# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 03:58:23 2022
#   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  51  33  .  2022-03-29  2022-03-29
;
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  -0.360   9.5148  -21.2559  11.3951
 VOP  C7   C  CR16   0  -0.333   8.8094  -19.7635   9.0880
 VOP  C6   C  CR56   0  -0.116   7.8152  -20.3379   9.8834
 VOP  C8   C  CR6    0   0.269  10.1217  -19.9430   9.4574
 VOP  C26  C  CR6    0   0.523  11.5568  -15.5444  14.4536
 VOP  C1   C  CH3    0  -0.660  12.3989  -22.2737  10.2144
 VOP  C2   C  CH1    0  -0.028  11.9506  -20.9909  10.8931
 VOP  C3   C  CR6    0   0.034  10.4915  -20.7032  10.5973
 VOP  C5   C  CR56   0   0.505   8.1791  -21.0507  11.0379
 VOP  N9   N  NR5    0  -0.382  11.1287  -19.3333   8.6645
 VOP  C10  C  CR15   0   0.031  11.4761  -19.6446   7.3984
 VOP  C11  C  CR15   0  -0.502  12.4538  -18.7546   7.0263
 VOP  C12  C  CR15   0  -0.036  12.6262  -17.9367   8.1558
 VOP  N13  N  N      0  -0.291  11.8177  -18.2903   9.1362
 VOP  C14  C  CR15   0  -0.124   6.3981  -20.3852   9.8827
 VOP  N15  N  N      0  -0.237   5.9629  -21.0443  10.9278
 VOP  N16  N  NR5    0  -0.377   7.0291  -21.4316  11.6336
 VOP  C17  C  CH2    0  -0.467   6.8846  -22.2477  12.8102
 VOP  O19  O  O      0  -0.584   7.4587  -24.1174  11.4373
 VOP  O20  O  OC    -1  -0.603   6.9200  -24.4597  13.5852
 VOP  O21  O  O2     0  -0.488  12.1591  -21.1706  12.2871
 VOP  C22  C  C      0   0.273  12.0401  -20.1115  13.1082
 VOP  C23  C  C1     0  -0.326  11.8949  -18.8122  12.7408
 VOP  C24  C  CR6    0   0.113  11.7951  -17.8132  13.7463
 VOP  C25  C  CR16   0  -0.502  11.6537  -16.4480  13.4337
 VOP  C27  C  CR16   0  -0.423  11.5929  -15.9255  15.7974
 VOP  C28  C  CR16   0  -0.285  11.7310  -17.2563  16.1073
 VOP  C29  C  CR6    0   0.188  11.8360  -18.2302  15.0944
 VOP  N30  N  N      0  -0.488  11.9639  -19.5350  15.4440
 VOP  C31  C  C      0   0.358  12.0621  -20.4440  14.5138
 VOP  N32  N  NH2    0  -0.829  12.2302  -21.7423  14.8700
 VOP  H1   H  HCR6   0   0.278   9.7733  -21.8393  12.2692
 VOP  H2   H  HCR6   0   0.271   8.5638  -19.1752   8.2127
 VOP  H3   H  HCH3   0   0.249  13.4517  -22.4701  10.4174
 VOP  H4   H  HCH3   0   0.240  11.8064  -23.1252  10.5504
 VOP  H5   H  HCH3   0   0.245  12.2770  -22.1817   9.1359
 VOP  H6   H  HCH1   0   0.256  12.5819  -20.1713  10.5402
 VOP  H7   H  HCR5   0   0.295  11.0126  -20.4635   6.8721
 VOP  H8   H  HCR5   0   0.266  12.9696  -18.7039   6.0824
 VOP  H9   H  HCR5   0   0.264  13.3039  -17.1065   8.2858
 VOP  H10  H  HCR5   0   0.268   5.7080  -19.9603   9.1699
 VOP  H11  H  HCH2   0   0.258   7.5875  -21.8943  13.5689
 VOP  H12  H  HCH2   0   0.271   5.8839  -22.0756  13.2059
 VOP  H14  H  H      0   0.304  11.8577  -18.5063  11.7015
 VOP  H15  H  HCR6   0   0.272  11.6220  -16.1250  12.3999
 VOP  H16  H  HCR6   0   0.275  11.5118  -15.1782  16.5760
 VOP  H17  H  HCR6   0   0.261  11.7609  -17.5761  17.1409
 VOP  H18  H  HNH2   0   0.388  12.0385  -21.9743  15.8305
 VOP  H19  H  HNH2   0   0.397  12.0216  -22.4651  14.2027
 VOP  C18  C  C      0   0.409   7.1110  -23.7629  12.5733
 VOP  F33  F  F      0  -0.321  11.4187  -14.2364  14.1689

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  1.349  0.020  1.349
 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  1.375  0.020  1.375
 VOP  C7   C6   aromatic  1.397  0.020  1.397
 VOP  C8   C3   aromatic  1.419  0.020  1.419
 VOP  C6   C14  aromatic  1.418  0.020  1.418
 VOP  C6   C5   aromatic  1.405  0.020  1.405
 VOP  C14  N15  aromatic  1.310  0.020  1.310
 VOP  C1   C2   single    1.519  0.020  1.519
 VOP  O19  C18  deloc     1.240  0.020  1.240
 VOP  C3   C2   single    1.516  0.020  1.516
 VOP  C3   C4   aromatic  1.377  0.020  1.377
 VOP  C2   O21  single    1.421  0.020  1.421
 VOP  N15  N16  aromatic  1.336  0.020  1.336
 VOP  C5   C4   aromatic  1.398  0.020  1.398
 VOP  C5   N16  aromatic  1.350  0.020  1.350
 VOP  N16  C17  single    1.439  0.020  1.439
 VOP  C18  O20  deloc     1.243  0.020  1.243
 VOP  C18  C17  single    1.550  0.020  1.550
 VOP  O21  C22  single    1.345  0.020  1.345
 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  1.445  0.020  1.445
 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  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   120.91  3.000
 VOP  H1   C4   C3   121.00  3.000
 VOP  C5   C4   C3   118.09  3.000
 VOP  H2   C7   C8   120.30  3.000
 VOP  H2   C7   C6   121.49  3.000
 VOP  C8   C7   C6   118.20  3.000
 VOP  C14  C6   C5   104.03  3.000
 VOP  C5   C6   C7   119.49  3.000
 VOP  C14  C6   C7   136.45  3.000
 VOP  N9   C8   C3   119.60  3.000
 VOP  C3   C8   C7   122.30  3.000
 VOP  N9   C8   C7   118.10  3.000
 VOP  F33  C26  C27  118.12  3.000
 VOP  C27  C26  C25  122.39  3.000
 VOP  F33  C26  C25  119.49  3.000
 VOP  H5   C1   H4   108.08  3.000
 VOP  H5   C1   H3   107.92  3.000
 VOP  H4   C1   H3   109.07  3.000
 VOP  H5   C1   C2   109.76  3.000
 VOP  H4   C1   C2   111.19  3.000
 VOP  H3   C1   C2   110.73  3.000
 VOP  H6   C2   O21  109.07  3.000
 VOP  H6   C2   C3   110.52  3.000
 VOP  O21  C2   C3   110.89  3.000
 VOP  H6   C2   C1   108.57  3.000
 VOP  O21  C2   C1   106.75  3.000
 VOP  C3   C2   C1   110.92  3.000
 VOP  C2   C3   C8   120.60  3.000
 VOP  C2   C3   C4   119.56  3.000
 VOP  C8   C3   C4   119.71  3.000
 VOP  N16  C5   C6   106.57  3.000
 VOP  N16  C5   C4   131.29  3.000
 VOP  C6   C5   C4   122.14  3.000
 VOP  N13  N9   C10  112.25  3.000
 VOP  N13  N9   C8   120.26  3.000
 VOP  C10  N9   C8   127.43  3.000
 VOP  H7   C10  C11  131.76  3.000
 VOP  H7   C10  N9   121.51  3.000
 VOP  C11  C10  N9   106.74  3.000
 VOP  H8   C11  C12  128.20  3.000
 VOP  H8   C11  C10  127.51  3.000
 VOP  C12  C11  C10  104.28  3.000
 VOP  H9   C12  N13  120.10  3.000
 VOP  H9   C12  C11  128.42  3.000
 VOP  N13  C12  C11  111.48  3.000
 VOP  C12  N13  N9   105.24  3.000
 VOP  H10  C14  N15  120.83  3.000
 VOP  H10  C14  C6   128.78  3.000
 VOP  N15  C14  C6   110.39  3.000
 VOP  N16  N15  C14  107.59  3.000
 VOP  C17  N16  N15  121.08  3.000
 VOP  C17  N16  C5   127.32  3.000
 VOP  N15  N16  C5   111.40  3.000
 VOP  H12  C17  H11  106.70  3.000
 VOP  H12  C17  N16  107.43  3.000
 VOP  H11  C17  N16  108.64  3.000
 VOP  H12  C17  C18  110.12  3.000
 VOP  H11  C17  C18  109.16  3.000
 VOP  N16  C17  C18  114.50  3.000
 VOP  C22  O21  C2   119.09  3.000
 VOP  C31  C22  C23  119.02  3.000
 VOP  C31  C22  O21  114.28  3.000
 VOP  C23  C22  O21  126.70  3.000
 VOP  H14  C23  C24  118.53  3.000
 VOP  H14  C23  C22  122.20  3.000
 VOP  C24  C23  C22  119.26  3.000
 VOP  C29  C24  C25  120.09  3.000
 VOP  C29  C24  C23  117.78  3.000
 VOP  C25  C24  C23  122.13  3.000
 VOP  H15  C25  C24  120.26  3.000
 VOP  H15  C25  C26  120.87  3.000
 VOP  C24  C25  C26  118.88  3.000
 VOP  H16  C27  C28  120.95  3.000
 VOP  H16  C27  C26  120.10  3.000
 VOP  C28  C27  C26  118.94  3.000
 VOP  H17  C28  C29  118.69  3.000
 VOP  H17  C28  C27  120.30  3.000
 VOP  C29  C28  C27  121.00  3.000
 VOP  N30  C29  C28  119.11  3.000
 VOP  C28  C29  C24  118.69  3.000
 VOP  N30  C29  C24  122.20  3.000
 VOP  C31  N30  C29  119.57  3.000
 VOP  N32  C31  N30  119.28  3.000
 VOP  N30  C31  C22  122.17  3.000
 VOP  N32  C31  C22  118.53  3.000
 VOP  H19  N32  H18  115.35  3.000
 VOP  H19  N32  C31  119.21  3.000
 VOP  H18  N32  C31  116.58  3.000
 VOP  O20  C18  O19  128.95  3.000
 VOP  O20  C18  C17  113.64  3.000
 VOP  O19  C18  C17  117.41  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  Var_01    N15  N16  C17  C18   97.75  30.0  2
 VOP  Var_02    C23  C22  O21  C2    -8.72  30.0  2
 VOP  Var_03    O19  C18  C17  N16    3.75  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  C18  0.020

