# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 16 11:28:35 2020
#   Inital geometry file: a 160 line input string
#   Ligand name: (6R)-6-[(1R,3R,7E,17beta)-1,3-dihydroxy-2-methylidene-9,10-secoestra-5,7-dien-17-yl]hept-1-en-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCC(=O)C=C)[C@H]1CC[C@H]2/C(CCC[C@]12C)=C/C=C/3C[C@@H](O)C(=C)[C@H](O)C/3
#
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
 9K0  9K0  (6R)-6-[(1R,3R,7E,17beta)-1,3-dihydroxy-2-methylidene-9,10-secoestra-5,7-dien-17-yl]hept-1-en-3-one  ligand  67  29  .  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_9K0
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
 9K0  O2   O  O     0  -0.409   7.1070   1.6923   1.4146
 9K0  C23  C  C     0   0.374   7.2651   1.2915   0.2803
 9K0  C24  C  C1    0  -0.287   8.4894   1.6094  -0.5005
 9K0  C25  C  C2    0  -0.466   9.4720   2.3613  -0.0128
 9K0  C22  C  CH2   0  -0.585   6.2510   0.4406  -0.4352
 9K0  C20  C  CH2   0  -0.410   4.9947   0.1383   0.3646
 9K0  C18  C  CH1   0  -0.234   3.9037  -0.5887  -0.4348
 9K0  C19  C  CH3   0  -0.675   4.4096  -1.9348  -0.9460
 9K0  C16  C  CH1   0  -0.168   2.6341  -0.7063   0.4237
 9K0  C15  C  CH2   0  -0.450   2.1120   0.6848   0.8748
 9K0  C14  C  CH2   0  -0.454   0.5769   0.5945   0.9598
 9K0  C9   C  CH1   0  -0.245   0.2926  -0.8894   0.7962
 9K0  C10  C  CT    0  -0.059   1.3835  -1.3829  -0.1889
 9K0  C17  C  CH3   0  -0.682   1.1294  -0.8556  -1.6030
 9K0  C11  C  CH2   0  -0.418   1.3585  -2.9133  -0.1649
 9K0  C12  C  CH2   0  -0.434  -0.0254  -3.4572  -0.5205
 9K0  C13  C  CH2   0  -0.506  -1.1386  -2.8694   0.3541
 9K0  C8   C  C     0   0.159  -1.0750  -1.3674   0.4165
 9K0  C7   C  C1    0  -0.368  -2.0952  -0.5308   0.1675
 9K0  C6   C  C1    0  -0.332  -3.4415  -0.8988  -0.2324
 9K0  C5   C  C     0   0.120  -4.4495  -0.0557  -0.5055
 9K0  C    C  CH2   0  -0.511  -5.7967  -0.5629  -0.9318
 9K0  C4   C  CH2   0  -0.529  -4.3703   1.4420  -0.4293
 9K0  C3   C  CH1   0   0.049  -5.4645   1.9992   0.4883
 9K0  O    O  OH1   0  -0.665  -5.3570   3.3999   0.4857
 9K0  C2   C  C     0   0.066  -6.8057   1.4896   0.0230
 9K0  C21  C  C2    0  -0.605  -7.8073   2.2763  -0.3548
 9K0  C1   C  CH1   0  -0.000  -6.9101  -0.0143  -0.0407
 9K0  O1   O  OH1   0  -0.662  -6.7592  -0.5982   1.2384
 9K0  H1   H  H     0   0.264   8.5582   1.2019  -1.5027
 9K0  H3   H  H     0   0.264  10.3543   2.5814  -0.5979
 9K0  H4   H  H     0   0.260   9.4271   2.7821   0.9839
 9K0  H6   H  HCH2  0   0.267   6.0018   0.9472  -1.3763
 9K0  H7   H  HCH2  0   0.272   6.7713  -0.4721  -0.7458
 9K0  H8   H  HCH2  0   0.218   5.2529  -0.4574   1.2466
 9K0  H9   H  HCH2  0   0.242   4.5977   1.0820   0.7431
 9K0  H10  H  HCH1  0   0.209   3.6606   0.0393  -1.3026
 9K0  H11  H  HCH3  0   0.232   3.7180  -2.3888  -1.6538
 9K0  H12  H  HCH3  0   0.235   5.3622  -1.8373  -1.4680
 9K0  H13  H  HCH3  0   0.213   4.5563  -2.6419  -0.1254
 9K0  H14  H  HCH1  0   0.208   2.8992  -1.2837   1.3209
 9K0  H15  H  HCH2  0   0.234   2.5500   0.9736   1.8308
 9K0  H16  H  HCH2  0   0.223   2.4082   1.4524   0.1546
 9K0  H17  H  HCH2  0   0.235   0.1826   0.9870   1.8984
 9K0  H18  H  HCH2  0   0.221   0.1162   1.1765   0.1587
 9K0  H19  H  HCH1  0   0.231   0.5362  -1.3719   1.7562
 9K0  H20  H  HCH3  0   0.232   1.2522   0.2272  -1.6657
 9K0  H21  H  HCH3  0   0.230   1.8267  -1.3013  -2.3150
 9K0  H22  H  HCH3  0   0.237   0.1225  -1.0820  -1.9546
 9K0  H23  H  HCH2  0   0.232   2.0931  -3.3410  -0.8488
 9K0  H24  H  HCH2  0   0.211   1.6351  -3.2535   0.8403
 9K0  H25  H  HCH2  0   0.222  -0.2441  -3.2535  -1.5721
 9K0  H26  H  HCH2  0   0.233  -0.0293  -4.5449  -0.4172
 9K0  H27  H  HCH2  0   0.245  -2.1068  -3.2304   0.0077
 9K0  H28  H  HCH2  0   0.231  -1.0126  -3.2524   1.3743
 9K0  H29  H  H     0   0.229  -1.8992   0.5301   0.2739
 9K0  H30  H  H     0   0.230  -3.6532  -1.9584  -0.3375
 9K0  H31  H  HCH2  0   0.248  -6.0076  -0.2327  -1.9552
 9K0  H32  H  HCH2  0   0.252  -5.8281  -1.6550  -0.9348
 9K0  H33  H  HCH2  0   0.257  -3.3995   1.7897  -0.0772
 9K0  H34  H  HCH2  0   0.244  -4.5214   1.8598  -1.4326
 9K0  H35  H  HCH1  0   0.221  -5.2806   1.6026   1.4967
 9K0  H36  H  HOH1  0   0.454  -5.9135   3.7504   1.1885
 9K0  H37  H  H     0   0.238  -7.7380   3.3562  -0.3476
 9K0  H38  H  H     0   0.240  -8.7454   1.8568  -0.6975
 9K0  H39  H  HCH1  0   0.225  -7.8783  -0.2856  -0.4816
 9K0  H40  H  HOH1  0   0.450  -7.4625  -0.2609   1.8024

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
 9K0  C21  C2   double  1.328  0.020  1.328
 9K0  O    C3   single  1.405  0.020  1.405
 9K0  C2   C3   single  1.508  0.020  1.508
 9K0  C2   C1   single  1.509  0.020  1.509
 9K0  C3   C4   single  1.533  0.020  1.533
 9K0  C1   O1   single  1.414  0.020  1.414
 9K0  C1   C    single  1.528  0.020  1.528
 9K0  C4   C5   single  1.502  0.020  1.502
 9K0  C    C5   single  1.501  0.020  1.501
 9K0  C5   C6   double  1.342  0.020  1.342
 9K0  C6   C7   single  1.452  0.020  1.452
 9K0  C7   C8   double  1.343  0.020  1.343
 9K0  C8   C13  single  1.505  0.020  1.505
 9K0  C8   C9   single  1.498  0.020  1.498
 9K0  C14  C9   single  1.520  0.020  1.520
 9K0  C14  C15  single  1.540  0.020  1.540
 9K0  C17  C10  single  1.530  0.020  1.530
 9K0  C13  C12  single  1.533  0.020  1.533
 9K0  C9   C10  single  1.550  0.020  1.550
 9K0  C15  C16  single  1.553  0.020  1.553
 9K0  C10  C16  single  1.548  0.020  1.548
 9K0  C10  C11  single  1.531  0.020  1.531
 9K0  C12  C11  single  1.529  0.020  1.529
 9K0  C20  C22  single  1.520  0.020  1.520
 9K0  C20  C18  single  1.536  0.020  1.536
 9K0  O2   C23  double  1.213  0.020  1.213
 9K0  C22  C23  single  1.505  0.020  1.505
 9K0  C16  C18  single  1.537  0.020  1.537
 9K0  C23  C24  single  1.486  0.020  1.486
 9K0  C18  C19  single  1.526  0.020  1.526
 9K0  C24  C25  double  1.330  0.020  1.330
 9K0  C24  H1   single  0.930  0.020  1.080
 9K0  C25  H3   single  0.930  0.020  1.080
 9K0  C25  H4   single  0.930  0.020  1.080
 9K0  C22  H6   single  0.970  0.020  1.090
 9K0  C22  H7   single  0.970  0.020  1.090
 9K0  C20  H8   single  0.970  0.020  1.090
 9K0  C20  H9   single  0.970  0.020  1.090
 9K0  C18  H10  single  0.970  0.020  1.090
 9K0  C19  H11  single  0.970  0.020  1.090
 9K0  C19  H12  single  0.970  0.020  1.090
 9K0  C19  H13  single  0.970  0.020  1.090
 9K0  C16  H14  single  0.970  0.020  1.090
 9K0  C15  H15  single  0.970  0.020  1.090
 9K0  C15  H16  single  0.970  0.020  1.090
 9K0  C14  H17  single  0.970  0.020  1.090
 9K0  C14  H18  single  0.970  0.020  1.090
 9K0  C9   H19  single  0.970  0.020  1.090
 9K0  C17  H20  single  0.970  0.020  1.090
 9K0  C17  H21  single  0.970  0.020  1.090
 9K0  C17  H22  single  0.970  0.020  1.090
 9K0  C11  H23  single  0.970  0.020  1.090
 9K0  C11  H24  single  0.970  0.020  1.090
 9K0  C12  H25  single  0.970  0.020  1.090
 9K0  C12  H26  single  0.970  0.020  1.090
 9K0  C13  H27  single  0.970  0.020  1.090
 9K0  C13  H28  single  0.970  0.020  1.090
 9K0  C7   H29  single  0.930  0.020  1.080
 9K0  C6   H30  single  0.930  0.020  1.080
 9K0  C    H31  single  0.970  0.020  1.090
 9K0  C    H32  single  0.970  0.020  1.090
 9K0  C4   H33  single  0.970  0.020  1.090
 9K0  C4   H34  single  0.970  0.020  1.090
 9K0  C3   H35  single  0.970  0.020  1.090
 9K0  O    H36  single  0.850  0.020  0.980
 9K0  C21  H37  single  0.930  0.020  1.080
 9K0  C21  H38  single  0.930  0.020  1.080
 9K0  C1   H39  single  0.970  0.020  1.090
 9K0  O1   H40  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
 9K0  C22  C23  C24  115.23  3.000
 9K0  C24  C23  O2   121.85  3.000
 9K0  C22  C23  O2   122.92  3.000
 9K0  H1   C24  C25  120.31  3.000
 9K0  H1   C24  C23  117.23  3.000
 9K0  C25  C24  C23  122.47  3.000
 9K0  H4   C25  H3   116.92  3.000
 9K0  H4   C25  C24  121.78  3.000
 9K0  H3   C25  C24  121.30  3.000
 9K0  H7   C22  H6   104.43  3.000
 9K0  H7   C22  C20  112.09  3.000
 9K0  H6   C22  C20  110.82  3.000
 9K0  H7   C22  C23  106.61  3.000
 9K0  H6   C22  C23  107.45  3.000
 9K0  C20  C22  C23  114.79  3.000
 9K0  H9   C20  H8   106.07  3.000
 9K0  H9   C20  C18  109.35  3.000
 9K0  H8   C20  C18  109.22  3.000
 9K0  H9   C20  C22  108.13  3.000
 9K0  H8   C20  C22  109.70  3.000
 9K0  C18  C20  C22  114.05  3.000
 9K0  H10  C18  C16  107.59  3.000
 9K0  H10  C18  C19  108.24  3.000
 9K0  C16  C18  C19  113.16  3.000
 9K0  H10  C18  C20  107.33  3.000
 9K0  C19  C18  C20  110.88  3.000
 9K0  C16  C18  C20  109.41  3.000
 9K0  H13  C19  H12  107.45  3.000
 9K0  H13  C19  H11  107.67  3.000
 9K0  H12  C19  H11  106.31  3.000
 9K0  H13  C19  C18  111.32  3.000
 9K0  H12  C19  C18  111.78  3.000
 9K0  H11  C19  C18  112.02  3.000
 9K0  H14  C16  C10  106.75  3.000
 9K0  H14  C16  C15  108.33  3.000
 9K0  C10  C16  C15  103.58  3.000
 9K0  H14  C16  C18  107.26  3.000
 9K0  C10  C16  C18  118.66  3.000
 9K0  C15  C16  C18  111.80  3.000
 9K0  H16  C15  H15  106.42  3.000
 9K0  H16  C15  C14  110.33  3.000
 9K0  H15  C15  C14  111.56  3.000
 9K0  H16  C15  C16  110.27  3.000
 9K0  H15  C15  C16  110.91  3.000
 9K0  C14  C15  C16  107.38  3.000
 9K0  H18  C14  H17  106.67  3.000
 9K0  H18  C14  C9   111.25  3.000
 9K0  H17  C14  C9   112.10  3.000
 9K0  H18  C14  C15  110.41  3.000
 9K0  H17  C14  C15  112.74  3.000
 9K0  C9   C14  C15  103.75  3.000
 9K0  H19  C9   C8   106.44  3.000
 9K0  H19  C9   C10  104.99  3.000
 9K0  C8   C9   C10  112.33  3.000
 9K0  H19  C9   C14  107.01  3.000
 9K0  C10  C9   C14  104.33  3.000
 9K0  C8   C9   C14  120.65  3.000
 9K0  C11  C10  C17  110.87  3.000
 9K0  C11  C10  C9   107.26  3.000
 9K0  C17  C10  C9   111.13  3.000
 9K0  C11  C10  C16  116.35  3.000
 9K0  C9   C10  C16  100.25  3.000
 9K0  C17  C10  C16  110.44  3.000
 9K0  H22  C17  H21  107.14  3.000
 9K0  H22  C17  H20  106.94  3.000
 9K0  H21  C17  H20  107.20  3.000
 9K0  H22  C17  C10  112.32  3.000
 9K0  H21  C17  C10  110.85  3.000
 9K0  H20  C17  C10  112.10  3.000
 9K0  H24  C11  H23  106.45  3.000
 9K0  H24  C11  C12  109.33  3.000
 9K0  H23  C11  C12  108.92  3.000
 9K0  H24  C11  C10  108.68  3.000
 9K0  H23  C11  C10  111.78  3.000
 9K0  C12  C11  C10  111.52  3.000
 9K0  H26  C12  H25  106.00  3.000
 9K0  H26  C12  C13  108.98  3.000
 9K0  H25  C12  C13  109.40  3.000
 9K0  H26  C12  C11  109.60  3.000
 9K0  H25  C12  C11  109.78  3.000
 9K0  C13  C12  C11  112.85  3.000
 9K0  H28  C13  H27  106.38  3.000
 9K0  H28  C13  C8   107.76  3.000
 9K0  H27  C13  C8   112.42  3.000
 9K0  H28  C13  C12  108.26  3.000
 9K0  H27  C13  C12  109.69  3.000
 9K0  C8   C13  C12  112.07  3.000
 9K0  C7   C8   C13  125.60  3.000
 9K0  C13  C8   C9   111.57  3.000
 9K0  C7   C8   C9   122.82  3.000
 9K0  H29  C7   C6   116.28  3.000
 9K0  H29  C7   C8   117.01  3.000
 9K0  C6   C7   C8   126.71  3.000
 9K0  H30  C6   C5   116.55  3.000
 9K0  H30  C6   C7   117.05  3.000
 9K0  C5   C6   C7   126.39  3.000
 9K0  C4   C5   C    113.50  3.000
 9K0  C    C5   C6   121.30  3.000
 9K0  C4   C5   C6   125.20  3.000
 9K0  H32  C    H31  107.04  3.000
 9K0  H32  C    C1   109.85  3.000
 9K0  H31  C    C1   107.23  3.000
 9K0  H32  C    C5   111.36  3.000
 9K0  H31  C    C5   109.64  3.000
 9K0  C1   C    C5   111.53  3.000
 9K0  H34  C4   H33  107.26  3.000
 9K0  H34  C4   C3   108.09  3.000
 9K0  H33  C4   C3   109.05  3.000
 9K0  H34  C4   C5   109.03  3.000
 9K0  H33  C4   C5   112.44  3.000
 9K0  C3   C4   C5   110.81  3.000
 9K0  H35  C3   C2   108.06  3.000
 9K0  H35  C3   O    110.41  3.000
 9K0  C2   C3   O    113.85  3.000
 9K0  H35  C3   C4   107.37  3.000
 9K0  C2   C3   C4   109.10  3.000
 9K0  O    C3   C4   107.86  3.000
 9K0  H36  O    C3   108.51  3.000
 9K0  C1   C2   C21  121.74  3.000
 9K0  C1   C2   C3   114.28  3.000
 9K0  C21  C2   C3   123.92  3.000
 9K0  H38  C21  H37  116.36  3.000
 9K0  H38  C21  C2   120.90  3.000
 9K0  H37  C21  C2   122.74  3.000
 9K0  H39  C1   O1   110.81  3.000
 9K0  H39  C1   C2   108.92  3.000
 9K0  O1   C1   C2   111.47  3.000
 9K0  H39  C1   C    108.65  3.000
 9K0  O1   C1   C    107.55  3.000
 9K0  C2   C1   C    109.39  3.000
 9K0  H40  O1   C1   107.89  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
 9K0  Var_01  C9   C14  C15  C16     9.56  30.0  1
 9K0  Var_02  C12  C13  C8   C9    -51.68  30.0  1
 9K0  Var_03  C13  C12  C11  C10   -53.91  30.0  1
 9K0  Var_04  C8   C13  C12  C11    50.00  30.0  1
 9K0  Var_05  C3   C4   C5   C      55.19  30.0  1
 9K0  Var_06  C1   C    C5   C4    -54.49  30.0  1
 9K0  Var_07  C6   C7   C8   C9    178.62  30.0  2
 9K0  Var_08  C5   C6   C7   C8   -178.58  30.0  2
 9K0  Var_09  C4   C5   C6   C7     -0.81  30.0  2
 9K0  Var_10  H37  C21  C2   C3     -0.62  30.0  2
 9K0  Var_11  C20  C22  C23  O2      1.02  30.0  1
 9K0  Var_12  C25  C24  C23  O2     -0.85  30.0  2
 9K0  Var_13  C18  C20  C22  C23   173.20  30.0  2
 9K0  Var_14  H3   C25  C24  C23  -179.95   0.0  2

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
 9K0  chir_01  C18  C20  C16  C19  positiv
 9K0  chir_02  C16  C18  C10  C15  positiv
 9K0  chir_03  C9   C10  C14  C8   negativ
 9K0  chir_04  C10  C16  C9   C11  positiv
 9K0  chir_05  C3   O    C2   C4   negativ
 9K0  chir_06  C1   O1   C    C2   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
 9K0  plan-1  O2   0.020
 9K0  plan-1  C23  0.020
 9K0  plan-1  C24  0.020
 9K0  plan-1  C22  0.020
 9K0  plan-2  C23  0.020
 9K0  plan-2  C24  0.020
 9K0  plan-2  C25  0.020
 9K0  plan-2  H1   0.020
 9K0  plan-2  H3   0.020
 9K0  plan-2  H4   0.020

