# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 09:10:03 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: 3-sulfanylpyridine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ncccc1S
#
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
 1WD  1WD  '3-sulfanylpyridine-2-carboxylic acid'  ligand  14  10  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1WD
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
 1WD  O10  O  OC    -1  -0.482  -1.8670  -1.8206  -0.1699
 1WD  C8   C  C      0   0.488  -1.4432  -0.6969  -0.1575
 1WD  O9   O  O      0  -0.625  -2.2348   0.3233  -0.1992
 1WD  C3   C  C      0   0.047   0.0206  -0.4046  -0.1012
 1WD  N4   N  N      0  -0.437   0.7712  -1.4982   0.0341
 1WD  C5   C  C1     0  -0.048   2.0803  -1.3886   0.0932
 1WD  C6   C  C1     0  -0.286   2.7259  -0.1504   0.0231
 1WD  C1   C  C1     0  -0.212   1.9604   0.9800  -0.1040
 1WD  C2   C  C      0  -0.130   0.5544   0.9065  -0.1608
 1WD  S7   S  S2     0  -0.534  -0.3547   2.3731  -0.2889
 1WD  H2   H  H      0   0.266   2.6552  -2.3070   0.1849
 1WD  H3   H  H      0   0.269   3.8073  -0.0903   0.0342
 1WD  H4   H  H      0   0.262   2.4250   1.9548  -0.1772
 1WD  H5   H  HSH1   0   0.421  -1.7085   1.1932  -0.2050

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
 1WD  S7  C2   single    1.730  0.020  1.730
 1WD  C1  C2   aromatic  1.409  0.020  1.409
 1WD  C1  C6   aromatic  1.371  0.020  1.371
 1WD  C2  C3   aromatic  1.417  0.020  1.417
 1WD  C6  C5   aromatic  1.398  0.020  1.398
 1WD  C3  N4   aromatic  1.333  0.020  1.333
 1WD  C3  C8   single    1.494  0.020  1.494
 1WD  C5  N4   aromatic  1.315  0.020  1.315
 1WD  C8  O9   deloc     1.292  0.020  1.292
 1WD  C8  O10  deloc     1.201  0.020  1.201
 1WD  C5  H2   single    0.930  0.020  1.080
 1WD  C6  H3   single    0.930  0.020  1.080
 1WD  C1  H4   single    0.930  0.020  1.080
 1WD  S7  H5   single    1.200  0.020  1.300

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
 1WD  C3  C8  O9   116.55  3.000
 1WD  O9  C8  O10  121.49  3.000
 1WD  C3  C8  O10  121.96  3.000
 1WD  C2  C3  N4   123.45  3.000
 1WD  N4  C3  C8   113.26  3.000
 1WD  C2  C3  C8   123.28  3.000
 1WD  C5  N4  C3   119.78  3.000
 1WD  H2  C5  C6   120.54  3.000
 1WD  H2  C5  N4   117.37  3.000
 1WD  C6  C5  N4   122.09  3.000
 1WD  H3  C6  C1   120.84  3.000
 1WD  H3  C6  C5   120.63  3.000
 1WD  C1  C6  C5   118.49  3.000
 1WD  H4  C1  C2   118.20  3.000
 1WD  H4  C1  C6   120.60  3.000
 1WD  C2  C1  C6   121.19  3.000
 1WD  S7  C2  C1   118.88  3.000
 1WD  C1  C2  C3   115.00  3.000
 1WD  S7  C2  C3   126.12  3.000
 1WD  H5  S7  C2    80.55  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
 1WD  CONST_01  C6  C1  C2  C3     0.00   0.0  0
 1WD  CONST_02  C6  C5  N4  C3     0.00   0.0  0
 1WD  CONST_03  C1  C2  C3  N4     0.00   0.0  0
 1WD  CONST_04  C1  C6  C5  N4     0.00   0.0  0
 1WD  CONST_05  C2  C1  C6  C5     0.00   0.0  0
 1WD  CONST_06  C2  C3  N4  C5     0.00   0.0  0
 1WD  CONST_07  C1  C2  C3  C8   180.00   0.0  0
 1WD  CONST_08  C5  N4  C3  C8   180.00   0.0  0
 1WD  CONST_09  S7  C2  C3  N4   180.00   0.0  0
 1WD  CONST_10  S7  C2  C1  C6   180.00   0.0  0
 1WD  CONST_11  H4  C1  C2  C3   180.00   0.0  0
 1WD  CONST_12  H2  C5  N4  C3   180.00   0.0  0
 1WD  CONST_13  H3  C6  C5  N4   180.00   0.0  0
 1WD  Var_01    C2  C3  C8  O10  176.34  30.0  2

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
 1WD  plan-1  C8   0.020
 1WD  plan-1  C3   0.020
 1WD  plan-1  N4   0.020
 1WD  plan-1  C5   0.020
 1WD  plan-1  C6   0.020
 1WD  plan-1  C1   0.020
 1WD  plan-1  C2   0.020
 1WD  plan-1  S7   0.020
 1WD  plan-1  H2   0.020
 1WD  plan-1  H3   0.020
 1WD  plan-1  H4   0.020
 1WD  plan-2  O10  0.020
 1WD  plan-2  C8   0.020
 1WD  plan-2  O9   0.020
 1WD  plan-2  C3   0.020

