# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 21:35:20 2021
#   Inital geometry file: a 131 line input string
#   Ligand name: [6-{(1S)-1-[(2-amino-6-fluoroquinolin-3-yl)oxy]ethyl}-5-(1H-pyrazol-1-yl)-1H-indazol-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Oc1cc2cc(F)ccc2nc1N)c3cc4n(CC(O)=O)ncc4cc3n5cccn5
#
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
 VOP  VOP  '[6-{(1S)-1-[(2-amino-6-fluoroquinolin-3-yl)oxy]ethyl}-5-(1H-pyrazol-1-yl)-1H-indazol-1-yl]acetic acid'  ligand  52  33  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VOP
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
 VOP  C4   C  CR16  0  -0.358   9.4753  -21.3231  11.3530
 VOP  C7   C  CR16  0  -0.329   8.7960  -19.7074   9.1233
 VOP  C6   C  CR56  0  -0.118   7.7948  -20.3208   9.8771
 VOP  C8   C  CR6   0   0.270  10.1052  -19.9138   9.4924
 VOP  C26  C  CR6   0   0.523  11.6168  -15.5286  14.3932
 VOP  C1   C  CH3   0  -0.658  12.3514  -22.3230  10.2454
 VOP  C2   C  CH1   0  -0.038  11.9153  -21.0274  10.9064
 VOP  C3   C  CR6   0   0.049  10.4616  -20.7276  10.5968
 VOP  C5   C  CR56  0   0.517   8.1469  -21.1031  10.9862
 VOP  N9   N  NR5   0  -0.383  11.1203  -19.2866   8.7252
 VOP  C10  C  CR15  0   0.027  11.4727  -19.5673   7.4526
 VOP  C11  C  CR15  0  -0.502  12.4675  -18.6832   7.1151
 VOP  C12  C  CR15  0  -0.033  12.6433  -17.9005   8.2692
 VOP  N13  N  N     0  -0.290  11.8222  -18.2693   9.2330
 VOP  C14  C  CR15  0  -0.103   6.3752  -20.3703   9.8502
 VOP  N15  N  N     0  -0.228   5.9219  -21.0977  10.8353
 VOP  N16  N  NR5   0  -0.401   6.9824  -21.5263  11.5345
 VOP  C17  C  CH2   0  -0.450   6.8096  -22.4362  12.6220
 VOP  O19  O  O     0  -0.422   7.2046  -24.2185  11.0540
 VOP  O20  O  OH1   0  -0.586   6.7043  -24.7021  13.1826
 VOP  O21  O  O2    0  -0.489  12.1115  -21.1944  12.3039
 VOP  C22  C  CR6   0   0.270  12.0224  -20.1202  13.1110
 VOP  C23  C  CR16  0  -0.332  11.8754  -18.8267  12.7256
 VOP  C24  C  CR66  0   0.114  11.8127  -17.8104  13.7168
 VOP  C25  C  CR16  0  -0.504  11.6718  -16.4496  13.3859
 VOP  C27  C  CR16  0  -0.423  11.6936  -15.8872  15.7417
 VOP  C28  C  CR16  0  -0.287  11.8298  -17.2137  16.0697
 VOP  C29  C  CR66  0   0.189  11.8933  -18.2048  15.0702
 VOP  N30  N  N     0  -0.490  12.0242  -19.5043  15.4372
 VOP  C31  C  CR6   0   0.359  12.0895  -20.4291  14.5202
 VOP  N32  N  NH2   0  -0.829  12.2688  -21.7205  14.8951
 VOP  H1   H  HCR6  0   0.275   9.7273  -21.9509  12.1981
 VOP  H2   H  HCR6  0   0.278   8.5589  -19.0761   8.2767
 VOP  H3   H  HCH3  0   0.253  13.4088  -22.5123  10.4298
 VOP  H4   H  HCH3  0   0.242  11.7694  -23.1682  10.6145
 VOP  H5   H  HCH3  0   0.244  12.2049  -22.2571   9.1680
 VOP  H6   H  HCH1  0   0.259  12.5579  -20.2185  10.5503
 VOP  H7   H  HCR5  0   0.299  11.0009  -20.3628   6.8990
 VOP  H8   H  HCR5  0   0.269  12.9920  -18.6125   6.1773
 VOP  H9   H  HCR5  0   0.268  13.3325  -17.0852   8.4275
 VOP  H10  H  HCR5  0   0.279   5.6986  -19.8998   9.1536
 VOP  H11  H  HCH2  0   0.315   7.5454  -22.2330  13.4037
 VOP  H12  H  HCH2  0   0.331   5.8284  -22.2690  13.0669
 VOP  H13  H  HOH1  0   0.489   6.7863  -25.6232  12.8925
 VOP  H14  H  HCR6  0   0.315  11.8139  -18.5387  11.6823
 VOP  H15  H  HCR6  0   0.271  11.6080  -16.1413  12.3493
 VOP  H16  H  HCR6  0   0.278  11.6456  -15.1260  16.5090
 VOP  H17  H  HCR6  0   0.264  11.8918  -17.5160  17.1072
 VOP  H18  H  HNH2  0   0.390  12.1193  -21.9320  15.8677
 VOP  H19  H  HNH2  0   0.396  12.0399  -22.4582  14.2521
 VOP  F33  F  F     0  -0.321  11.4827  -14.2244  14.0899
 VOP  C18  C  C     0   0.542   6.9321  -23.8786  12.1729

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
 VOP  C11  C10  aromatic  1.373  0.020  1.373
 VOP  C11  C12  aromatic  1.405  0.020  1.405
 VOP  C10  N9   aromatic  1.350  0.020  1.350
 VOP  C12  N13  aromatic  1.319  0.020  1.319
 VOP  N9   N13  aromatic  1.336  0.020  1.336
 VOP  N9   C8   single    1.419  0.020  1.419
 VOP  C7   C8   aromatic  1.376  0.020  1.376
 VOP  C7   C6   aromatic  1.395  0.020  1.395
 VOP  C8   C3   aromatic  1.417  0.020  1.417
 VOP  C6   C14  aromatic  1.421  0.020  1.421
 VOP  C6   C5   aromatic  1.402  0.020  1.402
 VOP  C14  N15  aromatic  1.306  0.020  1.306
 VOP  C1   C2   single    1.518  0.020  1.518
 VOP  O19  C18  double    1.201  0.020  1.201
 VOP  C3   C2   single    1.516  0.020  1.516
 VOP  C3   C4   aromatic  1.378  0.020  1.378
 VOP  C2   O21  single    1.421  0.020  1.421
 VOP  N15  N16  aromatic  1.341  0.020  1.341
 VOP  C5   C4   aromatic  1.396  0.020  1.396
 VOP  C5   N16  aromatic  1.355  0.020  1.355
 VOP  N16  C17  single    1.428  0.020  1.428
 VOP  C18  O20  single    1.323  0.020  1.323
 VOP  C18  C17  single    1.516  0.020  1.516
 VOP  O21  C22  single    1.347  0.020  1.347
 VOP  C23  C22  aromatic  1.358  0.020  1.358
 VOP  C23  C24  aromatic  1.421  0.020  1.421
 VOP  C25  C24  aromatic  1.408  0.020  1.408
 VOP  C25  C26  aromatic  1.366  0.020  1.366
 VOP  C22  C31  aromatic  1.444  0.020  1.444
 VOP  C24  C29  aromatic  1.412  0.020  1.412
 VOP  F33  C26  single    1.346  0.020  1.346
 VOP  C26  C27  aromatic  1.397  0.020  1.397
 VOP  C31  N32  single    1.357  0.020  1.357
 VOP  C31  N30  aromatic  1.304  0.020  1.304
 VOP  C29  N30  aromatic  1.357  0.020  1.357
 VOP  C29  C28  aromatic  1.409  0.020  1.409
 VOP  C27  C28  aromatic  1.373  0.020  1.373
 VOP  C4   H1   single    0.930  0.020  1.080
 VOP  C7   H2   single    0.930  0.020  1.080
 VOP  C1   H3   single    0.970  0.020  1.090
 VOP  C1   H4   single    0.970  0.020  1.090
 VOP  C1   H5   single    0.970  0.020  1.090
 VOP  C2   H6   single    0.970  0.020  1.090
 VOP  C10  H7   single    0.930  0.020  1.080
 VOP  C11  H8   single    0.930  0.020  1.080
 VOP  C12  H9   single    0.930  0.020  1.080
 VOP  C14  H10  single    0.930  0.020  1.080
 VOP  C17  H11  single    0.970  0.020  1.090
 VOP  C17  H12  single    0.970  0.020  1.090
 VOP  O20  H13  single    0.850  0.020  0.980
 VOP  C23  H14  single    0.930  0.020  1.080
 VOP  C25  H15  single    0.930  0.020  1.080
 VOP  C27  H16  single    0.930  0.020  1.080
 VOP  C28  H17  single    0.930  0.020  1.080
 VOP  N32  H18  single    0.890  0.020  1.040
 VOP  N32  H19  single    0.890  0.020  1.040

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
 VOP  H1   C4   C5   121.21  3.000
 VOP  H1   C4   C3   120.82  3.000
 VOP  C5   C4   C3   117.96  3.000
 VOP  H2   C7   C8   120.38  3.000
 VOP  H2   C7   C6   121.45  3.000
 VOP  C8   C7   C6   118.16  3.000
 VOP  C14  C6   C5   104.27  3.000
 VOP  C5   C6   C7   119.50  3.000
 VOP  C14  C6   C7   136.23  3.000
 VOP  N9   C8   C3   119.69  3.000
 VOP  C3   C8   C7   122.31  3.000
 VOP  N9   C8   C7   118.00  3.000
 VOP  F33  C26  C27  118.15  3.000
 VOP  C27  C26  C25  122.44  3.000
 VOP  F33  C26  C25  119.42  3.000
 VOP  H5   C1   H4   108.05  3.000
 VOP  H5   C1   H3   107.96  3.000
 VOP  H4   C1   H3   109.02  3.000
 VOP  H5   C1   C2   109.89  3.000
 VOP  H4   C1   C2   111.14  3.000
 VOP  H3   C1   C2   110.68  3.000
 VOP  H6   C2   O21  109.04  3.000
 VOP  H6   C2   C3   110.54  3.000
 VOP  O21  C2   C3   110.88  3.000
 VOP  H6   C2   C1   108.72  3.000
 VOP  O21  C2   C1   106.75  3.000
 VOP  C3   C2   C1   110.81  3.000
 VOP  C2   C3   C8   120.91  3.000
 VOP  C2   C3   C4   119.26  3.000
 VOP  C8   C3   C4   119.71  3.000
 VOP  N16  C5   C6   106.17  3.000
 VOP  N16  C5   C4   131.49  3.000
 VOP  C6   C5   C4   122.34  3.000
 VOP  N13  N9   C10  112.30  3.000
 VOP  N13  N9   C8   120.46  3.000
 VOP  C10  N9   C8   127.20  3.000
 VOP  H7   C10  C11  131.77  3.000
 VOP  H7   C10  N9   121.56  3.000
 VOP  C11  C10  N9   106.67  3.000
 VOP  H8   C11  C12  128.15  3.000
 VOP  H8   C11  C10  127.53  3.000
 VOP  C12  C11  C10  104.32  3.000
 VOP  H9   C12  N13  120.11  3.000
 VOP  H9   C12  C11  128.39  3.000
 VOP  N13  C12  C11  111.50  3.000
 VOP  C12  N13  N9   105.20  3.000
 VOP  H10  C14  N15  120.81  3.000
 VOP  H10  C14  C6   128.58  3.000
 VOP  N15  C14  C6   110.61  3.000
 VOP  N16  N15  C14  107.28  3.000
 VOP  C17  N16  N15  120.34  3.000
 VOP  C17  N16  C5   127.66  3.000
 VOP  N15  N16  C5   111.65  3.000
 VOP  H12  C17  H11  106.60  3.000
 VOP  H12  C17  N16  108.77  3.000
 VOP  H11  C17  N16  110.16  3.000
 VOP  H12  C17  C18  109.85  3.000
 VOP  H11  C17  C18  109.55  3.000
 VOP  N16  C17  C18  111.76  3.000
 VOP  H13  O20  C18  110.40  3.000
 VOP  C22  O21  C2   119.11  3.000
 VOP  C31  C22  C23  119.06  3.000
 VOP  C31  C22  O21  114.28  3.000
 VOP  C23  C22  O21  126.66  3.000
 VOP  H14  C23  C24  118.61  3.000
 VOP  H14  C23  C22  122.17  3.000
 VOP  C24  C23  C22  119.22  3.000
 VOP  C29  C24  C25  120.07  3.000
 VOP  C29  C24  C23  117.79  3.000
 VOP  C25  C24  C23  122.13  3.000
 VOP  H15  C25  C24  120.40  3.000
 VOP  H15  C25  C26  120.75  3.000
 VOP  C24  C25  C26  118.85  3.000
 VOP  H16  C27  C28  120.97  3.000
 VOP  H16  C27  C26  120.09  3.000
 VOP  C28  C27  C26  118.94  3.000
 VOP  H17  C28  C29  118.74  3.000
 VOP  H17  C28  C27  120.30  3.000
 VOP  C29  C28  C27  120.96  3.000
 VOP  N30  C29  C28  119.09  3.000
 VOP  C28  C29  C24  118.74  3.000
 VOP  N30  C29  C24  122.17  3.000
 VOP  C31  N30  C29  119.59  3.000
 VOP  N32  C31  N30  119.17  3.000
 VOP  N30  C31  C22  122.15  3.000
 VOP  N32  C31  C22  118.65  3.000
 VOP  H19  N32  H18  115.47  3.000
 VOP  H19  N32  C31  119.46  3.000
 VOP  H18  N32  C31  116.59  3.000
 VOP  O20  C18  O19  125.05  3.000
 VOP  O20  C18  C17  110.63  3.000
 VOP  O19  C18  C17  124.33  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
 VOP  CONST_01  N9   C8   C3   C4   180.00   0.0  0
 VOP  CONST_02  C7   C8   C3   C4     0.00   0.0  0
 VOP  CONST_03  C7   C6   C5   C4     0.00   0.0  0
 VOP  CONST_04  C14  C6   C5   C4   180.00   0.0  0
 VOP  CONST_05  N15  N16  C5   C4   180.00   0.0  0
 VOP  CONST_08  N15  C14  C6   C7   180.00   0.0  0
 VOP  CONST_09  N16  C5   C6   C7   180.00   0.0  0
 VOP  CONST_10  N9   C8   C7   C6   180.00   0.0  0
 VOP  CONST_11  C3   C8   C7   C6     0.00   0.0  0
 VOP  CONST_12  N16  N15  C14  C6     0.00   0.0  0
 VOP  CONST_13  C3   C4   C5   C6     0.00   0.0  0
 VOP  CONST_14  N15  N16  C5   C6     0.00   0.0  0
 VOP  CONST_15  C11  C10  N9   C8   180.00   0.0  0
 VOP  CONST_16  C12  N13  N9   C8   180.00   0.0  0
 VOP  CONST_17  C14  C6   C7   C8   180.00   0.0  0
 VOP  CONST_18  C5   C6   C7   C8     0.00   0.0  0
 VOP  CONST_19  C5   C4   C3   C8     0.00   0.0  0
 VOP  CONST_20  C23  C24  C25  C26  180.00   0.0  0
 VOP  CONST_21  C29  C24  C25  C26    0.00   0.0  0
 VOP  CONST_22  C29  C28  C27  C26    0.00   0.0  0
 VOP  CONST_25  N16  C5   C4   C3   180.00   0.0  0
 VOP  CONST_26  N15  C14  C6   C5     0.00   0.0  0
 VOP  CONST_27  C14  N15  N16  C5     0.00   0.0  0
 VOP  CONST_28  C12  C11  C10  N9     0.00   0.0  0
 VOP  CONST_29  C11  C12  N13  N9     0.00   0.0  0
 VOP  CONST_30  N13  C12  C11  C10    0.00   0.0  0
 VOP  CONST_31  C12  N13  N9   C10    0.00   0.0  0
 VOP  CONST_32  N13  N9   C10  C11    0.00   0.0  0
 VOP  CONST_33  N16  C5   C6   C14    0.00   0.0  0
 VOP  CONST_34  C25  C24  C23  C22  180.00   0.0  0
 VOP  CONST_35  C29  C24  C23  C22    0.00   0.0  0
 VOP  CONST_36  C29  N30  C31  C22    0.00   0.0  0
 VOP  CONST_37  N30  C31  C22  C23    0.00   0.0  0
 VOP  CONST_38  N30  C29  C24  C23    0.00   0.0  0
 VOP  CONST_39  C28  C29  C24  C23  180.00   0.0  0
 VOP  CONST_40  C31  C22  C23  C24    0.00   0.0  0
 VOP  CONST_41  C27  C26  C25  C24    0.00   0.0  0
 VOP  CONST_42  C31  N30  C29  C24    0.00   0.0  0
 VOP  CONST_43  C27  C28  C29  C24    0.00   0.0  0
 VOP  CONST_44  N30  C29  C24  C25  180.00   0.0  0
 VOP  CONST_45  C28  C29  C24  C25    0.00   0.0  0
 VOP  CONST_46  C28  C27  C26  C25    0.00   0.0  0
 VOP  CONST_47  N30  C29  C28  C27  180.00   0.0  0
 VOP  CONST_48  C31  N30  C29  C28  180.00   0.0  0
 VOP  CONST_49  C17  N16  C5   C4     0.00   0.0  0
 VOP  CONST_50  C2   C3   C8   C7   180.00   0.0  0
 VOP  CONST_51  C17  N16  C5   C6   180.00   0.0  0
 VOP  CONST_52  N9   C8   C3   C2     0.00   0.0  0
 VOP  CONST_53  C5   C4   C3   C2   180.00   0.0  0
 VOP  CONST_54  C17  N16  N15  C14  180.00   0.0  0
 VOP  CONST_55  C24  C23  C22  O21  180.00   0.0  0
 VOP  CONST_56  N30  C31  C22  O21  180.00   0.0  0
 VOP  CONST_57  N32  C31  C22  C23  180.00   0.0  0
 VOP  CONST_58  F33  C26  C25  C24  180.00   0.0  0
 VOP  CONST_59  F33  C26  C27  C28  180.00   0.0  0
 VOP  CONST_60  N32  C31  N30  C29  180.00   0.0  0
 VOP  CONST_61  H10  C14  C6   C7     0.00   0.0  0
 VOP  CONST_62  H1   C4   C5   C6   180.00   0.0  0
 VOP  CONST_63  H7   C10  N9   C8     0.00   0.0  0
 VOP  CONST_64  H17  C28  C27  C26  180.00   0.0  0
 VOP  CONST_65  H2   C7   C8   C3   180.00   0.0  0
 VOP  CONST_66  H8   C11  C10  N9   180.00   0.0  0
 VOP  CONST_67  H9   C12  N13  N9   180.00   0.0  0
 VOP  CONST_68  H15  C25  C24  C23    0.00   0.0  0
 VOP  CONST_69  H14  C23  C24  C25    0.00   0.0  0
 VOP  CONST_70  H16  C27  C26  C25  180.00   0.0  0
 VOP  CONST_71  H18  N32  C31  C22  180.00   0.0  0
 VOP  CONST_73  H13  O20  C18  C17  180.00   0.0  0
 VOP  Var_01    N15  N16  C17  C18   91.89  30.0  2
 VOP  Var_02    C23  C22  O21  C2    -6.34  30.0  2
 VOP  Var_03    O19  C18  C17  N16    3.34  30.0  2

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
 VOP  chir_01  C2  C1  C3  O21  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
 VOP  plan-1  C8   0.020
 VOP  plan-1  N9   0.020
 VOP  plan-1  C10  0.020
 VOP  plan-1  C11  0.020
 VOP  plan-1  C12  0.020
 VOP  plan-1  N13  0.020
 VOP  plan-1  H7   0.020
 VOP  plan-1  H8   0.020
 VOP  plan-1  H9   0.020
 VOP  plan-2  C4   0.020
 VOP  plan-2  C7   0.020
 VOP  plan-2  C6   0.020
 VOP  plan-2  C8   0.020
 VOP  plan-2  C2   0.020
 VOP  plan-2  C3   0.020
 VOP  plan-2  C5   0.020
 VOP  plan-2  N9   0.020
 VOP  plan-2  C14  0.020
 VOP  plan-2  N15  0.020
 VOP  plan-2  N16  0.020
 VOP  plan-2  C17  0.020
 VOP  plan-2  H1   0.020
 VOP  plan-2  H2   0.020
 VOP  plan-2  H10  0.020
 VOP  plan-3  C26  0.020
 VOP  plan-3  O21  0.020
 VOP  plan-3  C22  0.020
 VOP  plan-3  C23  0.020
 VOP  plan-3  C24  0.020
 VOP  plan-3  C25  0.020
 VOP  plan-3  C27  0.020
 VOP  plan-3  C28  0.020
 VOP  plan-3  C29  0.020
 VOP  plan-3  N30  0.020
 VOP  plan-3  C31  0.020
 VOP  plan-3  N32  0.020
 VOP  plan-3  H14  0.020
 VOP  plan-3  H15  0.020
 VOP  plan-3  H16  0.020
 VOP  plan-3  H17  0.020
 VOP  plan-3  F33  0.020
 VOP  plan-4  C31  0.020
 VOP  plan-4  N32  0.020
 VOP  plan-4  H18  0.020
 VOP  plan-4  H19  0.020
 VOP  plan-5  C17  0.020
 VOP  plan-5  O19  0.020
 VOP  plan-5  O20  0.020
 VOP  plan-5  H13  0.020
 VOP  plan-5  C18  0.020

