# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 21:07:26 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: 1'-{[5-(aminomethyl)-1-(4,4,4-trifluorobutyl)-1H-benzimidazol-2-yl]methyl}-6'-fluorospiro[cyclopropane-1,3'-indol]-2'(1'H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc2n(CCCC(F)(F)F)c(CN3C(=O)C4(CC4)c5ccc(F)cc35)nc2c1
#
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
 WVA  WVA  1'-{[5-(aminomethyl)-1-(4,4,4-trifluorobutyl)-1H-benzimidazol-2-yl]methyl}-6'-fluorospiro[cyclopropane-1,3'-indol]-2'(1'H)-one  ligand  54  32  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_WVA
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
 WVA  C10  C  CH2   0  -0.341  19.2225  16.0916  19.2431
 WVA  C13  C  CT    0   1.002  19.9045  14.0423  16.0492
 WVA  C17  C  CR5   0   0.458  20.0272  18.3810  19.9615
 WVA  C21  C  CR5   0   0.573  16.7664  18.9787  18.7944
 WVA  C24  C  CH2   0  -0.438  14.3233  18.8484  19.6330
 WVA  C26  C  CR56  0   0.101  16.1697  20.5662  20.4243
 WVA  C28  C  CR16  0  -0.424  16.4237  22.2455  22.1104
 WVA  C03  C  CR6   0   0.052  22.6913  16.6662  23.1188
 WVA  C04  C  CR16  0  -0.382  22.3122  17.8773  22.5684
 WVA  C05  C  CR56  0   0.170  21.3807  17.8744  21.5286
 WVA  C06  C  CR56  0   0.326  20.8375  16.6705  21.0659
 WVA  C07  C  CR16  0  -0.295  21.2087  15.4417  21.6030
 WVA  C08  C  CR16  0  -0.307  22.1390  15.4674  22.6236
 WVA  C11  C  CH2   0  -0.463  20.0395  15.5670  18.0680
 WVA  C12  C  CH2   0  -0.654  19.1733  14.6447  17.2162
 WVA  C19  C  CH2   0  -0.463  19.2423  19.1840  18.9712
 WVA  C23  C  CR5   0  -0.229  15.5979  19.6368  19.4385
 WVA  C25  C  CH2   0  -0.439  14.3633  19.9161  18.6132
 WVA  C27  C  CR16  0  -0.368  15.6003  21.4652  21.2995
 WVA  C29  C  CR6   0   0.531  17.7929  22.0921  22.0122
 WVA  C31  C  CR16  0  -0.468  18.4049  21.1943  21.1488
 WVA  C32  C  CR56  0   0.417  17.5592  20.4383  20.3580
 WVA  F14  F  F     0  -0.313  20.9285  13.2640  16.4333
 WVA  F15  F  F     0  -0.312  19.1034  13.2720  15.2962
 WVA  F16  F  F     0  -0.314  20.4182  14.9755  15.2321
 WVA  F30  F  F     0  -0.317  18.5818  22.8489  22.7935
 WVA  N01  N  NH2   0  -0.795  24.4159  17.8156  24.4599
 WVA  N09  N  NR5   0  -0.543  19.9632  17.0226  20.0673
 WVA  N18  N  N     0  -0.474  20.8559  18.9218  20.8137
 WVA  N20  N  NR5   0  -0.612  17.8930  19.4863  19.3961
 WVA  H1   H  HCH2  0   0.289  18.3193  16.5805  18.8839
 WVA  H2   H  HCH2  0   0.277  18.8954  15.2667  19.8782
 WVA  H3   H  HCH2  0   0.276  13.7919  19.0315  20.5578
 WVA  H4   H  HCH2  0   0.275  14.3378  17.8168  19.3053
 WVA  H5   H  HCR6  0   0.276  16.0033  22.9605  22.8047
 WVA  H6   H  HCH2  0   0.239  23.1158  16.3838  25.1832
 WVA  H7   H  HCH2  0   0.213  24.3115  15.7040  24.1089
 WVA  H8   H  HCR6  0   0.245  22.7298  18.8061  22.9341
 WVA  H9   H  HCR6  0   0.266  20.8022  14.5053  21.2424
 WVA  H10  H  HCR6  0   0.245  22.4587  14.5283  23.0605
 WVA  H11  H  HCH2  0   0.260  20.9200  15.0385  18.4391
 WVA  H12  H  HCH2  0   0.258  20.3937  16.4122  17.4739
 WVA  H13  H  HCH2  0   0.281  18.3120  15.1947  16.8288
 WVA  H14  H  HCH2  0   0.281  18.7789  13.8263  17.8240
 WVA  H15  H  HCH2  0   0.309  19.1825  18.6764  18.0083
 WVA  H16  H  HCH2  0   0.307  19.7797  20.1191  18.8069
 WVA  H17  H  HCH2  0   0.277  13.8626  20.8526  18.8214
 WVA  H18  H  HCH2  0   0.275  14.4048  19.6364  17.5683
 WVA  H19  H  HCR6  0   0.263  14.5246  21.5766  21.3598
 WVA  H20  H  HCR6  0   0.291  19.4815  21.0902  21.1208
 WVA  H21  H  HNH2  0   0.355  24.9560  17.7470  25.3122
 WVA  H22  H  HNH2  0   0.343  25.0877  17.9347  23.7118
 WVA  C02  C  CH2   0  -0.321  23.6737  16.5855  24.2637
 WVA  O22  O  O     0  -0.455  16.7542  18.1528  17.9048

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
 WVA  F16  C13  single    1.343  0.020  1.343
 WVA  F15  C13  single    1.342  0.020  1.342
 WVA  F14  C13  single    1.342  0.020  1.342
 WVA  C13  C12  single    1.503  0.020  1.503
 WVA  O22  C21  double    1.214  0.020  1.214
 WVA  C12  C11  single    1.525  0.020  1.525
 WVA  C11  C10  single    1.524  0.020  1.524
 WVA  C25  C23  single    1.511  0.020  1.511
 WVA  C25  C24  single    1.477  0.020  1.477
 WVA  C21  N20  single    1.374  0.020  1.374
 WVA  C21  C23  single    1.488  0.020  1.488
 WVA  C19  N20  single    1.447  0.020  1.447
 WVA  C19  C17  single    1.497  0.020  1.497
 WVA  N20  C32  single    1.394  0.020  1.394
 WVA  C23  C24  single    1.511  0.020  1.511
 WVA  C23  C26  single    1.471  0.020  1.471
 WVA  C10  N09  single    1.447  0.020  1.447
 WVA  C17  N09  aromatic  1.364  0.020  1.364
 WVA  C17  N18  aromatic  1.306  0.020  1.306
 WVA  C32  C26  aromatic  1.397  0.020  1.397
 WVA  C32  C31  aromatic  1.383  0.020  1.383
 WVA  C26  C27  aromatic  1.378  0.020  1.378
 WVA  N09  C06  aromatic  1.373  0.020  1.373
 WVA  N18  C05  aromatic  1.372  0.020  1.372
 WVA  C31  C29  aromatic  1.388  0.020  1.388
 WVA  C06  C05  aromatic  1.399  0.020  1.399
 WVA  C06  C07  aromatic  1.392  0.020  1.392
 WVA  C27  C28  aromatic  1.394  0.020  1.394
 WVA  C05  C04  aromatic  1.396  0.020  1.396
 WVA  C07  C08  aromatic  1.381  0.020  1.381
 WVA  C29  C28  aromatic  1.381  0.020  1.381
 WVA  C29  F30  single    1.344  0.020  1.344
 WVA  C04  C03  aromatic  1.383  0.020  1.383
 WVA  C08  C03  aromatic  1.410  0.020  1.410
 WVA  C03  C02  single    1.511  0.020  1.511
 WVA  N01  C02  single    1.450  0.020  1.450
 WVA  C10  H1   single    0.970  0.020  1.090
 WVA  C10  H2   single    0.970  0.020  1.090
 WVA  C24  H3   single    0.970  0.020  1.090
 WVA  C24  H4   single    0.970  0.020  1.090
 WVA  C28  H5   single    0.930  0.020  1.080
 WVA  C02  H6   single    0.970  0.020  1.090
 WVA  C02  H7   single    0.970  0.020  1.090
 WVA  C04  H8   single    0.930  0.020  1.080
 WVA  C07  H9   single    0.930  0.020  1.080
 WVA  C08  H10  single    0.930  0.020  1.080
 WVA  C11  H11  single    0.970  0.020  1.090
 WVA  C11  H12  single    0.970  0.020  1.090
 WVA  C12  H13  single    0.970  0.020  1.090
 WVA  C12  H14  single    0.970  0.020  1.090
 WVA  C19  H15  single    0.970  0.020  1.090
 WVA  C19  H16  single    0.970  0.020  1.090
 WVA  C25  H17  single    0.970  0.020  1.090
 WVA  C25  H18  single    0.970  0.020  1.090
 WVA  C27  H19  single    0.930  0.020  1.080
 WVA  C31  H20  single    0.930  0.020  1.080
 WVA  N01  H21  single    0.890  0.020  1.040
 WVA  N01  H22  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
 WVA  H2   C10  H1   106.44  3.000
 WVA  H2   C10  N09  107.95  3.000
 WVA  H1   C10  N09  108.89  3.000
 WVA  H2   C10  C11  110.44  3.000
 WVA  H1   C10  C11  110.19  3.000
 WVA  N09  C10  C11  112.71  3.000
 WVA  F16  C13  F15  106.61  3.000
 WVA  F15  C13  F14  106.45  3.000
 WVA  F16  C13  F14  106.57  3.000
 WVA  F14  C13  C12  112.41  3.000
 WVA  F15  C13  C12  112.03  3.000
 WVA  F16  C13  C12  112.34  3.000
 WVA  N18  C17  N09  113.05  3.000
 WVA  N18  C17  C19  122.84  3.000
 WVA  N09  C17  C19  124.11  3.000
 WVA  O22  C21  N20  125.47  3.000
 WVA  N20  C21  C23  106.91  3.000
 WVA  O22  C21  C23  127.62  3.000
 WVA  H4   C24  H3   115.25  3.000
 WVA  H4   C24  C25  118.66  3.000
 WVA  H3   C24  C25  118.75  3.000
 WVA  H4   C24  C23  116.55  3.000
 WVA  H3   C24  C23  115.83  3.000
 WVA  C25  C24  C23   60.74  3.000
 WVA  C32  C26  C27  120.06  3.000
 WVA  C27  C26  C23  132.65  3.000
 WVA  C32  C26  C23  107.28  3.000
 WVA  H5   C28  C29  120.29  3.000
 WVA  H5   C28  C27  120.90  3.000
 WVA  C29  C28  C27  118.81  3.000
 WVA  C08  C03  C04  119.83  3.000
 WVA  C08  C03  C02  118.39  3.000
 WVA  C04  C03  C02  121.77  3.000
 WVA  H8   C04  C05  120.74  3.000
 WVA  H8   C04  C03  120.75  3.000
 WVA  C05  C04  C03  118.51  3.000
 WVA  N18  C05  C06  109.63  3.000
 WVA  C06  C05  C04  120.47  3.000
 WVA  N18  C05  C04  129.91  3.000
 WVA  N09  C06  C07  132.61  3.000
 WVA  C07  C06  C05  121.91  3.000
 WVA  N09  C06  C05  105.49  3.000
 WVA  H9   C07  C08  121.01  3.000
 WVA  H9   C07  C06  122.35  3.000
 WVA  C08  C07  C06  116.64  3.000
 WVA  H10  C08  C07  118.71  3.000
 WVA  H10  C08  C03  118.66  3.000
 WVA  C07  C08  C03  122.63  3.000
 WVA  H12  C11  H11  107.34  3.000
 WVA  H12  C11  C12  110.39  3.000
 WVA  H11  C11  C12  110.80  3.000
 WVA  H12  C11  C10  109.08  3.000
 WVA  H11  C11  C10  109.68  3.000
 WVA  C12  C11  C10  109.52  3.000
 WVA  H14  C12  H13  106.84  3.000
 WVA  H14  C12  C11  110.31  3.000
 WVA  H13  C12  C11  109.95  3.000
 WVA  H14  C12  C13  107.89  3.000
 WVA  H13  C12  C13  108.05  3.000
 WVA  C11  C12  C13  113.55  3.000
 WVA  H16  C19  H15  107.04  3.000
 WVA  H16  C19  N20  108.94  3.000
 WVA  H15  C19  N20  107.79  3.000
 WVA  H16  C19  C17  107.52  3.000
 WVA  H15  C19  C17  111.30  3.000
 WVA  N20  C19  C17  114.00  3.000
 WVA  C25  C23  C26  124.54  3.000
 WVA  C26  C23  C24  124.85  3.000
 WVA  C25  C23  C24   58.51  3.000
 WVA  C26  C23  C21  105.33  3.000
 WVA  C24  C23  C21  119.17  3.000
 WVA  C25  C23  C21  119.14  3.000
 WVA  H18  C25  H17  115.28  3.000
 WVA  H18  C25  C23  116.63  3.000
 WVA  H17  C25  C23  115.65  3.000
 WVA  H18  C25  C24  118.74  3.000
 WVA  H17  C25  C24  118.69  3.000
 WVA  C23  C25  C24   60.75  3.000
 WVA  H19  C27  C28  119.77  3.000
 WVA  H19  C27  C26  120.86  3.000
 WVA  C28  C27  C26  119.37  3.000
 WVA  F30  C29  C31  117.85  3.000
 WVA  F30  C29  C28  118.56  3.000
 WVA  C31  C29  C28  123.59  3.000
 WVA  H20  C31  C32  122.76  3.000
 WVA  H20  C31  C29  121.14  3.000
 WVA  C32  C31  C29  116.09  3.000
 WVA  N20  C32  C31  128.43  3.000
 WVA  C31  C32  C26  122.08  3.000
 WVA  N20  C32  C26  109.48  3.000
 WVA  H22  N01  H21  106.04  3.000
 WVA  H22  N01  C02  109.84  3.000
 WVA  H21  N01  C02  109.26  3.000
 WVA  C06  N09  C17  106.37  3.000
 WVA  C06  N09  C10  125.10  3.000
 WVA  C17  N09  C10  128.35  3.000
 WVA  C05  N18  C17  105.46  3.000
 WVA  C32  N20  C19  124.66  3.000
 WVA  C32  N20  C21  110.98  3.000
 WVA  C19  N20  C21  123.98  3.000
 WVA  H7   C02  H6   105.45  3.000
 WVA  H7   C02  N01  113.73  3.000
 WVA  H6   C02  N01  107.68  3.000
 WVA  H7   C02  C03  108.27  3.000
 WVA  H6   C02  C03  108.37  3.000
 WVA  N01  C02  C03  112.96  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
 WVA  CONST_01  C05  C06  N09  C17     0.00   0.0  0
 WVA  CONST_02  C07  C06  N09  C17   180.00   0.0  0
 WVA  CONST_03  C06  C05  N18  C17     0.00   0.0  0
 WVA  CONST_04  C04  C05  N18  C17   180.00   0.0  0
 WVA  CONST_05  C29  C31  C32  C26     0.00   0.0  0
 WVA  CONST_06  C29  C28  C27  C26     0.00   0.0  0
 WVA  CONST_07  C32  C26  C27  C28     0.00   0.0  0
 WVA  CONST_08  C32  C31  C29  C28     0.00   0.0  0
 WVA  CONST_09  N18  C05  C04  C03   180.00   0.0  0
 WVA  CONST_10  C06  C05  C04  C03     0.00   0.0  0
 WVA  CONST_11  C06  C07  C08  C03     0.00   0.0  0
 WVA  CONST_12  N09  C06  C05  C04   180.00   0.0  0
 WVA  CONST_13  C07  C06  C05  C04     0.00   0.0  0
 WVA  CONST_14  C07  C08  C03  C04     0.00   0.0  0
 WVA  CONST_15  N09  C17  N18  C05     0.00   0.0  0
 WVA  CONST_16  C08  C07  C06  C05     0.00   0.0  0
 WVA  CONST_17  C08  C03  C04  C05     0.00   0.0  0
 WVA  CONST_18  N18  C17  N09  C06     0.00   0.0  0
 WVA  CONST_19  N18  C05  C06  C07   180.00   0.0  0
 WVA  CONST_20  N09  C06  C07  C08   180.00   0.0  0
 WVA  CONST_21  C31  C32  C26  C27     0.00   0.0  0
 WVA  CONST_22  C31  C29  C28  C27     0.00   0.0  0
 WVA  CONST_23  N18  C05  C06  N09     0.00   0.0  0
 WVA  CONST_24  C32  N20  C21  C23     0.00   0.0  0
 WVA  CONST_25  N18  C17  N09  C10   180.00   0.0  0
 WVA  CONST_26  C05  C06  N09  C10   180.00   0.0  0
 WVA  CONST_27  C07  C06  N09  C10     0.00   0.0  0
 WVA  CONST_28  C05  C04  C03  C02   180.00   0.0  0
 WVA  CONST_29  C07  C08  C03  C02   180.00   0.0  0
 WVA  CONST_30  C19  C17  N18  C05   180.00   0.0  0
 WVA  CONST_31  C19  C17  N09  C06   180.00   0.0  0
 WVA  CONST_32  F30  C29  C28  C27   180.00   0.0  0
 WVA  CONST_33  F30  C29  C31  C32   180.00   0.0  0
 WVA  CONST_34  C23  C21  N20  C19   180.00   0.0  0
 WVA  CONST_35  O22  C21  N20  C32   180.00   0.0  0
 WVA  CONST_36  H20  C31  C32  C26   180.00   0.0  0
 WVA  CONST_37  H5   C28  C27  C26   180.00   0.0  0
 WVA  CONST_38  H9   C07  C08  C03   180.00   0.0  0
 WVA  CONST_39  H10  C08  C03  C04   180.00   0.0  0
 WVA  CONST_40  H8   C04  C05  C06   180.00   0.0  0
 WVA  CONST_41  H19  C27  C26  C23     0.00   0.0  0
 WVA  CONST_42  O22  C21  N20  C19     0.00   0.0  0
 WVA  Var_01    C24  C25  C23  C21   108.23  30.0  3
 WVA  Var_02    N20  C21  C23  C24  -145.19  30.0  1
 WVA  Var_03    C32  C26  C23  C24   143.21  30.0  1
 WVA  Var_04    C21  N20  C19  C17  -112.83  30.0  3
 WVA  Var_05    N20  C19  C17  N09    83.42  30.0  1
 WVA  Var_06    C11  C10  N09  C17    91.45  30.0  2
 WVA  Var_07    N01  C02  C03  C04   -15.59  30.0  2
 WVA  Var_08    N09  C10  C11  C12  -177.49  30.0  3
 WVA  Var_09    H21  N01  C02  C03   172.04  30.0  3
 WVA  Var_10    C13  C12  C11  C10  -178.32  30.0  1
 WVA  Var_11    F16  C13  C12  C11   -57.97  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
 WVA  plan-1  C10  0.020
 WVA  plan-1  C17  0.020
 WVA  plan-1  C03  0.020
 WVA  plan-1  C04  0.020
 WVA  plan-1  C05  0.020
 WVA  plan-1  C06  0.020
 WVA  plan-1  C07  0.020
 WVA  plan-1  C08  0.020
 WVA  plan-1  C19  0.020
 WVA  plan-1  N09  0.020
 WVA  plan-1  N18  0.020
 WVA  plan-1  H8   0.020
 WVA  plan-1  H9   0.020
 WVA  plan-1  H10  0.020
 WVA  plan-1  C02  0.020
 WVA  plan-2  C21  0.020
 WVA  plan-2  C26  0.020
 WVA  plan-2  C28  0.020
 WVA  plan-2  C19  0.020
 WVA  plan-2  C23  0.020
 WVA  plan-2  C27  0.020
 WVA  plan-2  C29  0.020
 WVA  plan-2  C31  0.020
 WVA  plan-2  C32  0.020
 WVA  plan-2  F30  0.020
 WVA  plan-2  N20  0.020
 WVA  plan-2  H5   0.020
 WVA  plan-2  H19  0.020
 WVA  plan-2  H20  0.020
 WVA  plan-2  O22  0.020

