# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 04:36:02 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 1-methyl-3-oxidanyl-pyridine-2-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=CC=C(O)C1=S
#
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
 GQA  GQA  1-methyl-3-oxidanyl-pyridine-2-thione  ligand  16  9  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GQA
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
 GQA  N1  N  NR6   0  -0.441   0.1250   1.1880  -0.0226
 GQA  C4  C  CR16  0  -0.355   2.3548   0.4075  -0.0822
 GQA  C5  C  CR16  0   0.010   1.4607   1.4283  -0.0807
 GQA  C6  C  CH3   0  -0.511  -0.7793   2.3319  -0.0232
 GQA  C1  C  CR6   0   0.119  -0.4102  -0.0667   0.0356
 GQA  C2  C  CR6   0   0.285   0.5304  -1.1470   0.0328
 GQA  O1  O  OH1   0  -0.600  -0.0016  -2.3742   0.0862
 GQA  C3  C  CR16  0  -0.273   1.8783  -0.9104  -0.0224
 GQA  H1  H  HCR6  0   0.288   3.4126   0.6165  -0.1277
 GQA  H2  H  HCR6  0   0.314   1.7583   2.4643  -0.1265
 GQA  H3  H  HCH3  0   0.267  -1.3762   2.3366   0.8858
 GQA  H4  H  HCH3  0   0.260  -0.1917   3.2425  -0.0797
 GQA  H5  H  HCH3  0   0.267  -1.4526   2.2749  -0.8749
 GQA  H6  H  HOH1  0   0.479   0.6984  -3.0380   0.0674
 GQA  H7  H  HCR6  0   0.294   2.5793  -1.7368  -0.0200
 GQA  S1  S  S1    0  -0.402  -2.0693  -0.3259   0.1045

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
 GQA  C6  N1  single  1.458  0.020  1.458
 GQA  C5  N1  single  1.358  0.020  1.358
 GQA  C5  C4  double  1.357  0.020  1.357
 GQA  N1  C1  single  1.365  0.020  1.365
 GQA  C4  C3  single  1.403  0.020  1.403
 GQA  S1  C1  double  1.681  0.020  1.681
 GQA  C1  C2  single  1.432  0.020  1.432
 GQA  C2  C3  double  1.370  0.020  1.370
 GQA  C2  O1  single  1.339  0.020  1.339
 GQA  C4  H1  single  0.930  0.020  1.080
 GQA  C5  H2  single  0.930  0.020  1.080
 GQA  C6  H3  single  0.970  0.020  1.090
 GQA  C6  H4  single  0.970  0.020  1.090
 GQA  C6  H5  single  0.970  0.020  1.090
 GQA  O1  H6  single  0.850  0.020  0.980
 GQA  C3  H7  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
 GQA  C1  N1  C6  118.54  3.000
 GQA  C1  N1  C5  123.36  3.000
 GQA  C6  N1  C5  118.10  3.000
 GQA  H1  C4  C3  121.12  3.000
 GQA  H1  C4  C5  120.01  3.000
 GQA  C3  C4  C5  118.88  3.000
 GQA  H2  C5  C4  122.73  3.000
 GQA  H2  C5  N1  116.29  3.000
 GQA  C4  C5  N1  120.98  3.000
 GQA  H5  C6  H4  109.79  3.000
 GQA  H5  C6  H3  108.37  3.000
 GQA  H4  C6  H3  109.69  3.000
 GQA  H5  C6  N1  110.08  3.000
 GQA  H4  C6  N1  108.81  3.000
 GQA  H3  C6  N1  110.09  3.000
 GQA  C2  C1  S1  122.15  3.000
 GQA  C2  C1  N1  115.82  3.000
 GQA  S1  C1  N1  122.03  3.000
 GQA  C3  C2  O1  123.44  3.000
 GQA  O1  C2  C1  115.49  3.000
 GQA  C3  C2  C1  121.07  3.000
 GQA  H6  O1  C2  109.98  3.000
 GQA  H7  C3  C2  120.31  3.000
 GQA  H7  C3  C4  119.79  3.000
 GQA  C2  C3  C4  119.89  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
 GQA  Var_01  H3  C6  N1  C5  -119.90  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
 GQA  plan-1  N1  0.020
 GQA  plan-1  C4  0.020
 GQA  plan-1  C5  0.020
 GQA  plan-1  C6  0.020
 GQA  plan-1  C1  0.020
 GQA  plan-1  C2  0.020
 GQA  plan-1  O1  0.020
 GQA  plan-1  C3  0.020
 GQA  plan-1  H1  0.020
 GQA  plan-1  H2  0.020
 GQA  plan-1  H7  0.020
 GQA  plan-1  S1  0.020

