# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 16 16:22:55 2020
#   Inital geometry file: a 166 line input string
#   Ligand name: (2S,4E,6E)-2-[(1R,3R,7E,17beta)-1,3-dihydroxy-2-methylidene-9,10-secoestra-5,7-dien-17-yl]octa-4,6-dien-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C/C=C/C=C/C(=O)[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
 9KX  9KX  (2S,4E,6E)-2-[(1R,3R,7E,17beta)-1,3-dihydroxy-2-methylidene-9,10-secoestra-5,7-dien-17-yl]octa-4,6-dien-3-one  ligand  68  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 OK
;

data_comp_9KX
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
 9KX  O1   O  OH1   0  -0.665  -5.4852  -3.4729  -0.5236
 9KX  C1   C  CH1   0   0.048  -5.6269  -2.0758  -0.4872
 9KX  C2   C  C     0   0.067  -6.9886  -1.6131  -0.0307
 9KX  C3   C  CH1   0  -0.002  -7.1315  -0.1152   0.0800
 9KX  C4   C  CH2   0  -0.511  -6.0503   0.4275   1.0137
 9KX  C5   C  C     0   0.117  -4.6853  -0.0271   0.5852
 9KX  C6   C  C1    0  -0.331  -3.7061   0.8562   0.3358
 9KX  C7   C  C1    0  -0.368  -2.3531   0.5489  -0.0910
 9KX  C8   C  C     0   0.158  -1.3647   1.4303  -0.3116
 9KX  C9   C  C2    0  -0.604  -7.9767  -2.4354   0.3038
 9KX  C10  C  CH1   0  -0.245   0.0065   1.0186  -0.7471
 9KX  C11  C  CT    0  -0.061   1.1040   1.4885   0.2403
 9KX  C12  C  CH2   0  -0.417   1.0339   3.0150   0.3169
 9KX  C13  C  CH2   0  -0.435  -0.3588   3.4907   0.7314
 9KX  C14  C  CH2   0  -0.506  -1.4699   2.9239  -0.1604
 9KX  C15  C  CH2   0  -0.457   0.3386  -0.4422  -1.0067
 9KX  C16  C  CH2   0  -0.439   1.8787  -0.4629  -1.0089
 9KX  C17  C  CH1   0  -0.173   2.3566   0.9051  -0.4517
 9KX  C18  C  CH3   0  -0.683   0.9007   0.8654   1.6241
 9KX  C19  C  CH1   0  -0.388   3.6251   0.7482   0.3855
 9KX  C20  C  CH3   0  -0.665   4.1616   2.0465   1.0045
 9KX  C21  C  C     0   0.400   4.7701   0.1853  -0.4414
 9KX  C22  C  C1    0  -0.384   5.7557  -0.6231   0.2949
 9KX  C23  C  C1    0  -0.180   6.8980  -1.0533  -0.2672
 9KX  C24  C  C1    0  -0.237   7.8962  -1.8381   0.4180
 9KX  C25  C  C1    0  -0.204   9.0452  -2.2068  -0.1640
 9KX  C26  C  CH3   0  -0.715  10.1162  -3.0017   0.4923
 9KX  O    O  OH1   0  -0.664  -6.9645   0.5158  -1.1749
 9KX  C    C  CH2   0  -0.528  -4.5615  -1.5185   0.4639
 9KX  H1   H  HOH1  0   0.454  -6.0217  -3.8155  -1.2457
 9KX  H2   H  HCH1  0   0.221  -5.4359  -1.6457  -1.4805
 9KX  H3   H  HCH1  0   0.226  -8.1158   0.1189   0.5061
 9KX  H4   H  HCH2  0   0.252  -6.1107   1.5175   1.0589
 9KX  H5   H  HCH2  0   0.248  -6.2691   0.0514   2.0192
 9KX  H6   H  H     0   0.231  -3.9525   1.9041   0.4751
 9KX  H7   H  H     0   0.231  -2.1248  -0.4983  -0.2545
 9KX  H8   H  H     0   0.240  -8.9308  -2.0498   0.6422
 9KX  H9   H  H     0   0.238  -7.8800  -3.5125   0.2648
 9KX  H10  H  HCH1  0   0.232   0.2110   1.5631  -1.6831
 9KX  H11  H  HCH2  0   0.232   1.7710   3.4169   1.0151
 9KX  H12  H  HCH2  0   0.214   1.2812   3.4275  -0.6683
 9KX  H13  H  HCH2  0   0.223  -0.5506   3.2121   1.7706
 9KX  H14  H  HCH2  0   0.234  -0.3984   4.5819   0.6985
 9KX  H15  H  HCH2  0   0.231  -1.3739   3.3727  -1.1568
 9KX  H16  H  HCH2  0   0.245  -2.4414   3.2351   0.2228
 9KX  H17  H  HCH2  0   0.222  -0.0555  -1.0848  -0.2164
 9KX  H18  H  HCH2  0   0.236  -0.0893  -0.8002  -1.9442
 9KX  H19  H  HCH2  0   0.224   2.2551  -1.2847  -0.3934
 9KX  H20  H  HCH2  0   0.236   2.2696  -0.6288  -2.0126
 9KX  H21  H  HCH1  0   0.223   2.5913   1.5659  -1.2944
 9KX  H22  H  HCH3  0   0.233   1.0618  -0.2141   1.6208
 9KX  H23  H  HCH3  0   0.230   1.5926   1.2943   2.3516
 9KX  H24  H  HCH3  0   0.239  -0.1072   1.0366   2.0023
 9KX  H25  H  HCH1  0   0.251   3.4303   0.0401   1.1988
 9KX  H26  H  HCH3  0   0.244   3.4975   2.4219   1.7808
 9KX  H27  H  HCH3  0   0.245   5.1363   1.8904   1.4709
 9KX  H28  H  HCH3  0   0.231   4.2748   2.8247   0.2479
 9KX  H29  H  H     0   0.259   5.5366  -0.8571   1.3312
 9KX  H30  H  H     0   0.264   7.1023  -0.7946  -1.3026
 9KX  H31  H  H     0   0.253   7.6951  -2.1260   1.4460
 9KX  H32  H  H     0   0.257   9.2265  -1.9040  -1.1919
 9KX  H33  H  HCH3  0   0.251  11.0478  -2.4323   0.5337
 9KX  H34  H  HCH3  0   0.244   9.8479  -3.2934   1.5068
 9KX  H35  H  HCH3  0   0.250  10.3351  -3.9052  -0.0807
 9KX  H36  H  HOH1  0   0.451  -7.6463   0.1826  -1.7672
 9KX  H37  H  HCH2  0   0.244  -4.7161  -1.9711   1.4513
 9KX  H38  H  HCH2  0   0.257  -3.5756  -1.8276   0.1178
 9KX  O2   O  O     0  -0.424   4.8946   0.4405  -1.6258

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
 9KX  C9   C2   double  1.328  0.020  1.328
 9KX  O    C3   single  1.414  0.020  1.414
 9KX  C2   C3   single  1.509  0.020  1.509
 9KX  C2   C1   single  1.509  0.020  1.509
 9KX  C3   C4   single  1.528  0.020  1.528
 9KX  C1   O1   single  1.405  0.020  1.405
 9KX  C1   C    single  1.533  0.020  1.533
 9KX  C4   C5   single  1.501  0.020  1.501
 9KX  C    C5   single  1.501  0.020  1.501
 9KX  C5   C6   double  1.342  0.020  1.342
 9KX  C6   C7   single  1.452  0.020  1.452
 9KX  C7   C8   double  1.343  0.020  1.343
 9KX  C8   C10  single  1.496  0.020  1.496
 9KX  C8   C14  single  1.505  0.020  1.505
 9KX  C15  C10  single  1.520  0.020  1.520
 9KX  C15  C16  single  1.540  0.020  1.540
 9KX  C10  C11  single  1.549  0.020  1.549
 9KX  C14  C13  single  1.533  0.020  1.533
 9KX  C18  C11  single  1.531  0.020  1.531
 9KX  C16  C17  single  1.553  0.020  1.553
 9KX  O2   C21  double  1.218  0.020  1.218
 9KX  C11  C17  single  1.545  0.020  1.545
 9KX  C11  C12  single  1.530  0.020  1.530
 9KX  C13  C12  single  1.529  0.020  1.529
 9KX  C21  C22  single  1.472  0.020  1.472
 9KX  C21  C19  single  1.520  0.020  1.520
 9KX  C17  C19  single  1.528  0.020  1.528
 9KX  C25  C26  single  1.487  0.020  1.487
 9KX  C25  C24  double  1.340  0.020  1.340
 9KX  C22  C23  double  1.344  0.020  1.344
 9KX  C23  C24  single  1.443  0.020  1.443
 9KX  C19  C20  single  1.535  0.020  1.535
 9KX  O1   H1   single  0.850  0.020  0.980
 9KX  C1   H2   single  0.970  0.020  1.090
 9KX  C3   H3   single  0.970  0.020  1.090
 9KX  C4   H4   single  0.970  0.020  1.090
 9KX  C4   H5   single  0.970  0.020  1.090
 9KX  C6   H6   single  0.930  0.020  1.080
 9KX  C7   H7   single  0.930  0.020  1.080
 9KX  C9   H8   single  0.930  0.020  1.080
 9KX  C9   H9   single  0.930  0.020  1.080
 9KX  C10  H10  single  0.970  0.020  1.090
 9KX  C12  H11  single  0.970  0.020  1.090
 9KX  C12  H12  single  0.970  0.020  1.090
 9KX  C13  H13  single  0.970  0.020  1.090
 9KX  C13  H14  single  0.970  0.020  1.090
 9KX  C14  H15  single  0.970  0.020  1.090
 9KX  C14  H16  single  0.970  0.020  1.090
 9KX  C15  H17  single  0.970  0.020  1.090
 9KX  C15  H18  single  0.970  0.020  1.090
 9KX  C16  H19  single  0.970  0.020  1.090
 9KX  C16  H20  single  0.970  0.020  1.090
 9KX  C17  H21  single  0.970  0.020  1.090
 9KX  C18  H22  single  0.970  0.020  1.090
 9KX  C18  H23  single  0.970  0.020  1.090
 9KX  C18  H24  single  0.970  0.020  1.090
 9KX  C19  H25  single  0.970  0.020  1.090
 9KX  C20  H26  single  0.970  0.020  1.090
 9KX  C20  H27  single  0.970  0.020  1.090
 9KX  C20  H28  single  0.970  0.020  1.090
 9KX  C22  H29  single  0.930  0.020  1.080
 9KX  C23  H30  single  0.930  0.020  1.080
 9KX  C24  H31  single  0.930  0.020  1.080
 9KX  C25  H32  single  0.930  0.020  1.080
 9KX  C26  H33  single  0.970  0.020  1.090
 9KX  C26  H34  single  0.970  0.020  1.090
 9KX  C26  H35  single  0.970  0.020  1.090
 9KX  O    H36  single  0.850  0.020  0.980
 9KX  C    H37  single  0.970  0.020  1.090
 9KX  C    H38  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
 9KX  H1   O1   C1   108.49  3.000
 9KX  H2   C1   C    107.31  3.000
 9KX  H2   C1   C2   108.07  3.000
 9KX  C    C1   C2   109.14  3.000
 9KX  H2   C1   O1   110.38  3.000
 9KX  C    C1   O1   107.91  3.000
 9KX  C2   C1   O1   113.82  3.000
 9KX  C9   C2   C3   121.71  3.000
 9KX  C3   C2   C1   114.34  3.000
 9KX  C9   C2   C1   123.90  3.000
 9KX  H3   C3   O    110.80  3.000
 9KX  H3   C3   C4   108.75  3.000
 9KX  O    C3   C4   107.47  3.000
 9KX  H3   C3   C2   108.97  3.000
 9KX  C4   C3   C2   109.29  3.000
 9KX  O    C3   C2   111.50  3.000
 9KX  H5   C4   H4   107.06  3.000
 9KX  H5   C4   C5   109.86  3.000
 9KX  H4   C4   C5   111.35  3.000
 9KX  H5   C4   C3   107.31  3.000
 9KX  H4   C4   C3   109.90  3.000
 9KX  C5   C4   C3   111.19  3.000
 9KX  C    C5   C6   125.35  3.000
 9KX  C6   C5   C4   121.15  3.000
 9KX  C    C5   C4   113.50  3.000
 9KX  H6   C6   C7   116.98  3.000
 9KX  H6   C6   C5   116.48  3.000
 9KX  C7   C6   C5   126.54  3.000
 9KX  H7   C7   C8   117.02  3.000
 9KX  H7   C7   C6   116.42  3.000
 9KX  C8   C7   C6   126.55  3.000
 9KX  C14  C8   C10  111.49  3.000
 9KX  C14  C8   C7   125.70  3.000
 9KX  C10  C8   C7   122.81  3.000
 9KX  H9   C9   H8   116.38  3.000
 9KX  H9   C9   C2   122.72  3.000
 9KX  H8   C9   C2   120.90  3.000
 9KX  H10  C10  C15  106.81  3.000
 9KX  H10  C10  C11  105.07  3.000
 9KX  C15  C10  C11  104.21  3.000
 9KX  H10  C10  C8   106.34  3.000
 9KX  C11  C10  C8   112.34  3.000
 9KX  C15  C10  C8   120.94  3.000
 9KX  C18  C11  C17  111.02  3.000
 9KX  C17  C11  C12  115.86  3.000
 9KX  C18  C11  C12  110.77  3.000
 9KX  C12  C11  C10  107.58  3.000
 9KX  C17  C11  C10  100.04  3.000
 9KX  C18  C11  C10  111.01  3.000
 9KX  H12  C12  H11  106.49  3.000
 9KX  H12  C12  C13  109.39  3.000
 9KX  H11  C12  C13  109.09  3.000
 9KX  H12  C12  C11  108.67  3.000
 9KX  H11  C12  C11  111.61  3.000
 9KX  C13  C12  C11  111.45  3.000
 9KX  H14  C13  H13  106.08  3.000
 9KX  H14  C13  C14  108.99  3.000
 9KX  H13  C13  C14  109.37  3.000
 9KX  H14  C13  C12  109.61  3.000
 9KX  H13  C13  C12  109.78  3.000
 9KX  C14  C13  C12  112.79  3.000
 9KX  H16  C14  H15  106.30  3.000
 9KX  H16  C14  C13  109.63  3.000
 9KX  H15  C14  C13  108.28  3.000
 9KX  H16  C14  C8   112.40  3.000
 9KX  H15  C14  C8   107.98  3.000
 9KX  C13  C14  C8   112.00  3.000
 9KX  H18  C15  H17  106.69  3.000
 9KX  H18  C15  C16  112.73  3.000
 9KX  H17  C15  C16  110.73  3.000
 9KX  H18  C15  C10  112.11  3.000
 9KX  H17  C15  C10  111.29  3.000
 9KX  C16  C15  C10  103.39  3.000
 9KX  H20  C16  H19  106.29  3.000
 9KX  H20  C16  C17  110.75  3.000
 9KX  H19  C16  C17  110.74  3.000
 9KX  H20  C16  C15  111.23  3.000
 9KX  H19  C16  C15  110.70  3.000
 9KX  C17  C16  C15  107.18  3.000
 9KX  H21  C17  C19  107.78  3.000
 9KX  H21  C17  C16  108.73  3.000
 9KX  C19  C17  C16  111.20  3.000
 9KX  H21  C17  C11  106.87  3.000
 9KX  C19  C17  C11  117.80  3.000
 9KX  C16  C17  C11  104.11  3.000
 9KX  H24  C18  H23  107.04  3.000
 9KX  H24  C18  H22  107.03  3.000
 9KX  H23  C18  H22  107.28  3.000
 9KX  H24  C18  C11  111.87  3.000
 9KX  H23  C18  C11  110.99  3.000
 9KX  H22  C18  C11  112.35  3.000
 9KX  H25  C19  C21  107.35  3.000
 9KX  H25  C19  C20  108.02  3.000
 9KX  C21  C19  C20  105.61  3.000
 9KX  H25  C19  C17  109.00  3.000
 9KX  C20  C19  C17  115.10  3.000
 9KX  C21  C19  C17  111.43  3.000
 9KX  H28  C20  H27  107.79  3.000
 9KX  H28  C20  H26  108.17  3.000
 9KX  H27  C20  H26  106.82  3.000
 9KX  H28  C20  C19  111.08  3.000
 9KX  H27  C20  C19  111.31  3.000
 9KX  H26  C20  C19  111.47  3.000
 9KX  C22  C21  O2   122.21  3.000
 9KX  C22  C21  C19  115.82  3.000
 9KX  O2   C21  C19  121.88  3.000
 9KX  H29  C22  C23  120.15  3.000
 9KX  H29  C22  C21  117.45  3.000
 9KX  C23  C22  C21  122.40  3.000
 9KX  H30  C23  C24  116.87  3.000
 9KX  H30  C23  C22  118.82  3.000
 9KX  C24  C23  C22  124.31  3.000
 9KX  H31  C24  C25  119.79  3.000
 9KX  H31  C24  C23  117.74  3.000
 9KX  C25  C24  C23  122.46  3.000
 9KX  H32  C25  C26  116.51  3.000
 9KX  H32  C25  C24  118.51  3.000
 9KX  C26  C25  C24  124.98  3.000
 9KX  H35  C26  H34  108.46  3.000
 9KX  H35  C26  H33  106.26  3.000
 9KX  H34  C26  H33  108.33  3.000
 9KX  H35  C26  C25  110.80  3.000
 9KX  H34  C26  C25  112.14  3.000
 9KX  H33  C26  C25  110.63  3.000
 9KX  H36  O    C3   107.93  3.000
 9KX  H38  C    H37  107.24  3.000
 9KX  H38  C    C5   112.46  3.000
 9KX  H37  C    C5   109.00  3.000
 9KX  H38  C    C1   109.18  3.000
 9KX  H37  C    C1   108.08  3.000
 9KX  C5   C    C1   110.72  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
 9KX  Var_01  C4   C5   C    C1     55.50  30.0  1
 9KX  Var_02  C    C5   C4   C3    -55.21  30.0  1
 9KX  Var_03  C12  C13  C14  C8     50.40  30.0  1
 9KX  Var_04  C13  C14  C8   C10   -52.08  30.0  1
 9KX  Var_05  C17  C16  C15  C10    12.01  30.0  1
 9KX  Var_06  C14  C13  C12  C11   -53.83  30.0  1
 9KX  Var_07  C7   C6   C5   C4   -179.58  30.0  2
 9KX  Var_08  C8   C7   C6   C5   -178.39  30.0  2
 9KX  Var_09  C10  C8   C7   C6    179.77  30.0  2
 9KX  Var_10  H8   C9   C2   C1    178.91  30.0  2
 9KX  Var_11  C24  C23  C22  C21   179.50   0.0  2
 9KX  Var_12  C26  C25  C24  C23   179.36   0.0  2
 9KX  Var_13  C23  C22  C21  C19  -172.08  30.0  2
 9KX  Var_14  C25  C24  C23  C22  -177.52  30.0  2
 9KX  Var_15  H33  C26  C25  C24  -118.80  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
 9KX  chir_01  C1   C2   O1   C    positiv
 9KX  chir_02  C3   O    C4   C2   positiv
 9KX  chir_03  C10  C8   C15  C11  positiv
 9KX  chir_04  C11  C17  C12  C10  negativ
 9KX  chir_05  C17  C16  C11  C19  negativ
 9KX  chir_06  C19  C21  C17  C20  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
 9KX  plan-1  C19  0.020
 9KX  plan-1  C21  0.020
 9KX  plan-1  C22  0.020
 9KX  plan-1  O2   0.020
 9KX  plan-2  C23  0.020
 9KX  plan-2  C24  0.020
 9KX  plan-2  C25  0.020
 9KX  plan-2  C26  0.020
 9KX  plan-2  H31  0.020
 9KX  plan-2  H32  0.020
 9KX  plan-3  C21  0.020
 9KX  plan-3  C22  0.020
 9KX  plan-3  C23  0.020
 9KX  plan-3  C24  0.020
 9KX  plan-3  H29  0.020
 9KX  plan-3  H30  0.020

