N7", "C5", "N7", 1, { { 1.388, 0.006, "s" } } }, { "N7-C8", "C8-N7", "N7", "C8", 1, { { 1.311, 0.007, "s" } } }, { "C8-N9", "C8-N9", "C8", "N9", 1, { { 1.373, 0.008, "s" } } }, { "N9-C4", "C4-N9", "N9", "C4", 1, { { 1.374, 0.006, "s" } } }, { "C6-N6", "C6-N6", "C6", "N6", 1, { { 1.335, 0.008, "s" } } } }, { { "O1P-P-O2P", "O1P-P-O2P", "O1P", "P", "O2P", 1, { { 119.600, 1.5, "s" } } }, { "O5'-P-O1P/O2P", "O1P-P-O5*", "O5*", "P", "O1P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, { "O5'-P-O1P/O2P", "O2P-P-O5*", "O5*", "P", "O2P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, /* { "O3'-P-O5'", "O3*-P-O5*", "O3*", "P", "O5*", 1, { { 104.000, 1.9, "s" } } }, { "O3'-P-O2P/O2P", "O2P-P-O3*", "O2P", "P", "O3*", 2, {{ 110.500, 1.1, "large" } { 105.200, 2.2, "small" }} }, { "O3'-P-O1P/O2P", "O1P-P-O3*", "O1P", "P", "O3*", 2, {{ 110.500, 1.1, "large" } { 105.200, 2.2, "small" }} }, */ { "O5'-C5'-C4'", "C4*-C5*-O5*", "O5*", "C5*", "C4*", 3, {{ 109.400, 0.8, "(P)O5'-C5'-C4'" }, { 111.700, 1.9, "C2'-endo" }, { 111.500, 1.6, "C3'-endo" }} }, { "P-O5'-C5'", "C5*-O5*-P", "P", "O5*", "C5*", 1, { { 120.900, 1.6, "s" } } }, /* { "C3'-O3'-P", "C3*-O3*-P", "P", "O3*", "C3*", 1, { { 119.700, 1.2, "s" } } }, */ { "C3'-C4'-O4'", "C3*-C4*-O4*", "O4*", "C4*", "C3*", 2, {{ 106.100, 0.8, "C2'-endo" }, { 104.000, 1.0, "C3'-endo" }} }, { "C5'-C4'-C3'", "C3*-C4*-C5*", "C5*", "C4*", "C3*", 2, {{ 115.200, 1.4, "C2'-endo" }, { 116.000, 1.6, "C3'-endo" }} }, { "C5'-C4'-O4'", "C5*-C4*-O4*", "C5*", "C4*", "O4*", 2, {{ 109.100, 1.2, "C2'-endo" }, { 109.800, 0.9, "C3'-endo" }} }, { "C4'-O4'-C1'", "C1*-O4*-C4*", "C1*", "O4*", "C4*", 2, {{ 109.700, 0.7, "C2'-endo" }, { 109.900, 0.8, "C3'-endo" }} }, { "C4'-C3'-O3'", "C4*-C3*-O3*", "C4*", "C3*", "O3*", 2, {{ 109.400, 2.1, "C2'-endo" }, { 113.000, 2.0, "C3'-endo" }} }, { "C2'-C3'-O3'", "C2*-C3*-O3*", "C2*", "C3*", "O3*", 2, {{ 109.500, 2.2, "C2'-endo" }, { 113.700, 1.6, "C3'-endo" }} }, { "C2'-C3'-C4'", "C2*-C3*-C4*", "C4*", "C3*", "C2*", 2, {{ 102.600, 1.0, "C2'-endo" }, { 102.600, 1.0, "C3'-endo" }} }, { "C1'-C2'-C3'", "C1*-C2*-C3*", "C3*", "C2*", "C1*", 2, {{ 101.500, 0.8, "C2'-endo" }, { 101.300, 0.7, "C3'-endo" }} }, { "O4'-C1'-C2'", "C2*-C1*-O4*", "O4*", "C1*", "C2*", 2, {{ 105.800, 1.0, "C2'-endo" }, { 107.600, 0.9, "C3'-endo" }} }, { "C2'-C1'-N1/N9", "C2*-C1*-N9", "N9", "C1*", "C2*", 2, {{ 114.000, 1.3, "C2'-endo" }, { 112.000, 1.1, "C3'-endo" }} }, { "O4'-C1'-N1/N9", "N9-C1*-O4*", "O4*", "C1*", "N9", 2, {{ 108.200, 0.8, "C2'-endo" }, { 108.500, 0.7, "C3'-endo" }} }, { "C1'-C2'-O2'", "C1*-C2*-O2*", "C1*", "C2*", "O2*", 1, { { 110.600, 3.0, "s" } } }, { "C3'-C2'-O2'", "C3*-C2*-O2*", "C3*", "C2*", "O2*", 1, { { 113.300, 2.9, "s" } } }, { "C6-N1-C2", "C2-N1-C6", "C6", "N1", "C2", 1, { { 118.600, 0.6, "s" } } }, { "N1-C2-N3", "N1-C2-N3", "N1", "C2", "N3", 1, { { 129.300, 0.5, "s" } } }, { "C2-N3-C4", "C2-N3-C4", "C2", "N3", "C4", 1, { { 110.600, 0.5, "s" } } }, { "N3-C4-C5", "C5-C4-N3", "N3", "C4", "C5", 1, { { 126.800, 0.7, "s" } } }, { "C4-C5-C6", "C4-C5-C6", "C4", "C5", "C6", 1, { { 117.000, 0.5, "s" } } }, { "C5-C6-N1", "C5-C6-N1", "C5", "C6", "N1", 1, { { 117.700, 0.5, "s" } } }, { "C4-C5-N7", "C4-C5-N7", "C4", "C5", "N7", 1, { { 110.700, 0.5, "s" } } }, { "C5-N7-C8", "C5-N7-C8", "C5", "N7", "C8", 1, { { 103.900, 0.5, "s" } } }, { "N7-C8-N9", "N7-C8-N9", "N7", "C8", "N9", 1, { { 113.800, 0.5, "s" } } }, { "C8-N9-C4", "C4-N9-C8", "C8", "N9", "C4", 1, { { 105.800, 0.4, "s" } } }, { "N9-C4-C5", "C5-C4-N9", "N9", "C4", "C5", 1, { { 105.800, 0.4, "s" } } }, { "N3-C4-N9", "N3-C4-N9", "N3", "C4", "N9", 1, { { 127.400, 0.8, "s" } } }, { "C6-C5-N7", "C6-C5-N7", "C6", "C5", "N7", 1, { { 132.300, 0.7, "s" } } }, { "N1-C6-N6", "N1-C6-N6", "N1", "C6", "N6", 1, { { 118.600, 0.6, "s" } } }, { "C5-C6-N6", "C5-C6-N6", "C5", "C6", "N6", 1, { { 123.700, 0.8, "s" } } }, { "C8-N9-C1'", "C1*-N9-C8", "C8", "N9", "C1*", 1, { { 127.700, 1.8, "s" } } }, { "C4-N9-C1'", "C1*-N9-C4", "C4", "N9", "C1*", 1, { { 126.300, 1.8, "s" } } } } }; MONOMER DC = { "C", 20, 28, // 21, 32, { { "P-O1P/O2P", "O1P-P", "P", "O1P", 1, { { 1.485, 0.017, "s" } } }, { "P-O1P/O2P", "O2P-P", "P", "O2P", 1, { { 1.485, 0.017, "s" } } }, { "P-O5'", "O5*-P", "P", "O5*", 1, { { 1.593, 0.010, "s" } } }, // { "P-O3'", "O3*-P", "P", "O3*", 1, { { 1.607, 0.012, "s" } } }, { "O5'-C5'", "C5*-O5*", "O5*", "C5*", 3, {{ 1.440, 0.016, "(P)O5'-C5'" }, { 1.418, 0.025, "(H)C2'-endo" }, { 1.423, 0.011, "(H)C3'-endo" }} }, { "C5'-C4'", "C4*-C5*", "C5*", "C4*", 2, {{ 1.512, 0.007, "C2'-endo" }, { 1.509, 0.011, "C3'-endo" }} }, { "C3'-C4'", "C3*-C4*", "C4*", "C3*", 2, {{ 1.529, 0.010, "C2'-endo" }, { 1.521, 0.010, "C3'-endo" }} }, { "C2'-C3'", "C2*-C3*", "C3*", "C2*", 2, {{ 1.516, 0.008, "C2'-endo" }, { 1.518, 0.012, "C3'-endo" }} }, { "C1'-C2'", "C1*-C2*", "C2*", "C1*", 2, {{ 1.518, 0.010, "C2'-endo" }, { 1.519, 0.010, "C3'-endo" }} }, { "O4'-C1'", "C1*-O4*", "O4*", "C1*", 2, {{ 1.420, 0.011, "C2'-endo" }, { 1.418, 0.012, "C3'-endo" }} }, { "C4'-O4'", "C4*-O4*", "O4*", "C4*", 2, {{ 1.446, 0.010, "C2'-endo" }, { 1.449, 0.009, "C3'-endo" }} }, { "C3'-O3'", "C3*-O3*", "O3*", "C3*", 2, {{ 1.435, 0.013, "C2'-endo" }, { 1.419, 0.006, "C3'-endo" }} }, { "C1'-N1/N9", "C1*-N1", "C1*", "N1", 2, {{ 1.468, 0.014, "C2'-endo" }, { 1.488, 0.013, "C3'-endo" }} }, { "C2-O2", "C2-O2", "C2", "O2", 1, { { 1.240, 0.009, "s" } } }, { "C4-N4", "C4-N4", "C4", "N4", 1, { { 1.335, 0.009, "s" } } }, { "N1-C2", "C2-N1", "N1", "C2", 1, { { 1.397, 0.010, "s" } } }, { "C6-N1", "C6-N1", "N1", "C6", 1, { { 1.367, 0.006, "s" } } }, { "C2-N3", "C2-N3", "C2", "N3", 1, { { 1.353, 0.008, "s" } } }, { "N3-C4", "C4-N3", "N3", "C4", 1, { { 1.335, 0.007, "s" } } }, { "C4-C5", "C4-C5", "C4", "C5", 1, { { 1.425, 0.008, "s" } } }, { "C5-C6", "C5-C6", "C5", "C6", 1, { { 1.339, 0.008, "s" } } } }, { { "O1P-P-O2P", "O1P-P-O2P", "O1P", "P", "O2P", 1, { { 119.600, 1.5, "s" } } }, { "O5'-P-O1P/O2P", "O1P-P-O5*", "O5*", "P", "O1P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, { "O5'-P-O1P/O2P", "O2P-P-O5*", "O5*", "P", "O2P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, /* { "O3'-P-O5'", "O3*-P-O5*", "O3*", "P", "O5*", 1, { { 104.000, 1.9, "s" } } }, { "O3'-P-O2P/O2P", "O2P-P-O3*", "O2P", "P", "O3*", 2, {{ 110.500, 1.1, "large" } { 105.200, 2.2, "small" }} }, { "O3'-P-O1P/O2P", "O1P-P-O3*", "O1P", "P", "O3*", 2, {{ 110.500, 1.1, "large" } { 105.200, 2.2, "small" }} }, */ { "O5'-C5'-C4'", "C4*-C5*-O5*", "O5*", "C5*", "C4*", 3, {{ 109.400, 0.8, "(P)O5'-C5'-C4'" }, { 110.900, 1.7, "C2'-endo" }, { 111.000, 2.5, "C3'-endo" }} }, { "P-O5'-C5'", "C5*-O5*-P", "P", "O5*", "C5*", 1, { { 120.900, 1.6, "s" } } }, /* { "C3'-O3'-P", "C3*-O3*-P", "P", "O3*", "C3*", 1, { { 119.700, 1.2, "s" } } }, */ { "C3'-C4'-O4'", "C3*-C4*-O4*", "O4*", "C4*", "C3*", 2, {{ 106.000, 0.6, "C2'-endo" }, { 104.500, 0.4, "C3'-endo" }} }, { "C5'-C4'-C3'", "C3*-C4*-C5*", "C5*", "C4*", "C3*", 2, {{ 114.100, 1.8, "C2'-endo" }, { 115.700, 1.2, "C3'-endo" }} }, { "C5'-C4'-O4'", "C5*-C4*-O4*", "C5*", "C4*", "O4*", 2, {{ 109.300, 1.9, "C2'-endo" }, { 109.800, 1.1, "C3'-endo" }} }, { "C4'-O4'-C1'", "C1*-O4*-C4*", "C1*", "O4*", "C4*", 2, {{ 110.100, 1.0, "C2'-endo" }, { 110.300, 0.7, "C3'-endo" }} }, { "C4'-C3'-O3'", "C4*-C3*-O3*", "C4*", "C3*", "O3*", 2, {{ 109.700, 2.5, "C2'-endo" }, { 112.300, 2.0, "C3'-endo" }} }, { "C2'-C3'-O3'", "C2*-C3*-O3*", "C2*", "C3*", "O3*", 2, {{ 109.400, 2.5, "C2'-endo" }, { 112.600, 3.3, "C3'-endo" }} }, { "C2'-C3'-C4'", "C2*-C3*-C4*", "C4*", "C3*", "C2*", 2, {{ 103.100, 0.9, "C2'-endo" }, { 102.200, 0.7, "C3'-endo" }} }, { "C1'-C2'-C3'", "C1*-C2*-C3*", "C3*", "C2*", "C1*", 2, {{ 102.500, 1.2, "C2'-endo" }, { 102.400, 0.8, "C3'-endo" }} }, { "O4'-C1'-C2'", "C2*-C1*-O4*", "O4*", "C1*", "C2*", 2, {{ 105.900, 0.8, "C2'-endo" }, { 106.800, 0.5, "C3'-endo" }} }, { "C2'-C1'-N1/N9", "C2*-C1*-N1", "N1", "C1*", "C2*", 2, {{ 114.300, 1.4, "C2'-endo" }, { 112.600, 1.9, "C3'-endo" }} }, { "O4'-C1'-N1/N9", "N1-C1*-O4*", "O4*", "C1*", "N1", 2, {{ 108.000, 0.7, "C2'-endo" }, { 108.300, 0.3, "C3'-endo" }} }, { "C6-N1-C2", "C2-N1-C6", "C6", "N1", "C2", 1, { { 120.300, 0.4, "s" } } }, { "N1-C2-N3", "N1-C2-N3", "N1", "C2", "N3", 1, { { 119.200, 0.7, "s" } } }, { "C2-N3-C4", "C2-N3-C4", "C2", "N3", "C4", 1, { { 119.900, 0.5, "s" } } }, { "N3-C4-C5", "C5-C4-N3", "N3", "C4", "C5", 1, { { 121.900, 0.4, "s" } } }, { "C4-C5-C6", "C4-C5-C6", "C4", "C5", "C6", 1, { { 117.400, 0.5, "s" } } }, { "C5-C6-N1", "C5-C6-N1", "C5", "C6", "N1", 1, { { 121.000, 0.5, "s" } } }, { "N1-C2-O2", "N1-C2-O2", "N1", "C2", "O2", 1, { { 118.900, 0.6, "s" } } }, { "N3-C2-O2", "N3-C2-O2", "N3", "C2", "O2", 1, { { 121.900, 0.7, "s" } } }, { "N3-C4-N4", "N3-C4-N4", "N3", "C4", "N4", 1, { { 118.000, 0.7, "s" } } }, { "C5-C4-N4", "C5-C4-N4", "C5", "C4", "N4", 1, { { 120.200, 0.7, "s" } } }, { "C6-N1-C1'", "C1*-N1-C6", "C6", "N1", "C1*", 1, { { 120.800, 1.2, "s" } } }, { "C2-N1-C1'", "C1*-N1-C2", "C2", "N1", "C1*", 1, { { 118.800, 1.1, "s" } } } } }; MONOMER RC = { "C", 21, 30, // 22, 34, { { "P-O1P/O2P", "O1P-P", "P", "O1P", 1, { { 1.485, 0.017, "s" } } }, { "P-O1P/O2P", "O2P-P", "P", "O2P", 1, { { 1.485, 0.017, "s" } } }, { "P-O5'", "O5*-P", "P", "O5*", 1, { { 1.593, 0.010, "s" } } }, // { "P-O3'", "O3*-P", "P", "O3*", 1, { { 1.607, 0.012, "s" } } }, { "O5'-C5'", "C5*-O5*", "O5*", "C5*", 3, {{ 1.440, 0.016, "(P)O5'-C5'" }, { 1.424, 0.016, "(H)C2'-endo" }, { 1.420, 0.009, "(H)C3'-endo" }} }, { "C5'-C4'", "C4*-C5*", "C5*", "C4*", 2, {{ 1.509, 0.012, "C2'-endo" }, { 1.508, 0.007, "C3'-endo" }} }, { "C3'-C4'", "C3*-C4*", "C4*", "C3*", 2, {{ 1.527, 0.011, "C2'-endo" }, { 1.521, 0.010, "C3'-endo" }} }, { "C2'-C3'", "C2*-C3*", "C3*", "C2*", 2, {{ 1.525, 0.011, "C2'-endo" }, { 1.523, 0.011, "C3'-endo" }} }, { "C1'-C2'", "C1*-C2*", "C2*", "C1*", 2, {{ 1.526, 0.008, "C2'-endo" }, { 1.529, 0.011, "C3'-endo" }} }, { "O4'-C1'", "C1*-O4*", "O4*", "C1*", 2, {{ 1.415, 0.012, "C2'-endo" }, { 1.412, 0.013, "C3'-endo" }} }, { "C4'-O4'", "C4*-O4*", "O4*", "C4*", 2, {{ 1.454, 0.010, "C2'-endo" }, { 1.451, 0.013, "C3'-endo" }} }, { "C3'-O3'", "C3*-O3*", "O3*", "C3*", 2, {{ 1.427, 0.012, "C2'-endo" }, { 1.417, 0.014, "C3'-endo" }} }, { "C1'-N1/N9", "C1*-N1", "C1*", "N1", 2, {{ 1.464, 0.014, "C2'-endo" }, { 1.483, 0.015, "C3'-endo" }} }, { "C2'-O2'", "C2*-O2*", "C2*", "O2*", 2, {{ 1.412, 0.013, "C2'-endo" }, { 1.420, 0.010, "C3'-endo" }} }, { "C2-O2", "C2-O2", "C2", "O2", 1, { { 1.240, 0.009, "s" } } }, { "C4-N4", "C4-N4", "C4", "N4", 1, { { 1.335, 0.009, "s" } } }, { "N1-C2", "C2-N1", "N1", "C2", 1, { { 1.397, 0.010, "s" } } }, { "C6-N1", "C6-N1", "N1", "C6", 1, { { 1.367, 0.006, "s" } } }, { "C2-N3", "C2-N3", "C2", "N3", 1, { { 1.353, 0.008, "s" } } }, { "N3-C4", "C4-N3", "N3", "C4", 1, { { 1.335, 0.007, "s" } } }, { "C4-C5", "C4-C5", "C4", "C5", 1, { { 1.425, 0.008, "s" } } }, { "C5-C6", "C5-C6", "C5", "C6", 1, { { 1.339, 0.008, "s" } } } }, { { "O1P-P-O2P", "O1P-P-O2P", "O1P", "P", "O2P", 1, { { 119.600, 1.5, "s" } } }, { "O5'-P-O1P/O2P", "O1P-P-O5*", "O5*", "P", "O1P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, { "O5'-P-O1P/O2P", "O2P-P-O5*", "O5*", "P", "O2P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, /* { "O3'-P-O5'", "O3*-P-O5*", "O3*", "P", "O5*", 1, { { 104.000, 1.9, "s" } } }, { "O3'-P-O2P/O2P", "O2P-P-O3*", "O2P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, { "O3'-P-O1P/O2P", "O1P-P-O3*", "O1P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, */ { "O5'-C5'-C4'", "C4*-C5*-O5*", "O5*", "C5*", "C4*", 3, {{ 109.400, 0.8, "(P)O5'-C5'-C4'" }, { 111.700, 1.9, "C2'-endo" }, { 111.500, 1.6, "C3'-endo" }} }, { "P-O5'-C5'", "C5*-O5*-P", "P", "O5*", "C5*", 1, { { 120.900, 1.6, "s" } } }, /* { "C3'-O3'-P", "C3*-O3*-P", "P", "O3*", "C3*", 1, { { 119.700, 1.2, "s" } } }, */ { "C3'-C4'-O4'", "C3*-C4*-O4*", "O4*", "C4*", "C3*", 2, {{ 106.100, 0.8, "C2'-endo" }, { 104.000, 1.0, "C3'-endo" }} }, { "C5'-C4'-C3'", "C3*-C4*-C5*", "C5*", "C4*", "C3*", 2, {{ 115.200, 1.4, "C2'-endo" }, { 116.000, 1.6, "C3'-endo" }} }, { "C5'-C4'-O4'", "C5*-C4*-O4*", "C5*", "C4*", "O4*", 2, {{ 109.100, 1.2, "C2'-endo" }, { 109.800, 0.9, "C3'-endo" }} }, { "C4'-O4'-C1'", "C1*-O4*-C4*", "C1*", "O4*", "C4*", 2, {{ 109.700, 0.7, "C2'-endo" }, { 109.900, 0.8, "C3'-endo" }} }, { "C4'-C3'-O3'", "C4*-C3*-O3*", "C4*", "C3*", "O3*", 2, {{ 109.400, 2.1, "C2'-endo" }, { 113.000, 2.0, "C3'-endo" }} }, { "C2'-C3'-O3'", "C2*-C3*-O3*", "C2*", "C3*", "O3*", 2, {{ 109.500, 2.2, "C2'-endo" }, { 113.700, 1.6, "C3'-endo" }} }, { "C2'-C3'-C4'", "C2*-C3*-C4*", "C4*", "C3*", "C2*", 2, {{ 102.600, 1.0, "C2'-endo" }, { 102.600, 1.0, "C3'-endo" }} }, { "C1'-C2'-C3'", "C1*-C2*-C3*", "C3*", "C2*", "C1*", 2, {{ 101.500, 0.8, "C2'-endo" }, { 101.300, 0.7, "C3'-endo" }} }, { "O4'-C1'-C2'", "C2*-C1*-O4*", "O4*", "C1*", "C2*", 2, {{ 105.800, 1.0, "C2'-endo" }, { 107.600, 0.9, "C3'-endo" }} }, { "C2'-C1'-N1/N9", "C2*-C1*-N1", "N1", "C1*", "C2*", 2, {{ 114.000, 1.3, "C2'-endo" }, { 112.000, 1.1, "C3'-endo" }} }, { "O4'-C1'-N1/N9", "N1-C1*-O4*", "O4*", "C1*", "N1", 2, {{ 108.200, 0.8, "C2'-endo" }, { 108.500, 0.7, "C3'-endo" }} }, { "C1'-C2'-O2'", "C1*-C2*-O2*", "C1*", "C2*", "O2*", 1, { { 110.600, 3.0, "s" } } }, { "C3'-C2'-O2'", "C3*-C2*-O2*", "C3*", "C2*", "O2*", 1, { { 113.300, 2.9, "s" } } }, { "C6-N1-C2", "C2-N1-C6", "C6", "N1", "C2", 1, { { 120.300, 0.4, "s" } } }, { "N1-C2-N3", "N1-C2-N3", "N1", "C2", "N3", 1, { { 119.200, 0.7, "s" } } }, { "C2-N3-C4", "C2-N3-C4", "C2", "N3", "C4", 1, { { 119.900, 0.5, "s" } } }, { "N3-C4-C5", "C5-C4-N3", "N3", "C4", "C5", 1, { { 121.900, 0.4, "s" } } }, { "C4-C5-C6", "C4-C5-C6", "C4", "C5", "C6", 1, { { 117.400, 0.5, "s" } } }, { "C5-C6-N1", "C5-C6-N1", "C5", "C6", "N1", 1, { { 121.000, 0.5, "s" } } }, { "N1-C2-O2", "N1-C2-O2", "N1", "C2", "O2", 1, { { 118.900, 0.6, "s" } } }, { "N3-C2-O2", "N3-C2-O2", "N3", "C2", "O2", 1, { { 121.900, 0.7, "s" } } }, { "N3-C4-N4", "N3-C4-N4", "N3", "C4", "N4", 1, { { 118.000, 0.7, "s" } } }, { "C5-C4-N4", "C5-C4-N4", "C5", "C4", "N4", 1, { { 120.200, 0.7, "s" } } }, { "C6-N1-C1'", "C1*-N1-C6", "C6", "N1", "C1*", 1, { { 120.800, 1.2, "s" } } }, { "C2-N1-C1'", "C1*-N1-C2", "C2", "N1", "C1*", 1, { { 118.800, 1.1, "s" } } } } }; MONOMER DG = { "G", 24, 35, // 25, 39, { { "P-O1P/O2P", "O1P-P", "P", "O1P", 1, { { 1.485, 0.017, "s" } } }, { "P-O1P/O2P", "O2P-P", "P", "O2P", 1, { { 1.485, 0.017, "s" } } }, { "P-O5'", "O5*-P", "P", "O5*", 1, { { 1.593, 0.010, "s" } } }, // { "P-O3'", "O3*-P", "P", "O3*", 1, { { 1.607, 0.012, "s" } } }, { "O5'-C5'", "C5*-O5*", "O5*", "C5*", 3, {{ 1.440, 0.016, "(P)O5'-C5'" }, { 1.418, 0.025, "(H)C2'-endo" }, { 1.423, 0.011, "(H)C3'-endo" }} }, { "C5'-C4'", "C4*-C5*", "C5*", "C4*", 2, {{ 1.512, 0.007, "C2'-endo" }, { 1.509, 0.011, "C3'-endo" }} }, { "C3'-C4'", "C3*-C4*", "C4*", "C3*", 2, {{ 1.529, 0.010, "C2'-endo" }, { 1.521, 0.010, "C3'-endo" }} }, { "C2'-C3'", "C2*-C3*", "C3*", "C2*", 2, {{ 1.516, 0.008, "C2'-endo" }, { 1.518, 0.012, "C3'-endo" }} }, { "C1'-C2'", "C1*-C2*", "C2*", "C1*", 2, {{ 1.518, 0.010, "C2'-endo" }, { 1.519, 0.010, "C3'-endo" }} }, { "O4'-C1'", "C1*-O4*", "O4*", "C1*", 2, {{ 1.420, 0.011, "C2'-endo" }, { 1.418, 0.012, "C3'-endo" }} }, { "C4'-O4'", "C4*-O4*", "O4*", "C4*", 2, {{ 1.446, 0.010, "C2'-endo" }, { 1.449, 0.009, "C3'-endo" }} }, { "C3'-O3'", "C3*-O3*", "O3*", "C3*", 2, {{ 1.435, 0.013, "C2'-endo" }, { 1.419, 0.006, "C3'-endo" }} }, { "C1'-N1/N9", "C1*-N9", "C1*", "N9", 2, {{ 1.468, 0.014, "C2'-endo" }, { 1.488, 0.013, "C3'-endo" }} }, { "N1-C2", "C2-N1", "N1", "C2", 1, { { 1.373, 0.008, "s" } } }, { "C2-N3", "C2-N3", "C2", "N3", 1, { { 1.323, 0.008, "s" } } }, { "N3-C4", "C4-N3", "N3", "C4", 1, { { 1.350, 0.007, "s" } } }, { "C4-C5", "C4-C5", "C4", "C5", 1, { { 1.379, 0.007, "s" } } }, { "C5-C6", "C5-C6", "C5", "C6", 1, { { 1.419, 0.010, "s" } } }, { "C6-N1", "C6-N1", "C6", "N1", 1, { { 1.391, 0.007, "s" } } }, { "C5-N7", "C5-N7", "C5", "N7", 1, { { 1.388, 0.006, "s" } } }, { "N7-C8", "C8-N7", "N7", "C8", 1, { { 1.305, 0.006, "s" } } }, { "C8-N9", "C8-N9", "C8", "N9", 1, { { 1.374, 0.007, "s" } } }, { "N9-C4", "C4-N9", "N9", "C4", 1, { { 1.375, 0.008, "s" } } }, { "C2-N2", "C2-N2", "C2", "N2", 1, { { 1.341, 0.010, "s" } } }, { "C6-O6", "C6-O6", "C6", "O6", 1, { { 1.237, 0.009, "s" } } } }, { { "O1P-P-O2P", "O1P-P-O2P", "O1P", "P", "O2P", 1, { { 119.600, 1.5, "s" } } }, { "O5'-P-O1P/O2P", "O1P-P-O5*", "O5*", "P", "O1P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, { "O5'-P-O1P/O2P", "O2P-P-O5*", "O5*", "P", "O2P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, /* { "O3'-P-O5'", "O3*-P-O5*", "O3*", "P", "O5*", 1, { { 104.000, 1.9, "s" } } }, { "O3'-P-O2P/O2P", "O2P-P-O3*", "O2P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, { "O3'-P-O1P/O2P", "O1P-P-O3*", "O1P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, */ { "O5'-C5'-C4'", "C4*-C5*-O5*", "O5*", "C5*", "C4*", 3, {{ 109.400, 0.8, "(P)O5'-C5'-C4'" }, { 110.900, 1.7, "C2'-endo" }, { 111.000, 2.5, "C3'-endo" }} }, { "P-O5'-C5'", "C5*-O5*-P", "P", "O5*", "C5*", 1, { { 120.900, 1.6, "s" } } }, /* { "C3'-O3'-P", "C3*-O3*-P", "P", "O3*", "C3*", 1, { { 119.700, 1.2, "s" } } }, */ { "C3'-C4'-O4'", "C3*-C4*-O4*", "O4*", "C4*", "C3*", 2, {{ 106.000, 0.6, "C2'-endo" }, { 104.500, 0.4, "C3'-endo" }} }, { "C5'-C4'-C3'", "C3*-C4*-C5*", "C5*", "C4*", "C3*", 2, {{ 114.100, 1.8, "C2'-endo" }, { 115.700, 1.2, "C3'-endo" }} }, { "C5'-C4'-O4'", "C5*-C4*-O4*", "C5*", "C4*", "O4*", 2, {{ 109.300, 1.9, "C2'-endo" }, { 109.800, 1.1, "C3'-endo" }} }, { "C4'-O4'-C1'", "C1*-O4*-C4*", "C1*", "O4*", "C4*", 2, {{ 110.100, 1.0, "C2'-endo" }, { 110.300, 0.7, "C3'-endo" }} }, { "C4'-C3'-O3'", "C4*-C3*-O3*", "C4*", "C3*", "O3*", 2, {{ 109.700, 2.5, "C2'-endo" }, { 112.300, 2.0, "C3'-endo" }} }, { "C2'-C3'-O3'", "C2*-C3*-O3*", "C2*", "C3*", "O3*", 2, {{ 109.400, 2.5, "C2'-endo" }, { 112.600, 3.3, "C3'-endo" }} }, { "C2'-C3'-C4'", "C2*-C3*-C4*", "C4*", "C3*", "C2*", 2, {{ 103.100, 0.9, "C2'-endo" }, { 102.200, 0.7, "C3'-endo" }} }, { "C1'-C2'-C3'", "C1*-C2*-C3*", "C3*", "C2*", "C1*", 2, {{ 102.500, 1.2, "C2'-endo" }, { 102.400, 0.8, "C3'-endo" }} }, { "O4'-C1'-C2'", "C2*-C1*-O4*", "O4*", "C1*", "C2*", 2, {{ 105.900, 0.8, "C2'-endo" }, { 106.800, 0.5, "C3'-endo" }} }, { "C2'-C1'-N1/N9", "C2*-C1*-N9", "N9", "C1*", "C2*", 2, {{ 114.300, 1.4, "C2'-endo" }, { 112.600, 1.9, "C3'-endo" }} }, { "O4'-C1'-N1/N9", "N9-C1*-O4*", "O4*", "C1*", "N9", 2, {{ 108.000, 0.7, "C2'-endo" }, { 108.300, 0.3, "C3'-endo" }} }, { "C6-N1-C2", "C2-N1-C6", "C6", "N1", "C2", 1, { { 125.100, 0.6, "s" } } }, { "N1-C2-N3", "N1-C2-N3", "N1", "C2", "N3", 1, { { 123.900, 0.6, "s" } } }, { "C2-N3-C4", "C2-N3-C4", "C2", "N3", "C4", 1, { { 111.900, 0.5, "s" } } }, { "N3-C4-C5", "C5-C4-N3", "N3", "C4", "C5", 1, { { 128.600, 0.5, "s" } } }, { "C4-C5-C6", "C4-C5-C6", "C4", "C5", "C6", 1, { { 118.800, 0.6, "s" } } }, { "C5-C6-N1", "C5-C6-N1", "C5", "C6", "N1", 1, { { 111.500, 0.5, "s" } } }, { "C4-C5-N7", "C4-C5-N7", "C4", "C5", "N7", 1, { { 110.800, 0.4, "s" } } }, { "C5-N7-C8", "C5-N7-C8", "C5", "N7", "C8", 1, { { 104.300, 0.5, "s" } } }, { "N7-C8-N9", "N7-C8-N9", "N7", "C8", "N9", 1, { { 113.100, 0.5, "s" } } }, { "C8-N9-C4", "C4-N9-C8", "C8", "N9", "C4", 1, { { 106.400, 0.4, "s" } } }, { "N9-C4-C5", "C5-C4-N9", "N9", "C4", "C5", 1, { { 105.400, 0.4, "s" } } }, { "N3-C4-N9", "N3-C4-N9", "N3", "C4", "N9", 1, { { 126.000, 0.6, "s" } } }, { "C6-C5-N7", "C6-C5-N7", "C6", "C5", "N7", 1, { { 130.400, 0.6, "s" } } }, { "N1-C2-N2", "N1-C2-N2", "N1", "C2", "N2", 1, { { 116.200, 0.9, "s" } } }, { "N3-C2-N2", "N2-C2-N3", "N3", "C2", "N2", 1, { { 119.900, 0.7, "s" } } }, { "N1-C6-O6", "N1-C6-O6", "N1", "C6", "O6", 1, { { 119.900, 0.6, "s" } } }, { "C5-C6-O6", "C5-C6-O6", "C5", "C6", "O6", 1, { { 128.600, 0.6, "s" } } }, { "C8-N9-C1'", "C1*-N9-C8", "C8", "N9", "C1*", 1, { { 127.000, 1.3, "s" } } }, { "C4-N9-C1'", "C1*-N9-C4", "C4", "N9", "C1*", 1, { { 126.500, 1.3, "s" } } } } }; MONOMER RG = { "G", 25, 37, // 26, 41, { { "P-O1P/O2P", "O1P-P", "P", "O1P", 1, { { 1.485, 0.017, "s" } } }, { "P-O1P/O2P", "O2P-P", "P", "O2P", 1, { { 1.485, 0.017, "s" } } }, { "P-O5'", "O5*-P", "P", "O5*", 1, { { 1.593, 0.010, "s" } } }, // { "P-O3'", "O3*-P", "P", "O3*", 1, { { 1.607, 0.012, "s" } } }, { "O5'-C5'", "C5*-O5*", "O5*", "C5*", 3, {{ 1.440, 0.016, "(P)O5'-C5'" }, { 1.424, 0.016, "(H)C2'-endo" }, { 1.420, 0.009, "(H)C3'-endo" }} }, { "C5'-C4'", "C4*-C5*", "C5*", "C4*", 2, {{ 1.509, 0.012, "C2'-endo" }, { 1.508, 0.007, "C3'-endo" }} }, { "C3'-C4'", "C3*-C4*", "C4*", "C3*", 2, {{ 1.527, 0.011, "C2'-endo" }, { 1.521, 0.010, "C3'-endo" }} }, { "C2'-C3'", "C2*-C3*", "C3*", "C2*", 2, {{ 1.525, 0.011, "C2'-endo" }, { 1.523, 0.011, "C3'-endo" }} }, { "C1'-C2'", "C1*-C2*", "C2*", "C1*", 2, {{ 1.526, 0.008, "C2'-endo" }, { 1.529, 0.011, "C3'-endo" }} }, { "O4'-C1'", "C1*-O4*", "O4*", "C1*", 2, {{ 1.415, 0.012, "C2'-endo" }, { 1.412, 0.013, "C3'-endo" }} }, { "C4'-O4'", "C4*-O4*", "O4*", "C4*", 2, {{ 1.454, 0.010, "C2'-endo" }, { 1.451, 0.013, "C3'-endo" }} }, { "C3'-O3'", "C3*-O3*", "O3*", "C3*", 2, {{ 1.427, 0.012, "C2'-endo" }, { 1.417, 0.014, "C3'-endo" }} }, { "C1'-N1/N9", "C1*-N9", "C1*", "N9", 2, {{ 1.464, 0.014, "C2'-endo" }, { 1.483, 0.015, "C3'-endo" }} }, { "C2'-O2'", "C2*-O2*", "C2*", "O2*", 2, {{ 1.412, 0.013, "C2'-endo" }, { 1.420, 0.010, "C3'-endo" }} }, { "N1-C2", "C2-N1", "N1", "C2", 1, { { 1.373, 0.008, "s" } } }, { "C2-N3", "C2-N3", "C2", "N3", 1, { { 1.323, 0.008, "s" } } }, { "N3-C4", "C4-N3", "N3", "C4", 1, { { 1.350, 0.007, "s" } } }, { "C4-C5", "C4-C5", "C4", "C5", 1, { { 1.379, 0.007, "s" } } }, { "C5-C6", "C5-C6", "C5", "C6", 1, { { 1.419, 0.010, "s" } } }, { "C6-N1", "C6-N1", "C6", "N1", 1, { { 1.391, 0.007, "s" } } }, { "C5-N7", "C5-N7", "C5", "N7", 1, { { 1.388, 0.006, "s" } } }, { "N7-C8", "C8-N7", "N7", "C8", 1, { { 1.305, 0.006, "s" } } }, { "C8-N9", "C8-N9", "C8", "N9", 1, { { 1.374, 0.007, "s" } } }, { "N9-C4", "C4-N9", "N9", "C4", 1, { { 1.375, 0.008, "s" } } }, { "C2-N2", "C2-N2", "C2", "N2", 1, { { 1.341, 0.010, "s" } } }, { "C6-O6", "C6-O6", "C6", "O6", 1, { { 1.237, 0.009, "s" } } } }, { { "O1P-P-O2P", "O1P-P-O2P", "O1P", "P", "O2P", 1, { { 119.600, 1.5, "s" } } }, { "O5'-P-O1P/O2P", "O1P-P-O5*", "O5*", "P", "O1P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, { "O5'-P-O1P/O2P", "O2P-P-O5*", "O5*", "P", "O2P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, /* { "O3'-P-O5'", "O3*-P-O5*", "O3*", "P", "O5*", 1, { { 104.000, 1.9, "s" } } }, { "O3'-P-O2P/O2P", "O2P-P-O3*", "O2P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, { "O3'-P-O1P/O2P", "O1P-P-O3*", "O1P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, */ { "O5'-C5'-C4'", "C4*-C5*-O5*", "O5*", "C5*", "C4*", 3, {{ 109.400, 0.8, "(P)O5'-C5'-C4'" }, { 111.700, 1.9, "C2'-endo" }, { 111.500, 1.6, "C3'-endo" }} }, { "P-O5'-C5'", "C5*-O5*-P", "P", "O5*", "C5*", 1, { { 120.900, 1.6, "s" } } }, /* { "C3'-O3'-P", "C3*-O3*-P", "P", "O3*", "C3*", 1, { { 119.700, 1.2, "s" } } }, */ { "C3'-C4'-O4'", "C3*-C4*-O4*", "O4*", "C4*", "C3*", 2, {{ 106.100, 0.8, "C2'-endo" }, { 104.000, 1.0, "C3'-endo" }} }, { "C5'-C4'-C3'", "C3*-C4*-C5*", "C5*", "C4*", "C3*", 2, {{ 115.200, 1.4, "C2'-endo" }, { 116.000, 1.6, "C3'-endo" }} }, { "C5'-C4'-O4'", "C5*-C4*-O4*", "C5*", "C4*", "O4*", 2, {{ 109.100, 1.2, "C2'-endo" }, { 109.800, 0.9, "C3'-endo" }} }, { "C4'-O4'-C1'", "C1*-O4*-C4*", "C1*", "O4*", "C4*", 2, {{ 109.700, 0.7, "C2'-endo" }, { 109.900, 0.8, "C3'-endo" }} }, { "C4'-C3'-O3'", "C4*-C3*-O3*", "C4*", "C3*", "O3*", 2, {{ 109.400, 2.1, "C2'-endo" }, { 113.000, 2.0, "C3'-endo" }} }, { "C2'-C3'-O3'", "C2*-C3*-O3*", "C2*", "C3*", "O3*", 2, {{ 109.500, 2.2, "C2'-endo" }, { 113.700, 1.6, "C3'-endo" }} }, { "C2'-C3'-C4'", "C2*-C3*-C4*", "C4*", "C3*", "C2*", 2, {{ 102.600, 1.0, "C2'-endo" }, { 102.600, 1.0, "C3'-endo" }} }, { "C1'-C2'-C3'", "C1*-C2*-C3*", "C3*", "C2*", "C1*", 2, {{ 101.500, 0.8, "C2'-endo" }, { 101.300, 0.7, "C3'-endo" }} }, { "O4'-C1'-C2'", "C2*-C1*-O4*", "O4*", "C1*", "C2*", 2, {{ 105.800, 1.0, "C2'-endo" }, { 107.600, 0.9, "C3'-endo" }} }, { "C2'-C1'-N1/N9", "C2*-C1*-N9", "N9", "C1*", "C2*", 2, {{ 114.000, 1.3, "C2'-endo" }, { 112.000, 1.1, "C3'-endo" }} }, { "O4'-C1'-N1/N9", "N9-C1*-O4*", "O4*", "C1*", "N9", 2, {{ 108.200, 0.8, "C2'-endo" }, { 108.500, 0.7, "C3'-endo" }} }, { "C1'-C2'-O2'", "C1*-C2*-O2*", "C1*", "C2*", "O2*", 1, { { 110.600, 3.0, "s" } } }, { "C3'-C2'-O2'", "C3*-C2*-O2*", "C3*", "C2*", "O2*", 1, { { 113.300, 2.9, "s" } } }, { "C6-N1-C2", "C2-N1-C6", "C6", "N1", "C2", 1, { { 125.100, 0.6, "s" } } }, { "N1-C2-N3", "N1-C2-N3", "N1", "C2", "N3", 1, { { 123.900, 0.6, "s" } } }, { "C2-N3-C4", "C2-N3-C4", "C2", "N3", "C4", 1, { { 111.900, 0.5, "s" } } }, { "N3-C4-C5", "C5-C4-N3", "N3", "C4", "C5", 1, { { 128.600, 0.5, "s" } } }, { "C4-C5-C6", "C4-C5-C6", "C4", "C5", "C6", 1, { { 118.800, 0.6, "s" } } }, { "C5-C6-N1", "C5-C6-N1", "C5", "C6", "N1", 1, { { 111.500, 0.5, "s" } } }, { "C4-C5-N7", "C4-C5-N7", "C4", "C5", "N7", 1, { { 110.800, 0.4, "s" } } }, { "C5-N7-C8", "C5-N7-C8", "C5", "N7", "C8", 1, { { 104.300, 0.5, "s" } } }, { "N7-C8-N9", "N7-C8-N9", "N7", "C8", "N9", 1, { { 113.100, 0.5, "s" } } }, { "C8-N9-C4", "C4-N9-C8", "C8", "N9", "C4", 1, { { 106.400, 0.4, "s" } } }, { "N9-C4-C5", "C5-C4-N9", "N9", "C4", "C5", 1, { { 105.400, 0.4, "s" } } }, { "N3-C4-N9", "N3-C4-N9", "N3", "C4", "N9", 1, { { 126.000, 0.6, "s" } } }, { "C6-C5-N7", "C6-C5-N7", "C6", "C5", "N7", 1, { { 130.400, 0.6, "s" } } }, { "N1-C2-N2", "N1-C2-N2", "N1", "C2", "N2", 1, { { 116.200, 0.9, "s" } } }, { "N3-C2-N2", "N2-C2-N3", "N3", "C2", "N2", 1, { { 119.900, 0.7, "s" } } }, { "N1-C6-O6", "N1-C6-O6", "N1", "C6", "O6", 1, { { 119.900, 0.6, "s" } } }, { "C5-C6-O6", "C5-C6-O6", "C5", "C6", "O6", 1, { { 128.600, 0.6, "s" } } }, { "C8-N9-C1'", "C1*-N9-C8", "C8", "N9", "C1*", 1, { { 127.000, 1.3, "s" } } }, { "C4-N9-C1'", "C1*-N9-C4", "C4", "N9", "C1*", 1, { { 126.500, 1.3, "s" } } } } }; MONOMER DT = { "T", 21, 30, // 22, 34, { { "P-O1P/O2P", "O1P-P", "P", "O1P", 1, { { 1.485, 0.017, "s" } } }, { "P-O1P/O2P", "O2P-P", "P", "O2P", 1, { { 1.485, 0.017, "s" } } }, { "P-O5'", "O5*-P", "P", "O5*", 1, { { 1.593, 0.010, "s" } } }, // { "P-O3'", "O3*-P", "P", "O3*", 1, { { 1.607, 0.012, "s" } } }, { "O5'-C5'", "C5*-O5*", "O5*", "C5*", 3, {{ 1.440, 0.016, "(P)O5'-C5'" }, { 1.418, 0.025, "(H)C2'-endo" }, { 1.423, 0.011, "(H)C3'-endo" }} }, { "C5'-C4'", "C4*-C5*", "C5*", "C4*", 2, {{ 1.512, 0.007, "C2'-endo" }, { 1.509, 0.011, "C3'-endo" }} }, { "C3'-C4'", "C3*-C4*", "C4*", "C3*", 2, {{ 1.529, 0.010, "C2'-endo" }, { 1.521, 0.010, "C3'-endo" }} }, { "C2'-C3'", "C2*-C3*", "C3*", "C2*", 2, {{ 1.516, 0.008, "C2'-endo" }, { 1.518, 0.012, "C3'-endo" }} }, { "C1'-C2'", "C1*-C2*", "C2*", "C1*", 2, {{ 1.518, 0.010, "C2'-endo" }, { 1.519, 0.010, "C3'-endo" }} }, { "O4'-C1'", "C1*-O4*", "O4*", "C1*", 2, {{ 1.420, 0.011, "C2'-endo" }, { 1.418, 0.012, "C3'-endo" }} }, { "C4'-O4'", "C4*-O4*", "O4*", "C4*", 2, {{ 1.446, 0.010, "C2'-endo" }, { 1.449, 0.009, "C3'-endo" }} }, { "C3'-O3'", "C3*-O3*", "O3*", "C3*", 2, {{ 1.435, 0.013, "C2'-endo" }, { 1.419, 0.006, "C3'-endo" }} }, { "C1'-N1/N9", "C1*-N1", "C1*", "N1", 2, {{ 1.468, 0.014, "C2'-endo" }, { 1.488, 0.013, "C3'-endo" }} }, { "N1-C2", "C2-N1", "N1", "C2", 1, { { 1.376, 0.008, "s" } } }, { "C2-N3", "C2-N3", "C2", "N3", 1, { { 1.373, 0.008, "s" } } }, { "N3-C4", "C4-N3", "N3", "C4", 1, { { 1.382, 0.008, "s" } } }, { "C4-C5", "C4-C5", "C4", "C5", 1, { { 1.445, 0.009, "s" } } }, { "C5-C6", "C5-C6", "C5", "C6", 1, { { 1.339, 0.007, "s" } } }, { "C6-N1", "C6-N1", "C6", "N1", 1, { { 1.378, 0.007, "s" } } }, { "C2-O2", "C2-O2", "C2", "O2", 1, { { 1.220, 0.008, "s" } } }, { "C4-O4", "C4-O4", "C4", "O4", 1, { { 1.228, 0.009, "s" } } }, { "C5-C5M", "C5-C5M", "C5", "C5M", 1, { { 1.496, 0.006, "s" } } } }, { { "O1P-P-O2P", "O1P-P-O2P", "O1P", "P", "O2P", 1, { { 119.600, 1.5, "s" } } }, { "O5'-P-O1P/O2P", "O1P-P-O5*", "O5*", "P", "O1P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, { "O5'-P-O1P/O2P", "O2P-P-O5*", "O5*", "P", "O2P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, /* { "O3'-P-O5'", "O3*-P-O5*", "O3*", "P", "O5*", 1, { { 104.000, 1.9, "s" } } }, { "O3'-P-O2P/O2P", "O2P-P-O3*", "O2P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, { "O3'-P-O1P/O2P", "O1P-P-O3*", "O1P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, */ { "O5'-C5'-C4'", "C4*-C5*-O5*", "O5*", "C5*", "C4*", 3, {{ 109.400, 0.8, "(P)O5'-C5'-C4'" }, { 110.900, 1.7, "C2'-endo" }, { 111.000, 2.5, "C3'-endo" }} }, { "P-O5'-C5'", "C5*-O5*-P", "P", "O5*", "C5*", 1, { { 120.900, 1.6, "s" } } }, /* { "C3'-O3'-P", "C3*-O3*-P", "P", "O3*", "C3*", 1, { { 119.700, 1.2, "s" } } }, */ { "C3'-C4'-O4'", "C3*-C4*-O4*", "O4*", "C4*", "C3*", 2, {{ 106.000, 0.6, "C2'-endo" }, { 104.500, 0.4, "C3'-endo" }} }, { "C5'-C4'-C3'", "C3*-C4*-C5*", "C5*", "C4*", "C3*", 2, {{ 114.100, 1.8, "C2'-endo" }, { 115.700, 1.2, "C3'-endo" }} }, { "C5'-C4'-O4'", "C5*-C4*-O4*", "C5*", "C4*", "O4*", 2, {{ 109.300, 1.9, "C2'-endo" }, { 109.800, 1.1, "C3'-endo" }} }, { "C4'-O4'-C1'", "C1*-O4*-C4*", "C1*", "O4*", "C4*", 2, {{ 110.100, 1.0, "C2'-endo" }, { 110.300, 0.7, "C3'-endo" }} }, { "C4'-C3'-O3'", "C4*-C3*-O3*", "C4*", "C3*", "O3*", 2, {{ 109.700, 2.5, "C2'-endo" }, { 112.300, 2.0, "C3'-endo" }} }, { "C2'-C3'-O3'", "C2*-C3*-O3*", "C2*", "C3*", "O3*", 2, {{ 109.400, 2.5, "C2'-endo" }, { 112.600, 3.3, "C3'-endo" }} }, { "C2'-C3'-C4'", "C2*-C3*-C4*", "C4*", "C3*", "C2*", 2, {{ 103.100, 0.9, "C2'-endo" }, { 102.200, 0.7, "C3'-endo" }} }, { "C1'-C2'-C3'", "C1*-C2*-C3*", "C3*", "C2*", "C1*", 2, {{ 102.500, 1.2, "C2'-endo" }, { 102.400, 0.8, "C3'-endo" }} }, { "O4'-C1'-C2'", "C2*-C1*-O4*", "O4*", "C1*", "C2*", 2, {{ 105.900, 0.8, "C2'-endo" }, { 106.800, 0.5, "C3'-endo" }} }, { "C2'-C1'-N1/N9", "C2*-C1*-N1", "N1", "C1*", "C2*", 2, {{ 114.300, 1.4, "C2'-endo" }, { 112.600, 1.9, "C3'-endo" }} }, { "O4'-C1'-N1/N9", "N1-C1*-O4*", "O4*", "C1*", "N1", 2, {{ 108.000, 0.7, "C2'-endo" }, { 108.300, 0.3, "C3'-endo" }} }, { "C6-N1-C2", "C2-N1-C6", "C6", "N1", "C2", 1, { { 121.300, 0.5, "s" } } }, { "N1-C2-N3", "N1-C2-N3", "N1", "C2", "N3", 1, { { 114.600, 0.6, "s" } } }, { "C2-N3-C4", "C2-N3-C4", "C2", "N3", "C4", 1, { { 127.200, 0.6, "s" } } }, { "N3-C4-C5", "C5-C4-N3", "N3", "C4", "C5", 1, { { 115.200, 0.6, "s" } } }, { "C4-C5-C6", "C4-C5-C6", "C4", "C5", "C6", 1, { { 118.000, 0.6, "s" } } }, { "C5-C6-N1", "C5-C6-N1", "C5", "C6", "N1", 1, { { 123.700, 0.6, "s" } } }, { "N1-C2-O2", "N1-C2-O2", "N1", "C2", "O2", 1, { { 123.100, 0.8, "s" } } }, { "N3-C2-O2", "N3-C2-O2", "N3", "C2", "O2", 1, { { 122.300, 0.6, "s" } } }, { "N3-C4-O4", "N3-C4-O4", "N3", "C4", "O4", 1, { { 119.900, 0.6, "s" } } }, { "C5-C4-O4", "C5-C4-O4", "C5", "C4", "O4", 1, { { 124.900, 0.7, "s" } } }, { "C4-C5-C5M", "C4-C5-C5M", "C4", "C5", "C5M", 1, { { 119.000, 0.6, "s" } } }, { "C6-C5-C5M", "C5M-C5-C6", "C6", "C5", "C5M", 1, { { 122.900, 0.6, "s" } } }, { "C6-N1-C1'", "C1*-N1-C6", "C6", "N1", "C1*", 1, { { 120.400, 1.5, "s" } } }, { "C2-N1-C1'", "C1*-N1-C2", "C2", "N1", "C1*", 1, { { 118.200, 1.6, "s" } } } } }; MONOMER RT = { "T", 22, 32, // 23, 36, { { "P-O1P/O2P", "O1P-P", "P", "O1P", 1, { { 1.485, 0.017, "s" } } }, { "P-O1P/O2P", "O2P-P", "P", "O2P", 1, { { 1.485, 0.017, "s" } } }, { "P-O5'", "O5*-P", "P", "O5*", 1, { { 1.593, 0.010, "s" } } }, // { "P-O3'", "O3*-P", "P", "O3*", 1, { { 1.607, 0.012, "s" } } }, { "O5'-C5'", "C5*-O5*", "O5*", "C5*", 3, {{ 1.440, 0.016, "(P)O5'-C5'" }, { 1.424, 0.016, "(H)C2'-endo" }, { 1.420, 0.009, "(H)C3'-endo" }} }, { "C5'-C4'", "C4*-C5*", "C5*", "C4*", 2, {{ 1.509, 0.012, "C2'-endo" }, { 1.508, 0.007, "C3'-endo" }} }, { "C3'-C4'", "C3*-C4*", "C4*", "C3*", 2, {{ 1.527, 0.011, "C2'-endo" }, { 1.521, 0.010, "C3'-endo" }} }, { "C2'-C3'", "C2*-C3*", "C3*", "C2*", 2, {{ 1.525, 0.011, "C2'-endo" }, { 1.523, 0.011, "C3'-endo" }} }, { "C1'-C2'", "C1*-C2*", "C2*", "C1*", 2, {{ 1.526, 0.008, "C2'-endo" }, { 1.529, 0.011, "C3'-endo" }} }, { "O4'-C1'", "C1*-O4*", "O4*", "C1*", 2, {{ 1.415, 0.012, "C2'-endo" }, { 1.412, 0.013, "C3'-endo" }} }, { "C4'-O4'", "C4*-O4*", "O4*", "C4*", 2, {{ 1.454, 0.010, "C2'-endo" }, { 1.451, 0.013, "C3'-endo" }} }, { "C3'-O3'", "C3*-O3*", "O3*", "C3*", 2, {{ 1.427, 0.012, "C2'-endo" }, { 1.417, 0.014, "C3'-endo" }} }, { "C1'-N1/N9", "C1*-N1", "C1*", "N1", 2, {{ 1.464, 0.014, "C2'-endo" }, { 1.483, 0.015, "C3'-endo" }} }, { "C2'-O2'", "C2*-O2*", "C2*", "O2*", 2, {{ 1.412, 0.013, "C2'-endo" }, { 1.420, 0.010, "C3'-endo" }} }, { "N1-C2", "C2-N1", "N1", "C2", 1, { { 1.376, 0.008, "s" } } }, { "C2-N3", "C2-N3", "C2", "N3", 1, { { 1.373, 0.008, "s" } } }, { "N3-C4", "C4-N3", "N3", "C4", 1, { { 1.382, 0.008, "s" } } }, { "C4-C5", "C4-C5", "C4", "C5", 1, { { 1.445, 0.009, "s" } } }, { "C5-C6", "C5-C6", "C5", "C6", 1, { { 1.339, 0.007, "s" } } }, { "C6-N1", "C6-N1", "C6", "N1", 1, { { 1.378, 0.007, "s" } } }, { "C2-O2", "C2-O2", "C2", "O2", 1, { { 1.220, 0.008, "s" } } }, { "C4-O4", "C4-O4", "C4", "O4", 1, { { 1.228, 0.009, "s" } } }, { "C5-C5M", "C5-C5M", "C5", "C5M", 1, { { 1.496, 0.006, "s" } } } }, { { "O1P-P-O2P", "O1P-P-O2P", "O1P", "P", "O2P", 1, { { 119.600, 1.5, "s" } } }, { "O5'-P-O1P/O2P", "O1P-P-O5*", "O5*", "P", "O1P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, { "O5'-P-O1P/O2P", "O2P-P-O5*", "O5*", "P", "O2P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, /* { "O3'-P-O5'", "O3*-P-O5*", "O3*", "P", "O5*", 1, { { 104.000, 1.9, "s" } } }, { "O3'-P-O2P/O2P", "O2P-P-O3*", "O2P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, { "O3'-P-O1P/O2P", "O1P-P-O3*", "O1P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, */ { "O5'-C5'-C4'", "C4*-C5*-O5*", "O5*", "C5*", "C4*", 3, {{ 109.400, 0.8, "(P)O5'-C5'-C4'" }, { 111.700, 1.9, "C2'-endo" }, { 111.500, 1.6, "C3'-endo" }} }, { "P-O5'-C5'", "C5*-O5*-P", "P", "O5*", "C5*", 1, { { 120.900, 1.6, "s" } } }, /* { "C3'-O3'-P", "C3*-O3*-P", "P", "O3*", "C3*", 1, { { 119.700, 1.2, "s" } } }, */ { "C3'-C4'-O4'", "C3*-C4*-O4*", "O4*", "C4*", "C3*", 2, {{ 106.100, 0.8, "C2'-endo" }, { 104.000, 1.0, "C3'-endo" }} }, { "C5'-C4'-C3'", "C3*-C4*-C5*", "C5*", "C4*", "C3*", 2, {{ 115.200, 1.4, "C2'-endo" }, { 116.000, 1.6, "C3'-endo" }} }, { "C5'-C4'-O4'", "C5*-C4*-O4*", "C5*", "C4*", "O4*", 2, {{ 109.100, 1.2, "C2'-endo" }, { 109.800, 0.9, "C3'-endo" }} }, { "C4'-O4'-C1'", "C1*-O4*-C4*", "C1*", "O4*", "C4*", 2, {{ 109.700, 0.7, "C2'-endo" }, { 109.900, 0.8, "C3'-endo" }} }, { "C4'-C3'-O3'", "C4*-C3*-O3*", "C4*", "C3*", "O3*", 2, {{ 109.400, 2.1, "C2'-endo" }, { 113.000, 2.0, "C3'-endo" }} }, { "C2'-C3'-O3'", "C2*-C3*-O3*", "C2*", "C3*", "O3*", 2, {{ 109.500, 2.2, "C2'-endo" }, { 113.700, 1.6, "C3'-endo" }} }, { "C2'-C3'-C4'", "C2*-C3*-C4*", "C4*", "C3*", "C2*", 2, {{ 102.600, 1.0, "C2'-endo" }, { 102.600, 1.0, "C3'-endo" }} }, { "C1'-C2'-C3'", "C1*-C2*-C3*", "C3*", "C2*", "C1*", 2, {{ 101.500, 0.8, "C2'-endo" }, { 101.300, 0.7, "C3'-endo" }} }, { "O4'-C1'-C2'", "C2*-C1*-O4*", "O4*", "C1*", "C2*", 2, {{ 105.800, 1.0, "C2'-endo" }, { 107.600, 0.9, "C3'-endo" }} }, { "C2'-C1'-N1/N9", "C2*-C1*-N1", "N1", "C1*", "C2*", 2, {{ 114.000, 1.3, "C2'-endo" }, { 112.000, 1.1, "C3'-endo" }} }, { "O4'-C1'-N1/N9", "N1-C1*-O4*", "O4*", "C1*", "N1", 2, {{ 108.200, 0.8, "C2'-endo" }, { 108.500, 0.7, "C3'-endo" }} }, { "C1'-C2'-O2'", "C1*-C2*-O2*", "C1*", "C2*", "O2*", 1, { { 110.600, 3.0, "s" } } }, { "C3'-C2'-O2'", "C3*-C2*-O2*", "C3*", "C2*", "O2*", 1, { { 113.300, 2.9, "s" } } }, { "C6-N1-C2", "C2-N1-C6", "C6", "N1", "C2", 1, { { 121.300, 0.5, "s" } } }, { "N1-C2-N3", "N1-C2-N3", "N1", "C2", "N3", 1, { { 114.600, 0.6, "s" } } }, { "C2-N3-C4", "C2-N3-C4", "C2", "N3", "C4", 1, { { 127.200, 0.6, "s" } } }, { "N3-C4-C5", "C5-C4-N3", "N3", "C4", "C5", 1, { { 115.200, 0.6, "s" } } }, { "C4-C5-C6", "C4-C5-C6", "C4", "C5", "C6", 1, { { 118.000, 0.6, "s" } } }, { "C5-C6-N1", "C5-C6-N1", "C5", "C6", "N1", 1, { { 123.700, 0.6, "s" } } }, { "N1-C2-O2", "N1-C2-O2", "N1", "C2", "O2", 1, { { 123.100, 0.8, "s" } } }, { "N3-C2-O2", "N3-C2-O2", "N3", "C2", "O2", 1, { { 122.300, 0.6, "s" } } }, { "N3-C4-O4", "N3-C4-O4", "N3", "C4", "O4", 1, { { 119.900, 0.6, "s" } } }, { "C5-C4-O4", "C5-C4-O4", "C5", "C4", "O4", 1, { { 124.900, 0.7, "s" } } }, { "C4-C5-C5M", "C4-C5-C5M", "C4", "C5", "C5M", 1, { { 119.000, 0.6, "s" } } }, { "C6-C5-C5M", "C5M-C5-C6", "C6", "C5", "C5M", 1, { { 122.900, 0.6, "s" } } }, { "C6-N1-C1'", "C1*-N1-C6", "C6", "N1", "C1*", 1, { { 120.400, 1.5, "s" } } }, { "C2-N1-C1'", "C1*-N1-C2", "C2", "N1", "C1*", 1, { { 118.200, 1.6, "s" } } } } }; MONOMER DU = { "U", 20, 28, // 21, 32, { { "P-O1P/O2P", "O1P-P", "P", "O1P", 1, { { 1.485, 0.017, "s" } } }, { "P-O1P/O2P", "O2P-P", "P", "O2P", 1, { { 1.485, 0.017, "s" } } }, { "P-O5'", "O5*-P", "P", "O5*", 1, { { 1.593, 0.010, "s" } } }, // { "P-O3'", "O3*-P", "P", "O3*", 1, { { 1.607, 0.012, "s" } } }, { "O5'-C5'", "C5*-O5*", "O5*", "C5*", 3, {{ 1.440, 0.016, "(P)O5'-C5'" }, { 1.418, 0.025, "(H)C2'-endo" }, { 1.423, 0.011, "(H)C3'-endo" }} }, { "C5'-C4'", "C4*-C5*", "C5*", "C4*", 2, {{ 1.512, 0.007, "C2'-endo" }, { 1.509, 0.011, "C3'-endo" }} }, { "C3'-C4'", "C3*-C4*", "C4*", "C3*", 2, {{ 1.529, 0.010, "C2'-endo" }, { 1.521, 0.010, "C3'-endo" }} }, { "C2'-C3'", "C2*-C3*", "C3*", "C2*", 2, {{ 1.516, 0.008, "C2'-endo" }, { 1.518, 0.012, "C3'-endo" }} }, { "C1'-C2'", "C1*-C2*", "C2*", "C1*", 2, {{ 1.518, 0.010, "C2'-endo" }, { 1.519, 0.010, "C3'-endo" }} }, { "O4'-C1'", "C1*-O4*", "O4*", "C1*", 2, {{ 1.420, 0.011, "C2'-endo" }, { 1.418, 0.012, "C3'-endo" }} }, { "C4'-O4'", "C4*-O4*", "O4*", "C4*", 2, {{ 1.446, 0.010, "C2'-endo" }, { 1.449, 0.009, "C3'-endo" }} }, { "C3'-O3'", "C3*-O3*", "O3*", "C3*", 2, {{ 1.435, 0.013, "C2'-endo" }, { 1.419, 0.006, "C3'-endo" }} }, { "C1'-N1/N9", "C1*-N1", "C1*", "N1", 2, {{ 1.468, 0.014, "C2'-endo" }, { 1.488, 0.013, "C3'-endo" }} }, { "C2-O2", "C2-O2", "C2", "O2", 1, { { 1.219, 0.009, "s" } } }, { "C4-O4", "C4-O4", "C4", "O4", 1, { { 1.232, 0.008, "s" } } }, { "N1-C2", "C2-N1", "N1", "C2", 1, { { 1.381, 0.009, "s" } } }, { "C6-N1", "C6-N1", "N1", "C6", 1, { { 1.375, 0.009, "s" } } }, { "C2-N3", "C2-N3", "C2", "N3", 1, { { 1.373, 0.007, "s" } } }, { "N3-C4", "C4-N3", "N3", "C4", 1, { { 1.380, 0.009, "s" } } }, { "C4-C5", "C4-C5", "C4", "C5", 1, { { 1.431, 0.009, "s" } } }, { "C5-C6", "C5-C6", "C5", "C6", 1, { { 1.337, 0.009, "s" } } } }, { { "O1P-P-O2P", "O1P-P-O2P", "O1P", "P", "O2P", 1, { { 119.600, 1.5, "s" } } }, { "O5'-P-O1P/O2P", "O1P-P-O5*", "O5*", "P", "O1P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, { "O5'-P-O1P/O2P", "O2P-P-O5*", "O5*", "P", "O2P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, /* { "O3'-P-O5'", "O3*-P-O5*", "O3*", "P", "O5*", 1, { { 104.000, 1.9, "s" } } }, { "O3'-P-O2P/O2P", "O2P-P-O3*", "O2P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, { "O3'-P-O1P/O2P", "O1P-P-O3*", "O1P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, */ { "O5'-C5'-C4'", "C4*-C5*-O5*", "O5*", "C5*", "C4*", 3, {{ 109.400, 0.8, "(P)O5'-C5'-C4'" }, { 110.900, 1.7, "C2'-endo" }, { 111.000, 2.5, "C3'-endo" }} }, { "P-O5'-C5'", "C5*-O5*-P", "P", "O5*", "C5*", 1, { { 120.900, 1.6, "s" } } }, /* { "C3'-O3'-P", "C3*-O3*-P", "P", "O3*", "C3*", 1, { { 119.700, 1.2, "s" } } }, */ { "C3'-C4'-O4'", "C3*-C4*-O4*", "O4*", "C4*", "C3*", 2, {{ 106.000, 0.6, "C2'-endo" }, { 104.500, 0.4, "C3'-endo" }} }, { "C5'-C4'-C3'", "C3*-C4*-C5*", "C5*", "C4*", "C3*", 2, {{ 114.100, 1.8, "C2'-endo" }, { 115.700, 1.2, "C3'-endo" }} }, { "C5'-C4'-O4'", "C5*-C4*-O4*", "C5*", "C4*", "O4*", 2, {{ 109.300, 1.9, "C2'-endo" }, { 109.800, 1.1, "C3'-endo" }} }, { "C4'-O4'-C1'", "C1*-O4*-C4*", "C1*", "O4*", "C4*", 2, {{ 110.100, 1.0, "C2'-endo" }, { 110.300, 0.7, "C3'-endo" }} }, { "C4'-C3'-O3'", "C4*-C3*-O3*", "C4*", "C3*", "O3*", 2, {{ 109.700, 2.5, "C2'-endo" }, { 112.300, 2.0, "C3'-endo" }} }, { "C2'-C3'-O3'", "C2*-C3*-O3*", "C2*", "C3*", "O3*", 2, {{ 109.400, 2.5, "C2'-endo" }, { 112.600, 3.3, "C3'-endo" }} }, { "C2'-C3'-C4'", "C2*-C3*-C4*", "C4*", "C3*", "C2*", 2, {{ 103.100, 0.9, "C2'-endo" }, { 102.200, 0.7, "C3'-endo" }} }, { "C1'-C2'-C3'", "C1*-C2*-C3*", "C3*", "C2*", "C1*", 2, {{ 102.500, 1.2, "C2'-endo" }, { 102.400, 0.8, "C3'-endo" }} }, { "O4'-C1'-C2'", "C2*-C1*-O4*", "O4*", "C1*", "C2*", 2, {{ 105.900, 0.8, "C2'-endo" }, { 106.800, 0.5, "C3'-endo" }} }, { "C2'-C1'-N1/N9", "C2*-C1*-N1", "N1", "C1*", "C2*", 2, {{ 114.300, 1.4, "C2'-endo" }, { 112.600, 1.9, "C3'-endo" }} }, { "O4'-C1'-N1/N9", "N1-C1*-O4*", "O4*", "C1*", "N1", 2, {{ 108.000, 0.7, "C2'-endo" }, { 108.300, 0.3, "C3'-endo" }} }, { "C6-N1-C2", "C2-N1-C6", "C6", "N1", "C2", 1, { { 121.000, 0.6, "s" } } }, { "N1-C2-N3", "N1-C2-N3", "N1", "C2", "N3", 1, { { 114.900, 0.6, "s" } } }, { "C2-N3-C4", "C2-N3-C4", "C2", "N3", "C4", 1, { { 127.000, 0.6, "s" } } }, { "N3-C4-C5", "C5-C4-N3", "N3", "C4", "C5", 1, { { 114.600, 0.6, "s" } } }, { "C4-C5-C6", "C4-C5-C6", "C4", "C5", "C6", 1, { { 119.700, 0.6, "s" } } }, { "C5-C6-N1", "C5-C6-N1", "C5", "C6", "N1", 1, { { 122.700, 0.5, "s" } } }, { "N1-C2-O2", "N1-C2-O2", "N1", "C2", "O2", 1, { { 122.800, 0.7, "s" } } }, { "N3-C2-O2", "N3-C2-O2", "N3", "C2", "O2", 1, { { 122.200, 0.7, "s" } } }, { "N3-C4-O4", "N3-C4-O4", "N3", "C4", "O4", 1, { { 119.400, 0.7, "s" } } }, { "C5-C4-O4", "C5-C4-O4", "C5", "C4", "O4", 1, { { 125.900, 0.6, "s" } } }, { "C6-N1-C1'", "C1*-N1-C6", "C6", "N1", "C1*", 1, { { 121.200, 1.4, "s" } } }, { "C2-N1-C1'", "C1*-N1-C2", "C2", "N1", "C1*", 1, { { 117.700, 1.2, "s" } } } } }; MONOMER RU = { "U", 21, 30, // 22, 34, { { "P-O1P/O2P", "O1P-P", "P", "O1P", 1, { { 1.485, 0.017, "s" } } }, { "P-O1P/O2P", "O2P-P", "P", "O2P", 1, { { 1.485, 0.017, "s" } } }, { "P-O5'", "O5*-P", "P", "O5*", 1, { { 1.593, 0.010, "s" } } }, // { "P-O3'", "O3*-P", "P", "O3*", 1, { { 1.607, 0.012, "s" } } }, { "O5'-C5'", "C5*-O5*", "O5*", "C5*", 3, {{ 1.440, 0.016, "(P)O5'-C5'" }, { 1.424, 0.016, "(H)C2'-endo" }, { 1.420, 0.009, "(H)C3'-endo" }} }, { "C5'-C4'", "C4*-C5*", "C5*", "C4*", 2, {{ 1.509, 0.012, "C2'-endo" }, { 1.508, 0.007, "C3'-endo" }} }, { "C3'-C4'", "C3*-C4*", "C4*", "C3*", 2, {{ 1.527, 0.011, "C2'-endo" }, { 1.521, 0.010, "C3'-endo" }} }, { "C2'-C3'", "C2*-C3*", "C3*", "C2*", 2, {{ 1.525, 0.011, "C2'-endo" }, { 1.523, 0.011, "C3'-endo" }} }, { "C1'-C2'", "C1*-C2*", "C2*", "C1*", 2, {{ 1.526, 0.008, "C2'-endo" }, { 1.529, 0.011, "C3'-endo" }} }, { "O4'-C1'", "C1*-O4*", "O4*", "C1*", 2, {{ 1.415, 0.012, "C2'-endo" }, { 1.412, 0.013, "C3'-endo" }} }, { "C4'-O4'", "C4*-O4*", "O4*", "C4*", 2, {{ 1.454, 0.010, "C2'-endo" }, { 1.451, 0.013, "C3'-endo" }} }, { "C3'-O3'", "C3*-O3*", "O3*", "C3*", 2, {{ 1.427, 0.012, "C2'-endo" }, { 1.417, 0.014, "C3'-endo" }} }, { "C1'-N1/N9", "C1*-N1", "C1*", "N1", 2, {{ 1.464, 0.014, "C2'-endo" }, { 1.483, 0.015, "C3'-endo" }} }, { "C2'-O2'", "C2*-O2*", "C2*", "O2*", 2, {{ 1.412, 0.013, "C2'-endo" }, { 1.420, 0.010, "C3'-endo" }} }, { "C2-O2", "C2-O2", "C2", "O2", 1, { { 1.219, 0.009, "s" } } }, { "C4-O4", "C4-O4", "C4", "O4", 1, { { 1.232, 0.008, "s" } } }, { "N1-C2", "C2-N1", "N1", "C2", 1, { { 1.381, 0.009, "s" } } }, { "C6-N1", "C6-N1", "N1", "C6", 1, { { 1.375, 0.009, "s" } } }, { "C2-N3", "C2-N3", "C2", "N3", 1, { { 1.373, 0.007, "s" } } }, { "N3-C4", "C4-N3", "N3", "C4", 1, { { 1.380, 0.009, "s" } } }, { "C4-C5", "C4-C5", "C4", "C5", 1, { { 1.431, 0.009, "s" } } }, { "C5-C6", "C5-C6", "C5", "C6", 1, { { 1.337, 0.009, "s" } } } }, { { "O1P-P-O2P", "O1P-P-O2P", "O1P", "P", "O2P", 1, { { 119.600, 1.5, "s" } } }, { "O5'-P-O1P/O2P", "O1P-P-O5*", "O5*", "P", "O1P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, { "O5'-P-O1P/O2P", "O2P-P-O5*", "O5*", "P", "O2P", 2, {{ 110.700, 1.2, "large" }, { 105.700, 0.9, "small" }} }, /* { "O3'-P-O5'", "O3*-P-O5*", "O3*", "P", "O5*", 1, { { 104.000, 1.9, "s" } } }, { "O3'-P-O2P/O2P", "O2P-P-O3*", "O2P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, { "O3'-P-O1P/O2P", "O1P-P-O3*", "O1P", "P", "O3*", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, */ { "O5'-C5'-C4'", "C4*-C5*-O5*", "O5*", "C5*", "C4*", 3, {{ 109.400, 0.8, "(P)O5'-C5'-C4'" }, { 111.700, 1.9, "C2'-endo" }, { 111.500, 1.6, "C3'-endo" }} }, { "P-O5'-C5'", "C5*-O5*-P", "P", "O5*", "C5*", 1, { { 120.900, 1.6, "s" } } }, /* { "C3'-O3'-P", "C3*-O3*-P", "P", "O3*", "C3*", 1, { { 119.700, 1.2, "s" } } }, */ { "C3'-C4'-O4'", "C3*-C4*-O4*", "O4*", "C4*", "C3*", 2, {{ 106.100, 0.8, "C2'-endo" }, { 104.000, 1.0, "C3'-endo" }} }, { "C5'-C4'-C3'", "C3*-C4*-C5*", "C5*", "C4*", "C3*", 2, {{ 115.200, 1.4, "C2'-endo" }, { 116.000, 1.6, "C3'-endo" }} }, { "C5'-C4'-O4'", "C5*-C4*-O4*", "C5*", "C4*", "O4*", 2, {{ 109.100, 1.2, "C2'-endo" }, { 109.800, 0.9, "C3'-endo" }} }, { "C4'-O4'-C1'", "C1*-O4*-C4*", "C1*", "O4*", "C4*", 2, {{ 109.700, 0.7, "C2'-endo" }, { 109.900, 0.8, "C3'-endo" }} }, { "C4'-C3'-O3'", "C4*-C3*-O3*", "C4*", "C3*", "O3*", 2, {{ 109.400, 2.1, "C2'-endo" }, { 113.000, 2.0, "C3'-endo" }} }, { "C2'-C3'-O3'", "C2*-C3*-O3*", "C2*", "C3*", "O3*", 2, {{ 109.500, 2.2, "C2'-endo" }, { 113.700, 1.6, "C3'-endo" }} }, { "C2'-C3'-C4'", "C2*-C3*-C4*", "C4*", "C3*", "C2*", 2, {{ 102.600, 1.0, "C2'-endo" }, { 102.600, 1.0, "C3'-endo" }} }, { "C1'-C2'-C3'", "C1*-C2*-C3*", "C3*", "C2*", "C1*", 2, {{ 101.500, 0.8, "C2'-endo" }, { 101.300, 0.7, "C3'-endo" }} }, { "O4'-C1'-C2'", "C2*-C1*-O4*", "O4*", "C1*", "C2*", 2, {{ 105.800, 1.0, "C2'-endo" }, { 107.600, 0.9, "C3'-endo" }} }, { "C2'-C1'-N1/N9", "C2*-C1*-N1", "N1", "C1*", "C2*", 2, {{ 114.000, 1.3, "C2'-endo" }, { 112.000, 1.1, "C3'-endo" }} }, { "O4'-C1'-N1/N9", "N1-C1*-O4*", "O4*", "C1*", "N1", 2, {{ 108.200, 0.8, "C2'-endo" }, { 108.500, 0.7, "C3'-endo" }} }, { "C1'-C2'-O2'", "C1*-C2*-O2*", "C1*", "C2*", "O2*", 1, { { 110.600, 3.0, "s" } } }, { "C3'-C2'-O2'", "C3*-C2*-O2*", "C3*", "C2*", "O2*", 1, { { 113.300, 2.9, "s" } } }, { "C6-N1-C2", "C2-N1-C6", "C6", "N1", "C2", 1, { { 121.000, 0.6, "s" } } }, { "N1-C2-N3", "N1-C2-N3", "N1", "C2", "N3", 1, { { 114.900, 0.6, "s" } } }, { "C2-N3-C4", "C2-N3-C4", "C2", "N3", "C4", 1, { { 127.000, 0.6, "s" } } }, { "N3-C4-C5", "C5-C4-N3", "N3", "C4", "C5", 1, { { 114.600, 0.6, "s" } } }, { "C4-C5-C6", "C4-C5-C6", "C4", "C5", "C6", 1, { { 119.700, 0.6, "s" } } }, { "C5-C6-N1", "C5-C6-N1", "C5", "C6", "N1", 1, { { 122.700, 0.5, "s" } } }, { "N1-C2-O2", "N1-C2-O2", "N1", "C2", "O2", 1, { { 122.800, 0.7, "s" } } }, { "N3-C2-O2", "N3-C2-O2", "N3", "C2", "O2", 1, { { 122.200, 0.7, "s" } } }, { "N3-C4-O4", "N3-C4-O4", "N3", "C4", "O4", 1, { { 119.400, 0.7, "s" } } }, { "C5-C4-O4", "C5-C4-O4", "C5", "C4", "O4", 1, { { 125.900, 0.6, "s" } } }, { "C6-N1-C1'", "C1*-N1-C6", "C6", "N1", "C1*", 1, { { 121.200, 1.4, "s" } } }, { "C2-N1-C1'", "C1*-N1-C2", "C2", "N1", "C1*", 1, { { 117.700, 1.2, "s" } } } } }; MONOMER ALA = { "ALA", 4, 4, // 5, 7, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"}} }, { "CA-CB (Ala)", "CA-CB", "CA", "CB", 1, { { 1.521, 0.033, "CH1E-CH3E" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (Ala)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.500, 1.500, "CH3E-CH1E-C" } } }, { "N-CA-CB (Ala)", "N-CA-CB", "N", "CA", "CB", 1, { { 110.400, 1.500, "NH1-CH1E-CH3E" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER ARG = { "ARG", 10, 11, // 11, 14, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (the rest)", "CA-CB", "CA", "CB", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CB-CG", "CB-CG", "CB", "CG", 1, { { 1.520, 0.030, "CH2E-CH2E" } } }, { "CG-CD", "CG-CD", "CG", "CD", 1, { { 1.520, 0.030, "CH2E-CH2E" } } }, { "CD-NE", "CD-NE", "CD", "NE", 1, { { 1.460, 0.018, "CH2E-NH1" } } }, { "NE-CZ", "NE-CZ", "NE", "CZ", 1, { { 1.329, 0.014, "NH1-C" } } }, { "CZ-NH1", "CZ-NH1", "CZ", "NH1", 1, { { 1.326, 0.018, "C-NC2" } } }, { "CZ-NH2", "CZ-NH2", "CZ", "NH2", 1, { { 1.326, 0.018, "C-NC2" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (the rest)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.100, 1.900, "CH2E-CH1E-C" } } }, { "N-CA-CB (the rest)", "N-CA-CB", "N", "CA", "CB", 1, { { 110.500, 1.700, "NH1-CH1E-CH2E" } } }, { "CA-CB-CG", "CA-CB-CG", "CA", "CB", "CG", 1, { { 114.100, 2.000, "CH1E-CH2E-CH2E" } } }, { "CB-CG-CD", "CB-CG-CD", "CB", "CG", "CD", 1, { { 111.300, 2.300, "CH2E-CH2E-CH2E" } } }, { "CG-CD-NE", "CG-CD-NE", "CG", "CD", "NE", 1, { { 112.000, 2.200, "CH2E-CH2E-NH1" } } }, { "CD-NE-CZ", "CD-NE-CZ", "CD", "NE", "CZ", 1, { { 124.200, 1.500, "CH2E-NH1-C" } } }, { "NH1-CZ-NH2", "NH1-CZ-NH2", "NH1", "CZ", "NH2", 1, { { 119.700, 1.800, "NC2-C-NC2" } } }, { "NE-CZ-NH1", "NE-CZ-NH1", "NE", "CZ", "NH1", 1, { { 120.000, 1.900, "NH1-C-NC2" } } }, { "NE-CZ-NH2", "NE-CZ-NH2", "NE", "CZ", "NH2", 1, { { 120.000, 1.900, "NH1-C-NC2" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER ASN = { "ASN", 7, 8, // 8, 11, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (the rest)", "CA-CB", "CA", "CB", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CB-CG", "CB-CG", "CB", "CG", 1, { { 1.516, 0.025, "CH2E-C" } } }, { "CG-OD1", "CG-OD1", "CG", "OD1", 1, { { 1.231, 0.020, "C-O" } } }, { "CG-ND2", "CG-ND2", "CG", "ND2", 1, { { 1.328, 0.021, "C-NH2" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (the rest)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.100, 1.900, "CH2E-CH1E-C" } } }, { "N-CA-CB (the rest)", "N-CA-CB", "N", "CA", "CB", 1, { { 110.500, 1.700, "NH1-CH1E-CH2E" } } }, { "CA-CB-CG", "CA-CB-CG", "CA", "CB", "CG", 1, { { 112.600, 1.000, "CH1E-CH2E-C" } } }, { "OD1-CG-ND2", "OD1-CG-ND2", "OD1", "CG", "ND2", 1, { { 122.600, 1.000, "O-C-NH2" } } }, { "CB-CG-OD1", "CB-CG-OD1", "CB", "CG", "OD1", 1, { { 120.800, 2.000, "CH2E-C-O" } } }, { "CB-CG-ND2", "CB-CG-ND2", "CB", "CG", "ND2", 1, { { 116.400, 1.500, "CH2E-C-NH2" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER ASP = { "ASP", 7, 8, // 8, 11, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (the rest)", "CA-CB", "CA", "CB", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CB-CG", "CB-CG", "CB", "CG", 1, { { 1.516, 0.025, "CH2E-C" } } }, { "CG-OD1", "CG-OD1", "CG", "OD1", 1, { { 1.249, 0.019, "C-OC" } } }, { "CG-OD2", "CG-OD2", "CG", "OD2", 1, { { 1.249, 0.019, "C-OC" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (the rest)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.100, 1.900, "CH2E-CH1E-C" } } }, { "N-CA-CB (the rest)", "N-CA-CB", "N", "CA", "CB", 1, { { 110.500, 1.700, "NH1-CH1E-CH2E" } } }, { "CA-CB-CG", "CA-CB-CG", "CA", "CB", "CG", 1, { { 112.600, 1.000, "CH1E-CH2E-C" } } }, { "OD1-CG-OD2", "OD1-CG-OD2", "OD1", "CG", "OD2", 1, { { 122.900, 2.400, "OC-C-OC" } } }, { "CB-CG-OD1", "CB-CG-OD1", "CB", "CG", "OD1", 1, { { 118.400, 2.300, "CH2E-C-OC" } } }, { "CB-CG-OD2", "CB-CG-OD2", "CB", "CG", "OD2", 1, { { 118.400, 2.300, "CH2E-C-OC" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER CYS = { "CYS", 5, 5, // 6, 8, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (the rest)", "CA-CB", "CA", "CB", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CB-SG", "CB-SG", "CB", "SG", 2, {{1.808, 0.033, "CH2E-SH1E" }, {1.822, 0.020, "CH2E-S" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (the rest)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.100, 1.900, "CH2E-CH1E-C" } } }, { "N-CA-CB (the rest)", "N-CA-CB", "N", "CA", "CB", 1, { { 110.500, 1.700, "NH1-CH1E-CH2E" } } }, { "CA-CB-SG", "CA-CB-SG", "CA", "CB", "SG", 1, { { 114.400, 2.300, "CH1E-CH2E-SH1E" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER GLN = { "GLN", 8, 9, // 9, 12, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (the rest)", "CA-CB", "CA", "CB", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CB-CG", "CB-CG", "CB", "CG", 1, { { 1.520, 0.030, "CH2E-CH2E" } } }, { "CG-CD", "CG-CD", "CG", "CD", 1, { { 1.516, 0.025, "CH2E-C" } } }, { "CD-OE1", "CD-OE1", "CD", "OE1", 1, { { 1.231, 0.020, "C-O" } } }, { "CD-NE2", "CD-NE2", "CD", "NE2", 1, { { 1.328, 0.021, "C-NH2" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (the rest)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.100, 1.900, "CH2E-CH1E-C" } } }, { "N-CA-CB (the rest)", "N-CA-CB", "N", "CA", "CB", 1, { { 110.500, 1.700, "NH1-CH1E-CH2E" } } }, { "CA-CB-CG", "CA-CB-CG", "CA", "CB", "CG", 1, { { 114.100, 2.000, "CH1E-CH2E-CH2E" } } }, { "CB-CG-CD", "CB-CG-CD", "CB", "CG", "CD", 1, { { 112.600, 1.700, "CH2E-CH2E-C" } } }, { "OE1-CD-NE2", "OE1-CD-NE2", "OE1", "CD", "NE2", 1, { { 122.600, 1.000, "O-C-NH2" } } }, { "CG-CD-OE1", "CG-CD-OE1", "CG", "CD", "OE1", 1, { { 120.800, 2.000, "CH2E-C-O" } } }, { "CG-CD-NE2", "CG-CD-NE2", "CG", "CD", "NE2", 1, { { 116.400, 1.500, "CH2E-C-NH2" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER GLU = { "GLU", 8, 9, // 9, 12, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (the rest)", "CA-CB", "CA", "CB", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CB-CG", "CB-CG", "CB", "CG", 1, { { 1.520, 0.030, "CH2E-CH2E" } } }, { "CG-CD", "CG-CD", "CG", "CD", 1, { { 1.516, 0.025, "CH2E-C" } } }, { "CD-OE1", "CD-OE1", "CD", "OE1", 1, { { 1.249, 0.019, "C-OC" } } }, { "CD-OE2", "CD-OE2", "CD", "OE2", 1, { { 1.249, 0.019, "C-OC" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (the rest)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.100, 1.900, "CH2E-CH1E-C" } } }, { "N-CA-CB (the rest)", "N-CA-CB", "N", "CA", "CB", 1, { { 110.500, 1.700, "NH1-CH1E-CH2E" } } }, { "CA-CB-CG", "CA-CB-CG", "CA", "CB", "CG", 1, { { 114.100, 2.000, "CH1E-CH2E-CH2E" } } }, { "CB-CG-CD", "CB-CG-CD", "CB", "CG", "CD", 1, { { 112.600, 1.700, "CH2E-CH2E-C" } } }, { "OE1-CD-OE2", "OE1-CD-OE2", "OE1", "CD", "OE2", 1, { { 122.900, 2.400, "OC-C-OC" } } }, { "CG-CD-OE1", "CG-CD-OE1", "CG", "CD", "OE1", 1, { { 118.400, 2.300, "CH2E-C-OC" } } }, { "CG-CD-OE2", "CG-CD-OE2", "CG", "CD", "OE2", 1, { { 118.400, 2.300, "CH2E-C-OC" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER GLY = { "GLY", 3, 2, // 4, 5, { { "N-CA (Gly)", "N-CA", "N", "CA", 1, { { 1.451, 0.016, "NH1-CH2G*" } } }, { "CA-C (Gly)", "CA-C", "CA", "C", 1, { { 1.516, 0.018, "CH2G*-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "N-CA-C (Gly)", "N-CA-C", "N", "CA", "C", 1, { { 112.500, 2.900, "NH1-CH2G*-C" } } }, { "CA-C-O (Gly)", "CA-C-O", "CA", "C", "O", 2, {{120.800, 2.100, "CH2G*-C-O" }, {118.400, 2.300, "CH2G*-C-OC"} } } // { "CA-C-N (Gly)", "CA-C-N", "CA", "C", "N", 1, { { 116.400, 2.100, "CH2G*-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (Gly)", "C-N-CA", "C", "N", "CA", 1, { { 120.600, 1.700, "C-NH1-CH2G*" } } }, } }; MONOMER HIS = { "HIS", 10, 12, // 11, 15, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (the rest)", "CA-CB", "CA", "CB", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CB-CG", "CB-CG", "CB", "CG", 1, { { 1.497, 0.014, "CH2E-C5" } } }, { "CG-CD2", "CG-CD2", "CG", "CD2", 1, { { 1.354, 0.011, "C5-CR1H" } } }, { "CG-ND1", "CG-ND1", "CG", "ND1", 1, { { 1.378, 0.011, "C5-NH1" } } }, { "ND1-CE1", "ND1-CE1", "ND1", "CE1", 1, { { 1.321, 0.010, "NH1-CRHH" } } }, { "CE1-NE2", "CE1-NE2", "CE1", "NE2", 1, { { 1.321, 0.010, "CRHH-NH1" } } }, { "NE2-CD2", "NE2-CD2", "NE2", "CD2", 1, { { 1.374, 0.011, "NH1-CR1H" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (the rest)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.100, 1.900, "CH2E-CH1E-C" } } }, { "N-CA-CB (the rest)", "N-CA-CB", "N", "CA", "CB", 1, { { 110.500, 1.700, "NH1-CH1E-CH2E" } } }, { "CA-CB-CG", "CA-CB-CG", "CA", "CB", "CG", 1, { { 113.800, 1.000, "CH1E-CH2E-C5" } } }, { "CB-CG-CD2", "CB-CG-CD2", "CB", "CG", "CD2", 1, { { 131.200, 1.300, "CH2E-C5-CR1H" } } }, { "ND1-CG-CD2", "ND1-CG-CD2", "ND1", "CG", "CD2", 1, { { 106.100, 1.000, "NH1-C5-CR1H" } } }, { "CB-CG-ND1", "CB-CG-ND1", "CB", "CG", "ND1", 1, { { 122.700, 1.500, "CH2E-C5-NH1" } } }, { "CG-ND1-CE1", "CG-ND1-CE1", "CG", "ND1", "CE1", 1, { { 109.300, 1.700, "C5-NH1-CRHH" } } }, { "ND1-CE1-NE2", "ND1-CE1-NE2", "ND1", "CE1", "NE2", 1, { { 108.400, 1.000, "NH1-CRHH-NH1" } } }, { "CE1-NE2-CD2", "CE1-NE2-CD2", "CE1", "NE2", "CD2", 1, { { 109.000, 1.000, "CRHH-NH1-CR1H" } } }, { "CG-CD2-NE2", "CG-CD2-NE2", "CG", "CD2", "NE2", 1, { { 107.200, 1.000, "C5-CR1H-NH1" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER ILE = { "ILE", 7, 8, // 8, 11, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (Ile,Thr,Val)", "CA-CB", "CA", "CB", 1, { { 1.540, 0.027, "CH1E-CH1E" } } }, { "CB-CG1", "CB-CG1", "CB", "CG1", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CG1-CD", "CG1-CD", "CG1", "CD", 1, { { 1.513, 0.039, "CH2E-CH3E" } } }, { "CB-CG2", "CB-CG2", "CB", "CG2", 1, { { 1.521, 0.033, "CH1E-CH3E" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (Ile,Thr,Val)", "CB-CA-C", "CB", "CA", "C", 1, { { 109.100, 2.200, "CH1E-CH1E-C" } } }, { "N-CA-CB (Ile,Thr,Val)", "N-CA-CB", "N", "CA", "CB", 1, { { 111.500, 1.700, "NH1-CH1E-CH1E" } } }, { "CG1-CB-CG2", "CG1-CB-CG2", "CG1", "CB", "CG2", 1, { { 110.700, 3.000, "CH2E-CH1E-CH3E" } } }, { "CA-CB-CG1", "CA-CB-CG1", "CA", "CB", "CG1", 1, { { 110.400, 1.700, "CH1E-CH1E-CH2E" } } }, { "CB-CG1-CD", "CB-CG1-CD", "CB", "CG1", "CD", 1, { { 113.800, 2.100, "CH1E-CH2E-CH3E" } } }, { "CA-CB-CG2", "CA-CB-CG2", "CA", "CB", "CG2", 1, { { 110.500, 1.700, "CH1E-CH1E-CH3E" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER LEU = { "LEU", 7, 8, // 8, 11, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (the rest)", "CA-CB", "CA", "CB", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CB-CG", "CB-CG", "CB", "CG", 1, { { 1.530, 0.020, "CH2E-CH1E" } } }, { "CG-CD1", "CG-CD1", "CG", "CD1", 1, { { 1.521, 0.033, "CH1E-CH3E" } } }, { "CG-CD2", "CG-CD2", "CG", "CD2", 1, { { 1.521, 0.033, "CH1E-CH3E" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (the rest)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.100, 1.900, "CH2E-CH1E-C" } } }, { "N-CA-CB (the rest)", "N-CA-CB", "N", "CA", "CB", 1, { { 110.500, 1.700, "NH1-CH1E-CH2E" } } }, { "CA-CB-CG", "CA-CB-CG", "CA", "CB", "CG", 1, { { 116.300, 3.500, "CH1E-CH2E-CH1E" } } }, { "CD1-CG-CD2", "CD1-CG-CD2", "CD1", "CG", "CD2", 1, { { 110.800, 2.200, "CH3E-CH1E-CH3E" } } }, { "CB-CG-CD1", "CB-CG-CD1", "CB", "CG", "CD1", 1, { { 110.700, 3.000, "CH2E-CH1E-CH3E" } } }, { "CB-CG-CD2", "CB-CG-CD2", "CB", "CG", "CD2", 1, { { 110.700, 3.000, "CH2E-CH1E-CH3E" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER LYS = { "LYS", 8, 8, // 9, 11, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (the rest)", "CA-CB", "CA", "CB", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CB-CG", "CB-CG", "CB", "CG", 1, { { 1.520, 0.030, "CH2E-CH2E" } } }, { "CG-CD", "CG-CD", "CG", "CD", 1, { { 1.520, 0.030, "CH2E-CH2E" } } }, { "CD-CE", "CD-CE", "CD", "CE", 1, { { 1.520, 0.030, "CH2E-CH2E" } } }, { "CE-NZ", "CE-NZ", "CE", "NZ", 1, { { 1.489, 0.030, "CH2E-NH3" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (the rest)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.100, 1.900, "CH2E-CH1E-C" } } }, { "N-CA-CB (the rest)", "N-CA-CB", "N", "CA", "CB", 1, { { 110.500, 1.700, "NH1-CH1E-CH2E" } } }, { "CA-CB-CG", "CA-CB-CG", "CA", "CB", "CG", 1, { { 114.100, 2.000, "CH1E-CH2E-CH2E" } } }, { "CB-CG-CD", "CB-CG-CD", "CB", "CG", "CD", 1, { { 111.300, 2.300, "CH2E-CH2E-CH2E" } } }, { "CG-CD-CE", "CG-CD-CE", "CG", "CD", "CE", 1, { { 111.300, 2.300, "CH2E-CH2E-CH2E" } } }, { "CD-CE-NZ", "CD-CE-NZ", "CD", "CE", "NZ", 1, { { 111.900, 3.200, "CH2E-CH2E-NH3" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER MET = { "MET", 7, 7, // 8, 10, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (the rest)", "CA-CB", "CA", "CB", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CB-CG", "CB-CG", "CB", "CG", 1, { { 1.520, 0.030, "CH2E-CH2E" } } }, { "CG-SD", "CG-SD", "CG", "SD", 1, { { 1.803, 0.034, "CH2E-SM" } } }, { "SD-CE", "SD-CE", "SD", "CE", 1, { { 1.791, 0.059, "SM-CH3E" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (the rest)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.100, 1.900, "CH2E-CH1E-C" } } }, { "N-CA-CB (the rest)", "N-CA-CB", "N", "CA", "CB", 1, { { 110.500, 1.700, "NH1-CH1E-CH2E" } } }, { "CA-CB-CG", "CA-CB-CG", "CA", "CB", "CG", 1, { { 114.100, 2.000, "CH1E-CH2E-CH2E" } } }, { "CB-CG-SD", "CB-CG-SD", "CB", "CG", "SD", 1, { { 112.700, 3.000, "CH2E-CH2E-SM" } } }, { "CG-SD-CE", "CG-SD-CE", "CG", "SD", "CE", 1, { { 100.900, 2.200, "CH2E-SM-CH3E" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER PHE = { "PHE", 11, 13, // 12, 16, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (the rest)", "CA-CB", "CA", "CB", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CB-CG", "CB-CG", "CB", "CG", 1, { { 1.502, 0.023, "CH2E-CF" } } }, { "CG-CD2", "CG-CD2", "CG", "CD2", 1, { { 1.384, 0.021, "CF-CR1E" } } }, { "CG-CD1", "CG-CD1", "CG", "CD1", 1, { { 1.384, 0.021, "CF-CR1E" } } }, { "CD1-CE1", "CD1-CE1", "CD1", "CE1", 1, { { 1.382, 0.030, "CR1E-CR1E" } } }, { "CE1-CZ", "CE1-CZ", "CE1", "CZ", 1, { { 1.382, 0.030, "CR1E-CR1E" } } }, { "CZ-CE2", "CZ-CE2", "CZ", "CE2", 1, { { 1.382, 0.030, "CR1E-CR1E" } } }, { "CE2-CD2", "CE2-CD2", "CE2", "CD2", 1, { { 1.382, 0.030, "CR1E-CR1E" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (the rest)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.100, 1.900, "CH2E-CH1E-C" } } }, { "N-CA-CB (the rest)", "N-CA-CB", "N", "CA", "CB", 1, { { 110.500, 1.700, "NH1-CH1E-CH2E" } } }, { "CA-CB-CG", "CA-CB-CG", "CA", "CB", "CG", 1, { { 113.800, 1.000, "CH1E-CH2E-CF" } } }, { "CB-CG-CD2", "CB-CG-CD2", "CB", "CG", "CD2", 1, { { 120.700, 1.700, "CH2E-CF-CR1E" } } }, { "CD1-CG-CD2", "CD1-CG-CD2", "CD1", "CG", "CD2", 1, { { 118.600, 1.500, "CR1E-CF-CR1E" } } }, { "CB-CG-CD1", "CB-CG-CD1", "CB", "CG", "CD1", 1, { { 120.700, 1.700, "CH2E-CF-CR1E" } } }, { "CG-CD1-CE1", "CG-CD1-CE1", "CG", "CD1", "CE1", 1, { { 120.700, 1.700, "CF-CR1E-CR1E" } } }, { "CG-CD2-CE2", "CG-CD2-CE2", "CG", "CD2", "CE2", 1, { { 120.700, 1.700, "CF-CR1E-CR1E" } } }, { "CD1-CE1-CZ", "CD1-CE1-CZ", "CD1", "CE1", "CZ", 1, { { 120.000, 1.800, "CR1E-CR1E-CR1E" } } }, { "CE1-CZ-CE2", "CE1-CZ-CE2", "CE1", "CZ", "CE2", 1, { { 120.000, 1.800, "CR1E-CR1E-CR1E" } } }, { "CZ-CE2-CD2", "CZ-CE2-CD2", "CZ", "CE2", "CD2", 1, { { 120.000, 1.800, "CR1E-CR1E-CR1E" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER PRO = { "PRO", 7, 8, // 8, 11, { { "N-CA (Pro)", "N-CA", "N", "CA", 1, { { 1.466, 0.015, "N-CH1E" } } }, { "CA-CB (the rest)", "CA-CB", "CA", "CB", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CB-CG", "CB-CG", "CB", "CG", 1, { { 1.492, 0.050, "CH2E-CH2P" } } }, { "CG-CD", "CG-CD", "CG", "CD", 1, { { 1.503, 0.034, "CH2P-CH2P" } } }, { "CD-N", "CD-N", "CD", "N", 1, { { 1.473, 0.014, "CH2P-N" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (Pro)", "C-N", "C", "N", 1, { { 1.341, 0.016, "C-NH1" } } }, }, { { "CA-N-CD", "CA-N-CD", "CA", "N", "CD", 1, { { 112.000, 1.400, "CH1E-N-CH2P" } } }, { "CB-CA-C (the rest)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.100, 1.900, "CH2E-CH1E-C" } } }, { "N-CA-CB (Pro)", "N-CA-CB", "N", "CA", "CB", 1, { { 103.000, 1.100, "N-CH1E-CH2E" } } }, { "CA-CB-CG", "CA-CB-CG", "CA", "CB", "CG", 1, { { 104.500, 1.900, "CH1E-CH2E-CH2P" } } }, { "CB-CG-CD", "CB-CG-CD", "CB", "CG", "CD", 1, { { 106.100, 3.200, "CH2E-CH2P-CH2P" } } }, { "N-CD-CG", "N-CD-CG", "N", "CD", "CG", 1, { { 103.200, 1.500, "N-CH2P-CH2P" } } }, { "N-CA-C (Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.800, 2.500, "N-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.900, 1.500, "CH1E-C-N" } } }, // { "O-C-N (Pro)", "O-C-N", "O", "C", "N", 1, { { 122.000, 1.400, "O-C-N" } } }, // { "C-N-CA (Pro)", "C-N-CA", "C", "N", "CA", 1, { { 122.600, 5.000, "C-N-CH1E" } } }, } }; MONOMER SER = { "SER", 5, 5, // 6, 8, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (the rest)", "CA-CB", "CA", "CB", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CB-OG", "CB-OG", "CB", "OG", 1, { { 1.417, 0.020, "CH2E-OH1" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (the rest)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.100, 1.900, "CH2E-CH1E-C" } } }, { "N-CA-CB (the rest)", "N-CA-CB", "N", "CA", "CB", 1, { { 110.500, 1.700, "NH1-CH1E-CH2E" } } }, { "CA-CB-OG", "CA-CB-OG", "CA", "CB", "OG", 1, { { 111.100, 2.000, "CH1E-CH2E-OH1" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER THR = { "THR", 6, 7, // 7, 10, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (Ile,Thr,Val)", "CA-CB", "CA", "CB", 1, { { 1.540, 0.027, "CH1E-CH1E" } } }, { "CB-OG1", "CB-OG1", "CB", "OG1", 1, { { 1.433, 0.016, "CH1E-OH1" } } }, { "CB-CG2", "CB-CG2", "CB", "CG2", 1, { { 1.521, 0.033, "CH1E-CH3E" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (Ile,Thr,Val)", "CB-CA-C", "CB", "CA", "C", 1, { { 109.100, 2.200, "CH1E-CH1E-C" } } }, { "N-CA-CB (Ile,Thr,Val)", "N-CA-CB", "N", "CA", "CB", 1, { { 111.500, 1.700, "NH1-CH1E-CH1E" } } }, { "OG1-CB-CG2", "OG1-CB-CG2", "OG1", "CB", "CG2", 1, { { 109.300, 2.000, "OH1-CH1E-CH3E" } } }, { "CA-CB-OG1", "CA-CB-OG1", "CA", "CB", "OG1", 1, { { 109.600, 1.500, "CH1E-CH1E-OH1" } } }, { "CA-CB-CG2", "CA-CB-CG2", "CA", "CB", "CG2", 1, { { 110.500, 1.700, "CH1E-CH1E-CH3E" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER TRP = { "TRP", 15, 20, // 16, 23, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (the rest)", "CA-CB", "CA", "CB", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CB-CG", "CB-CG", "CB", "CG", 1, { { 1.498, 0.031, "CH2E-C5W" } } }, { "CG-CD2", "CG-CD2", "CG", "CD2", 1, { { 1.433, 0.018, "C5W-CW" } } }, { "CG-CD1", "CG-CD1", "CG", "CD1", 1, { { 1.365, 0.025, "C5W-CR1E" } } }, { "CD1-NE1", "CD1-NE1", "CD1", "NE1", 1, { { 1.374, 0.021, "CR1E-NH1" } } }, { "NE1-CE2", "NE1-CE2", "NE1", "CE2", 1, { { 1.370, 0.011, "NH1-CW" } } }, { "CE2-CZ2", "CE2-CZ2", "CE2", "CZ2", 1, { { 1.394, 0.021, "CW-CR1W" } } }, { "CE2-CD2", "CE2-CD2", "CE2", "CD2", 1, { { 1.409, 0.017, "CW-CW" } } }, { "CD2-CE3", "CD2-CE3", "CD2", "CE3", 1, { { 1.398, 0.016, "CW-CR1E" } } }, { "CE3-CZ3", "CE3-CZ3", "CE3", "CZ3", 1, { { 1.382, 0.030, "CR1E-CR1E" } } }, { "CZ3-CH2", "CZ3-CH2", "CZ3", "CH2", 1, { { 1.400, 0.025, "CR1E-CR1W" } } }, { "CH2-CZ2", "CH2-CZ2", "CH2", "CZ2", 1, { { 1.368, 0.019, "CR1W-CR1W" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (the rest)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.100, 1.900, "CH2E-CH1E-C" } } }, { "N-CA-CB (the rest)", "N-CA-CB", "N", "CA", "CB", 1, { { 110.500, 1.700, "NH1-CH1E-CH2E" } } }, { "CA-CB-CG", "CA-CB-CG", "CA", "CB", "CG", 1, { { 113.600, 1.900, "CH1E-CH2E-C5W" } } }, { "CB-CG-CD2", "CB-CG-CD2", "CB", "CG", "CD2", 1, { { 126.800, 1.400, "CH2E-C5W-CW" } } }, { "CD1-CG-CD2", "CD1-CG-CD2", "CD1", "CG", "CD2", 1, { { 106.300, 1.600, "CR1E-C5W-CW" } } }, { "CB-CG-CD1", "CB-CG-CD1", "CB", "CG", "CD1", 1, { { 126.900, 1.500, "CH2E-C5W-CR1E" } } }, { "CG-CD1-NE1", "CG-CD1-NE1", "CG", "CD1", "NE1", 1, { { 110.200, 1.300, "C5W-CR1E-NH1" } } }, { "CD1-NE1-CE2", "CD1-NE1-CE2", "CD1", "NE1", "CE2", 1, { { 108.900, 1.800, "CR1E-NH1-CW" } } }, { "NE1-CE2-CZ2", "NE1-CE2-CZ2", "NE1", "CE2", "CZ2", 1, { { 130.100, 1.500, "NH1-CW-CR1W" } } }, { "CD2-CE2-CZ2", "CD2-CE2-CZ2", "CD2", "CE2", "CZ2", 1, { { 122.400, 1.000, "CW-CW-CR1W" } } }, { "NE1-CE2-CD2", "NE1-CE2-CD2", "NE1", "CE2", "CD2", 1, { { 107.400, 1.300, "NH1-CW-CW" } } }, { "CE2-CD2-CE3", "CE2-CD2-CE3", "CE2", "CD2", "CE3", 1, { { 118.800, 1.000, "CW-CW-CR1E" } } }, { "CE2-CD2-CG", "CE2-CD2-CG", "CE2", "CD2", "CG", 1, { { 107.200, 1.200, "CW-CW-C5W" } } }, { "CG-CD2-CE3", "CG-CD2-CE3", "CG", "CD2", "CE3", 1, { { 133.900, 1.000, "C5W-CW-CR1E" } } }, { "CD2-CE3-CZ3", "CD2-CE3-CZ3", "CD2", "CE3", "CZ3", 1, { { 118.600, 1.300, "CW-CR1E-CR1E" } } }, { "CE3-CZ3-CH2", "CE3-CZ3-CH2", "CE3", "CZ3", "CH2", 1, { { 121.100, 1.300, "CR1E-CR1E-CR1W" } } }, { "CZ3-CH2-CZ2", "CZ3-CH2-CZ2", "CZ3", "CH2", "CZ2", 1, { { 121.500, 1.300, "CR1E-CR1W-CR1W" } } }, { "CH2-CZ2-CE2", "CH2-CZ2-CE2", "CH2", "CZ2", "CE2", 1, { { 117.500, 1.300, "CR1W-CR1W-CW" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER TYR = { "TYR", 12, 15, // 13, 18, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"} } }, { "CA-CB (the rest)", "CA-CB", "CA", "CB", 1, { { 1.530, 0.020, "CH1E-CH2E" } } }, { "CB-CG", "CB-CG", "CB", "CG", 1, { { 1.512, 0.022, "CH2E-CY" } } }, { "CG-CD2", "CG-CD2", "CG", "CD2", 1, { { 1.389, 0.021, "CY-CR1E" } } }, { "CG-CD1", "CG-CD1", "CG", "CD1", 1, { { 1.389, 0.021, "CY-CR1E" } } }, { "CD1-CE1", "CD1-CE1", "CD1", "CE1", 1, { { 1.382, 0.030, "CR1E-CR1E" } } }, { "CE1-CZ", "CE1-CZ", "CE1", "CZ", 1, { { 1.378, 0.024, "CR1E-CY2" } } }, { "CZ-OH", "CZ-OH", "CZ", "OH", 1, { { 1.376, 0.021, "CY2-OH1" } } }, { "CZ-CE2", "CZ-CE2", "CZ", "CE2", 1, { { 1.378, 0.024, "CY2-CR1E" } } }, { "CE2-CD2", "CE2-CD2", "CE2", "CD2", 1, { { 1.382, 0.030, "CR1E-CR1E" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (the rest)", "CB-CA-C", "CB", "CA", "C", 1, { { 110.100, 1.900, "CH2E-CH1E-C" } } }, { "N-CA-CB (the rest)", "N-CA-CB", "N", "CA", "CB", 1, { { 110.500, 1.700, "NH1-CH1E-CH2E" } } }, { "CA-CB-CG", "CA-CB-CG", "CA", "CB", "CG", 1, { { 113.900, 1.800, "CH1E-CH2E-CY" } } }, { "CB-CG-CD2", "CB-CG-CD2", "CB", "CG", "CD2", 1, { { 120.800, 1.500, "CH2E-CY-CR1E" } } }, { "CD1-CG-CD2", "CD1-CG-CD2", "CD1", "CG", "CD2", 1, { { 118.100, 1.500, "CR1E-CY-CR1E" } } }, { "CB-CG-CD1", "CB-CG-CD1", "CB", "CG", "CD1", 1, { { 120.800, 1.500, "CH2E-CY-CR1E" } } }, { "CG-CD1-CE1", "CG-CD1-CE1", "CG", "CD1", "CE1", 1, { { 121.200, 1.500, "CY-CR1E-CR1E" } } }, { "CG-CD2-CE2", "CG-CD2-CE2", "CG", "CD2", "CE2", 1, { { 121.200, 1.500, "CY-CR1E-CR1E" } } }, { "CD1-CE1-CZ", "CD1-CE1-CZ", "CD1", "CE1", "CZ", 1, { { 119.600, 1.800, "CR1E-CR1E-CY2" } } }, { "OH-CZ-CE2", "OH-CZ-CE2", "OH", "CZ", "CE2", 1, { { 119.900, 3.000, "OH1-CY2-CR1E" } } }, { "CE1-CZ-OH", "CE1-CZ-OH", "CE1", "CZ", "OH", 1, { { 119.900, 3.000, "CR1E-CY2-OH1" } } }, { "CE1-CZ-CE2", "CE1-CZ-CE2", "CE1", "CZ", "CE2", 1, { { 120.300, 2.000, "CR1E-CY2-CR1E" } } }, { "CZ-CE2-CD2", "CZ-CE2-CD2", "CZ", "CE2", "CD2", 1, { { 119.600, 1.800, "CY2-CR1E-CR1E" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER VAL = { "VAL", 6, 7, // 7, 10, { { "N-CA (except Gly,Pro)", "N-CA", "N", "CA", 2, {{1.458, 0.019, "NH1-CH1E"}, {1.491, 0.021, "NH3-CH1E"}} }, { "CA-CB (Ile,Thr,Val)", "CA-CB", "CA", "CB", 1, { { 1.540, 0.027, "CH1E-CH1E" } } }, { "CB-CG1", "CB-CG1", "CB", "CG1", 1, { { 1.521, 0.033, "CH1E-CH3E" } } }, { "CB-CG2", "CB-CG2", "CB", "CG2", 1, { { 1.521, 0.033, "CH1E-CH3E" } } }, { "CA-C (except Gly)", "CA-C", "CA", "C", 1, { { 1.525, 0.021, "CH1E-C" } } }, { "C-O", "C-O", "C", "O", 2, {{1.231, 0.020, "C-O" }, {1.249, 0.019, "C-OC"} } } // { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }, }, { { "CB-CA-C (Ile,Thr,Val)", "CB-CA-C", "CB", "CA", "C", 1, { { 109.100, 2.200, "CH1E-CH1E-C" } } }, { "N-CA-CB (Ile,Thr,Val)", "N-CA-CB", "N", "CA", "CB", 1, { { 111.500, 1.700, "NH1-CH1E-CH1E" } } }, { "CG1-CB-CG2", "CG1-CB-CG2", "CG1", "CB", "CG2", 1, { { 110.800, 2.200, "CH3E-CH1E-CH3E" } } }, { "CA-CB-CG1", "CA-CB-CG1", "CA", "CB", "CG1", 1, { { 110.500, 1.700, "CH1E-CH1E-CH3E" } } }, { "CA-CB-CG2", "CA-CB-CG2", "CA", "CB", "CG2", 1, { { 110.500, 1.700, "CH1E-CH1E-CH3E" } } }, { "N-CA-C (except Gly,Pro)", "N-CA-C", "N", "CA", "C", 1, { { 111.200, 2.800, "NH1-CH1E-C" } } }, { "CA-C-O (except Gly)", "CA-C-O", "CA", "C", "O", 2, {{ 120.800, 1.700, "CH1E-C-O" }, { 117.000, 2.500, "CH1E-C-OC"} } } // { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, // { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } }, // { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }, } }; MONOMER_DB params[MAX_MONOMER] = { { "A", MONOMER_TYPE_DNA, &DA }, { "A", MONOMER_TYPE_RNA, &RA }, { "ALA", MONOMER_TYPE_A_A, &ALA }, { "ARG", MONOMER_TYPE_A_A, &ARG }, { "ASN", MONOMER_TYPE_A_A, &ASN }, { "ASP", MONOMER_TYPE_A_A, &ASP }, { "C", MONOMER_TYPE_DNA, &DC }, { "C", MONOMER_TYPE_RNA, &RC }, { "CYS", MONOMER_TYPE_A_A, &CYS }, { "G", MONOMER_TYPE_DNA, &DG }, { "G", MONOMER_TYPE_RNA, &RG }, { "GLN", MONOMER_TYPE_A_A, &GLN }, { "GLU", MONOMER_TYPE_A_A, &GLU }, { "GLY", MONOMER_TYPE_A_A, &GLY }, { "HIS", MONOMER_TYPE_A_A, &HIS }, { "ILE", MONOMER_TYPE_A_A, &ILE }, { "LEU", MONOMER_TYPE_A_A, &LEU }, { "LYS", MONOMER_TYPE_A_A, &LYS }, { "MET", MONOMER_TYPE_A_A, &MET }, { "PHE", MONOMER_TYPE_A_A, &PHE }, { "PRO", MONOMER_TYPE_A_A, &PRO }, { "SER", MONOMER_TYPE_A_A, &SER }, { "T", MONOMER_TYPE_DNA, &DT }, { "T", MONOMER_TYPE_RNA, &RT }, { "THR", MONOMER_TYPE_A_A, &THR }, { "TRP", MONOMER_TYPE_A_A, &TRP }, { "TYR", MONOMER_TYPE_A_A, &TYR }, { "U", MONOMER_TYPE_DNA, &DU }, { "U", MONOMER_TYPE_RNA, &RU }, { "VAL", MONOMER_TYPE_A_A, &VAL } }; MONOMER_BOND A_LINK = { "C-N (except Pro)", "C-N", "C", "N", 1, { { 1.329, 0.014, "C-NH1" } } }; MONOMER_BOND PRO_LINK = { "C-N (Pro)", "C-N", "C", "N", 1, { { 1.341, 0.016, "C-NH1" } } }; MONOMER_BOND N_LINK = { "P-O3'", "O3*-P", "O3*", "P", 1, { { 1.607, 0.012, "s" } } }; MONOMER_ANGLE GLY_ANG1[2] = { { "CA-C-N (Gly)", "CA-C-N", "CA", "C", "N", 1, { { 116.400, 2.100, "CH2G*-C-NH1" } } }, { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } } }; MONOMER_ANGLE GLY_ANG2 = { "C-N-CA (Gly)", "C-N-CA", "C", "N", "CA", 1, { { 120.600, 1.700, "C-NH1-CH2G*" } } }; MONOMER_ANGLE PRO_ANG1[2] = { { "CA-C-N (Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.900, 1.500, "CH1E-C-N" } } }, { "O-C-N (Pro)", "O-C-N", "O", "C", "N", 1, { { 122.000, 1.400, "O-C-N" } } } }; MONOMER_ANGLE PRO_ANG2 = { "C-N-CA (Pro)", "C-N-CA", "C", "N", "CA", 1, { { 122.600, 5.000, "C-N-CH1E" } } }; MONOMER_ANGLE AA_ANG1[2] = { { "CA-C-N (except Gly,Pro)", "CA-C-N", "CA", "C", "N", 1, { { 116.200, 2.000, "CH1E-C-NH1" } } }, { "O-C-N (except Pro)", "O-C-N", "O", "C", "N", 1, { { 123.000, 1.600, "O-C-NH1" } } } }; MONOMER_ANGLE AA_ANG2 = { "C-N-CA (except Gly,Pro)", "C-N-CA", "C", "N", "CA", 1, { { 121.700, 1.800, "C-NH1-CH1E" } } }; MONOMER_ANGLE NN_ANG1 = { "C3'-O3'-P", "C3*-O3*-P", "C3*", "O3*", "P", 1, { { 119.700, 1.2, "s" } } }; MONOMER_ANGLE NN_ANG2[3] = { { "O3'-P-O5'", "O3*-P-O5*", "O3*", "P", "O5*", 1, { { 104.000, 1.9, "s" } } }, { "O3'-P-O1P/O2P", "O2P-P-O3*", "O3*", "P", "O2P", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} }, { "O3'-P-O1P/O2P", "O1P-P-O3*", "O3*", "P", "O1P", 2, {{ 110.500, 1.1, "large" }, { 105.200, 2.2, "small" }} } }; static int _dbIndex_flag = 0; static TblIndexObj _dbIndex; static void _dbIndex_init() { CifString index; if (_dbIndex_flag) return; _dbIndex_flag = 1; _dbIndex.Clear(); for (int i = 0; i < MAX_MONOMER; i++) { index.Copy(params[i].resname); index += params[i].type; _dbIndex.Add(index); } } static MONOMER_DB *find_monomer_db(CifString &index) { int ret = _dbIndex.Seek(index); if (ret >= 0) return (¶ms[ret]); return NULL; } #endif