# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 07:26:15 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  15  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  OH1   0  -0.574  -1.7103  -2.0434  -0.0853
 1WD  C8   C  C     0   0.534  -1.4499  -0.7524  -0.1477
 1WD  O9   O  O     0  -0.443  -2.3187   0.0861  -0.2431
 1WD  C3   C  CR6   0   0.095   0.0110  -0.4550  -0.0861
 1WD  N4   N  N     0  -0.392   0.7937  -1.5247   0.0586
 1WD  C5   C  CR16  0  -0.082   2.0988  -1.3865   0.1272
 1WD  C6   C  CR16  0  -0.297   2.7179  -0.1414   0.0514
 1WD  C1   C  CR16  0  -0.137   1.9267   0.9727  -0.0984
 1WD  C2   C  CR6   0  -0.159   0.5336   0.8445  -0.1718
 1WD  S7   S  S2    0  -0.166  -0.3173   2.3666  -0.3695
 1WD  H1   H  HOH1  0   0.489  -2.6693  -2.1777  -0.1289
 1WD  H2   H  HCR6  0   0.275   2.6841  -2.2905   0.2468
 1WD  H3   H  HCR6  0   0.286   3.7937  -0.0542   0.1099
 1WD  H4   H  HCR6  0   0.291   2.3795   1.9546  -0.1594
 1WD  H5   H  HSH1  0   0.279  -1.5681   1.8994  -0.3634

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    1.755  0.020  1.755
 1WD  C1   C2   aromatic  1.401  0.020  1.401
 1WD  C1   C6   aromatic  1.375  0.020  1.375
 1WD  C2   C3   aromatic  1.403  0.020  1.403
 1WD  C6   C5   aromatic  1.393  0.020  1.393
 1WD  C3   N4   aromatic  1.333  0.020  1.333
 1WD  C3   C8   single    1.492  0.020  1.492
 1WD  C5   N4   aromatic  1.314  0.020  1.314
 1WD  C8   O9   double    1.211  0.020  1.211
 1WD  C8   O10  single    1.319  0.020  1.319
 1WD  O10  H1   single    0.850  0.020  0.980
 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  H1  O10  C8   109.21  3.000
 1WD  C3  C8   O9   124.59  3.000
 1WD  O9  C8   O10  122.67  3.000
 1WD  C3  C8   O10  112.74  3.000
 1WD  C2  C3   N4   122.07  3.000
 1WD  N4  C3   C8   114.79  3.000
 1WD  C2  C3   C8   123.13  3.000
 1WD  C5  N4   C3   120.28  3.000
 1WD  H2  C5   C6   120.78  3.000
 1WD  H2  C5   N4   117.03  3.000
 1WD  C6  C5   N4   122.19  3.000
 1WD  H3  C6   C1   120.89  3.000
 1WD  H3  C6   C5   120.77  3.000
 1WD  C1  C6   C5   118.34  3.000
 1WD  H4  C1   C2   119.72  3.000
 1WD  H4  C1   C6   120.02  3.000
 1WD  C2  C1   C6   120.26  3.000
 1WD  S7  C2   C1   114.12  3.000
 1WD  C1  C2   C3   116.86  3.000
 1WD  S7  C2   C3   129.02  3.000
 1WD  H5  S7   C2    98.64  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  CONST_14  H1  O10  C8  C3   180.00   0.0  0
 1WD  Var_01    C2  C3   C8  O10  178.20  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
 1WD  plan-2  H1   0.020

