# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 22:20:07 2021
#   Inital geometry file: a 111 line input string
#   Ligand name: 6-[(2R)-1-amino-4-methylpentan-2-yl]-3-(pyridin-3-yl)-5,6-dihydrothieno[2,3-c]pyridin-7(4H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](CN)N1CCc2c(scc2c3cccnc3)C1=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
 91A  91A  6-[(2R)-1-amino-4-methylpentan-2-yl]-3-(pyridin-3-yl)-5,6-dihydrothieno[2,3-c]pyridin-7(4H)-one  ligand  46  23  .  2022-03-11  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_91A
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
 91A  C4   C  CH2   0  -0.411  -0.4825  108.8211  43.7684
 91A  C5   C  CH1   0  -0.148   0.1899  107.5385  44.2583
 91A  C7   C  CH2   0  -0.258  -0.6671  106.8357  45.3116
 91A  C10  C  C     0  -0.307   1.7129  108.7641  45.8236
 91A  C13  C  CR5   0   0.158   5.3740  108.0478  46.5253
 91A  C17  C  CR6   0   0.571   2.6045  107.1965  44.1804
 91A  C20  C  CR16  0  -0.200   5.2101  108.2117  49.0185
 91A  C21  C  CR16  0  -0.315   5.7057  108.7130  50.2104
 91A  C22  C  CR16  0  -0.069   6.8230  109.5331  50.1724
 91A  C24  C  CR16  0  -0.097   6.9488  109.3938  47.9054
 91A  C2   C  CH1   0  -0.233   0.2536  109.5731  42.6592
 91A  C3   C  CH3   0  -0.663   0.3416  108.7616  41.3703
 91A  N8   N  NH2   0  -0.787  -0.0362  105.6189  45.7867
 91A  N9   N  NR6   0  -0.461   1.5376  107.7851  44.7551
 91A  C11  C  C     0  -0.532   2.7607  108.3436  46.8409
 91A  C12  C  CR56  0   0.182   4.0102  107.9704  46.1135
 91A  C14  C  CR15  0  -0.554   6.2155  107.6035  45.5379
 91A  S15  S  S2    0   0.279   5.3885  107.0761  44.1420
 91A  C16  C  CR56  0  -0.383   3.8809  107.4753  44.8503
 91A  O18  O  O     0  -0.502   2.5654  106.4638  43.1965
 91A  C19  C  CR6   0  -0.023   5.8384  108.5522  47.8228
 91A  N23  N  N     0  -0.398   7.4353  109.8685  49.0422
 91A  H1   H  HCH2  0   0.223  -0.6378  109.4978  44.6161
 91A  H2   H  HCH2  0   0.230  -1.4843  108.5571  43.4130
 91A  H3   H  HCH1  0   0.262   0.2932  106.8535  43.4164
 91A  H4   H  HCH2  0   0.216  -0.8249  107.4983  46.1673
 91A  H5   H  HCH2  0   0.208  -1.6586  106.6803  44.8631
 91A  H6   H  H     0   0.252   1.9878  109.7359  45.3991
 91A  H7   H  H     0   0.268   0.7586  108.8944  46.3291
 91A  H9   H  HCR6  0   0.275   5.2414  108.4664  51.1551
 91A  H10  H  HCR6  0   0.268   7.2400  109.9343  51.0892
 91A  H11  H  HCR6  0   0.261   7.4576  109.7016  46.9971
 91A  H12  H  HCH3  0   0.224  -0.4676  111.5184  43.3112
 91A  H13  H  HCH3  0   0.225   0.0873  111.4868  41.6383
 91A  H14  H  HCH3  0   0.213  -1.4635  110.7655  42.0662
 91A  H15  H  HCH1  0   0.218   1.2742  109.7823  43.0013
 91A  H16  H  HCH3  0   0.233   0.9114  107.8410  41.4986
 91A  H17  H  HCH3  0   0.211  -0.6552  108.4912  41.0122
 91A  H18  H  HCH3  0   0.225   0.8302  109.3372  40.5822
 91A  H19  H  HNH2  0   0.349  -0.6091  105.2076  46.5120
 91A  H20  H  HNH2  0   0.338  -0.0113  104.9365  45.0388
 91A  H22  H  H     0   0.268   2.9278  109.1663  47.5375
 91A  H23  H  H     0   0.266   2.3940  107.4936  47.4241
 91A  H24  H  HCR5  0   0.301   7.2933  107.5493  45.5782
 91A  H8   H  HCR6  0   0.271   4.3564  107.5463  49.0238
 91A  C1   C  CH3   0  -0.651  -0.4344  110.9112  42.4047

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
 91A  C3   C2   single    1.526  0.020  1.526
 91A  C1   C2   single    1.526  0.020  1.526
 91A  C2   C4   single    1.529  0.020  1.529
 91A  O18  C17  double    1.227  0.020  1.227
 91A  C4   C5   single    1.529  0.020  1.529
 91A  S15  C16  aromatic  1.713  0.020  1.713
 91A  S15  C14  aromatic  1.706  0.020  1.706
 91A  C17  C16  single    1.468  0.020  1.468
 91A  C17  N9   single    1.347  0.020  1.347
 91A  C5   N9   single    1.457  0.020  1.457
 91A  C5   C7   single    1.529  0.020  1.529
 91A  C16  C12  aromatic  1.363  0.020  1.363
 91A  N9   C10  single    1.460  0.020  1.460
 91A  C7   N8   single    1.451  0.020  1.451
 91A  C14  C13  aromatic  1.371  0.020  1.371
 91A  C10  C11  single    1.520  0.020  1.520
 91A  C12  C13  aromatic  1.427  0.020  1.427
 91A  C12  C11  single    1.493  0.020  1.493
 91A  C13  C19  single    1.467  0.020  1.467
 91A  C24  C19  aromatic  1.396  0.020  1.396
 91A  C24  N23  aromatic  1.325  0.020  1.325
 91A  C19  C20  aromatic  1.393  0.020  1.393
 91A  N23  C22  aromatic  1.328  0.020  1.328
 91A  C20  C21  aromatic  1.385  0.020  1.385
 91A  C22  C21  aromatic  1.386  0.020  1.386
 91A  C4   H1   single    0.970  0.020  1.090
 91A  C4   H2   single    0.970  0.020  1.090
 91A  C5   H3   single    0.970  0.020  1.090
 91A  C7   H4   single    0.970  0.020  1.090
 91A  C7   H5   single    0.970  0.020  1.090
 91A  C10  H6   single    0.970  0.020  1.090
 91A  C10  H7   single    0.970  0.020  1.090
 91A  C20  H8   single    0.930  0.020  1.080
 91A  C21  H9   single    0.930  0.020  1.080
 91A  C22  H10  single    0.930  0.020  1.080
 91A  C24  H11  single    0.930  0.020  1.080
 91A  C1   H12  single    0.970  0.020  1.090
 91A  C1   H13  single    0.970  0.020  1.090
 91A  C1   H14  single    0.970  0.020  1.090
 91A  C2   H15  single    0.970  0.020  1.090
 91A  C3   H16  single    0.970  0.020  1.090
 91A  C3   H17  single    0.970  0.020  1.090
 91A  C3   H18  single    0.970  0.020  1.090
 91A  N8   H19  single    0.890  0.020  1.040
 91A  N8   H20  single    0.890  0.020  1.040
 91A  C11  H22  single    0.970  0.020  1.090
 91A  C11  H23  single    0.970  0.020  1.090
 91A  C14  H24  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
 91A  H2   C4   H1   105.68  3.000
 91A  H2   C4   C2   108.87  3.000
 91A  H1   C4   C2   109.01  3.000
 91A  H2   C4   C5   107.70  3.000
 91A  H1   C4   C5   109.43  3.000
 91A  C2   C4   C5   115.68  3.000
 91A  H3   C5   N9   106.38  3.000
 91A  H3   C5   C7   107.23  3.000
 91A  N9   C5   C7   111.18  3.000
 91A  H3   C5   C4   108.75  3.000
 91A  C7   C5   C4   111.09  3.000
 91A  N9   C5   C4   111.96  3.000
 91A  H5   C7   H4   105.95  3.000
 91A  H5   C7   N8   114.04  3.000
 91A  H4   C7   N8   108.34  3.000
 91A  H5   C7   C5   106.83  3.000
 91A  H4   C7   C5   109.96  3.000
 91A  N8   C7   C5   111.55  3.000
 91A  H7   C10  H6   107.09  3.000
 91A  H7   C10  C11  109.08  3.000
 91A  H6   C10  C11  109.38  3.000
 91A  H7   C10  N9   108.37  3.000
 91A  H6   C10  N9   109.97  3.000
 91A  C11  C10  N9   112.78  3.000
 91A  C19  C13  C14  123.63  3.000
 91A  C19  C13  C12  125.19  3.000
 91A  C14  C13  C12  111.17  3.000
 91A  O18  C17  C16  120.45  3.000
 91A  C16  C17  N9   114.25  3.000
 91A  O18  C17  N9   125.29  3.000
 91A  H8   C20  C19  120.68  3.000
 91A  H8   C20  C21  120.04  3.000
 91A  C19  C20  C21  119.27  3.000
 91A  H9   C21  C22  120.33  3.000
 91A  H9   C21  C20  121.05  3.000
 91A  C22  C21  C20  118.62  3.000
 91A  H10  C22  N23  116.67  3.000
 91A  H10  C22  C21  120.37  3.000
 91A  N23  C22  C21  122.96  3.000
 91A  H11  C24  N23  116.37  3.000
 91A  H11  C24  C19  119.63  3.000
 91A  N23  C24  C19  124.00  3.000
 91A  H15  C2   C3   108.15  3.000
 91A  H15  C2   C1   107.72  3.000
 91A  C3   C2   C1   110.58  3.000
 91A  H15  C2   C4   108.40  3.000
 91A  C1   C2   C4   109.58  3.000
 91A  C3   C2   C4   112.27  3.000
 91A  H18  C3   H17  107.59  3.000
 91A  H18  C3   H16  107.24  3.000
 91A  H17  C3   H16  107.83  3.000
 91A  H18  C3   C2   110.81  3.000
 91A  H17  C3   C2   110.84  3.000
 91A  H16  C3   C2   112.32  3.000
 91A  H20  N8   H19  105.63  3.000
 91A  H20  N8   C7   109.51  3.000
 91A  H19  N8   C7   109.24  3.000
 91A  C17  N9   C10  120.68  3.000
 91A  C10  N9   C5   118.30  3.000
 91A  C17  N9   C5   120.86  3.000
 91A  H23  C11  H22  107.27  3.000
 91A  H23  C11  C12  110.24  3.000
 91A  H22  C11  C12  111.80  3.000
 91A  H23  C11  C10  109.92  3.000
 91A  H22  C11  C10  108.93  3.000
 91A  C12  C11  C10  108.66  3.000
 91A  C16  C12  C11  117.58  3.000
 91A  C11  C12  C13  130.22  3.000
 91A  C16  C12  C13  112.21  3.000
 91A  H24  C14  S15  119.92  3.000
 91A  H24  C14  C13  127.00  3.000
 91A  S15  C14  C13  113.07  3.000
 91A  C16  S15  C14   90.93  3.000
 91A  S15  C16  C12  112.61  3.000
 91A  C12  C16  C17  125.05  3.000
 91A  S15  C16  C17  122.15  3.000
 91A  C24  C19  C20  117.09  3.000
 91A  C20  C19  C13  122.15  3.000
 91A  C24  C19  C13  120.75  3.000
 91A  C24  N23  C22  118.06  3.000
 91A  H14  C1   H13  107.63  3.000
 91A  H14  C1   H12  107.62  3.000
 91A  H13  C1   H12  107.72  3.000
 91A  H14  C1   C2   111.05  3.000
 91A  H13  C1   C2   111.35  3.000
 91A  H12  C1   C2   111.29  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
 91A  CONST_01  C16  S15  C14  C13     0.00   0.0  0
 91A  CONST_02  S15  C16  C12  C13     0.00   0.0  0
 91A  CONST_03  N23  C24  C19  C13   180.00   0.0  0
 91A  CONST_04  C21  C20  C19  C13   180.00   0.0  0
 91A  CONST_07  N23  C24  C19  C20     0.00   0.0  0
 91A  CONST_08  N23  C22  C21  C20     0.00   0.0  0
 91A  CONST_09  C24  C19  C20  C21     0.00   0.0  0
 91A  CONST_10  C24  N23  C22  C21     0.00   0.0  0
 91A  CONST_11  C19  C24  N23  C22     0.00   0.0  0
 91A  CONST_12  C19  C20  C21  C22     0.00   0.0  0
 91A  CONST_15  C14  S15  C16  C12     0.00   0.0  0
 91A  CONST_16  S15  C14  C13  C12     0.00   0.0  0
 91A  CONST_17  C16  C12  C13  C14     0.00   0.0  0
 91A  CONST_18  C19  C13  C14  S15   180.00   0.0  0
 91A  CONST_19  C19  C13  C12  C16   180.00   0.0  0
 91A  CONST_20  C19  C13  C12  C11     0.00   0.0  0
 91A  CONST_21  C16  C17  N9   C10     0.00   0.0  0
 91A  CONST_22  C16  C17  N9   C5    180.00   0.0  0
 91A  CONST_23  O18  C17  N9   C10   180.00   0.0  0
 91A  CONST_24  H11  C24  C19  C13     0.00   0.0  0
 91A  CONST_25  H8   C20  C19  C13     0.00   0.0  0
 91A  CONST_26  H10  C22  C21  C20   180.00   0.0  0
 91A  CONST_27  H24  C14  C13  C12   180.00   0.0  0
 91A  CONST_28  H9   C21  C20  C19   180.00   0.0  0
 91A  CONST_29  O18  C17  N9   C5      0.00   0.0  0
 91A  Var_01    C16  C12  C11  C10   -29.15  30.0  1
 91A  Var_02    C11  C10  N9   C17   -43.11  30.0  1
 91A  Var_03    S15  C16  C17  N9   -168.58  30.0  1
 91A  Var_04    C12  C11  C10  N9     51.17  30.0  1
 91A  Var_05    C3   C2   C4   C5     64.03  30.0  1
 91A  Var_06    H16  C3   C2   C4    -62.67  30.0  3
 91A  Var_07    H12  C1   C2   C4     58.00  30.0  3
 91A  Var_08    H19  N8   C7   C5    177.26  30.0  3

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
 91A  chir_01  C5  C4  N9  C7  negativ

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
 91A  plan-1  C13  0.020
 91A  plan-1  C20  0.020
 91A  plan-1  C21  0.020
 91A  plan-1  C22  0.020
 91A  plan-1  C24  0.020
 91A  plan-1  C19  0.020
 91A  plan-1  N23  0.020
 91A  plan-1  H9   0.020
 91A  plan-1  H10  0.020
 91A  plan-1  H11  0.020
 91A  plan-1  H8   0.020
 91A  plan-2  C13  0.020
 91A  plan-2  C17  0.020
 91A  plan-2  C11  0.020
 91A  plan-2  C12  0.020
 91A  plan-2  C14  0.020
 91A  plan-2  S15  0.020
 91A  plan-2  C16  0.020
 91A  plan-2  C19  0.020
 91A  plan-2  H24  0.020
 91A  plan-3  C5   0.020
 91A  plan-3  C10  0.020
 91A  plan-3  C17  0.020
 91A  plan-3  N9   0.020
 91A  plan-3  C16  0.020
 91A  plan-3  O18  0.020

