# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 17 01:20:05 2020
#   Inital geometry file: a 166 line input string
#   Ligand name: (2E,7R)-7-[(1R,3R,7E,17beta)-1,3-dihydroxy-2-methylidene-9,10-secoestra-5,7-dien-17-yl]oct-2-en-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C/C=C/C(=O)CC[C@@H](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
 9KR  9KR  (2E,7R)-7-[(1R,3R,7E,17beta)-1,3-dihydroxy-2-methylidene-9,10-secoestra-5,7-dien-17-yl]oct-2-en-4-one  ligand  70  30  .  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_9KR
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
 9KR  O2   O  O     0  -0.422   6.7824   1.2150   1.5824
 9KR  C23  C  C     0   0.379   6.9320   0.9121   0.4145
 9KR  C24  C  C1    0  -0.342   8.1539   1.2582  -0.3429
 9KR  C25  C  C1    0  -0.154   9.1798   1.9101   0.2089
 9KR  C26  C  CH3   0  -0.715  10.4320   2.2841  -0.4978
 9KR  C22  C  CH2   0  -0.584   5.8901   0.1490  -0.3621
 9KR  C20  C  CH2   0  -0.410   4.6176  -0.1590   0.4099
 9KR  C18  C  CH1   0  -0.234   3.5072  -0.7899  -0.4437
 9KR  C19  C  CH3   0  -0.674   3.9611  -2.1320  -1.0101
 9KR  C16  C  CH1   0  -0.167   2.2204  -0.8857   0.3912
 9KR  C15  C  CH2   0  -0.449   1.7486   0.5096   0.8824
 9KR  C14  C  CH2   0  -0.454   0.2102   0.4813   0.9404
 9KR  C9   C  CH1   0  -0.245  -0.1301  -0.9852   0.7312
 9KR  C10  C  CT    0  -0.060   0.9520  -1.4917  -0.2567
 9KR  C17  C  CH3   0  -0.680   0.7341  -0.9108  -1.6566
 9KR  C11  C  CH2   0  -0.419   0.8654  -3.0198  -0.2828
 9KR  C12  C  CH2   0  -0.434  -0.5361  -3.4949  -0.6675
 9KR  C13  C  CH2   0  -0.506  -1.6321  -2.8946   0.2200
 9KR  C8   C  C     0   0.158  -1.5117  -1.3987   0.3296
 9KR  C7   C  C1    0  -0.368  -2.4985  -0.5164   0.1045
 9KR  C6   C  C1    0  -0.331  -3.8582  -0.8234  -0.3008
 9KR  C5   C  C     0   0.120  -4.8385   0.0611  -0.5413
 9KR  C    C  CH2   0  -0.511  -6.2061  -0.3905  -0.9647
 9KR  C4   C  CH2   0  -0.529  -4.7099   1.5524  -0.4219
 9KR  C3   C  CH1   0   0.049  -5.7734   2.1150   0.5283
 9KR  O    O  OH1   0  -0.665  -5.6243   3.5114   0.5644
 9KR  C2   C  C     0   0.066  -7.1363   1.6593   0.0695
 9KR  C21  C  C2    0  -0.605  -8.1187   2.4864  -0.2702
 9KR  C1   C  CH1   0  -0.000  -7.2875   0.1619  -0.0372
 9KR  O1   O  OH1   0  -0.662  -7.1316  -0.4655   1.2204
 9KR  H1   H  H     0   0.254   8.1945   0.9582  -1.3853
 9KR  H3   H  H     0   0.259   9.1123   2.1958   1.2547
 9KR  H5   H  HCH3  0   0.245  10.4220   1.9865  -1.5450
 9KR  H6   H  HCH3  0   0.253  10.5926   3.3628  -0.4430
 9KR  H7   H  HCH3  0   0.253  11.2948   1.8220  -0.0132
 9KR  H8   H  HCH2  0   0.263   5.6622   0.7219  -1.2695
 9KR  H9   H  HCH2  0   0.269   6.3779  -0.7609  -0.7283
 9KR  H10  H  HCH2  0   0.216   4.8432  -0.8242   1.2503
 9KR  H11  H  HCH2  0   0.241   4.2526   0.7711   0.8501
 9KR  H12  H  HCH1  0   0.208   3.3143  -0.1074  -1.2824
 9KR  H13  H  HCH3  0   0.213   4.0732  -2.8774  -0.2183
 9KR  H14  H  HCH3  0   0.232   3.2594  -2.5287  -1.7419
 9KR  H15  H  HCH3  0   0.235   4.9224  -2.0507  -1.5191
 9KR  H16  H  HCH1  0   0.208   2.4528  -1.5031   1.2710
 9KR  H17  H  HCH2  0   0.234   2.1799   0.7479   1.8554
 9KR  H18  H  HCH2  0   0.222   2.0918   1.2888   0.1962
 9KR  H19  H  HCH2  0   0.235  -0.1833   0.8634   1.8837
 9KR  H20  H  HCH2  0   0.221  -0.2142   1.1031   0.1492
 9KR  H21  H  HCH1  0   0.230   0.0858  -1.5030   1.6795
 9KR  H22  H  HCH3  0   0.232   0.9018   0.1673  -1.6864
 9KR  H23  H  HCH3  0   0.229   1.4170  -1.3641  -2.3776
 9KR  H24  H  HCH3  0   0.236  -0.2786  -1.0862  -2.0204
 9KR  H25  H  HCH2  0   0.231   1.5881  -3.4539  -0.9753
 9KR  H26  H  HCH2  0   0.211   1.1188  -3.4038   0.7126
 9KR  H27  H  HCH2  0   0.222  -0.7371  -3.2439  -1.7121
 9KR  H28  H  HCH2  0   0.233  -0.5840  -4.5846  -0.6040
 9KR  H29  H  HCH2  0   0.245  -2.6111  -3.2073  -0.1425
 9KR  H30  H  HCH2  0   0.230  -1.5271  -3.3147   1.2279
 9KR  H31  H  H     0   0.230  -2.2630   0.5328   0.2426
 9KR  H32  H  H     0   0.230  -4.1079  -1.8712  -0.4352
 9KR  H33  H  HCH2  0   0.248  -6.4226  -0.0202  -1.9730
 9KR  H34  H  HCH2  0   0.252  -6.2705  -1.4805  -1.0033
 9KR  H35  H  HCH2  0   0.257  -3.7232   1.8585  -0.0753
 9KR  H36  H  HCH2  0   0.244  -4.8627   2.0050  -1.4096
 9KR  H37  H  HCH1  0   0.221  -5.5857   1.6840   1.5219
 9KR  H38  H  HOH1  0   0.454  -6.1618   3.8577   1.2839
 9KR  H39  H  H     0   0.240  -9.0739   2.1052  -0.6106
 9KR  H40  H  H     0   0.238  -8.0164   3.5631  -0.2337
 9KR  H41  H  HCH1  0   0.225  -8.2710  -0.0672  -0.4681
 9KR  H42  H  HOH1  0   0.450  -7.8113  -0.1214   1.8089

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
 9KR  C21  C2   double  1.328  0.020  1.328
 9KR  O1   C1   single  1.414  0.020  1.414
 9KR  C2   C1   single  1.509  0.020  1.509
 9KR  C2   C3   single  1.509  0.020  1.509
 9KR  C1   C    single  1.528  0.020  1.528
 9KR  C3   O    single  1.405  0.020  1.405
 9KR  C3   C4   single  1.533  0.020  1.533
 9KR  C    C5   single  1.501  0.020  1.501
 9KR  C4   C5   single  1.502  0.020  1.502
 9KR  C5   C6   double  1.342  0.020  1.342
 9KR  C6   C7   single  1.452  0.020  1.452
 9KR  C7   C8   double  1.343  0.020  1.343
 9KR  C8   C9   single  1.497  0.020  1.497
 9KR  C8   C13  single  1.505  0.020  1.505
 9KR  C14  C9   single  1.520  0.020  1.520
 9KR  C14  C15  single  1.540  0.020  1.540
 9KR  C17  C10  single  1.531  0.020  1.531
 9KR  C9   C10  single  1.550  0.020  1.550
 9KR  C13  C12  single  1.533  0.020  1.533
 9KR  C15  C16  single  1.553  0.020  1.553
 9KR  C10  C16  single  1.548  0.020  1.548
 9KR  C10  C11  single  1.531  0.020  1.531
 9KR  C12  C11  single  1.529  0.020  1.529
 9KR  C20  C22  single  1.520  0.020  1.520
 9KR  C20  C18  single  1.536  0.020  1.536
 9KR  C16  C18  single  1.537  0.020  1.537
 9KR  C22  C23  single  1.507  0.020  1.507
 9KR  O2   C23  double  1.216  0.020  1.216
 9KR  C18  C19  single  1.526  0.020  1.526
 9KR  C23  C24  single  1.479  0.020  1.479
 9KR  C24  C25  double  1.335  0.020  1.335
 9KR  C25  C26  single  1.486  0.020  1.486
 9KR  C24  H1   single  0.930  0.020  1.080
 9KR  C25  H3   single  0.930  0.020  1.080
 9KR  C26  H5   single  0.970  0.020  1.090
 9KR  C26  H6   single  0.970  0.020  1.090
 9KR  C26  H7   single  0.970  0.020  1.090
 9KR  C22  H8   single  0.970  0.020  1.090
 9KR  C22  H9   single  0.970  0.020  1.090
 9KR  C20  H10  single  0.970  0.020  1.090
 9KR  C20  H11  single  0.970  0.020  1.090
 9KR  C18  H12  single  0.970  0.020  1.090
 9KR  C19  H13  single  0.970  0.020  1.090
 9KR  C19  H14  single  0.970  0.020  1.090
 9KR  C19  H15  single  0.970  0.020  1.090
 9KR  C16  H16  single  0.970  0.020  1.090
 9KR  C15  H17  single  0.970  0.020  1.090
 9KR  C15  H18  single  0.970  0.020  1.090
 9KR  C14  H19  single  0.970  0.020  1.090
 9KR  C14  H20  single  0.970  0.020  1.090
 9KR  C9   H21  single  0.970  0.020  1.090
 9KR  C17  H22  single  0.970  0.020  1.090
 9KR  C17  H23  single  0.970  0.020  1.090
 9KR  C17  H24  single  0.970  0.020  1.090
 9KR  C11  H25  single  0.970  0.020  1.090
 9KR  C11  H26  single  0.970  0.020  1.090
 9KR  C12  H27  single  0.970  0.020  1.090
 9KR  C12  H28  single  0.970  0.020  1.090
 9KR  C13  H29  single  0.970  0.020  1.090
 9KR  C13  H30  single  0.970  0.020  1.090
 9KR  C7   H31  single  0.930  0.020  1.080
 9KR  C6   H32  single  0.930  0.020  1.080
 9KR  C    H33  single  0.970  0.020  1.090
 9KR  C    H34  single  0.970  0.020  1.090
 9KR  C4   H35  single  0.970  0.020  1.090
 9KR  C4   H36  single  0.970  0.020  1.090
 9KR  C3   H37  single  0.970  0.020  1.090
 9KR  O    H38  single  0.850  0.020  0.980
 9KR  C21  H39  single  0.930  0.020  1.080
 9KR  C21  H40  single  0.930  0.020  1.080
 9KR  C1   H41  single  0.970  0.020  1.090
 9KR  O1   H42  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
 9KR  C22  C23  C24  115.21  3.000
 9KR  C24  C23  O2   122.37  3.000
 9KR  C22  C23  O2   122.42  3.000
 9KR  H1   C24  C25  120.22  3.000
 9KR  H1   C24  C23  117.26  3.000
 9KR  C25  C24  C23  122.52  3.000
 9KR  H3   C25  C26  116.37  3.000
 9KR  H3   C25  C24  118.60  3.000
 9KR  C26  C25  C24  125.03  3.000
 9KR  H7   C26  H6   106.23  3.000
 9KR  H7   C26  H5   108.57  3.000
 9KR  H6   C26  H5   108.64  3.000
 9KR  H7   C26  C25  110.38  3.000
 9KR  H6   C26  C25  110.41  3.000
 9KR  H5   C26  C25  112.40  3.000
 9KR  H9   C22  H8   104.46  3.000
 9KR  H9   C22  C20  111.98  3.000
 9KR  H8   C22  C20  110.61  3.000
 9KR  H9   C22  C23  106.56  3.000
 9KR  H8   C22  C23  107.79  3.000
 9KR  C20  C22  C23  114.82  3.000
 9KR  H11  C20  H10  106.07  3.000
 9KR  H11  C20  C18  109.41  3.000
 9KR  H10  C20  C18  109.02  3.000
 9KR  H11  C20  C22  108.18  3.000
 9KR  H10  C20  C22  109.89  3.000
 9KR  C18  C20  C22  113.97  3.000
 9KR  H12  C18  C16  107.84  3.000
 9KR  H12  C18  C19  108.39  3.000
 9KR  C16  C18  C19  113.32  3.000
 9KR  H12  C18  C20  107.22  3.000
 9KR  C19  C18  C20  110.64  3.000
 9KR  C16  C18  C20  109.20  3.000
 9KR  H15  C19  H14  106.34  3.000
 9KR  H15  C19  H13  107.37  3.000
 9KR  H14  C19  H13  107.73  3.000
 9KR  H15  C19  C18  111.71  3.000
 9KR  H14  C19  C18  112.23  3.000
 9KR  H13  C19  C18  111.19  3.000
 9KR  H16  C16  C10  106.75  3.000
 9KR  H16  C16  C15  108.40  3.000
 9KR  C10  C16  C15  103.61  3.000
 9KR  H16  C16  C18  107.02  3.000
 9KR  C10  C16  C18  118.89  3.000
 9KR  C15  C16  C18  111.73  3.000
 9KR  H18  C15  H17  106.26  3.000
 9KR  H18  C15  C14  110.50  3.000
 9KR  H17  C15  C14  111.44  3.000
 9KR  H18  C15  C16  110.27  3.000
 9KR  H17  C15  C16  111.01  3.000
 9KR  C14  C15  C16  107.40  3.000
 9KR  H20  C14  H19  106.67  3.000
 9KR  H20  C14  C9   111.26  3.000
 9KR  H19  C14  C9   112.09  3.000
 9KR  H20  C14  C15  110.52  3.000
 9KR  H19  C14  C15  112.73  3.000
 9KR  C9   C14  C15  103.66  3.000
 9KR  H21  C9   C8   106.38  3.000
 9KR  H21  C9   C10  104.96  3.000
 9KR  C8   C9   C10  112.52  3.000
 9KR  H21  C9   C14  106.92  3.000
 9KR  C10  C9   C14  104.28  3.000
 9KR  C8   C9   C14  120.67  3.000
 9KR  C11  C10  C17  110.80  3.000
 9KR  C11  C10  C9   107.30  3.000
 9KR  C17  C10  C9   111.06  3.000
 9KR  C11  C10  C16  116.38  3.000
 9KR  C9   C10  C16  100.21  3.000
 9KR  C17  C10  C16  110.54  3.000
 9KR  H24  C17  H23  107.09  3.000
 9KR  H24  C17  H22  107.01  3.000
 9KR  H23  C17  H22  107.22  3.000
 9KR  H24  C17  C10  112.10  3.000
 9KR  H23  C17  C10  110.93  3.000
 9KR  H22  C17  C10  112.20  3.000
 9KR  H26  C11  H25  106.48  3.000
 9KR  H26  C11  C12  109.35  3.000
 9KR  H25  C11  C12  108.89  3.000
 9KR  H26  C11  C10  108.73  3.000
 9KR  H25  C11  C10  111.75  3.000
 9KR  C12  C11  C10  111.49  3.000
 9KR  H28  C12  H27  106.05  3.000
 9KR  H28  C12  C13  109.00  3.000
 9KR  H27  C12  C13  109.39  3.000
 9KR  H28  C12  C11  109.60  3.000
 9KR  H27  C12  C11  109.74  3.000
 9KR  C13  C12  C11  112.83  3.000
 9KR  H30  C13  H29  106.36  3.000
 9KR  H30  C13  C8   107.83  3.000
 9KR  H29  C13  C8   112.42  3.000
 9KR  H30  C13  C12  108.28  3.000
 9KR  H29  C13  C12  109.72  3.000
 9KR  C8   C13  C12  111.98  3.000
 9KR  C7   C8   C13  125.61  3.000
 9KR  C13  C8   C9   111.59  3.000
 9KR  C7   C8   C9   122.80  3.000
 9KR  H31  C7   C6   116.34  3.000
 9KR  H31  C7   C8   117.06  3.000
 9KR  C6   C7   C8   126.59  3.000
 9KR  H32  C6   C5   116.48  3.000
 9KR  H32  C6   C7   117.02  3.000
 9KR  C5   C6   C7   126.50  3.000
 9KR  C4   C5   C    113.53  3.000
 9KR  C4   C5   C6   125.29  3.000
 9KR  C    C5   C6   121.18  3.000
 9KR  H34  C    H33  107.04  3.000
 9KR  H34  C    C1   109.90  3.000
 9KR  H33  C    C1   107.25  3.000
 9KR  H34  C    C5   111.33  3.000
 9KR  H33  C    C5   109.75  3.000
 9KR  C1   C    C5   111.40  3.000
 9KR  H36  C4   H35  107.25  3.000
 9KR  H36  C4   C3   108.06  3.000
 9KR  H35  C4   C3   109.14  3.000
 9KR  H36  C4   C5   109.04  3.000
 9KR  H35  C4   C5   112.44  3.000
 9KR  C3   C4   C5   110.75  3.000
 9KR  H37  C3   C2   108.10  3.000
 9KR  H37  C3   O    110.39  3.000
 9KR  C2   C3   O    113.82  3.000
 9KR  H37  C3   C4   107.34  3.000
 9KR  O    C3   C4   107.88  3.000
 9KR  C2   C3   C4   109.11  3.000
 9KR  H38  O    C3   108.52  3.000
 9KR  C1   C2   C21  121.72  3.000
 9KR  C1   C2   C3   114.32  3.000
 9KR  C21  C2   C3   123.91  3.000
 9KR  H40  C21  H39  116.37  3.000
 9KR  H40  C21  C2   122.75  3.000
 9KR  H39  C21  C2   120.88  3.000
 9KR  H41  C1   O1   110.81  3.000
 9KR  H41  C1   C2   108.94  3.000
 9KR  O1   C1   C2   111.49  3.000
 9KR  H41  C1   C    108.69  3.000
 9KR  C2   C1   C    109.32  3.000
 9KR  O1   C1   C    107.54  3.000
 9KR  H42  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
 9KR  Var_01  C9   C14  C15  C16     9.98  30.0  1
 9KR  Var_02  C12  C13  C8   C9    -51.72  30.0  1
 9KR  Var_03  C13  C12  C11  C10   -54.13  30.0  1
 9KR  Var_04  C8   C13  C12  C11    50.31  30.0  1
 9KR  Var_05  C3   C4   C5   C      55.29  30.0  1
 9KR  Var_06  C1   C    C5   C4    -54.78  30.0  1
 9KR  Var_07  C6   C7   C8   C9    179.28  30.0  2
 9KR  Var_08  C5   C6   C7   C8   -179.11  30.0  1
 9KR  Var_09  C    C5   C6   C7    179.61  30.0  2
 9KR  Var_10  H39  C21  C2   C3    178.87  30.0  2
 9KR  Var_11  C26  C25  C24  C23   179.93   0.0  2
 9KR  Var_12  C20  C22  C23  O2      2.48  30.0  2
 9KR  Var_13  C25  C24  C23  O2      0.89  30.0  2
 9KR  Var_14  C18  C20  C22  C23   173.24  30.0  2
 9KR  Var_15  H5   C26  C25  C24     1.34  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
 9KR  chir_01  C18  C20  C16  C19  positiv
 9KR  chir_02  C16  C18  C10  C15  positiv
 9KR  chir_03  C9   C10  C14  C8   negativ
 9KR  chir_04  C10  C16  C9   C11  positiv
 9KR  chir_05  C3   O    C4   C2   positiv
 9KR  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
 9KR  plan-1  O2   0.020
 9KR  plan-1  C23  0.020
 9KR  plan-1  C24  0.020
 9KR  plan-1  C22  0.020
 9KR  plan-2  C23  0.020
 9KR  plan-2  C24  0.020
 9KR  plan-2  C25  0.020
 9KR  plan-2  C26  0.020
 9KR  plan-2  H1   0.020
 9KR  plan-2  H3   0.020

