# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 23:29:25 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: (3alpha,8alpha)-17-(1H-benzimidazol-1-yl)androsta-5,16-dien-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CC[C@H](O)CC1=CC[C@@H]3[C@@H]2CC[C@@]4(C)[C@H]3CC=C4n5cnc6ccccc56
#
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
 TOK  TOK  (3alpha,8alpha)-17-(1H-benzimidazol-1-yl)androsta-5,16-dien-3-ol  ligand  61  29  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TOK
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
 TOK  C1    C  CH2   0  -0.433  -4.0649   1.5959  -0.6654
 TOK  C2    C  CH2   0  -0.467  -5.5433   1.8208  -0.3771
 TOK  C3    C  CH1   0   0.090  -6.3113   0.5224  -0.5246
 TOK  O3    O  OH1   0  -0.678  -7.6759   0.7736  -0.2574
 TOK  C4    C  CH2   0  -0.548  -5.7295  -0.5250   0.4220
 TOK  C5    C  C     0   0.207  -4.2497  -0.7200   0.2198
 TOK  C6    C  C1    0  -0.328  -3.7429  -1.9418   0.0600
 TOK  C7    C  CH2   0  -0.451  -2.2896  -2.2509  -0.0893
 TOK  C8    C  CH1   0  -0.246  -1.3944  -1.0654   0.2521
 TOK  C9    C  CH1   0  -0.185  -1.9889   0.2191  -0.3536
 TOK  C10   C  CT    0  -0.130  -3.3901   0.5342   0.2284
 TOK  C11   C  CH2   0  -0.452  -1.0359   1.4268  -0.2933
 TOK  C12   C  CH2   0  -0.428   0.3978   1.1346  -0.7525
 TOK  C13   C  CT    0  -0.117   0.9405  -0.0852  -0.0171
 TOK  C14   C  CH1   0  -0.202  -0.0032  -1.2575  -0.3152
 TOK  C15   C  CH2   0  -0.473   0.8270  -2.5028   0.0034
 TOK  C16   C  C1    0  -0.261   2.1997  -2.0396  -0.4024
 TOK  C17   C  C     0   0.346   2.2481  -0.7097  -0.4660
 TOK  C18   C  CH3   0  -0.668   1.1087   0.2170   1.4814
 TOK  C19   C  CH3   0  -0.673  -3.3010   1.0497   1.6752
 TOK  N48   N  NR5   0  -0.609   3.4136   0.0492  -0.6782
 TOK  C49   C  CR56  0   0.312   4.6045  -0.0401   0.0120
 TOK  C50   C  CR56  0   0.128   5.4293   0.9415  -0.5585
 TOK  N51   N  N     0  -0.464   4.7557   1.5981  -1.5635
 TOK  C52   C  CR15  0   0.103   3.5804   1.0461  -1.5946
 TOK  C53   C  CR16  0  -0.295   5.0179  -0.8433   1.0682
 TOK  C54   C  CR16  0  -0.275   6.3041  -0.6395   1.5359
 TOK  C55   C  CR16  0  -0.272   7.1472   0.3297   0.9701
 TOK  C56   C  CR16  0  -0.323   6.7242   1.1294  -0.0753
 TOK  H1    H  HCH2  0   0.222  -3.9559   1.2878  -1.7120
 TOK  H1A   H  HCH2  0   0.238  -3.5330   2.5449  -0.5719
 TOK  H2    H  HCH2  0   0.221  -5.6853   2.2144   0.6352
 TOK  H2A   H  HCH2  0   0.238  -5.9379   2.5733  -1.0652
 TOK  H3    H  HCH1  0   0.190  -6.1841   0.1627  -1.5576
 TOK  HO3   H  HOH1  0   0.446  -8.1679  -0.0381  -0.4158
 TOK  H4    H  HCH2  0   0.230  -5.9295  -0.1937   1.4484
 TOK  H4A   H  HCH2  0   0.241  -6.2483  -1.4798   0.2947
 TOK  H6    H  H     0   0.222  -4.4233  -2.7889   0.0421
 TOK  H7    H  HCH2  0   0.239  -2.0306  -3.1087   0.5392
 TOK  H7A   H  HCH2  0   0.224  -2.0920  -2.5804  -1.1185
 TOK  H8    H  HCH1  0   0.225  -1.3409  -0.9712   1.3428
 TOK  H9    H  HCH1  0   0.211  -2.1404  -0.0055  -1.4201
 TOK  H11   H  HCH2  0   0.243  -1.4340   2.2317  -0.9147
 TOK  H11A  H  HCH2  0   0.227  -1.0040   1.8313   0.7199
 TOK  H12   H  HCH2  0   0.226   0.4095   0.9480  -1.8318
 TOK  H12A  H  HCH2  0   0.233   1.0166   2.0200  -0.5767
 TOK  H14   H  HCH1  0   0.227  -0.1208  -1.2687  -1.4093
 TOK  H15   H  HCH2  0   0.241   0.8079  -2.7600   1.0697
 TOK  H16   H  H     0   0.260   3.0369  -2.7055  -0.5687
 TOK  H18   H  HCH3  0   0.240   0.2021   0.6024   1.9452
 TOK  H18A  H  HCH3  0   0.239   1.4094  -0.6716   2.0386
 TOK  H18B  H  HCH3  0   0.237   1.8866   0.9707   1.6243
 TOK  H19   H  HCH3  0   0.233  -2.6836   0.3960   2.2935
 TOK  H19A  H  HCH3  0   0.228  -2.8763   2.0535   1.7225
 TOK  H19B  H  HCH3  0   0.236  -4.2819   1.1001   2.1481
 TOK  H52   H  HCR5  0   0.289   2.7884   1.3108  -2.2795
 TOK  H53   H  HCR6  0   0.270   4.3709  -1.5902   1.5088
 TOK  H54   H  HCR6  0   0.257   6.6699  -1.2418   2.3572
 TOK  H55   H  HCR6  0   0.254   8.1475   0.4517   1.3645
 TOK  H56   H  HCR6  0   0.256   7.3731   1.8806  -0.5070
 TOK  H15A  H  HCH2  0   0.250   0.4981  -3.3904  -0.5398

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
 TOK  C1   H1    single    0.970  0.020  1.090
 TOK  C1   H1A   single    0.970  0.020  1.090
 TOK  C2   C1    single    1.523  0.020  1.523
 TOK  C2   H2    single    0.970  0.020  1.090
 TOK  C2   H2A   single    0.970  0.020  1.090
 TOK  C3   C2    single    1.516  0.020  1.516
 TOK  C3   H3    single    0.970  0.020  1.090
 TOK  O3   C3    single    1.413  0.020  1.413
 TOK  O3   HO3   single    0.850  0.020  0.980
 TOK  C4   C3    single    1.527  0.020  1.527
 TOK  C4   C5    single    1.506  0.020  1.506
 TOK  C4   H4    single    0.970  0.020  1.090
 TOK  C4   H4A   single    0.970  0.020  1.090
 TOK  C5   C10   single    1.520  0.020  1.520
 TOK  C6   C5    double    1.332  0.020  1.332
 TOK  C6   C7    single    1.493  0.020  1.493
 TOK  C6   H6    single    0.930  0.020  1.080
 TOK  C7   C8    single    1.524  0.020  1.524
 TOK  C7   H7    single    0.970  0.020  1.090
 TOK  C7   H7A   single    0.970  0.020  1.090
 TOK  C8   C14   single    1.515  0.020  1.515
 TOK  C8   C9    single    1.540  0.020  1.540
 TOK  C8   H8    single    0.970  0.020  1.090
 TOK  C9   C11   single    1.540  0.020  1.540
 TOK  C9   H9    single    0.970  0.020  1.090
 TOK  C10  C1    single    1.543  0.020  1.543
 TOK  C10  C9    single    1.550  0.020  1.550
 TOK  C11  C12   single    1.534  0.020  1.534
 TOK  C11  H11   single    0.970  0.020  1.090
 TOK  C11  H11A  single    0.970  0.020  1.090
 TOK  C12  H12   single    0.970  0.020  1.090
 TOK  C12  H12A  single    0.970  0.020  1.090
 TOK  C13  C12   single    1.524  0.020  1.524
 TOK  C13  C17   single    1.517  0.020  1.517
 TOK  C14  C13   single    1.534  0.020  1.534
 TOK  C14  H14   single    0.970  0.020  1.090
 TOK  C15  C14   single    1.530  0.020  1.530
 TOK  C15  C16   single    1.505  0.020  1.505
 TOK  C15  H15   single    0.970  0.020  1.090
 TOK  C16  C17   double    1.332  0.020  1.332
 TOK  C16  H16   single    0.930  0.020  1.080
 TOK  C17  N48   single    1.407  0.020  1.407
 TOK  C18  C13   single    1.538  0.020  1.538
 TOK  C18  H18   single    0.970  0.020  1.090
 TOK  C18  H18A  single    0.970  0.020  1.090
 TOK  C18  H18B  single    0.970  0.020  1.090
 TOK  C19  C10   single    1.538  0.020  1.538
 TOK  C19  H19   single    0.970  0.020  1.090
 TOK  C19  H19A  single    0.970  0.020  1.090
 TOK  C19  H19B  single    0.970  0.020  1.090
 TOK  N48  C52   aromatic  1.364  0.020  1.364
 TOK  N48  C49   aromatic  1.379  0.020  1.379
 TOK  C49  C53   aromatic  1.390  0.020  1.390
 TOK  C49  C50   aromatic  1.403  0.020  1.403
 TOK  C50  C56   aromatic  1.395  0.020  1.395
 TOK  N51  C50   aromatic  1.377  0.020  1.377
 TOK  C52  N51   aromatic  1.299  0.020  1.299
 TOK  C52  H52   single    0.930  0.020  1.080
 TOK  C53  C54   aromatic  1.384  0.020  1.384
 TOK  C53  H53   single    0.930  0.020  1.080
 TOK  C54  C55   aromatic  1.404  0.020  1.404
 TOK  C54  H54   single    0.930  0.020  1.080
 TOK  C55  H55   single    0.930  0.020  1.080
 TOK  C56  C55   aromatic  1.383  0.020  1.383
 TOK  C56  H56   single    0.930  0.020  1.080
 TOK  C15  H15A  single    0.970  0.020  1.090

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
 TOK  H1A   C1   H1    106.12  3.000
 TOK  H1A   C1   C10   109.59  3.000
 TOK  H1    C1   C10   108.43  3.000
 TOK  C10   C1   C2    114.61  3.000
 TOK  H1A   C1   C2    109.17  3.000
 TOK  H1    C1   C2    108.59  3.000
 TOK  H2A   C2   H2    106.71  3.000
 TOK  H2A   C2   C3    110.21  3.000
 TOK  H2    C2   C3    109.39  3.000
 TOK  C3    C2   C1    110.30  3.000
 TOK  H2A   C2   C1    109.44  3.000
 TOK  H2    C2   C1    110.73  3.000
 TOK  H3    C3   C4    108.27  3.000
 TOK  C4    C3   O3    111.89  3.000
 TOK  H3    C3   O3    110.30  3.000
 TOK  C4    C3   C2    109.52  3.000
 TOK  O3    C3   C2    108.58  3.000
 TOK  H3    C3   C2    108.21  3.000
 TOK  HO3   O3   C3    108.22  3.000
 TOK  H4A   C4   H4    106.62  3.000
 TOK  H4A   C4   C5    109.71  3.000
 TOK  H4    C4   C5    110.11  3.000
 TOK  H4A   C4   C3    110.23  3.000
 TOK  H4    C4   C3    107.66  3.000
 TOK  C5    C4   C3    112.33  3.000
 TOK  C10   C5   C6    122.82  3.000
 TOK  C6    C5   C4    120.56  3.000
 TOK  C10   C5   C4    116.61  3.000
 TOK  H6    C6   C7    116.52  3.000
 TOK  H6    C6   C5    118.59  3.000
 TOK  C7    C6   C5    124.89  3.000
 TOK  H7A   C7   H7    105.09  3.000
 TOK  H7A   C7   C8    109.72  3.000
 TOK  H7    C7   C8    110.00  3.000
 TOK  H7A   C7   C6    109.31  3.000
 TOK  H7    C7   C6    109.58  3.000
 TOK  C8    C7   C6    112.85  3.000
 TOK  H8    C8   C14   109.80  3.000
 TOK  H8    C8   C9    109.79  3.000
 TOK  C14   C8   C9    108.25  3.000
 TOK  H8    C8   C7    108.56  3.000
 TOK  C9    C8   C7    109.52  3.000
 TOK  C14   C8   C7    110.91  3.000
 TOK  H9    C9   C11   106.46  3.000
 TOK  H9    C9   C10   106.32  3.000
 TOK  C11   C9   C10   112.68  3.000
 TOK  C10   C9   C8    111.78  3.000
 TOK  H9    C9   C8    105.31  3.000
 TOK  C11   C9   C8    113.59  3.000
 TOK  C19   C10  C9    111.65  3.000
 TOK  C19   C10  C5    108.33  3.000
 TOK  C9    C10  C5    109.96  3.000
 TOK  C19   C10  C1    109.85  3.000
 TOK  C9    C10  C1    108.52  3.000
 TOK  C5    C10  C1    108.48  3.000
 TOK  H11A  C11  H11   105.41  3.000
 TOK  H11A  C11  C12   108.74  3.000
 TOK  H11   C11  C12   108.11  3.000
 TOK  H11A  C11  C9    110.19  3.000
 TOK  H11   C11  C9    109.28  3.000
 TOK  C12   C11  C9    114.68  3.000
 TOK  H12A  C12  H12   106.86  3.000
 TOK  H12A  C12  C13   111.63  3.000
 TOK  H12   C12  C13   109.59  3.000
 TOK  C13   C12  C11   109.93  3.000
 TOK  H12A  C12  C11   109.05  3.000
 TOK  H12   C12  C11   109.73  3.000
 TOK  C18   C13  C17   105.96  3.000
 TOK  C18   C13  C14   114.00  3.000
 TOK  C17   C13  C14    99.10  3.000
 TOK  C18   C13  C12   110.59  3.000
 TOK  C14   C13  C12   107.38  3.000
 TOK  C17   C13  C12   119.58  3.000
 TOK  H14   C14  C15   104.87  3.000
 TOK  C15   C14  C13   104.34  3.000
 TOK  H14   C14  C13   105.47  3.000
 TOK  C15   C14  C8    121.57  3.000
 TOK  H14   C14  C8    105.99  3.000
 TOK  C13   C14  C8    113.29  3.000
 TOK  H15A  C15  H15   106.73  3.000
 TOK  H15A  C15  C16   113.02  3.000
 TOK  H15   C15  C16   110.50  3.000
 TOK  H15A  C15  C14   113.25  3.000
 TOK  H15   C15  C14   112.56  3.000
 TOK  C16   C15  C14   100.86  3.000
 TOK  H16   C16  C17   125.35  3.000
 TOK  H16   C16  C15   123.89  3.000
 TOK  C17   C16  C15   110.69  3.000
 TOK  N48   C17  C16   125.15  3.000
 TOK  N48   C17  C13   122.46  3.000
 TOK  C16   C17  C13   111.43  3.000
 TOK  H18B  C18  H18A  107.38  3.000
 TOK  H18B  C18  H18   107.03  3.000
 TOK  H18A  C18  H18   107.47  3.000
 TOK  H18B  C18  C13   109.93  3.000
 TOK  H18A  C18  C13   111.57  3.000
 TOK  H18   C18  C13   113.18  3.000
 TOK  H19B  C19  H19A  106.80  3.000
 TOK  H19B  C19  H19   106.92  3.000
 TOK  H19A  C19  H19   107.84  3.000
 TOK  H19B  C19  C10   111.80  3.000
 TOK  H19A  C19  C10   111.82  3.000
 TOK  H19   C19  C10   111.40  3.000
 TOK  C52   N48  C49   106.14  3.000
 TOK  C49   N48  C17   127.22  3.000
 TOK  C52   N48  C17   126.63  3.000
 TOK  C53   C49  C50   122.57  3.000
 TOK  C50   C49  N48   104.99  3.000
 TOK  C53   C49  N48   132.42  3.000
 TOK  C56   C50  N51   130.01  3.000
 TOK  N51   C50  C49   110.05  3.000
 TOK  C56   C50  C49   119.94  3.000
 TOK  C52   N51  C50   104.93  3.000
 TOK  H52   C52  N51   125.08  3.000
 TOK  H52   C52  N48   121.02  3.000
 TOK  N51   C52  N48   113.89  3.000
 TOK  H53   C53  C54   121.32  3.000
 TOK  H53   C53  C49   122.05  3.000
 TOK  C54   C53  C49   116.63  3.000
 TOK  H54   C54  C55   119.16  3.000
 TOK  H54   C54  C53   119.26  3.000
 TOK  C55   C54  C53   121.59  3.000
 TOK  H55   C55  C56   119.55  3.000
 TOK  C56   C55  C54   121.36  3.000
 TOK  H55   C55  C54   119.09  3.000
 TOK  H56   C56  C55   121.30  3.000
 TOK  H56   C56  C50   120.79  3.000
 TOK  C55   C56  C50   117.91  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
 TOK  CONST_01  C50  N51  C52  N48     0.00   0.0  0
 TOK  CONST_02  C54  C53  C49  N48   180.00   0.0  0
 TOK  CONST_03  C56  C50  C49  N48   180.00   0.0  0
 TOK  CONST_04  N51  C50  C49  N48     0.00   0.0  0
 TOK  CONST_05  N51  C52  N48  C49     0.00   0.0  0
 TOK  CONST_06  C55  C54  C53  C49     0.00   0.0  0
 TOK  CONST_07  C55  C56  C50  C49     0.00   0.0  0
 TOK  CONST_08  C52  N51  C50  C49     0.00   0.0  0
 TOK  CONST_09  C52  N48  C49  C50     0.00   0.0  0
 TOK  CONST_10  C54  C53  C49  C50     0.00   0.0  0
 TOK  CONST_11  C54  C55  C56  C50     0.00   0.0  0
 TOK  CONST_12  C53  C49  C50  N51   180.00   0.0  0
 TOK  CONST_13  C55  C56  C50  N51   180.00   0.0  0
 TOK  CONST_14  C53  C49  N48  C52   180.00   0.0  0
 TOK  CONST_15  C56  C50  N51  C52   180.00   0.0  0
 TOK  CONST_16  C56  C50  C49  C53     0.00   0.0  0
 TOK  CONST_17  C56  C55  C54  C53     0.00   0.0  0
 TOK  CONST_18  N51  C52  N48  C17   180.00   0.0  0
 TOK  CONST_19  C53  C49  N48  C17     0.00   0.0  0
 TOK  CONST_20  C50  C49  N48  C17   180.00   0.0  0
 TOK  CONST_21  H52  C52  N48  C17     0.00   0.0  0
 TOK  CONST_22  H53  C53  C49  N48     0.00   0.0  0
 TOK  CONST_23  H54  C54  C53  C49   180.00   0.0  0
 TOK  CONST_24  H56  C56  C50  C49   180.00   0.0  0
 TOK  CONST_25  H55  C55  C56  C50   180.00   0.0  0
 TOK  Var_01    C10  C1   C2   C3    -57.68  30.0  1
 TOK  Var_02    C10  C5   C4   C3     51.31  30.0  1
 TOK  Var_03    C7   C6   C5   C4   -177.29  30.0  1
 TOK  Var_04    C8   C7   C6   C5     12.24  30.0  1
 TOK  Var_05    C13  C12  C11  C9    -51.59  30.0  1
 TOK  Var_06    C15  C16  C17  C13     4.00  30.0  1
 TOK  Var_07    C52  N48  C17  C13   -62.10  30.0  2
 TOK  Var_08    C17  C16  C15  C14    18.92  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
 TOK  chir_01  C3   C2   O3   C4   positiv
 TOK  chir_02  C8   C7   C14  C9   negativ
 TOK  chir_03  C9   C10  C11  C8   negativ
 TOK  chir_04  C10  C9   C1   C5   negativ
 TOK  chir_05  C13  C14  C17  C12  negativ
 TOK  chir_06  C14  C15  C13  C8   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
 TOK  plan-1  C17  0.020
 TOK  plan-1  N48  0.020
 TOK  plan-1  C49  0.020
 TOK  plan-1  C50  0.020
 TOK  plan-1  N51  0.020
 TOK  plan-1  C52  0.020
 TOK  plan-1  C53  0.020
 TOK  plan-1  C54  0.020
 TOK  plan-1  C55  0.020
 TOK  plan-1  C56  0.020
 TOK  plan-1  H52  0.020
 TOK  plan-1  H53  0.020
 TOK  plan-1  H54  0.020
 TOK  plan-1  H55  0.020
 TOK  plan-1  H56  0.020

