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Re: coreCIFchem #5
- To: Chemical information in core CIF <[email protected]>
- Subject: Re: coreCIFchem #5
- From: Howard Flack <[email protected]>
- Date: Fri, 30 Jul 2004 12:53:29 +0200
- In-reply-to: <[email protected]>
- References: <[email protected]>
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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