############################################################################## # # # MIF DATA DICTIONARY # # # ############################################################################## data_on_this_dictionary _dictionary_name mif_core.dic _dictionary_version 1.2.3 _dictionary_update 2005-06-17 _dictionary_history ; 1993-02-22 Created from document "The Molecular Information File (MIF): A Standard File Format for Molecuar Information" J M Barnard and A P F Cook (4 Dec 1992). SRH 1993-02-25 Adjustments and refinement of data name definitions. SRH 1993-03-12 Corrections and refinements. SRH 1993-03-25 Amendments resulting from the Cambridge Workshop. SRH 1993-04-28 Amendments resulting from J M Barnard fax (25 Apr). SRH 1993-04-28 Amendments resulting from A P F Cook email (26 Apr). SRH 1993-05-21 Apply new DDL commands from ddldic.c93. SRH 1993-05-27 Added periodic table symbols to _atom_type. SRH 1993-05-28 Some major trial definition changes -- testing only. SRH 1993-06-02 Expansion of the trial definitions. SRH 1993-06-04 Some fine tuning and corrections. SRH 1993-07-09 Changes following Dutch 'Chemical Structures' meeting. SRH 1993-12-12 Changes following Cambridge meetings with APFC and FHA. SRH 1993-12-17 Changes for _include_file and _type_conditions. SRH 1994-02-22 Adapt include to new naming convention. SRH 1994-04-18 Update the codes for _define_stereo_relationship. SRH 1994-06-15 Make include filenames systematic. SRH 1994-08-23 General check and tidy before publication. SRH 1994-09-09 Adjustments to _atom_id and other definitions. SRH 1994-09-27 Replace 'null' enumeration in _display_object with '.' SRH 1994-10-15 Additions as per FHA mail and JB/TC suggestions. SRH 1994-12-21 Change _include_file to include_ construction. SRH 1995-07-17 Changes related to DDL (JCICS, 35, 819-825). SRH 2001-03-09 Changes to conform with the ddl_core_1.4.dic definitions. SRH 2001-05-02 Add three new items _atom_environment, *_frag_key, *_frag_id. SRH 2005-01-12 Change datablock name atom_model_ to atom_coord_ SRH 2005-02_11 Change data names _display_origin, *_scale and *_span_x, _y to the names _display_define_origin, etc. SRH 2005-02-28 Style changes for International Tables Volume G. BMcM 2005-06-17 Minor corrections to reflect proof corrections for IT G Chapter 4.8. NJA ; global_ _list no _list_mandatory no _list_level 1 _type_conditions seq data_atom_attach_ loop_ _name '_atom_attach_all' '_atom_attach_ring' '_atom_attach_nh' '_atom_attach_h' _category atom _type numb _list yes _list_reference '_atom_id' _enumeration_range 0: _definition ; The number of atom sites considered to be attached (i.e. chemically bonded) to this site. The extensions are: all all sites ring all sites forming rings nh all sites excluding H atoms and unshared electron pairs h H-atom sites ; data_atom_charge _name '_atom_charge' _category atom _type numb _list yes _list_reference '_atom_id' _enumeration_range -99:99 _definition ; Specifies the formal electronic charge on the atom for the different atomic representation conventions. The convention for charge is specified by _define_bonding_convention. ; data_atom_cip _name '_atom_cip' _category atom _type char _list yes _list_reference '_atom_id' _definition ; Specifies the Cahn-Ingold-Prelog designation for the atom. The designators are by Prelog & Helmchen (1982). Reference: Prelog, V. & Helmchen, G. (1982). Angew. Chem. Int. Ed. Engl. 21, 567-583. ; data_atom_coord_ loop_ _name '_atom_coord_x' '_atom_coord_y' '_atom_coord_z' _category atom _type numb _list yes _list_reference '_atom_id' _units angstr _units_detail 'Angstroems' _definition ; Specifies the Cartesian coordinates for the atom with an arbitrary origin and arbitrary orthogonal axes. ; data_atom_environment _name '_atom_environment' _category atom _type char _list yes _list_reference '_atom_id' loop_ _enumeration _enumeration_detail atom 'a single atom site' frag 'atom site in molecular fragment' _enumeration_default atom _definition ; Environment of the atom site. ; data_atom_frag_key _name '_atom_frag_key' _category atom _type char _list yes _list_reference '_atom_id' _definition ; Name of save frame containing atom data on molecular fragment. ; data_atom_frag_id _name '_atom_frag_id' _category atom _type numb _list yes _list_reference '_atom_id' _definition ; ID of atom site within the molecular fragment. ; data_atom_id _name '_atom_id' _category atom _type char _list yes _list_mandatory yes _list_uniqueness '_atom_id' loop_ _list_link_child '_bond_id_1' '_bond_id_2' '_stereo_vertex_id' _definition ; This specifies a unique code for an 'atom site' in a molecule or fragment. A designated atom site may be occupied by a 'dummy' atom (see _atom_type). A special syntax exists for this code which permits a template molecular fragment to be referred to as an 'atom site', and for the atom within that template to be identified. The syntax is m>n where m is the code identifying the template fragment (contained within a save frame) and n is the code matching an _atom_id value stored within the save frame. ; data_atom_mass_number _name '_atom_mass_number' _category atom _type numb _list yes _list_reference '_atom_id' _enumeration_range 1: _definition ; Specifies the mass number or the isotopic state of the atom. The default is the 'most abundant naturally occurring' value. ; data_atom_label _name '_atom_label' _category atom _type char _list yes _list_reference '_atom_id' _definition ; The code providing unique identification of the atom site for display purposes. See also _atom_type. ; data_atom_radical_count _name '_atom_radical_count' _category atom _type numb _list yes _list_reference '_atom_id' _enumeration_range 0: _definition ; Specifies the formal radical state of the atom site identified by _atom_id. This is the number of unpaired electrons associated with the atom, e.g. the value of 1 specifies one singly occupied orbital on the atom that is not involved in bonding. ; data_atom_spin_multiplicity _name '_atom_spin_multiplicity' _category atom _type numb _list yes _list_reference '_atom_id' _enumeration_range 1: _definition ; The spin multiplicity applies only if the _atom_radical_count value is nonzero, and is derived from the formula 2S+1, where S is the absolute value of the sum of the electron spins (+1/2 or -1/2) on the atom. Thus, a biradical atom may have the values 1 or 3 [2(1/2-1/2)+1 or 2(1/2+1/2)+1] to represent a singlet or a triplet biradical. ; data_atom_type _name '_atom_type' _category atom _type char _list yes _list_reference '_atom_id' loop_ _enumeration_detail _enumeration 1 H 2 He 3 Li 4 Be 5 B 6 C 7 N 8 O 9 F 10 Ne 11 Na 12 Mg 13 Al 14 Si 15 P 16 S 17 Cl 18 Ar 19 K 20 Ca 21 Sc 22 Ti 23 V 24 Cr 25 Mn 26 Fe 27 Co 28 Ni 29 Cu 30 Zn 31 Ga 32 Ge 33 As 34 Se 35 Br 36 Kr 37 Rb 38 Sr 39 Y 40 Zr 41 Nb 42 Mo 43 Tc 44 Ru 45 Rh 46 Pd 47 Ag 48 Cd 49 In 50 Sn 51 Sb 52 Te 53 I 54 Xe 55 Cs 56 Ba 57 La 58 Ce 59 Pr 60 Nd 61 Pm 62 Sm 63 Eu 64 Gd 65 Tb 66 Dy 67 Ho 68 Er 69 Tm 70 Yb 71 Lu 72 Hf 73 Ta 74 W 75 Re 76 Os 77 Ir 78 Pt 79 Au 80 Hg 81 Tl 82 Pb 83 Bi 84 Po 85 At 86 Rn 87 Fr 88 Ra 89 Ac 90 Th 91 Pa 92 U 93 Np 94 Pu 95 Am 96 Cm 97 Bk 98 Cf 99 Es 100 Fm 101 Md 102 No 103 Lr 'un-shared electron pair' usp 'dummy atom' dum _definition ; Specifies the type of atom site identified by _atom_id. Hydrogen atoms will usually not be assigned to sites except where they are connected to more than one other atom, or where it is necessary to reference them, for example, in describing stereochemistry. ; data_atom_valency _name '_atom_valency' _category atom _type numb _list yes _list_reference '_atom_id' _enumeration_range -99:99 _definition ; Specifies the valency state of the atom site identified by _atom_id. ; data_bond_cip _name '_bond_cip' _category bond _type char _list yes loop_ _list_reference '_bond_id_1' '_bond_id_2' _definition ; Specifies the Cahn-Ingold-Prelog designation for the bond. The designators are by Prelog & Helmchen (1982). Reference: Prelog, V. & Helmchen, G. (1982). Angew. Chem. Int. Ed. Engl. 21, 567-583. ; data_bond_environment _name '_bond_environment' _category bond _type char _list yes loop_ _list_reference '_bond_id_1' '_bond_id_2' loop_ _enumeration _enumeration_detail ring 'in a ring' chain 'in a chain' _definition ; Specifies the connection environment of the bond. ; data_bond_id_ loop_ _name '_bond_id_1' '_bond_id_2' _category bond _type char _list yes _list_mandatory yes _list_link_parent '_atom_id' loop_ _list_uniqueness '_bond_id_1' '_bond_id_2' _definition ; Specify the atom-site codes of 'chemically connected' sites. The atom ID codes may appear in either order except for asymmetric bonds. Each 'bond' pair may be represented only once. The special syntax for representing atom sites within molecular templates is described in the _atom_id definition. ; data_bond_type_casreg3 _name '_bond_type_casreg3' _category bond _type char _list yes loop_ _list_reference '_bond_id_1' '_bond_id_2' loop_ _related_item _related_function '_bond_type_mif' convention '_bond_type_ccdc' convention loop_ _enumeration _enumeration_detail S 'single exact bond' D 'double exact bond' T 'triple exact bond' A 'ring alternating normalized bond' U 'tautomer normalized bond' _definition ; Code indicating the nature of the bond according to the Chemical Abstracts Service Registry III bonding convention. The convention is specified with _define_bonding_convention. Reference: Mockus, J. & Stobaugh, R. E. (1980). J. Chem. Inf. Comput. Sci. 20, 18-22. ; data_bond_type_ccdc _name '_bond_type_ccdc' _category bond _type char _list yes loop_ _list_reference '_bond_id_1' '_bond_id_2' loop_ _related_item _related_function '_bond_type_casreg3' convention '_bond_type_mif' convention loop_ _enumeration _enumeration_detail S 'single (two-electron) bond or sigma bond to metal' D 'double (four-electron) bond' T 'triple (six-electron) bond' Q 'quadruple (eight-electron, metal-metal) bond' A 'alternating normalized ring bond (aromatic)' C 'catena-forming bond in crystal structure' E 'equivalent (delocalized double) bond' P 'pi bond (metal-ligand pi interaction)' _definition ; Code indicating the nature of the bond according to the Cambridge Crystallographic Data Centre (CCDC) bonding convention. The convention is specified with _define_bonding_convention. Reference: Allen, F. H., Davies, J. E., Galloy, J. J., Johnson, O., Kennard, O., Macrae, C. F., Mitchell, E. M., Mitchell, G. F., Smith, J. M. & Watson, D. G. (1991). J. Chem. Inf. Comput. Sci. 31, 187-204. ; data_bond_type_mif _name '_bond_type_mif' _category bond _type char _list yes loop_ _list_reference '_bond_id_1' '_bond_id_2' loop_ _related_item _related_function '_bond_type_casreg3' convention '_bond_type_ccdc' convention loop_ _enumeration _enumeration_detail S 'single (two-electron) bond' D 'double (four-electron) bond' T 'triple (six-electron) bond' O 'other (e.g. coordination) bond' _definition ; Code indicating the nature of the bond according to the MIF bonding convention. Aromatic and normalized tautomeric bonds cannot be shown. The convention is specified with _define_bonding_convention. ; data_define_bonding_convention _name '_define_bonding_convention' _category define _type char loop_ _enumeration _enumeration_detail casreg3 'Chemical Abstracts Service Registry III' ccdc 'Cambridge Crystallographic Data Centre' mif 'basic MIF' _enumeration_default mif _definition ; Specifies the convention used for the values of the items: _atom_charge _atom_radical_count _atom_spin_multiplicity _atom_valency ; data_define_stereo_relationship _name '_define_stereo_relationship' _category define _type char loop_ _enumeration _enumeration_detail absolute 'configuration is as shown' relative 'configuration is relative' unknown 'configuration is unknown' racemic 'two stereoisomers: equal mix of d and l' absolute_excess 'two stereoisomers; excess as shown' relative_excess 'two stereoisomers; excess unknown' _enumeration_default unknown _definition ; Defines the enantiomorphic relationship of the stereo geometry in the data cell (data block or save frame). The descriptions of independently defined stereo regions, whose centres all have the same inter-centre relationship, may be grouped together. For each such group, the inter-centre relationship is specified by _define_stereo_relationship. Where there is only one such group, all the relevant data may be included in the data block or save frame for the molecule as a whole. Where there are several different such groups, each should be shown in a separate save frame and _reference_stereo_group should be used to reference the different save frames. For each stereo group, a two-level loop structure will be used to define the stereocentres it contains. Each stereogenic atom site is defined by _stereo_atom_id and _stereo_geometry at the first loop level, and by _stereo_vertex_id at the second. Each stereogenic bond is defined by _stereo_bond_id_1, _stereo_bond_id_2 and _stereo_geometry at the first level, and by _stereo_vertex_id at the second level. ; data_display_colour _name '_display_colour' _category display _type char _list yes _list_reference '_display_id' loop_ _enumeration _enumeration_detail black 000:000:000_RGB white 255:255:255_RGB grey 192:192:192_RGB grey_light 211:211:211_RGB grey_slate 112:128:144_RGB blue 000:000:255_RGB blue_light 176:224:230_RGB blue_medium 000:000:205_RGB blue_dark 025:025:112_RGB blue_navy 000:000:128_RGB blue_royal 065:105:225_RGB blue_sky 135:206:235_RGB blue_steel 070:130:180_RGB turquoise 064:224:208_RGB cyan 000:255:255_RGB cyan_light 224:255:255_RGB green 000:255:000_RGB green_light 152:251:152_RGB green_dark 000:100:000_RGB green_sea 046:139:087_RGB green_lime 050:205:050_RGB green_olive 107:142:035_RGB green_khaki 240:230:140_RGB yellow 255:255:000_RGB yellow_light 255:255:224_RGB yellow_gold 255:215:000_RGB brown 165:042:042_RGB brown_sienna 160:082:045_RGB brown_beige 245:245:220_RGB brown_tan 210:180:140_RGB salmon 250:128:114_RGB salmon_light 255:160:122_RGB salmon_dark 233:150:122_RGB orange 255:165:000_RGB orange_dark 255:140:000_RGB red 255:000:000_RGB red_coral 255:127:080_RGB red_tomato 255:099:071_RGB red_orange 255:069:000_RGB red_violet 219:112:147_RGB red_maroon 176:048:096_RGB pink 255:192:203_RGB pink_light 255:182:193_RGB pink_deep 255:020:147_RGB pink_hot 255:105:180_RGB violet 238:130:238_RGB violet_red 208:032:144_RGB violet_magenta 255:000:255_RGB violet_dark 148:000:211_RGB violet_blue 138:043:226_RGB _enumeration_default black _definition ; The colour code specifying the colour of the object identified by _display_symbol. The permitted colour codes are stored with the RGB ratios as a separate validation file 'mif_core_colours.val'. ; data_display_conn_colour _name '_display_conn_colour' _category display_conn _type char _list yes _list_level 2 _list_reference '_display_conn_id' loop_ _enumeration _enumeration_detail black 000:000:000_RGB white 255:255:255_RGB grey 192:192:192_RGB grey_light 211:211:211_RGB grey_slate 112:128:144_RGB blue 000:000:255_RGB blue_light 176:224:230_RGB blue_medium 000:000:205_RGB blue_dark 025:025:112_RGB blue_navy 000:000:128_RGB blue_royal 065:105:225_RGB blue_sky 135:206:235_RGB blue_steel 070:130:180_RGB turquoise 064:224:208_RGB cyan 000:255:255_RGB cyan_light 224:255:255_RGB green 000:255:000_RGB green_light 152:251:152_RGB green_dark 000:100:000_RGB green_sea 046:139:087_RGB green_lime 050:205:050_RGB green_olive 107:142:035_RGB green_khaki 240:230:140_RGB yellow 255:255:000_RGB yellow_light 255:255:224_RGB yellow_gold 255:215:000_RGB brown 165:042:042_RGB brown_sienna 160:082:045_RGB brown_beige 245:245:220_RGB brown_tan 210:180:140_RGB salmon 250:128:114_RGB salmon_light 255:160:122_RGB salmon_dark 233:150:122_RGB orange 255:165:000_RGB orange_dark 255:140:000_RGB red 255:000:000_RGB red_coral 255:127:080_RGB red_tomato 255:099:071_RGB red_orange 255:069:000_RGB red_violet 219:112:147_RGB red_maroon 176:048:096_RGB pink 255:192:203_RGB pink_light 255:182:193_RGB pink_deep 255:020:147_RGB pink_hot 255:105:180_RGB violet 238:130:238_RGB violet_red 208:032:144_RGB violet_magenta 255:000:255_RGB violet_dark 148:000:211_RGB violet_blue 138:043:226_RGB _enumeration_default black _definition ; The colour code specifying the colour of the object identified by _display_conn_symbol. The permitted colour codes are stored with the RGB ratios as a separate validation file 'mif_core_colours.val'. ; data_display_conn_id _name '_display_conn_id' _category display_conn _type numb _list yes _list_level 2 _list_mandatory yes _list_link_parent '_display_id' _definition ; The identifying number of a display object which is connected to another display object in level 1 of the loop packet which is designated as _display_id. The ID number appearing as the _display_conn_id MUST appear elsewhere in the loop structure as a value for _display_id. ; data_display_conn_symbol _name '_display_conn_symbol' _category display_conn _type char _list yes _list_level 2 _list_reference '_display_conn_id' loop_ _enumeration _enumeration_detail .c 'dotted line to object centres' -c 'dashed line to object centres' +c 'dashed+solid line to object centres' 1c 'solid line to object centres' 2c 'double solid line to object centres' 3c 'triple solid line to object centres' 4c 'quadruple solid line to object centres' .b 'dotted line to object boundary' -b 'dashed line to object boundary' +b 'dashed+solid line to object boundary' 1b 'solid line to object boundary' 2b 'double solid line to object boundary' 3b 'triple solid line to object boundary' 4b 'quadruple solid line to object boundary' >b 'wedge with apex at _display_conn_id'