# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 02:31:25 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: 3-[(carboxymethyl)sulfanyl]pyridine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CSc1cccnc1C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 O2Y  O2Y  '3-[(carboxymethyl)sulfanyl]pyridine-2-carboxylic acid'  ligand  19  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_O2Y
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 O2Y  O14  O  O      0  -0.541  -3.5829  -1.2942   0.1965
 O2Y  C12  C  C      0   0.424  -3.5627  -0.0785  -0.0519
 O2Y  O13  O  OC    -1  -0.754  -4.5344   0.6484  -0.3272
 O2Y  C11  C  CH2    0  -0.720  -2.2024   0.6456  -0.0168
 O2Y  S10  S  S2     0   0.074  -0.8585  -0.5668   0.0554
 O2Y  C6   C  CR6    0  -0.188   0.5633   0.4813   0.0392
 O2Y  C5   C  CR16   0  -0.106   0.4515   1.8747   0.0531
 O2Y  C4   C  CR16   0  -0.341   1.5852   2.6642   0.0167
 O2Y  C3   C  CR16   0  -0.134   2.8189   2.0414  -0.0474
 O2Y  N2   N  N      0  -0.302   2.9445   0.7243  -0.0587
 O2Y  C1   C  CR6    0  -0.001   1.8682  -0.0549  -0.0216
 O2Y  C7   C  C      0   0.421   2.1390  -1.5588  -0.0174
 O2Y  O8   O  O      0  -0.512   1.1894  -2.2716   0.3627
 O2Y  O9   O  OC    -1  -0.702   3.2679  -1.9259  -0.3711
 O2Y  H2   H  HCH2   0   0.298  -2.1207   1.3019  -0.8857
 O2Y  H3   H  HCH2   0   0.295  -2.1753   1.2793   0.8752
 O2Y  H4   H  HCR6   0   0.285  -0.5120   2.3605   0.1124
 O2Y  H5   H  HCR6   0   0.265   1.5065   3.7429   0.0271
 O2Y  H6   H  HCR6   0   0.239   3.7336   2.6236  -0.0877

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 O2Y  O14  C12  deloc     1.241  0.020  1.241
 O2Y  C12  C11  single    1.541  0.020  1.541
 O2Y  C12  O13  deloc     1.244  0.020  1.244
 O2Y  C11  S10  single    1.811  0.020  1.811
 O2Y  C5   C4   aromatic  1.382  0.020  1.382
 O2Y  C5   C6   aromatic  1.398  0.020  1.398
 O2Y  S10  C6   single    1.766  0.020  1.766
 O2Y  C4   C3   aromatic  1.383  0.020  1.383
 O2Y  C6   C1   aromatic  1.412  0.020  1.412
 O2Y  C3   N2   aromatic  1.323  0.020  1.323
 O2Y  C1   N2   aromatic  1.329  0.020  1.329
 O2Y  C1   C7   single    1.528  0.020  1.528
 O2Y  C7   O8   deloc     1.247  0.020  1.247
 O2Y  C7   O9   deloc     1.239  0.020  1.239
 O2Y  C11  H2   single    0.970  0.020  1.090
 O2Y  C11  H3   single    0.970  0.020  1.090
 O2Y  C5   H4   single    0.930  0.020  1.080
 O2Y  C4   H5   single    0.930  0.020  1.080
 O2Y  C3   H6   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 O2Y  C11  C12  O13  114.82  3.000
 O2Y  O13  C12  O14  127.15  3.000
 O2Y  C11  C12  O14  118.03  3.000
 O2Y  H3   C11  H2   107.38  3.000
 O2Y  H3   C11  S10  109.68  3.000
 O2Y  H2   C11  S10  112.24  3.000
 O2Y  H3   C11  C12  108.20  3.000
 O2Y  H2   C11  C12  109.28  3.000
 O2Y  S10  C11  C12  109.95  3.000
 O2Y  C6   S10  C11  101.51  3.000
 O2Y  C1   C6   C5   116.92  3.000
 O2Y  C1   C6   S10  121.26  3.000
 O2Y  C5   C6   S10  121.80  3.000
 O2Y  H4   C5   C4   118.42  3.000
 O2Y  H4   C5   C6   121.33  3.000
 O2Y  C4   C5   C6   120.24  3.000
 O2Y  H5   C4   C3   120.95  3.000
 O2Y  H5   C4   C5   120.65  3.000
 O2Y  C3   C4   C5   118.40  3.000
 O2Y  H6   C3   N2   116.99  3.000
 O2Y  H6   C3   C4   120.80  3.000
 O2Y  N2   C3   C4   122.22  3.000
 O2Y  C1   N2   C3   120.43  3.000
 O2Y  C7   C1   N2   115.69  3.000
 O2Y  C7   C1   C6   122.50  3.000
 O2Y  N2   C1   C6   121.79  3.000
 O2Y  O9   C7   O8   127.72  3.000
 O2Y  O9   C7   C1   116.90  3.000
 O2Y  O8   C7   C1   115.38  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 O2Y  CONST_01  C3   C4   C5   C6     0.00   0.0  0
 O2Y  CONST_02  C3   N2   C1   C6     0.00   0.0  0
 O2Y  CONST_03  N2   C3   C4   C5     0.00   0.0  0
 O2Y  CONST_04  N2   C1   C6   C5     0.00   0.0  0
 O2Y  CONST_05  C1   C6   C5   C4     0.00   0.0  0
 O2Y  CONST_06  C1   N2   C3   C4     0.00   0.0  0
 O2Y  CONST_07  C4   C5   C6   S10  180.00   0.0  0
 O2Y  CONST_08  N2   C1   C6   S10  180.00   0.0  0
 O2Y  CONST_09  C7   C1   C6   C5   180.00   0.0  0
 O2Y  CONST_10  C7   C1   N2   C3   180.00   0.0  0
 O2Y  CONST_11  H5   C4   C5   C6   180.00   0.0  0
 O2Y  CONST_12  H6   C3   C4   C5   180.00   0.0  0
 O2Y  CONST_13  H4   C5   C4   C3   180.00   0.0  0
 O2Y  Var_01    C5   C6   S10  C11    3.43  30.0  2
 O2Y  Var_02    O8   C7   C1   C6   -16.61  30.0  2
 O2Y  Var_03    H2   C11  S10  C6    56.57  30.0  2
 O2Y  Var_04    S10  C11  C12  O14   11.87  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 O2Y  plan-1  S10  0.020
 O2Y  plan-1  C6   0.020
 O2Y  plan-1  C5   0.020
 O2Y  plan-1  C4   0.020
 O2Y  plan-1  C3   0.020
 O2Y  plan-1  N2   0.020
 O2Y  plan-1  C1   0.020
 O2Y  plan-1  C7   0.020
 O2Y  plan-1  H4   0.020
 O2Y  plan-1  H5   0.020
 O2Y  plan-1  H6   0.020
 O2Y  plan-2  O14  0.020
 O2Y  plan-2  C12  0.020
 O2Y  plan-2  O13  0.020
 O2Y  plan-2  C11  0.020
 O2Y  plan-3  C1   0.020
 O2Y  plan-3  C7   0.020
 O2Y  plan-3  O8   0.020
 O2Y  plan-3  O9   0.020

