# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 27 01:56:55 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(1R)-1-methylpropyl]hexadecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3[C@H](O)C[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[C@]12C
#
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
 BNC  BNC  '(3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(1R)-1-methylpropyl]hexadecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol (non-preferred name)'  ligand  66  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BNC
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
 BNC  C1    C  CH2   0  -0.429  -1.3291   5.7020   3.6708
 BNC  C2    C  CH2   0  -0.478  -2.0463   4.9467   4.7800
 BNC  C3    C  CH1   0   0.087  -1.0249   4.2605   5.6755
 BNC  O3    O  OH1   0  -0.679  -1.6259   3.5033   6.7079
 BNC  C4    C  CH2   0  -0.451  -0.1599   3.3244   4.8515
 BNC  C5    C  CH1   0  -0.225   0.5481   4.0513   3.6987
 BNC  C6    C  CH2   0  -0.448   1.4615   3.1302   2.8853
 BNC  C7    C  CH1   0   0.052   0.7372   2.1584   1.9548
 BNC  O7    O  OH1   0  -0.675   0.2345   1.0239   2.6439
 BNC  C8    C  CH1   0  -0.298  -0.3228   2.8806   1.1126
 BNC  C9    C  CH1   0  -0.207  -1.2430   3.7892   1.9548
 BNC  C10   C  CT    0  -0.056  -0.4322   4.8207   2.7832
 BNC  C11   C  CH2   0  -0.461  -2.3201   4.4308   1.0721
 BNC  C12   C  CH1   0   0.075  -3.1281   3.4450   0.2302
 BNC  O12   O  OH1   0  -0.675  -3.9261   2.6923   1.1236
 BNC  C13   C  CT    0  -0.088  -2.1919   2.5737  -0.6312
 BNC  C14   C  CH1   0  -0.159  -1.1672   1.9055   0.3037
 BNC  C15   C  CH2   0  -0.447  -0.4403   0.9199  -0.6003
 BNC  C16   C  CH2   0  -0.446  -1.5372   0.4302  -1.5640
 BNC  C17   C  CH1   0  -0.199  -2.7897   1.3159  -1.3218
 BNC  C18   C  CH3   0  -0.700  -1.5263   3.4631  -1.6876
 BNC  C19   C  CH3   0  -0.676   0.3486   5.7819   1.8785
 BNC  C20   C  CH1   0  -0.220  -3.6317   1.4859  -2.5943
 BNC  C21   C  CH3   0  -0.680  -4.8403   2.3987  -2.3983
 BNC  C22   C  CH2   0  -0.420  -4.0893   0.1141  -3.1139
 BNC  C23   C  CH3   0  -0.669  -4.6320   0.1330  -4.5379
 BNC  H1C1  H  HCH2  0   0.233  -2.0448   6.2559   3.0599
 BNC  H1C2  H  HCH2  0   0.220  -0.6886   6.4637   4.1314
 BNC  H2C1  H  HCH2  0   0.233  -2.6566   5.6415   5.3660
 BNC  H2C2  H  HCH2  0   0.219  -2.7308   4.2015   4.3617
 BNC  H3    H  HCH1  0   0.182  -0.3765   5.0416   6.1051
 BNC  HA    H  HOH1  0   0.445  -2.1828   4.0932   7.2257
 BNC  H4C1  H  HCH2  0   0.197  -0.8047   2.5155   4.4980
 BNC  H4C2  H  HCH2  0   0.237   0.5964   2.8548   5.4879
 BNC  H5    H  HCH1  0   0.220   1.1945   4.8035   4.1714
 BNC  H6C1  H  HCH2  0   0.231   2.1254   3.7465   2.2723
 BNC  H6C2  H  HCH2  0   0.231   2.1174   2.5668   3.5562
 BNC  H7    H  HCH1  0   0.228   1.4809   1.7452   1.2657
 BNC  HB    H  HOH1  0   0.443  -0.5880   1.2552   3.0825
 BNC  H8    H  HCH1  0   0.222   0.2391   3.5073   0.4095
 BNC  H9    H  HCH1  0   0.211  -1.7742   3.1420   2.6653
 BNC  H11   H  HCH2  0   0.240  -3.0258   4.9942   1.6876
 BNC  H111  H  HCH2  0   0.231  -1.8642   5.1625   0.4016
 BNC  H112  H  HCH1  0   0.204  -3.7736   4.0395  -0.4298
 BNC  H14   H  HCH1  0   0.211  -1.7572   1.3166   1.0172
 BNC  H151  H  HCH2  0   0.231   0.0163   0.1032  -0.0404
 BNC  H152  H  HCH2  0   0.215   0.3657   1.4189  -1.1464
 BNC  H161  H  HCH2  0   0.220  -1.2094   0.5142  -2.6033
 BNC  H162  H  HCH2  0   0.232  -1.7679  -0.6231  -1.4006
 BNC  H17   H  HCH1  0   0.204  -3.4172   0.7931  -0.5873
 BNC  H181  H  HCH3  0   0.233  -2.2718   4.0074  -2.2707
 BNC  H182  H  HCH3  0   0.237  -0.8650   4.2094  -1.2490
 BNC  H183  H  HCH3  0   0.240  -0.9271   2.8868  -2.3932
 BNC  H191  H  HCH3  0   0.228   0.9657   6.4474   2.4864
 BNC  H192  H  HCH3  0   0.232   1.0144   5.2842   1.1745
 BNC  H193  H  HCH3  0   0.231  -0.3263   6.4116   1.2970
 BNC  H20   H  HCH1  0   0.206  -2.9890   1.9333  -3.3638
 BNC  H211  H  HCH3  0   0.207  -5.4618   2.0568  -1.5657
 BNC  H212  H  HCH3  0   0.238  -5.4758   2.4092  -3.2841
 BNC  H213  H  HCH3  0   0.232  -4.5549   3.4318  -2.2057
 BNC  H221  H  HCH2  0   0.207  -4.8489  -0.2871  -2.4332
 BNC  H222  H  HCH2  0   0.234  -3.2558  -0.5895  -3.0787
 BNC  H231  H  HCH3  0   0.228  -4.9132  -0.8695  -4.8624
 BNC  H232  H  HCH3  0   0.216  -3.8783   0.5057  -5.2349
 BNC  H233  H  HCH3  0   0.219  -5.5138   0.7666  -4.6396
 BNC  HO1   H  HOH1  0   0.444  -4.5019   2.1175   0.6117

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
 BNC  C1   C2    single  1.522  0.020  1.522
 BNC  C1   C10   single  1.539  0.020  1.539
 BNC  C1   H1C1  single  0.970  0.020  1.090
 BNC  C1   H1C2  single  0.970  0.020  1.090
 BNC  C2   C3    single  1.522  0.020  1.522
 BNC  C2   H2C1  single  0.970  0.020  1.090
 BNC  C2   H2C2  single  0.970  0.020  1.090
 BNC  C3   O3    single  1.414  0.020  1.414
 BNC  C3   C4    single  1.518  0.020  1.518
 BNC  C3   H3    single  0.970  0.020  1.090
 BNC  O3   HA    single  0.850  0.020  0.980
 BNC  C4   C5    single  1.536  0.020  1.536
 BNC  C4   H4C1  single  0.970  0.020  1.090
 BNC  C4   H4C2  single  0.970  0.020  1.090
 BNC  C5   C6    single  1.531  0.020  1.531
 BNC  C5   C10   single  1.546  0.020  1.546
 BNC  C5   H5    single  0.970  0.020  1.090
 BNC  C6   C7    single  1.528  0.020  1.528
 BNC  C6   H6C1  single  0.970  0.020  1.090
 BNC  C6   H6C2  single  0.970  0.020  1.090
 BNC  C7   O7    single  1.419  0.020  1.419
 BNC  C7   C8    single  1.534  0.020  1.534
 BNC  C7   H7    single  0.970  0.020  1.090
 BNC  O7   HB    single  0.850  0.020  0.980
 BNC  C8   C9    single  1.543  0.020  1.543
 BNC  C8   C14   single  1.523  0.020  1.523
 BNC  C8   H8    single  0.970  0.020  1.090
 BNC  C9   C10   single  1.552  0.020  1.552
 BNC  C9   C11   single  1.533  0.020  1.533
 BNC  C9   H9    single  0.970  0.020  1.090
 BNC  C10  C19   single  1.534  0.020  1.534
 BNC  C11  C12   single  1.528  0.020  1.528
 BNC  C11  H11   single  0.970  0.020  1.090
 BNC  C11  H111  single  0.970  0.020  1.090
 BNC  C12  O12   single  1.415  0.020  1.415
 BNC  C12  C13   single  1.542  0.020  1.542
 BNC  C12  H112  single  0.970  0.020  1.090
 BNC  C13  C14   single  1.540  0.020  1.540
 BNC  C13  C17   single  1.554  0.020  1.554
 BNC  C13  C18   single  1.533  0.020  1.533
 BNC  C14  C15   single  1.522  0.020  1.522
 BNC  C14  H14   single  0.970  0.020  1.090
 BNC  C15  C16   single  1.540  0.020  1.540
 BNC  C15  H151  single  0.970  0.020  1.090
 BNC  C15  H152  single  0.970  0.020  1.090
 BNC  C16  C17   single  1.553  0.020  1.553
 BNC  C16  H161  single  0.970  0.020  1.090
 BNC  C16  H162  single  0.970  0.020  1.090
 BNC  C17  C20   single  1.535  0.020  1.535
 BNC  C17  H17   single  0.970  0.020  1.090
 BNC  C18  H181  single  0.970  0.020  1.090
 BNC  C18  H182  single  0.970  0.020  1.090
 BNC  C18  H183  single  0.970  0.020  1.090
 BNC  C19  H191  single  0.970  0.020  1.090
 BNC  C19  H192  single  0.970  0.020  1.090
 BNC  C19  H193  single  0.970  0.020  1.090
 BNC  C20  C21   single  1.527  0.020  1.527
 BNC  C20  C22   single  1.537  0.020  1.537
 BNC  C20  H20   single  0.970  0.020  1.090
 BNC  C21  H211  single  0.970  0.020  1.090
 BNC  C21  H212  single  0.970  0.020  1.090
 BNC  C21  H213  single  0.970  0.020  1.090
 BNC  C22  C23   single  1.524  0.020  1.524
 BNC  C22  H221  single  0.970  0.020  1.090
 BNC  C22  H222  single  0.970  0.020  1.090
 BNC  C23  H231  single  0.970  0.020  1.090
 BNC  C23  H232  single  0.970  0.020  1.090
 BNC  C23  H233  single  0.970  0.020  1.090
 BNC  HO1  O12   single  0.850  0.020  0.980

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
 BNC  H1C2  C1   H1C1  105.40  3.000
 BNC  H1C2  C1   C10   107.43  3.000
 BNC  H1C1  C1   C10   110.47  3.000
 BNC  H1C2  C1   C2    108.30  3.000
 BNC  H1C1  C1   C2    110.53  3.000
 BNC  C10   C1   C2    114.26  3.000
 BNC  H2C2  C2   H2C1  106.74  3.000
 BNC  H2C2  C2   C3    109.72  3.000
 BNC  H2C1  C2   C3    110.21  3.000
 BNC  H2C2  C2   C1    110.73  3.000
 BNC  H2C1  C2   C1    109.75  3.000
 BNC  C3    C2   C1    109.66  3.000
 BNC  H3    C3   C4    108.26  3.000
 BNC  H3    C3   O3    110.17  3.000
 BNC  C4    C3   O3    107.95  3.000
 BNC  H3    C3   C2    107.74  3.000
 BNC  C4    C3   C2    109.95  3.000
 BNC  O3    C3   C2    112.69  3.000
 BNC  HA    O3   C3    108.08  3.000
 BNC  H4C2  C4   H4C1  106.16  3.000
 BNC  H4C2  C4   C5    108.72  3.000
 BNC  H4C1  C4   C5    112.30  3.000
 BNC  H4C2  C4   C3    110.05  3.000
 BNC  H4C1  C4   C3    107.20  3.000
 BNC  C5    C4   C3    112.23  3.000
 BNC  H5    C5   C10   106.68  3.000
 BNC  H5    C5   C6    106.83  3.000
 BNC  C10   C5   C6    111.28  3.000
 BNC  H5    C5   C4    105.81  3.000
 BNC  C10   C5   C4    112.81  3.000
 BNC  C6    C5   C4    112.89  3.000
 BNC  H6C2  C6   H6C1  105.66  3.000
 BNC  H6C2  C6   C7    109.27  3.000
 BNC  H6C1  C6   C7    107.74  3.000
 BNC  H6C2  C6   C5    109.97  3.000
 BNC  H6C1  C6   C5    108.72  3.000
 BNC  C7    C6   C5    115.05  3.000
 BNC  H7    C7   C8    107.54  3.000
 BNC  H7    C7   O7    104.15  3.000
 BNC  C8    C7   O7    113.45  3.000
 BNC  H7    C7   C6    107.54  3.000
 BNC  C8    C7   C6    111.24  3.000
 BNC  O7    C7   C6    112.37  3.000
 BNC  HB    O7   C7    109.42  3.000
 BNC  H8    C8   C14   108.03  3.000
 BNC  H8    C8   C9    108.60  3.000
 BNC  C14   C8   C9    109.65  3.000
 BNC  H8    C8   C7    105.48  3.000
 BNC  C14   C8   C7    111.92  3.000
 BNC  C9    C8   C7    112.92  3.000
 BNC  H9    C9   C11   106.22  3.000
 BNC  H9    C9   C10   107.41  3.000
 BNC  C11   C9   C10   113.34  3.000
 BNC  H9    C9   C8    107.13  3.000
 BNC  C11   C9   C8    110.55  3.000
 BNC  C10   C9   C8    111.79  3.000
 BNC  C19   C10  C9    111.58  3.000
 BNC  C19   C10  C5    109.77  3.000
 BNC  C9    C10  C5    108.46  3.000
 BNC  C19   C10  C1    106.14  3.000
 BNC  C9    C10  C1    112.59  3.000
 BNC  C5    C10  C1    108.23  3.000
 BNC  H111  C11  H11   105.66  3.000
 BNC  H111  C11  C12   108.35  3.000
 BNC  H11   C11  C12   107.55  3.000
 BNC  H111  C11  C9    109.91  3.000
 BNC  H11   C11  C9    110.19  3.000
 BNC  C12   C11  C9    114.76  3.000
 BNC  H112  C12  C13   109.09  3.000
 BNC  H112  C12  O12   109.64  3.000
 BNC  C13   C12  O12   113.24  3.000
 BNC  H112  C12  C11   107.02  3.000
 BNC  C13   C12  C11   110.57  3.000
 BNC  O12   C12  C11   107.08  3.000
 BNC  HO1   O12  C12   108.64  3.000
 BNC  C18   C13  C17   109.28  3.000
 BNC  C18   C13  C14   112.41  3.000
 BNC  C17   C13  C14   100.05  3.000
 BNC  C18   C13  C12   108.71  3.000
 BNC  C17   C13  C12   118.16  3.000
 BNC  C14   C13  C12   108.07  3.000
 BNC  H14   C14  C15   107.18  3.000
 BNC  H14   C14  C13   105.66  3.000
 BNC  C15   C14  C13   103.78  3.000
 BNC  H14   C14  C8    107.25  3.000
 BNC  C15   C14  C8    117.73  3.000
 BNC  C13   C14  C8    114.44  3.000
 BNC  H152  C15  H151  106.83  3.000
 BNC  H152  C15  C16   110.94  3.000
 BNC  H151  C15  C16   112.42  3.000
 BNC  H152  C15  C14   110.67  3.000
 BNC  H151  C15  C14   112.34  3.000
 BNC  C16   C15  C14   103.73  3.000
 BNC  H162  C16  H161  106.26  3.000
 BNC  H162  C16  C17   110.91  3.000
 BNC  H161  C16  C17   110.26  3.000
 BNC  H162  C16  C15   111.35  3.000
 BNC  H161  C16  C15   110.92  3.000
 BNC  C17   C16  C15   107.19  3.000
 BNC  H17   C17  C20   107.07  3.000
 BNC  H17   C17  C16   107.07  3.000
 BNC  C20   C17  C16   112.10  3.000
 BNC  H17   C17  C13   107.92  3.000
 BNC  C20   C17  C13   119.31  3.000
 BNC  C16   C17  C13   102.74  3.000
 BNC  H183  C18  H182  106.80  3.000
 BNC  H183  C18  H181  107.04  3.000
 BNC  H182  C18  H181  106.74  3.000
 BNC  H183  C18  C13   112.20  3.000
 BNC  H182  C18  C13   112.56  3.000
 BNC  H181  C18  C13   111.15  3.000
 BNC  H193  C19  H192  107.30  3.000
 BNC  H193  C19  H191  107.13  3.000
 BNC  H192  C19  H191  107.02  3.000
 BNC  H193  C19  C10   111.17  3.000
 BNC  H192  C19  C10   113.95  3.000
 BNC  H191  C19  C10   109.95  3.000
 BNC  H20   C20  C22   107.53  3.000
 BNC  H20   C20  C21   108.04  3.000
 BNC  C22   C20  C21   109.96  3.000
 BNC  H20   C20  C17   107.76  3.000
 BNC  C22   C20  C17   110.17  3.000
 BNC  C21   C20  C17   113.19  3.000
 BNC  H213  C21  H212  106.70  3.000
 BNC  H213  C21  H211  108.11  3.000
 BNC  H212  C21  H211  106.87  3.000
 BNC  H213  C21  C20   112.48  3.000
 BNC  H212  C21  C20   111.27  3.000
 BNC  H211  C21  C20   111.13  3.000
 BNC  H222  C22  H221  105.86  3.000
 BNC  H222  C22  C23   108.06  3.000
 BNC  H221  C22  C23   109.76  3.000
 BNC  H222  C22  C20   109.71  3.000
 BNC  H221  C22  C20   108.86  3.000
 BNC  C23   C22  C20   114.26  3.000
 BNC  H233  C23  H232  107.47  3.000
 BNC  H233  C23  H231  107.33  3.000
 BNC  H232  C23  H231  107.57  3.000
 BNC  H233  C23  C22   112.47  3.000
 BNC  H232  C23  C22   110.78  3.000
 BNC  H231  C23  C22   111.00  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
 BNC  Var_01  C10   C1   C2   C3    58.53  30.0  1
 BNC  Var_02  C17   C16  C15  C14    8.77  30.0  1
 BNC  Var_03  H231  C23  C22  C20  178.34  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
 BNC  chir_01  C3   C2   O3   C4   negativ
 BNC  chir_02  C5   C4   C6   C10  negativ
 BNC  chir_03  C7   O7   C6   C8   positiv
 BNC  chir_04  C8   C7   C9   C14  positiv
 BNC  chir_05  C9   C11  C10  C8   positiv
 BNC  chir_06  C10  C5   C9   C1   negativ
 BNC  chir_07  C12  O12  C11  C13  negativ
 BNC  chir_08  C13  C17  C14  C12  positiv
 BNC  chir_09  C14  C15  C13  C8   positiv
 BNC  chir_10  C17  C20  C16  C13  negativ
 BNC  chir_11  C20  C17  C21  C22  positiv

