############################################################################## # # # MIF DATA DICTIONARY # # # # Standard definitions for DATA stored in a Molecular Information File. # # The DDL commands used in this dictionary are defined in "ddldic.c93". # # # ############################################################################## global_ _dictionary_name mifdic.t93 _dictionary_version 0.7 _dictionary_update 1993-07-09 _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 symbils 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 ; _list no _list_mandatory no _list_level 1 _enumeration ? _enumeration_default ? _esd no 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 to this site. all all sites ring all sites forming rings nh all sites excl. hydrogens and unshared electron pairs h hydrogen 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_atom_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 and Helmchen (Angew. Chem. Int. Ed. Engl. 1982, 21, 567-583). ; data_atom_model_ loop_ _name '_atom_coord_x' '_atom_coord_y' '_atom_coord_z' _category atom _type numb _list yes _list_reference '_atom_id' loop_ _units_extension _units_description _units_conversion ' ' 'Angstroms' *1.0 '_pm' 'picometres' /100. '_nm' 'nanometres' *10. _definition ; Specifies the Cartesian coordinates for the atom at an arbitary origin and arbitary orthogonal axes. ; data_atom_id _name '_atom_id' _category atom _type numb _list yes _list_mandatory yes _list_uniqueness '_atom_id' loop_ _list_link_child '_bond_id_1' '_bond_id_2' '_stereo_centre_id' '_stereo_vertex_id' _enumeration_range 1: _definition ; This specifies a unique numeric identifier for an 'atom site' in a molecule or fragment. A designated atom site may be occupied by a 'dummy' atom (see _atom_type). ; 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 isotopic state of the atom. The default is the most abundant naturally occuring 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. See also _atom_type. ; data_atom_radical _name '_atom_radical' _category atom _type numb _list yes _list_reference '_atom_id' loop_ _enumeration _enumeration_detail none 'not a radical' singlet 'singlet biradical' doublet 'doublet (i.e. ordinary) radical' triplet 'triplet biradiacal' _enumeration_default none _definition ; Specifies the formal radical state of the atom. ; 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 C1 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 'unshared electron pair' usp 'dummy atom' dum _definition ; Specifies the type of atom site identified by _atom_id. Hydrogen atoms will usually not 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. ; data_bond_cip _name '_bond_cip' _category bond _type char _list yes _list_reference '_bond_id_' _definition ; Specifies the Cahn-Ingold-Prelog designation for the bond. The designators are by Prelog and Helmchen (Angew. Chem. Int. Ed. Engl. 1982, 21 567-583). ; data_bond_environment _name '_bond_environment' _category bond _type char _list yes _list_reference '_bond_id_' 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 numb _list yes _list_mandatory yes _list_link_parent '_atom_id' loop_ _list_uniqueness '_bond_id_1' '_bond_id_2' _enumeration_range 1: _definition ; Specify the atoms joined by a covalent bond in the applicable bonding convention; the atom id's may appear in either order except for asymmetric bonds. Each covalent bond shall be represented only once. ; data_bond_type_casreg3 _name '_bond_type_casreg3' _category bond _type char _list yes _list_reference '_bond_id_' 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 normalised bond' U 'tautomer normalised bond' _definition ; Specifies the nature of the covalent bond using the CASREG3 bonding convention. ; data_bond_type_ccdc _name '_bond_type_ccdc' _category bond _type char _list yes _list_reference '_bond_id_' loop_ _related_item _related_function '_bond_type_casreg3' convention '_bond_type_mif' convention loop_ _enumeration _enumeration_detail S 'single (2-electron) bond or sigma bond to metal' D 'double (4-electron) bond' T 'triple (6-electron) bond' Q 'quadruple (8-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 ; Specifies the nature of the covalent bond using the Cambridge Crystallographic Data Centre (CCDC) bonding convention. ; data_bond_type_mif _name '_bond_type_mif' _category bond _type char _list yes _list_reference '_bond_id_' loop_ _related_item _related_function '_bond_type_casreg3' convention '_bond_type_ccdc' convention loop_ _enumeration _enumeration_detail S 'single (2-electron) bond' D 'Double (4-electron) bond' T 'Triple (6-electron) bond' O 'Other (e.g. coordination) bond' _definition ; Specifies the nature of the covalent bond using the MIF bonding convention. Aromatic and normalised tautomeric bonds cannot be shown. ; data_conformance_ loop_ _name '_conformance_primary' '_conformance_secondary' _category conformance _type char _list both _definition ; File names of the DDL dictionaries containing definitions to which the contained data conforms. The "primary" dictionaries are used for standard conformance (_type, _enumeration, etc.) testing by STAR compliant software. The "secondary" files, if specified, contain additional definitions used by applications. E.g. if data uses the "query" construction (as defined in _define_object_conformance), the primary dictionary will contain definitions for this construction and the secondary dictionary will contain definitions for the standard data as "unwrapped" by the application. ; data_define_atom_convention _name '_define_atom_convention' _category define _type char loop_ _enumeration _enumeration_detail casreg3 'Chemical Abstracts Reg 3' ccdc 'Cambridge Cryst. Data Centre' mif 'basic MIF' _enumeration_default mif _definition ; Specifies the convention used for the values of the items: _atom_charge _atom_radical _atom_valency ; data_define_object_class _name '_define_object_class' _category define _type char loop_ _enumeration _enumeration_detail molecule 'molecular structure data' conformation 'molecular conformation data' stereo-group 'stereo data in same group' _enumeration_default molecule _definition ; Specifies the nature of the object being represented by the data block or save frame. ; data_define_object_conformance _name '_define_object_conformance' _category define _type char loop_ _enumeration _enumeration_detail data 'primary conformance to data dictionary' query 'primary conformance to query dictionary' _enumeration_default data _definition ; Specifies the dictionary definitions which the data in this object conforms to. If the value is "data" the definitions are contained within the standard DDL file(s) specified by _conformance_primary. The value "query" indicates that the primary definitions are contained within a DDL query file specified by _conformance_primary, but the standard DDL data file is specified by _conformance_secondary. ; 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 '2 stereoisomers: equal mix of d & l' abs-xs '2 stereoisomers; excess as shown' rel-xs '2 stereoisomers; excess unknown' _enumeration_default unknown _definition ; Defines the enantiomorphic relationship of the stereo geometry in this data set (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 used to reference the different save frames. For each stereo group, a 2 level loop structure may be used to define the stereocentres it contains. Each stereocentre is defined by a _stereo_geometry and _stereo_centre_id items in the first loop level, and _stereo_vertex_id in the second. ; data_display_colour _name '_display_colour' _category display _type char _list yes _list_reference '_display_id' loop_ _enumeration white black grey red pink dark_red blue light_blue dark_blue green light_green dark_green yellow lemon orange violet mauve magenta _enumeration_default black _definition ; The colour of the _display_object. ; 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 white black grey red pink dark_red blue light_blue dark_blue green light_green dark_green yellow lemon orange violet mauve magenta _enumeration_default black _definition ; The colour of the _display_conn_symbol. ; 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 connect site. ; 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' 1c 'solid line to object centres' 2c 'double solid line to object centres' 3c 'triple solid line to object centres' .b 'dotted line to object boundary' -b 'dashed line to object boundary' 1b 'solid line to object boundary' 2b 'double solid line to object boundary' 3b 'triple solid line to object boundary' >b 'wedge with apex at _display_conn_id'