# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 07:53:53 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (5beta,8alpha,17beta)-17-hydroxyandrostan-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CC[C@H]3[C@@H](CC[C@@H]4CC(=O)CC[C@]34C)[C@@H]1CC[C@@H]2O
#
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
 BDT  BDT  (5beta,8alpha,17beta)-17-hydroxyandrostan-3-one  ligand  51  21  .  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_BDT
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
 BDT  C1    C  CH2   0  -0.439   2.6922  -1.4678   0.7180
 BDT  C2    C  CH2   0  -0.562   3.1685  -1.6107  -0.7267
 BDT  C3    C  C     0   0.421   3.8455  -0.3481  -1.1821
 BDT  O3    O  O     0  -0.412   4.9283  -0.3444  -1.7285
 BDT  C4    C  CH2   0  -0.562   3.0692   0.9117  -0.9153
 BDT  C5    C  CH1   0  -0.219   2.5243   1.0097   0.5211
 BDT  C6    C  CH2   0  -0.431   1.6646   2.2635   0.6762
 BDT  C7    C  CH2   0  -0.429   0.3268   2.1404  -0.0430
 BDT  C8    C  CH1   0  -0.219  -0.4375   0.8865   0.3763
 BDT  C9    C  CH1   0  -0.196   0.4343  -0.3728   0.1861
 BDT  C10   C  CT    0  -0.068   1.7695  -0.2654   0.9667
 BDT  C11   C  CH2   0  -0.443  -0.3347  -1.6697   0.4701
 BDT  C12   C  CH2   0  -0.403  -1.6717  -1.7580  -0.2711
 BDT  C13   C  CT    0  -0.101  -2.5292  -0.5255  -0.0171
 BDT  C14   C  CH1   0  -0.186  -1.7219   0.7171  -0.4152
 BDT  C15   C  CH2   0  -0.448  -2.7568   1.8443  -0.4077
 BDT  C16   C  CH2   0  -0.488  -4.0611   1.1520  -0.8659
 BDT  C17   C  CH1   0   0.102  -3.7264  -0.3542  -0.9553
 BDT  O17   O  OH1   0  -0.676  -4.7869  -1.2169  -0.6230
 BDT  C18   C  CH3   0  -0.669  -2.9957  -0.4891   1.4423
 BDT  C19   C  CH3   0  -0.668   1.5313  -0.2126   2.4822
 BDT  H1    H  HCH2  0   0.247   2.2110  -2.3951   1.0343
 BDT  H1A   H  HCH2  0   0.236   3.5713  -1.3601   1.3636
 BDT  H2    H  HCH2  0   0.261   3.8493  -2.4568  -0.8321
 BDT  H2A   H  HCH2  0   0.259   2.3164  -1.7993  -1.3897
 BDT  H4    H  HCH2  0   0.260   3.6956   1.7785  -1.1362
 BDT  H4A   H  HCH2  0   0.260   2.2449   0.9265  -1.6366
 BDT  H5    H  HCH1  0   0.231   3.3946   1.1105   1.1817
 BDT  H6    H  HCH2  0   0.230   1.4896   2.4527   1.7390
 BDT  H6A   H  HCH2  0   0.229   2.2129   3.1333   0.3033
 BDT  H7    H  HCH2  0   0.236  -0.2777   3.0292   0.1562
 BDT  H7A   H  HCH2  0   0.208   0.4804   2.1211  -1.1284
 BDT  H8    H  HCH1  0   0.209  -0.6952   0.9954   1.4367
 BDT  H9    H  HCH1  0   0.208   0.6752  -0.3972  -0.8870
 BDT  H11   H  HCH2  0   0.231   0.2752  -2.5262   0.1708
 BDT  H11A  H  HCH2  0   0.220  -0.5014  -1.7826   1.5447
 BDT  H12   H  HCH2  0   0.210  -1.4844  -1.8457  -1.3480
 BDT  H12A  H  HCH2  0   0.222  -2.1934  -2.6715   0.0283
 BDT  H14   H  HCH1  0   0.208  -1.4220   0.5658  -1.4645
 BDT  H15   H  HCH2  0   0.220  -2.8683   2.2597   0.5973
 BDT  H15A  H  HCH2  0   0.232  -2.4712   2.6717  -1.0585
 BDT  H16   H  HCH2  0   0.227  -4.8668   1.3103  -0.1460
 BDT  H16A  H  HCH2  0   0.233  -4.4142   1.5350  -1.8247
 BDT  H17   H  HCH1  0   0.194  -3.3727  -0.5712  -1.9755
 BDT  HO17  H  HOH1  0   0.447  -5.5078  -1.0579  -1.2395
 BDT  H18   H  HCH3  0   0.227  -2.1634  -0.3827   2.1367
 BDT  H18A  H  HCH3  0   0.231  -3.6877   0.3295   1.6438
 BDT  H18B  H  HCH3  0   0.229  -3.5102  -1.4151   1.7032
 BDT  H19   H  HCH3  0   0.228   2.4675   0.0024   3.0016
 BDT  H19A  H  HCH3  0   0.234   0.8112   0.5475   2.7802
 BDT  H19B  H  HCH3  0   0.231   1.1668  -1.1686   2.8608

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
 BDT  C1   C2    single  1.528  0.020  1.528
 BDT  C1   C10   single  1.536  0.020  1.536
 BDT  C2   C3    single  1.503  0.020  1.503
 BDT  C3   O3    double  1.213  0.020  1.213
 BDT  C3   C4    single  1.504  0.020  1.504
 BDT  C4   C5    single  1.539  0.020  1.539
 BDT  C5   C6    single  1.528  0.020  1.528
 BDT  C5   C10   single  1.547  0.020  1.547
 BDT  C6   C7    single  1.524  0.020  1.524
 BDT  C7   C8    single  1.527  0.020  1.527
 BDT  C8   C9    single  1.543  0.020  1.543
 BDT  C8   C14   single  1.518  0.020  1.518
 BDT  C9   C10   single  1.550  0.020  1.550
 BDT  C9   C11   single  1.534  0.020  1.534
 BDT  C10  C19   single  1.535  0.020  1.535
 BDT  C11  C12   single  1.531  0.020  1.531
 BDT  C12  C13   single  1.523  0.020  1.523
 BDT  C13  C14   single  1.534  0.020  1.534
 BDT  C13  C17   single  1.531  0.020  1.531
 BDT  C13  C18   single  1.533  0.020  1.533
 BDT  C14  C15   single  1.530  0.020  1.530
 BDT  C15  C16   single  1.546  0.020  1.546
 BDT  C16  C17   single  1.546  0.020  1.546
 BDT  C17  O17   single  1.407  0.020  1.407
 BDT  C1   H1    single  0.970  0.020  1.090
 BDT  C1   H1A   single  0.970  0.020  1.090
 BDT  C2   H2    single  0.970  0.020  1.090
 BDT  C2   H2A   single  0.970  0.020  1.090
 BDT  C4   H4    single  0.970  0.020  1.090
 BDT  C4   H4A   single  0.970  0.020  1.090
 BDT  C5   H5    single  0.970  0.020  1.090
 BDT  C6   H6    single  0.970  0.020  1.090
 BDT  C6   H6A   single  0.970  0.020  1.090
 BDT  C7   H7    single  0.970  0.020  1.090
 BDT  C7   H7A   single  0.970  0.020  1.090
 BDT  C8   H8    single  0.970  0.020  1.090
 BDT  C9   H9    single  0.970  0.020  1.090
 BDT  C11  H11   single  0.970  0.020  1.090
 BDT  C11  H11A  single  0.970  0.020  1.090
 BDT  C12  H12   single  0.970  0.020  1.090
 BDT  C12  H12A  single  0.970  0.020  1.090
 BDT  C14  H14   single  0.970  0.020  1.090
 BDT  C15  H15   single  0.970  0.020  1.090
 BDT  C15  H15A  single  0.970  0.020  1.090
 BDT  C16  H16   single  0.970  0.020  1.090
 BDT  C16  H16A  single  0.970  0.020  1.090
 BDT  C17  H17   single  0.970  0.020  1.090
 BDT  O17  HO17  single  0.850  0.020  0.980
 BDT  C18  H18   single  0.970  0.020  1.090
 BDT  C18  H18A  single  0.970  0.020  1.090
 BDT  C18  H18B  single  0.970  0.020  1.090
 BDT  C19  H19   single  0.970  0.020  1.090
 BDT  C19  H19A  single  0.970  0.020  1.090
 BDT  C19  H19B  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
 BDT  H1A   C1   H1    105.44  3.000
 BDT  H1A   C1   C10   108.03  3.000
 BDT  H1    C1   C10   110.69  3.000
 BDT  H1A   C1   C2    108.43  3.000
 BDT  H1    C1   C2    109.39  3.000
 BDT  C10   C1   C2    114.44  3.000
 BDT  H2A   C2   H2    107.05  3.000
 BDT  H2A   C2   C3    108.15  3.000
 BDT  H2    C2   C3    109.94  3.000
 BDT  H2A   C2   C1    110.23  3.000
 BDT  H2    C2   C1    111.00  3.000
 BDT  C3    C2   C1    110.38  3.000
 BDT  C4    C3   O3    122.56  3.000
 BDT  C4    C3   C2    114.67  3.000
 BDT  O3    C3   C2    122.76  3.000
 BDT  H4A   C4   H4    106.72  3.000
 BDT  H4A   C4   C5    110.32  3.000
 BDT  H4    C4   C5    109.95  3.000
 BDT  H4A   C4   C3    106.43  3.000
 BDT  H4    C4   C3    109.45  3.000
 BDT  C5    C4   C3    113.68  3.000
 BDT  H5    C5   C10   106.81  3.000
 BDT  H5    C5   C6    108.05  3.000
 BDT  C10   C5   C6    111.86  3.000
 BDT  H5    C5   C4    106.67  3.000
 BDT  C10   C5   C4    112.89  3.000
 BDT  C6    C5   C4    110.25  3.000
 BDT  H6A   C6   H6    105.90  3.000
 BDT  H6A   C6   C7    110.08  3.000
 BDT  H6    C6   C7    109.40  3.000
 BDT  H6A   C6   C5    109.62  3.000
 BDT  H6    C6   C5    109.31  3.000
 BDT  C7    C6   C5    112.32  3.000
 BDT  H7A   C7   H7    105.79  3.000
 BDT  H7A   C7   C8    109.12  3.000
 BDT  H7    C7   C8    109.92  3.000
 BDT  H7A   C7   C6    110.22  3.000
 BDT  H7    C7   C6    109.50  3.000
 BDT  C8    C7   C6    112.09  3.000
 BDT  H8    C8   C14   108.44  3.000
 BDT  H8    C8   C9    109.45  3.000
 BDT  C14   C8   C9    108.82  3.000
 BDT  H8    C8   C7    107.55  3.000
 BDT  C14   C8   C7    111.83  3.000
 BDT  C9    C8   C7    110.70  3.000
 BDT  H9    C9   C11   105.75  3.000
 BDT  H9    C9   C10   107.71  3.000
 BDT  C11   C9   C10   113.39  3.000
 BDT  H9    C9   C8    105.19  3.000
 BDT  C11   C9   C8    112.57  3.000
 BDT  C10   C9   C8    111.59  3.000
 BDT  C19   C10  C9    111.46  3.000
 BDT  C19   C10  C5    109.37  3.000
 BDT  C9    C10  C5    109.40  3.000
 BDT  C19   C10  C1    106.26  3.000
 BDT  C9    C10  C1    112.43  3.000
 BDT  C5    C10  C1    107.78  3.000
 BDT  H11A  C11  H11   105.86  3.000
 BDT  H11A  C11  C12   109.67  3.000
 BDT  H11   C11  C12   108.03  3.000
 BDT  H11A  C11  C9    110.22  3.000
 BDT  H11   C11  C9    109.39  3.000
 BDT  C12   C11  C9    113.38  3.000
 BDT  H12A  C12  H12   106.47  3.000
 BDT  H12A  C12  C13   111.20  3.000
 BDT  H12   C12  C13   108.95  3.000
 BDT  H12A  C12  C11   109.39  3.000
 BDT  H12   C12  C11   109.32  3.000
 BDT  C13   C12  C11   111.37  3.000
 BDT  C18   C13  C17   110.06  3.000
 BDT  C18   C13  C14   112.83  3.000
 BDT  C17   C13  C14    99.31  3.000
 BDT  C18   C13  C12   110.46  3.000
 BDT  C17   C13  C12   115.39  3.000
 BDT  C14   C13  C12   108.41  3.000
 BDT  H14   C14  C15   106.85  3.000
 BDT  H14   C14  C13   106.21  3.000
 BDT  C15   C14  C13   103.85  3.000
 BDT  H14   C14  C8    106.36  3.000
 BDT  C15   C14  C8    119.17  3.000
 BDT  C13   C14  C8    113.59  3.000
 BDT  H15A  C15  H15   106.68  3.000
 BDT  H15A  C15  C16   112.57  3.000
 BDT  H15   C15  C16   110.89  3.000
 BDT  H15A  C15  C14   112.26  3.000
 BDT  H15   C15  C14   110.69  3.000
 BDT  C16   C15  C14   103.84  3.000
 BDT  H16A  C16  H16   106.84  3.000
 BDT  H16A  C16  C17   111.18  3.000
 BDT  H16   C16  C17   109.83  3.000
 BDT  H16A  C16  C15   112.10  3.000
 BDT  H16   C16  C15   111.23  3.000
 BDT  C17   C16  C15   105.71  3.000
 BDT  H17   C17  O17   109.88  3.000
 BDT  H17   C17  C16   108.38  3.000
 BDT  O17   C17  C16   114.88  3.000
 BDT  H17   C17  C13   107.13  3.000
 BDT  O17   C17  C13   112.09  3.000
 BDT  C16   C17  C13   104.06  3.000
 BDT  HO17  O17  C17   108.19  3.000
 BDT  H18B  C18  H18A  107.08  3.000
 BDT  H18B  C18  H18   106.90  3.000
 BDT  H18A  C18  H18   107.08  3.000
 BDT  H18B  C18  C13   110.56  3.000
 BDT  H18A  C18  C13   112.76  3.000
 BDT  H18   C18  C13   112.14  3.000
 BDT  H19B  C19  H19A  107.21  3.000
 BDT  H19B  C19  H19   107.09  3.000
 BDT  H19A  C19  H19   107.43  3.000
 BDT  H19B  C19  C10   111.37  3.000
 BDT  H19A  C19  C10   113.39  3.000
 BDT  H19   C19  C10   110.08  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
 BDT  Var_01  C4   C3   C2   C1   -49.57  30.0  1
 BDT  Var_02  C5   C4   C3   C2    48.05  30.0  1
 BDT  Var_03  C10  C1   C2   C3    55.62  30.0  1
 BDT  Var_04  C8   C7   C6   C5    53.73  30.0  1
 BDT  Var_05  C13  C12  C11  C9   -52.91  30.0  1
 BDT  Var_06  C17  C16  C15  C14    6.08  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
 BDT  chir_01  C5   C4   C6   C10  negativ
 BDT  chir_02  C8   C14  C9   C7   negativ
 BDT  chir_03  C9   C11  C10  C8   positiv
 BDT  chir_04  C10  C5   C9   C1   negativ
 BDT  chir_05  C13  C14  C17  C12  negativ
 BDT  chir_06  C14  C8   C13  C15  negativ
 BDT  chir_07  C17  O17  C16  C13  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
 BDT  plan-1  C2  0.020
 BDT  plan-1  C3  0.020
 BDT  plan-1  O3  0.020
 BDT  plan-1  C4  0.020

