# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 05:39:27 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: (6alpha,8alpha)-6-(pent-2-yn-1-yloxy)androsta-1,4-diene-3,17-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC#CCO[C@@H]1C[C@H]2[C@@H]3CCC(=O)[C@@]3(C)CC[C@@H]2[C@@]4(C)C=CC(=O)C=C14
#
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
 0XJ  0XJ  (6alpha,8alpha)-6-(pent-2-yn-1-yloxy)androsta-1,4-diene-3,17-dione  ligand  57  27  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0XJ
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
 0XJ  C8   C  CH1   0  -0.241  -1.1215  -0.2775   0.5111
 0XJ  C5   C  CR6   0   0.213   1.1194   1.5342   0.6734
 0XJ  C6   C  CH1   0  -0.004   1.1169   0.2933   1.5342
 0XJ  C2   C  CR16  0  -0.388   0.9060   3.9550  -0.7973
 0XJ  C4   C  CR16  0  -0.458   1.7210   2.6369   1.1364
 0XJ  C17  C  C     0   0.432  -4.7170  -1.2817   0.1329
 0XJ  C13  C  CT    0  -0.204  -3.4049  -0.8146  -0.4583
 0XJ  C18  C  CH3   0  -0.670  -2.9296  -1.9909  -1.3325
 0XJ  C12  C  CH2   0  -0.408  -3.4260   0.4840  -1.2464
 0XJ  C11  C  CH2   0  -0.456  -1.9962   0.9342  -1.5618
 0XJ  C16  C  CH2   0  -0.567  -4.4164  -2.0067   1.4374
 0XJ  C15  C  CH2   0  -0.462  -2.9072  -1.8426   1.6696
 0XJ  C14  C  CH1   0  -0.203  -2.5698  -0.6222   0.8113
 0XJ  C9   C  CH1   0  -0.187  -1.1076   1.0288  -0.3113
 0XJ  C7   C  CH2   0  -0.452  -0.3200  -0.1191   1.7962
 0XJ  C10  C  CR6   0  -0.232   0.3522   1.5052  -0.6250
 0XJ  C19  C  CH3   0  -0.661   1.0502   0.5816  -1.6513
 0XJ  C1   C  CR16  0  -0.109   0.3073   2.8580  -1.2642
 0XJ  C3   C  CR6   0   0.400   1.6776   3.9254   0.4436
 0XJ  O1   O  O     0  -0.445   2.2458   4.9142   0.8849
 0XJ  O    O  O2    0  -0.488   1.7825  -0.7986   0.9352
 0XJ  C20  C  CH2   0  -0.326   3.1829  -0.6436   0.8824
 0XJ  C21  C  CSP   0   0.028   3.7542  -1.7735   0.1624
 0XJ  C22  C  CSP   0   0.082   4.2343  -2.6998  -0.4373
 0XJ  C23  C  CH2   0  -0.605   4.8274  -3.8178  -1.1619
 0XJ  C24  C  CH3   0  -0.663   6.3195  -3.9812  -0.8734
 0XJ  H1   H  HCH1  0   0.235  -0.6816  -1.0905  -0.0761
 0XJ  H2   H  HCH1  0   0.246   1.5992   0.5386   2.4913
 0XJ  H3   H  HCR6  0   0.265   0.8423   4.8945  -1.3331
 0XJ  H4   H  HCR6  0   0.261   2.2555   2.6087   2.0811
 0XJ  H5   H  HCH3  0   0.247  -3.5881  -2.0969  -2.1955
 0XJ  H6   H  HCH3  0   0.247  -1.9183  -1.8398  -1.7071
 0XJ  H7   H  HCH3  0   0.247  -2.9301  -2.9424  -0.7988
 0XJ  H8   H  HCH2  0   0.238  -3.9930   0.3814  -2.1747
 0XJ  H9   H  HCH2  0   0.232  -3.9241   1.2586  -0.6548
 0XJ  H10  H  HCH2  0   0.235  -1.5476   0.2567  -2.2919
 0XJ  H11  H  HCH2  0   0.248  -2.0521   1.9072  -2.0527
 0XJ  H12  H  HCH2  0   0.279  -4.9971  -1.5324   2.2334
 0XJ  H13  H  HCH2  0   0.280  -4.7510  -3.0447   1.3848
 0XJ  H14  H  HCH2  0   0.253  -2.6729  -1.6922   2.7229
 0XJ  H15  H  HCH2  0   0.235  -2.3539  -2.7245   1.3391
 0XJ  H16  H  HCH1  0   0.233  -2.9968   0.2491   1.3325
 0XJ  H17  H  HCH1  0   0.236  -1.5480   1.8017   0.3351
 0XJ  H18  H  HCH2  0   0.241  -0.7848   0.6463   2.4259
 0XJ  H19  H  HCH2  0   0.259  -0.3242  -1.0459   2.3757
 0XJ  H20  H  HCH3  0   0.247   0.5938   0.6933  -2.6343
 0XJ  H21  H  HCH3  0   0.246   2.1023   0.8513  -1.7499
 0XJ  H22  H  HCH3  0   0.257   0.9927  -0.4661  -1.3686
 0XJ  H23  H  HCR6  0   0.282  -0.2295   2.9206  -2.2039
 0XJ  H24  H  HCH2  0   0.242   3.4716   0.2895   0.3822
 0XJ  H25  H  HCH2  0   0.250   3.6046  -0.5937   1.8958
 0XJ  H26  H  HCH2  0   0.265   4.2978  -4.7355  -0.8943
 0XJ  H27  H  HCH2  0   0.264   4.6698  -3.6754  -2.2336
 0XJ  H28  H  HCH3  0   0.240   6.7187  -4.8208  -1.4412
 0XJ  H29  H  HCH3  0   0.233   6.8754  -3.0875  -1.1546
 0XJ  H30  H  HCH3  0   0.233   6.4961  -4.1726   0.1844
 0XJ  O2   O  O     0  -0.399  -5.8140  -1.1156  -0.3430

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
 0XJ  O2   C17  double  1.207  0.020  1.207
 0XJ  C12  C11  single  1.532  0.020  1.532
 0XJ  C12  C13  single  1.519  0.020  1.519
 0XJ  C18  C13  single  1.541  0.020  1.541
 0XJ  C11  C9   single  1.537  0.020  1.537
 0XJ  C13  C17  single  1.513  0.020  1.513
 0XJ  C13  C14  single  1.532  0.020  1.532
 0XJ  C17  C16  single  1.522  0.020  1.522
 0XJ  C1   C2   double  1.334  0.020  1.334
 0XJ  C1   C10  single  1.497  0.020  1.497
 0XJ  C19  C10  single  1.547  0.020  1.547
 0XJ  C9   C10  single  1.567  0.020  1.567
 0XJ  C9   C8   single  1.544  0.020  1.544
 0XJ  C2   C3   single  1.462  0.020  1.462
 0XJ  C16  C15  single  1.536  0.020  1.536
 0XJ  C10  C5   single  1.508  0.020  1.508
 0XJ  C14  C8   single  1.519  0.020  1.519
 0XJ  C14  C15  single  1.530  0.020  1.530
 0XJ  C8   C7   single  1.523  0.020  1.523
 0XJ  C3   O1   double  1.223  0.020  1.223
 0XJ  C3   C4   single  1.464  0.020  1.464
 0XJ  C5   C4   double  1.339  0.020  1.339
 0XJ  C5   C6   single  1.510  0.020  1.510
 0XJ  C7   C6   single  1.518  0.020  1.518
 0XJ  O    C6   single  1.412  0.020  1.412
 0XJ  O    C20  single  1.410  0.020  1.410
 0XJ  C20  C21  single  1.457  0.020  1.457
 0XJ  C21  C22  triple  1.203  0.020  1.203
 0XJ  C22  C23  single  1.458  0.020  1.458
 0XJ  C23  C24  single  1.529  0.020  1.529
 0XJ  C8   H1   single  0.970  0.020  1.090
 0XJ  C6   H2   single  0.970  0.020  1.090
 0XJ  C2   H3   single  0.930  0.020  1.080
 0XJ  C4   H4   single  0.930  0.020  1.080
 0XJ  C18  H5   single  0.970  0.020  1.090
 0XJ  C18  H6   single  0.970  0.020  1.090
 0XJ  C18  H7   single  0.970  0.020  1.090
 0XJ  C12  H8   single  0.970  0.020  1.090
 0XJ  C12  H9   single  0.970  0.020  1.090
 0XJ  C11  H10  single  0.970  0.020  1.090
 0XJ  C11  H11  single  0.970  0.020  1.090
 0XJ  C16  H12  single  0.970  0.020  1.090
 0XJ  C16  H13  single  0.970  0.020  1.090
 0XJ  C15  H14  single  0.970  0.020  1.090
 0XJ  C15  H15  single  0.970  0.020  1.090
 0XJ  C14  H16  single  0.970  0.020  1.090
 0XJ  C9   H17  single  0.970  0.020  1.090
 0XJ  C7   H18  single  0.970  0.020  1.090
 0XJ  C7   H19  single  0.970  0.020  1.090
 0XJ  C19  H20  single  0.970  0.020  1.090
 0XJ  C19  H21  single  0.970  0.020  1.090
 0XJ  C19  H22  single  0.970  0.020  1.090
 0XJ  C1   H23  single  0.930  0.020  1.080
 0XJ  C20  H24  single  0.970  0.020  1.090
 0XJ  C20  H25  single  0.970  0.020  1.090
 0XJ  C23  H26  single  0.970  0.020  1.090
 0XJ  C23  H27  single  0.970  0.020  1.090
 0XJ  C24  H28  single  0.970  0.020  1.090
 0XJ  C24  H29  single  0.970  0.020  1.090
 0XJ  C24  H30  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
 0XJ  H1   C8   C7   108.56  3.000
 0XJ  H1   C8   C9   109.82  3.000
 0XJ  C7   C8   C9   110.91  3.000
 0XJ  H1   C8   C14  108.69  3.000
 0XJ  C7   C8   C14  111.02  3.000
 0XJ  C9   C8   C14  107.81  3.000
 0XJ  C10  C5   C4   122.83  3.000
 0XJ  C4   C5   C6   118.71  3.000
 0XJ  C10  C5   C6   118.29  3.000
 0XJ  H2   C6   O    109.57  3.000
 0XJ  H2   C6   C7   109.01  3.000
 0XJ  O    C6   C7   108.02  3.000
 0XJ  H2   C6   C5   108.19  3.000
 0XJ  O    C6   C5   113.13  3.000
 0XJ  C7   C6   C5   108.86  3.000
 0XJ  H3   C2   C3   117.94  3.000
 0XJ  H3   C2   C1   120.90  3.000
 0XJ  C3   C2   C1   121.16  3.000
 0XJ  H4   C4   C3   116.70  3.000
 0XJ  H4   C4   C5   120.05  3.000
 0XJ  C3   C4   C5   123.24  3.000
 0XJ  C16  C17  C13  108.10  3.000
 0XJ  C16  C17  O2   125.64  3.000
 0XJ  C13  C17  O2   126.26  3.000
 0XJ  C14  C13  C12  109.28  3.000
 0XJ  C14  C13  C18  113.45  3.000
 0XJ  C12  C13  C18  111.26  3.000
 0XJ  C14  C13  C17  100.82  3.000
 0XJ  C18  C13  C17  104.69  3.000
 0XJ  C12  C13  C17  117.04  3.000
 0XJ  H7   C18  H6   106.84  3.000
 0XJ  H7   C18  H5   107.58  3.000
 0XJ  H6   C18  H5   107.58  3.000
 0XJ  H7   C18  C13  112.84  3.000
 0XJ  H6   C18  C13  112.07  3.000
 0XJ  H5   C18  C13  109.68  3.000
 0XJ  H9   C12  H8   106.82  3.000
 0XJ  H9   C12  C11  109.15  3.000
 0XJ  H8   C12  C11  109.70  3.000
 0XJ  H9   C12  C13  109.32  3.000
 0XJ  H8   C12  C13  111.57  3.000
 0XJ  C11  C12  C13  110.19  3.000
 0XJ  H11  C11  H10  105.87  3.000
 0XJ  H11  C11  C9   109.92  3.000
 0XJ  H10  C11  C9   110.16  3.000
 0XJ  H11  C11  C12  107.87  3.000
 0XJ  H10  C11  C12  109.79  3.000
 0XJ  C9   C11  C12  112.96  3.000
 0XJ  H13  C16  H12  106.54  3.000
 0XJ  H13  C16  C15  114.21  3.000
 0XJ  H12  C16  C15  111.43  3.000
 0XJ  H13  C16  C17  110.55  3.000
 0XJ  H12  C16  C17  108.20  3.000
 0XJ  C15  C16  C17  105.83  3.000
 0XJ  H15  C15  H14  107.16  3.000
 0XJ  H15  C15  C14  111.26  3.000
 0XJ  H14  C15  C14  112.63  3.000
 0XJ  H15  C15  C16  111.46  3.000
 0XJ  H14  C15  C16  111.86  3.000
 0XJ  C14  C15  C16  102.54  3.000
 0XJ  H16  C14  C15  106.26  3.000
 0XJ  H16  C14  C13  106.27  3.000
 0XJ  C15  C14  C13  104.16  3.000
 0XJ  H16  C14  C8   106.48  3.000
 0XJ  C15  C14  C8   120.16  3.000
 0XJ  C13  C14  C8   112.62  3.000
 0XJ  H17  C9   C10  106.08  3.000
 0XJ  H17  C9   C11  106.86  3.000
 0XJ  C10  C9   C11  113.22  3.000
 0XJ  H17  C9   C8   106.15  3.000
 0XJ  C10  C9   C8   111.85  3.000
 0XJ  C11  C9   C8   112.10  3.000
 0XJ  H19  C7   H18  106.64  3.000
 0XJ  H19  C7   C6   108.99  3.000
 0XJ  H18  C7   C6   108.14  3.000
 0XJ  H19  C7   C8   110.93  3.000
 0XJ  H18  C7   C8   109.56  3.000
 0XJ  C6   C7   C8   112.39  3.000
 0XJ  C1   C10  C19  105.65  3.000
 0XJ  C19  C10  C9   111.81  3.000
 0XJ  C1   C10  C9   109.40  3.000
 0XJ  C9   C10  C5   107.90  3.000
 0XJ  C19  C10  C5   110.67  3.000
 0XJ  C1   C10  C5   111.44  3.000
 0XJ  H22  C19  H21  108.24  3.000
 0XJ  H22  C19  H20  108.14  3.000
 0XJ  H21  C19  H20  107.29  3.000
 0XJ  H22  C19  C10  112.28  3.000
 0XJ  H21  C19  C10  110.34  3.000
 0XJ  H20  C19  C10  110.39  3.000
 0XJ  H23  C1   C10  115.92  3.000
 0XJ  H23  C1   C2   118.57  3.000
 0XJ  C10  C1   C2   125.46  3.000
 0XJ  O1   C3   C4   121.83  3.000
 0XJ  C4   C3   C2   115.81  3.000
 0XJ  O1   C3   C2   122.36  3.000
 0XJ  C20  O    C6   113.52  3.000
 0XJ  H25  C20  H24  106.31  3.000
 0XJ  H25  C20  C21  109.91  3.000
 0XJ  H24  C20  C21  109.34  3.000
 0XJ  H25  C20  O    110.58  3.000
 0XJ  H24  C20  O    111.83  3.000
 0XJ  C21  C20  O    108.83  3.000
 0XJ  C22  C21  C20  180.00  3.000
 0XJ  C23  C22  C21  180.00  3.000
 0XJ  H27  C23  H26  106.24  3.000
 0XJ  H27  C23  C24  109.87  3.000
 0XJ  H26  C23  C24  109.70  3.000
 0XJ  H27  C23  C22  109.20  3.000
 0XJ  H26  C23  C22  108.97  3.000
 0XJ  C24  C23  C22  112.66  3.000
 0XJ  H30  C24  H29  108.19  3.000
 0XJ  H30  C24  H28  108.14  3.000
 0XJ  H29  C24  H28  108.10  3.000
 0XJ  H30  C24  C23  111.12  3.000
 0XJ  H29  C24  C23  111.20  3.000
 0XJ  H28  C24  C23  109.98  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
 0XJ  Var_01  C2   C3   C4   C5      1.06  30.0  1
 0XJ  Var_02  C3   C4   C5   C6   -174.19  30.0  1
 0XJ  Var_03  C1   C2   C3   C4     -1.19  30.0  1
 0XJ  Var_04  C14  C15  C16  C17    21.06  30.0  1
 0XJ  Var_05  C9   C11  C12  C13   -53.66  30.0  1
 0XJ  Var_06  C15  C16  C17  C13     5.16  30.0  1
 0XJ  Var_07  C3   C2   C1   C10    -0.77  30.0  1
 0XJ  Var_08  C21  C20  O    C6   -175.88  30.0  3
 0XJ  Var_09  C24  C23  C22  C21    16.74  30.0  3
 0XJ  Var_10  H28  C24  C23  C22  -179.54  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
 0XJ  chir_01  C8   C9   C14  C7   positiv
 0XJ  chir_02  C6   O    C7   C5   positiv
 0XJ  chir_03  C13  C12  C17  C14  positiv
 0XJ  chir_04  C14  C15  C8   C13  negativ
 0XJ  chir_05  C9   C11  C10  C8   positiv
 0XJ  chir_06  C10  C1   C9   C5   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
 0XJ  plan-1  C17  0.020
 0XJ  plan-1  C13  0.020
 0XJ  plan-1  C16  0.020
 0XJ  plan-1  O2   0.020
 0XJ  plan-2  C2   0.020
 0XJ  plan-2  C4   0.020
 0XJ  plan-2  C3   0.020
 0XJ  plan-2  O1   0.020

