# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 01:19:10 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: 1-methylethyl (2S)-7-methoxy-2-[(methylsulfanyl)methyl]-3-thioxo-3,4-dihydroquinoxaline-1(2H)-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2NC(=S)[C@H](CSC)N(C(=O)OC(C)C)c2c1
#
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
 HBY  HBY  '1-methylethyl (2S)-7-methoxy-2-[(methylsulfanyl)methyl]-3-thioxo-3,4-dihydroquinoxaline-1(2H)-carboxylate'  ligand  42  22  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HBY
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
 HBY  C1    C  CH1   0  -0.234  -0.2713  -0.1813  -1.8543
 HBY  C2    C  C     0   0.198   0.8850  -1.0846  -2.2329
 HBY  C3    C  CR6   0   0.322   1.7739  -0.5352  -0.0611
 HBY  C4    C  CR6   0   0.345   0.5383  -0.0854   0.4080
 HBY  C5    C  CR16  0  -0.379   0.4637   0.6111   1.5993
 HBY  C6    C  CR6   0   0.386   1.6119   0.8052   2.3673
 HBY  C7    C  CR16  0  -0.384   2.8405   0.3280   1.9126
 HBY  C8    C  CR16  0  -0.311   2.9154  -0.3272   0.6934
 HBY  C10   C  CH1   0   0.015  -2.9744  -1.6361   1.8613
 HBY  C12   C  CH3   0  -0.671  -2.5439  -2.3630   3.1175
 HBY  C11   C  CH3   0  -0.678  -3.9016  -0.4717   2.1496
 HBY  C13   C  CH2   0  -0.531   0.0682   1.2624  -2.2259
 HBY  C14   C  CH3   0  -0.763  -0.6951   3.8968  -2.4043
 HBY  C15   C  CH3   0  -0.440   2.5699   1.7279   4.3310
 HBY  N1    N  NT    0  -0.592  -0.5590  -0.3249  -0.4378
 HBY  N2    N  NH1   0  -0.645   1.8243  -1.1860  -1.2980
 HBY  O1    O  O     0  -0.491  -2.6670  -1.0919  -0.8067
 HBY  O2    O  O2    0  -0.472  -1.7563  -1.1554   1.2464
 HBY  O3    O  O2    0  -0.471   1.4385   1.4734   3.5216
 HBY  S1    S  S1    0  -0.311   0.9721  -1.8180  -3.7099
 HBY  S2    S  S2    0  -0.018  -1.2717   2.3496  -1.6721
 HBY  H1    H  HCH1  0   0.318  -1.1485  -0.4960  -2.4124
 HBY  H5    H  HCR6  0   0.275  -0.4806   1.0017   1.9514
 HBY  H7    H  HCR6  0   0.288   3.7490   0.4655   2.4814
 HBY  H8    H  HCR6  0   0.286   3.8741  -0.6765   0.3317
 HBY  H10   H  HCH1  0   0.244  -3.4592  -2.3391   1.1809
 HBY  H121  H  HCH3  0   0.238  -3.4208  -2.7712   3.6191
 HBY  H122  H  HCH3  0   0.243  -1.8748  -3.1922   2.8883
 HBY  H123  H  HCH3  0   0.232  -2.0403  -1.6909   3.8138
 HBY  H111  H  HCH3  0   0.232  -3.4206   0.2605   2.8003
 HBY  H112  H  HCH3  0   0.243  -4.2241   0.0297   1.2376
 HBY  H113  H  HCH3  0   0.242  -4.7952  -0.8345   2.6577
 HBY  H131  H  HCH2  0   0.278   1.0100   1.5828  -1.7744
 HBY  H132  H  HCH2  0   0.293   0.1754   1.3257  -3.3096
 HBY  H141  H  HCH3  0   0.277  -1.4138   4.6696  -2.1379
 HBY  H142  H  HCH3  0   0.265   0.2801   4.1769  -2.0092
 HBY  H143  H  HCH3  0   0.264  -0.6427   3.8261  -3.4895
 HBY  H151  H  HCH3  0   0.262   2.2102   2.2704   5.2016
 HBY  H152  H  HCH3  0   0.231   3.0489   0.8040   4.6649
 HBY  H153  H  HCH3  0   0.231   3.3111   2.3444   3.8159
 HBY  HN2   H  HNH1  0   0.421   2.6475  -1.7330  -1.5155
 HBY  C9    C  C     0   0.762  -1.7525  -0.8814  -0.0436

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
 HBY  C1   C2    single    1.515  0.020  1.515
 HBY  C1   C13   single    1.529  0.020  1.529
 HBY  C1   N1    single    1.453  0.020  1.453
 HBY  C1   H1    single    0.970  0.020  1.090
 HBY  C2   N2    single    1.329  0.020  1.329
 HBY  C2   S1    double    1.651  0.020  1.651
 HBY  C3   C4    aromatic  1.396  0.020  1.396
 HBY  C3   C8    aromatic  1.384  0.020  1.384
 HBY  C3   N2    single    1.398  0.020  1.398
 HBY  C4   C5    aromatic  1.382  0.020  1.382
 HBY  C4   N1    single    1.406  0.020  1.406
 HBY  C5   C6    aromatic  1.395  0.020  1.395
 HBY  C5   H5    single    0.930  0.020  1.080
 HBY  C6   C7    aromatic  1.394  0.020  1.394
 HBY  C6   O3    single    1.345  0.020  1.345
 HBY  C7   C8    aromatic  1.386  0.020  1.386
 HBY  C7   H7    single    0.930  0.020  1.080
 HBY  C8   H8    single    0.930  0.020  1.080
 HBY  C9   N1    single    1.375  0.020  1.375
 HBY  C9   O1    double    1.210  0.020  1.210
 HBY  C9   O2    single    1.319  0.020  1.319
 HBY  C10  C12   single    1.514  0.020  1.514
 HBY  C10  C11   single    1.516  0.020  1.516
 HBY  C10  O2    single    1.447  0.020  1.447
 HBY  C10  H10   single    0.970  0.020  1.090
 HBY  C12  H121  single    0.970  0.020  1.090
 HBY  C12  H122  single    0.970  0.020  1.090
 HBY  C12  H123  single    0.970  0.020  1.090
 HBY  C11  H111  single    0.970  0.020  1.090
 HBY  C11  H112  single    0.970  0.020  1.090
 HBY  C11  H113  single    0.970  0.020  1.090
 HBY  C13  S2    single    1.812  0.020  1.812
 HBY  C13  H131  single    0.970  0.020  1.090
 HBY  C13  H132  single    0.970  0.020  1.090
 HBY  C14  S2    single    1.806  0.020  1.806
 HBY  C14  H141  single    0.970  0.020  1.090
 HBY  C14  H142  single    0.970  0.020  1.090
 HBY  C14  H143  single    0.970  0.020  1.090
 HBY  C15  O3    single    1.414  0.020  1.414
 HBY  C15  H151  single    0.970  0.020  1.090
 HBY  C15  H152  single    0.970  0.020  1.090
 HBY  C15  H153  single    0.970  0.020  1.090
 HBY  N2   HN2   single    0.860  0.020  1.020

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
 HBY  H1    C1   N1    108.20  3.000
 HBY  H1    C1   C13   109.15  3.000
 HBY  N1    C1   C13   111.98  3.000
 HBY  H1    C1   C2    108.37  3.000
 HBY  N1    C1   C2    109.63  3.000
 HBY  C13   C1   C2    109.43  3.000
 HBY  S1    C2   N2    123.92  3.000
 HBY  S1    C2   C1    121.90  3.000
 HBY  N2    C2   C1    114.14  3.000
 HBY  N2    C3   C8    121.49  3.000
 HBY  N2    C3   C4    118.62  3.000
 HBY  C8    C3   C4    119.89  3.000
 HBY  N1    C4   C5    124.21  3.000
 HBY  N1    C4   C3    115.71  3.000
 HBY  C5    C4   C3    119.98  3.000
 HBY  H5    C5   C6    119.30  3.000
 HBY  H5    C5   C4    120.67  3.000
 HBY  C6    C5   C4    120.02  3.000
 HBY  O3    C6   C7    124.30  3.000
 HBY  O3    C6   C5    115.82  3.000
 HBY  C7    C6   C5    119.87  3.000
 HBY  H7    C7   C8    118.53  3.000
 HBY  H7    C7   C6    121.71  3.000
 HBY  C8    C7   C6    119.75  3.000
 HBY  H8    C8   C7    119.62  3.000
 HBY  H8    C8   C3    119.98  3.000
 HBY  C7    C8   C3    120.40  3.000
 HBY  H10   C10  O2    108.84  3.000
 HBY  H10   C10  C11   109.96  3.000
 HBY  O2    C10  C11   109.91  3.000
 HBY  H10   C10  C12   109.52  3.000
 HBY  O2    C10  C12   105.83  3.000
 HBY  C11   C10  C12   112.64  3.000
 HBY  H123  C12  H122  108.64  3.000
 HBY  H123  C12  H121  107.97  3.000
 HBY  H122  C12  H121  107.81  3.000
 HBY  H123  C12  C10   111.41  3.000
 HBY  H122  C12  C10   111.43  3.000
 HBY  H121  C12  C10   109.45  3.000
 HBY  H113  C11  H112  107.50  3.000
 HBY  H113  C11  H111  107.86  3.000
 HBY  H112  C11  H111  108.71  3.000
 HBY  H113  C11  C10   109.53  3.000
 HBY  H112  C11  C10   112.04  3.000
 HBY  H111  C11  C10   111.05  3.000
 HBY  H132  C13  H131  107.99  3.000
 HBY  H132  C13  S2    109.96  3.000
 HBY  H131  C13  S2    109.58  3.000
 HBY  H132  C13  C1    108.55  3.000
 HBY  H131  C13  C1    111.59  3.000
 HBY  S2    C13  C1    109.15  3.000
 HBY  H143  C14  H142  109.59  3.000
 HBY  H143  C14  H141  108.77  3.000
 HBY  H142  C14  H141  108.66  3.000
 HBY  H143  C14  S2    111.33  3.000
 HBY  H142  C14  S2    111.05  3.000
 HBY  H141  C14  S2    107.35  3.000
 HBY  H153  C15  H152  108.87  3.000
 HBY  H153  C15  H151  108.68  3.000
 HBY  H152  C15  H151  108.80  3.000
 HBY  H153  C15  O3    111.98  3.000
 HBY  H152  C15  O3    111.92  3.000
 HBY  H151  C15  O3    106.47  3.000
 HBY  C9    N1   C4    125.03  3.000
 HBY  C9    N1   C1    119.45  3.000
 HBY  C4    N1   C1    114.53  3.000
 HBY  HN2   N2   C3    118.10  3.000
 HBY  HN2   N2   C2    117.70  3.000
 HBY  C3    N2   C2    124.13  3.000
 HBY  C10   O2   C9    119.16  3.000
 HBY  C15   O3   C6    118.52  3.000
 HBY  C14   S2   C13    98.86  3.000
 HBY  O2    C9   O1    125.37  3.000
 HBY  O2    C9   N1    111.54  3.000
 HBY  O1    C9   N1    123.09  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
 HBY  CONST_01  C6    C5   C4   C3      0.00   0.0  0
 HBY  CONST_02  C6    C7   C8   C3      0.00   0.0  0
 HBY  CONST_03  C7    C8   C3   C4      0.00   0.0  0
 HBY  CONST_04  C7    C6   C5   C4      0.00   0.0  0
 HBY  CONST_05  C8    C3   C4   C5      0.00   0.0  0
 HBY  CONST_06  C8    C7   C6   C5      0.00   0.0  0
 HBY  CONST_07  O3    C6   C5   C4    180.00   0.0  0
 HBY  CONST_08  O3    C6   C7   C8    180.00   0.0  0
 HBY  CONST_09  H5    C5   C4   C3    180.00   0.0  0
 HBY  CONST_10  H7    C7   C8   C3    180.00   0.0  0
 HBY  CONST_11  H8    C8   C3   C4    180.00   0.0  0
 HBY  Var_01    C3    N2   C2   C1      0.37  30.0  1
 HBY  Var_02    C3    C4   N1   C1    -37.39  30.0  1
 HBY  Var_03    C4    C3   N2   C2     20.08  30.0  1
 HBY  Var_04    O1    C9   N1   C1    -10.75  30.0  2
 HBY  Var_05    N1    C9   O2   C10   174.52  30.0  1
 HBY  Var_06    H151  C15  O3   C6   -179.98  30.0  3
 HBY  Var_07    C12   C10  O2   C9    157.77  30.0  2
 HBY  Var_08    H111  C11  C10  C12    59.58  30.0  3
 HBY  Var_09    H121  C12  C10  C11    61.13  30.0  3
 HBY  Var_10    H141  C14  S2   C13  -179.27  30.0  3
 HBY  Var_11    H131  C13  S2   C14    63.83  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 HBY  chir_01  C1  C2  C13  N1  positiv

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
 HBY  plan-1  C2   0.020
 HBY  plan-1  C3   0.020
 HBY  plan-1  N2   0.020
 HBY  plan-1  HN2  0.020
 HBY  plan-2  C3   0.020
 HBY  plan-2  C4   0.020
 HBY  plan-2  C5   0.020
 HBY  plan-2  C6   0.020
 HBY  plan-2  C7   0.020
 HBY  plan-2  C8   0.020
 HBY  plan-2  N1   0.020
 HBY  plan-2  N2   0.020
 HBY  plan-2  O3   0.020
 HBY  plan-2  H5   0.020
 HBY  plan-2  H7   0.020
 HBY  plan-2  H8   0.020
 HBY  plan-3  C1   0.020
 HBY  plan-3  C2   0.020
 HBY  plan-3  N2   0.020
 HBY  plan-3  S1   0.020
 HBY  plan-4  N1   0.020
 HBY  plan-4  O1   0.020
 HBY  plan-4  O2   0.020
 HBY  plan-4  C9   0.020

