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Re: coreCIFchem #5

Here is the first part of my contribution to coreCIFchem #5.
It is a very highly modified cif of David's TNT example and represents 
my best effort to date to try and clarify and simplify his very 
stimulating offering. I have not as yet had time to tidy up my file of 
comments on #5 but you should receive that fairly soon.

In accordance with the sloppy way that I work, I have concentrated on 
the information that needs to be encapsulated in the file and have more 
or less ignored the CIF syntax rules.

H.



HDF's modified TNT CIF
----------------------


loop_
_tecton_id          # List reference / short name
_tecton_name        # name e.g. full IUPAC name  
_tecton_formula
_tecton_symmetry    # point group if geometry present otherwise topological
_tecton_chirality   # time-averaged if no geometry given
_tecton_type
TNTaa   'aa 2,4,6 trinitrotoluene'  'C7 H5 N3 O6'  Cs   achiral  conformer
TNTbb   'ab 2,4,6 trinitrotoluene'  'C7 H5 N3 O6'  Cs   achiral  conformer
TNTab   'ab 2,4,6 trinitrotoluene'  'C7 H5 N3 O6'  C1   *TNTba   conformer
TNTba   'ba 2,4,6 trinitrotoluene'  'C7 H5 N3 O6'  C1   *TNTab   conformer
TNT     '2,4,6 trinitrotoluene'     'C7 H5 N3 O6'  C2h  achiral  molecule
subnz   '1,2,4,6 benzene ring'      'C6 H2'        C2h  achiral  moeity
nitro   'nitro group'               'N O2'         C2h  achiral  group
# Need to find out about IUPAC rules for naming conformers
# *TNTba means chiral being the enantiomer of TNTba



loop_
_tecton_topology_atom_tecton_id          # Child of _tecton_id
_tecton_topology_atom_label
_tecton_topology_atom_type_symbol        # Child of _atom_type_symbol
_tecton_topology_atom_valence            # WHAT IS THIS EXACTLY?????
_tecton_topology_atom_coord_number
_tecton_topology_atom_details
TNT     C1   C    4   3  ?
TNT     C2   C    4   3  ?
TNT     C3   C    4   3  ?
TNT     C4   C    4   3  ?
TNT     C5   C    4   3  ?
TNT     C6   C    4   3  ?
TNT     C7   C    4   4  ?
TNT     H3   H    1   1  ?
TNT     H5   H    1   1  ?
TNT     H71  H    1   1  ?
TNT     H72  H    1   1  ?
TNT     H73  H    1   1  ?
TNT     N2   N    3   3  ?
TNT     O21  O    2   1  ?
TNT     O22  O    2   1  ?
TNT     N4   N    3   3  ?
TNT     O41  O    2   1  ?
TNT     O42  O    2   1  ?
TNT     N6   N    3   3  ?
TNT     O61  O    2   1  ?
TNT     O62  O    2   1  ?
subnz   C1   C    4   3  ?
subnz   C2   C    4   3  ?
subnz   C3   C    4   3  ?
subnz   C4   C    4   3  ?
subnz   C5   C    4   3  ?
subnz   C6   C    4   3  ?
subnz   H3   C    1   1  ?
subnz   H5   H    1   1  ?
nitro   N1   N    3   3  ?
nitro   O1   O    2   1  ?
nitro   O2   O    2   1  ?



loop_
_tecton_topology_bond_tecton_id   # Child of _tecton_id
_tecton_topology_bond_atom1_label # Child of _tecton_topology_atom_label
_tecton_topology_bond_atom2_label # Child of _tecton_topology_atom_label
_tecton_topology_bond_order
_tecton_topology_bond_type
TNT     C1   C2   1.5  delocalized     # TNT benzene ring
TNT     C2   C3   1.5  delocalized
TNT     C3   C4   1.5  delocalized
TNT     C4   C5   1.5  delocalized
TNT     C5   C6   1.5  delocalized
TNT     C6   C1   1.5  delocalized
TNT     C3   H3   1.0  single
TNT     C5   H5   1.0  single
TNT     C7   C1   1.0  single          # TNT Methyl group
TNT     C7   H71  1.0  single
TNT     C7   H72  1.0  single
TNT     C7   H73  1.0  single
TNT     N2   C2   1.0  single          # TNT N2 nitro group
TNT     N2   O21  1.5  delocalized
TNT     N2   O22  1.5  delocalized
TNT     N4   C4   1.0  single          # TNT N4 nitro group
TNT     N4   O41  1.5  delocalized
TNT     N4   O42  1.5  delocalized
TNT     N6   C6   1.0  single          # TNT N6 nitro group
TNT     N6   O61  1.5  delocalized
TNT     N6   O62  1.5  delocalized
subnz   C1   C2   1.5  delocalized     # 1,2,4,6 substituted benzene ring
subnz   C2   C3   1.5  delocalized
subnz   C3   C4   1.5  delocalized
subnz   C4   C5   1.5  delocalized
subnz   C5   C6   1.5  delocalized
subnz   C6   C1   1.5  delocalized
subnz   C3   H3   1.0  single
subnz   C5   H5   1.0  single
subnz   C1   .    1.0  single          # A dangling bond
subnz   C2   .    1.0  single
subnz   C4   .    1.0  single
subnz   C6   .    1.0  single
nitro   N1   O1   1.5  delocalized     # Nitro group
nitro   N1   O2   1.5  delocalized
nitro   N1   .    1.0  single


----------------------------------------------------------------------------------
EITHER - Minimal geometry information necessary to distinguish conformers
----------------------------------------------------------------------------------


loop_
_tecton_geometry_dihedral_id           # Child of _tecton_id
_tecton_geometry_dihedral_atom1_label  # Child of _tecton_topology_atom_label
_tecton_geometry_dihedral_atom2_label  # Child of _tecton_topology_atom_label
_tecton_geometry_dihedral_atom3_label  # Child of _tecton_topology_atom_label
_tecton_geometry_dihedral_atom4_label  # Child of _tecton_topology_atom_label
TNTaa   C1   C2   N2   O21   10.5
TNTaa   C1   C6   N6   O61   10.5
TNTbb   C1   C2   N2   O21  -10.5
TNTbb   C1   C6   N6   O61  -10.5
TNTab   C1   C2   N2   O21   10.5
TNTab   C1   C6   N6   O61  -10.5
TNTba   C1   C2   N2   O21  -10.5
TNTba   C1   C6   N6   O61   10.5


----------------------------------------------------------------------------------
OR - Maximal geometry information
----------------------------------------------------------------------------------



loop_
_tecton_geometry_coord_id              # Child of _tecton_id
_tecton_geometry_ooord_atom_label      # Child of _tecton_topology_atom_label
_tecton_geometry_coord_atom_coord_x    # Coordinates of atom in Angstrom
_tecton_geometry_coord_atom_coord_y    # THERE IS A PROBLEM HERE IF YOU HAVE
_tecton_geometry_coord_atom_coord_z    # COORDINATE SETS ON DIFFERENT BASES
_tecton_geometry_coord_atom_details
TNT     C1  0.037  0.146  -0.124  ?
TNT     C2  1.378  0.562   0.134  ?
TNT     C3  1.846  1.421   0.204  ?
TNT     C4  2.567  1.834   0.304  ?
TNT     C5  1.745  1.563   0.245  ?
TNT     C6  0.962  0 498   0.103  ?
TNT     H3      ?      ?       ?  ?    # NEED SOME VALUES HERE
TNT     H5      ?      ?       ?  ?    # NEED SOME VALUES HERE



loop_
_tecton_geometry_distance_id           # Child of _tecton_id
_tecton_geometry_distance_atom1_label  # Child of _tecton_topology_atom_label
_tecton_geometry_distance_atom2_label  # Child of _tecton_topology_atom_label
_tecton_geometry_distance_distance     # Distance atom1-atom2 in Angstroms
TNT     C7   C1    1.54                # TNT methyl group
TNT     C7   H71   1.05
TNT     C7   H72   1.05
TNT     C7   H73   1.05
TNT     N4   C4    1.43                # TNT N4 nitro group
TNT     N4   O41   1.18
TNT     N4   O42   1.18
TNT     N2   C2    1.43                # TNT N2 nitro group
TNT     N2   O21   1.18
TNT     N2   O22   1.18
TNT     N6   C6    1.43                # TNT N6 nitro group
TNT     N6   O61   1.18
TNT     N6   O62   1.18



loop_
_tecton_geometry_angle_id              # Child of _tecton_id
_tecton_geometry_angle_atom1_label     # Child of _tecton_topology_atom_label
_tecton_geometry_angle_atom2_label     # Child of _tecton_topology_atom_label
_tecton_geometry_angle_atom3_label     # Child of _tecton_topology_atom_label
_tecton_geometry_angle_angle           # Angle in degrees
TNT     C1   C7   H71  109             # TNT Methyl group
TNT     C1   C7   H72  109
TNT     C1   C7   H73  109
TNT     H71  C7   H72  109
TNT     H72  C7   H73  109
TNT     H73  C7   H71  109
TNT     O41  N4   C4   117             # TNT N4 nitro group
TNT     O42  N4   C4   117 
TNT     O41  N4   O42  126
TNT     O21  N2   C2   117             # TNT N2 nitro group
TNT     O22  N2   C2   117 
TNT     O21  N2   O22  126 
TNT     O61  N6   C6   117             # TNT N6 nitro group
TNT     O62  N6   C6   117 
TNT     O61  N6   O62  126 



loop_
_tecton_geometry_dihedral_id           # Child of _tecton_id
_tecton_geometry_dihedral_atom1_label  # Child of _tecton_topology_atom_label
_tecton_geometry_dihedral_atom2_label  # Child of _tecton_topology_atom_label
_tecton_geometry_dihedral_atom3_label  # Child of _tecton_topology_atom_label
_tecton_geometry_dihedral_atom4_label  # Child of _tecton_topology_atom_label
TNT     C3   C4   N4   O41   90
TNTaa   C1   C2   N2   O21   10.5
TNTaa   C1   C6   N6   O61   10.5
TNTbb   C1   C2   N2   O21  -10.5
TNTbb   C1   C6   N6   O61  -10.5
TNTab   C1   C2   N2   O21   10.5
TNTab   C1   C6   N6   O61  -10.5
TNTba   C1   C2   N2   O21  -10.5
TNTba   C1   C6   N6   O61   10.5



----------------------------------------------------------------------------------
ENDOR
----------------------------------------------------------------------------------



loop_
_tecton_topology_combine_id              # Child of _tecton_id
_tecton_topology_combine_source_id       # Child of _tecton_id
TNTaa   TNT  # Means any information about TNT also applies, as such, to TNTaa
TNTbb   TNT
TNTab   TNT
TNTba   TNT
# MAY BE THIS CAN BE DONE LEGALLY WITHIN CURRENT CIF SYNTAX BY SAVE FRAMES ???


#
# AT LEAST SOME OF THE FOLLOWING "MAPS" ARE NOT MAPS IN THE STRICT 
# MATHEMATICAL SENSE. MAYBE ANOTHER WORD IS NEEDED.
#
loop_
_map_tecton2tecton_id           # List reference / Map Name
_map_tecton2tecton_source_id    # Child of tecton_id
_map_tecton2tecton_image_id     # Child of tecton_id     
MAPsubnz2TNT         subnz   TNT
MAPnitro2TNTnitroN2  nitro   TNT
MAPnitro2TNTnitroN4  nitro   TNT
MAPnitro2TNTnitroN6  nitro   TNT



loop_
_map_tecton2tecton_atom_map_id        # _map_tecton2tecton_id (Map name)
_map_tecton2tecton_atom_atom1_label   # Child of _tecton_topology_atom_label
_map_tecton2tecton_atom_atom2_label   # Child of _tecton_topology_atom_label
MAPsubnz2TNT          C1    C1        # mapping 1,2,4,6 benzene moeity onto TNT
MAPsubnz2TNT          C2    C2
MAPsubnz2TNT          C3    C3
MAPsubnz2TNT          C4    C4
MAPsubnz2TNT          C5    C5
MAPsubnz2TNT          C6    C6
MAPsubnz2TNT          H3    H3
MAPsubnz2TNT          H5    H5
MAPnitro2TNTnitroN2   N1    N2    # mapping the nitro group onto the TNT N2 group
MAPnitro2TNTnitroN2   O1    O21
MAPnitro2TNTnitroN2   O2    O22
MAPnitro2TNTnitroN4   N1    N4    # mapping the nitro group onto the TNT N4 group
MAPnitro2TNTnitroN4   O1    O41
MAPnitro2TNTnitroN4   O2    O42
MAPnitro2TNTnitroN6   N1    N6    # mapping the nitro group onto the TNT N6 group
MAPnitro2TNTnitroN6   O1    O61
MAPnitro2TNTnitroN6   O2    O62



loop_
_map_tecton2crystal_id          # List reference / Map Name
_map_tecton2crystal_tecton_id   # Child of tecton_id
                                # CRYSTAL ID ????
                                # OCCUPATION PARAMETER? 
MAPTNTaa2crystal     TNTaa
MAPTNTbb2crystal     TNTbb
MAPTNTab2crystal     TNTab
MAPTNTba2crystal     TNTba
MAPTNT2crystal       TNT



loop_
map_tecton2crystal_atom_id               # Child of _map_tecton2crystal_id
map_tecton2crystal_atom_atom_id          # Child of _tecton_topology_atom_label
map_tecton2crystal_atom_site_label       # child of _atom_site_label
map_tecton2crystal_atom_symop_id         # child of _space_group_symop_id
MAPTNT2crystal    C1    C1    1
MAPTNT2crystal    C2    C2    1
MAPTNT2crystal    C3    C3    1
MAPTNT2crystal    C4    C4    1
MAPTNT2crystal    C5    C3    2
MAPTNT2crystal    C6    C2    2
MAPTNT2crystal    H3    H3    1
MAPTNT2crystal    H5    H3    2
MAPTNT2crystal    C7    C7    1
MAPTNT2crystal    H71   H71   1
MAPTNT2crystal    H72   H72   1
MAPTNT2crystal    H73   H71   2
MAPTNT2crystal    N4    N4    1
MAPTNT2crystal    O41   O41   1
MAPTNT2crystal    O42   O42   1
# SIDE CHAINS
MAPTNTaa2crystal  N2    N2a   1
MAPTNTaa2crystal  O21   O21a  1
MAPTNTaa2crystal  O22   O22a  1
MAPTNTaa2crystal  N6    N2a   2
MAPTNTaa2crystal  O61   O21a  2
MAPTNTaa2crystal  O62   O22a  2
MAPTNTbb2crystal  N2    N2b   1
MAPTNTbb2crystal  O21   O21b  1
MAPTNTbb2crystal  O22   O22b  1
MAPTNTbb2crystal  N6    N2b   2
MAPTNTbb2crystal  O61   O21b  2
MAPTNTbb2crystal  O62   O22b  2
MAPTNTab2crystal  N2    N2a   1
MAPTNTab2crystal  O21   O21a  1
MAPTNTab2crystal  O22   O22a  1
MAPTNTab2crystal  N6    N2b   2
MAPTNTab2crystal  O61   O21b  2
MAPTNTab2crystal  O62   O22b  2
MAPTNTba2crystal  N2    N2b   1
MAPTNTba2crystal  O21   O21b  1
MAPTNTba2crystal  O22   O22b  1
MAPTNTba2crystal  N6    N2a   2
MAPTNTba2crystal  O61   O21a  2
MAPTNTba2crystal  O62   O22a  2
# IF THE SIDE CHAINS WERE LONGER, EVEN THE ABOVE SYNTAX WOULD BE TOO CUMBERSOME.

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