# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jul  4 22:09:04 2020
#   Inital geometry file: a 167 line input string
#   Ligand name: (1R,3R,7E,17beta)-17-[(1S)-5-hydroxy-1,5-dimethylhexyl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CCCC(C)(C)O)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3C[C@@H](O)C(=C)[C@H](O)C3
#
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
 VDZ  VDZ  (1R,3R,7E,17beta)-17-[(1S)-5-hydroxy-1,5-dimethylhexyl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol  ligand  74  30  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VDZ
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
 VDZ  O1    O  OH1   0  -0.659  -4.9650   1.3112   1.8093
 VDZ  C1    C  CH1   0  -0.001  -5.9760   0.3461   1.5946
 VDZ  C2    C  C     0   0.064  -7.0926   0.8931   0.7391
 VDZ  C28   C  C2    0  -0.604  -8.3433   0.9617   1.1817
 VDZ  C3    C  CH1   0   0.048  -6.6699   1.2803  -0.6563
 VDZ  O2    O  OH1   0  -0.665  -7.7220   1.7437  -1.4632
 VDZ  C4    C  CH2   0  -0.514  -6.0476   0.0577  -1.3391
 VDZ  C10   C  CH2   0  -0.524  -5.3293  -0.8463   0.8917
 VDZ  C5    C  C     0   0.119  -4.9241  -0.4984  -0.5105
 VDZ  C6    C  C1    0  -0.329  -3.6914  -0.6446  -1.0199
 VDZ  C7    C  C1    0  -0.361  -2.5168  -1.1266  -0.3160
 VDZ  C8    C  CR6   0   0.155  -1.3041  -1.3382  -0.8516
 VDZ  C9    C  C     0  -0.502  -0.9496  -1.1686  -2.3040
 VDZ  C11   C  C     0  -0.433   0.2775  -0.2721  -2.4954
 VDZ  C14   C  CR16  0  -0.242  -0.1232  -1.7936  -0.0533
 VDZ  C13   C  CR6   0  -0.064   1.0663  -0.8006  -0.1415
 VDZ  C12   C  C     0  -0.417   1.4604  -0.6807  -1.6172
 VDZ  C18   C  CH3   0  -0.674   0.6774   0.5646   0.4296
 VDZ  C15   C  CH2   0  -0.454  -0.2557  -2.0844   1.4337
 VDZ  C16   C  CH2   0  -0.446   1.1971  -2.0433   1.9457
 VDZ  C17   C  CH1   0  -0.162   2.0789  -1.5200   0.7822
 VDZ  C20   C  CH1   0  -0.228   3.3198  -0.7684   1.2867
 VDZ  C21   C  CH3   0  -0.674   4.1477  -1.6923   2.1818
 VDZ  C22   C  CH2   0  -0.402   4.1689  -0.2056   0.1414
 VDZ  C23   C  CH2   0  -0.425   5.5237   0.3726   0.5406
 VDZ  C24   C  CH2   0  -0.426   6.2122   1.0335  -0.6477
 VDZ  C25   C  CT    0   0.205   7.6013   1.6291  -0.3759
 VDZ  C26   C  CH3   0  -0.668   8.5842   0.5667   0.1019
 VDZ  C27   C  CH3   0  -0.670   8.1283   2.2711  -1.6597
 VDZ  O3    O  OH1   0  -0.683   7.5374   2.5992   0.6621
 VDZ  HO1   H  HOH1  0   0.449  -5.3624   2.0588   2.2675
 VDZ  H1    H  HCH1  0   0.225  -6.3956   0.0014   2.5491
 VDZ  H281  H  H     0   0.239  -8.5950   0.6510   2.1884
 VDZ  H282  H  H     0   0.238  -9.1629   1.3140   0.5692
 VDZ  H3    H  HCH1  0   0.219  -5.8841   2.0443  -0.5723
 VDZ  HO2   H  HOH1  0   0.453  -8.0206   2.5907  -1.1168
 VDZ  H41   H  HCH2  0   0.239  -6.8331  -0.6993  -1.4579
 VDZ  H42   H  HCH2  0   0.250  -5.6973   0.3324  -2.3364
 VDZ  H101  H  HCH2  0   0.259  -4.4980  -1.2137   1.4941
 VDZ  H102  H  HCH2  0   0.251  -6.0731  -1.6502   0.8604
 VDZ  H6    H  H     0   0.229  -3.5585  -0.3609  -2.0594
 VDZ  H7    H  H     0   0.230  -2.6321  -1.3225   0.7443
 VDZ  H91   H  H     0   0.229  -0.7196  -2.1615  -2.7106
 VDZ  H92   H  H     0   0.242  -1.7819  -0.7834  -2.8938
 VDZ  H111  H  H     0   0.231   0.5789  -0.2975  -3.5454
 VDZ  H112  H  H     0   0.221   0.0003   0.7641  -2.2855
 VDZ  H14   H  HCR6  0   0.229   0.2367  -2.7166  -0.5356
 VDZ  H121  H  H     0   0.210   1.8517  -1.6472  -1.9563
 VDZ  H122  H  H     0   0.230   2.2658   0.0414  -1.7597
 VDZ  H181  H  HCH3  0   0.231   0.4343   0.5096   1.4915
 VDZ  H182  H  HCH3  0   0.228   1.4907   1.2836   0.3173
 VDZ  H183  H  HCH3  0   0.236  -0.1985   0.9752  -0.0733
 VDZ  H151  H  HCH2  0   0.222  -0.8591  -1.3208   1.9298
 VDZ  H152  H  HCH2  0   0.232  -0.7416  -3.0426   1.6251
 VDZ  H161  H  HCH2  0   0.219   1.2788  -1.3818   2.8123
 VDZ  H162  H  HCH2  0   0.232   1.5325  -3.0263   2.2778
 VDZ  H17   H  HCH1  0   0.204   2.4417  -2.3904   0.2161
 VDZ  H20   H  HCH1  0   0.204   2.9843   0.0776   1.9010
 VDZ  H211  H  HCH3  0   0.237   3.5614  -2.0885   3.0103
 VDZ  H212  H  HCH3  0   0.209   4.5313  -2.5423   1.6109
 VDZ  H213  H  HCH3  0   0.231   5.0016  -1.1730   2.6164
 VDZ  H221  H  HCH2  0   0.201   4.3291  -0.9920  -0.6063
 VDZ  H222  H  HCH2  0   0.215   3.6023   0.5805  -0.3652
 VDZ  H231  H  HCH2  0   0.209   5.3981   1.0977   1.3504
 VDZ  H232  H  HCH2  0   0.220   6.1590  -0.4240   0.9331
 VDZ  H241  H  HCH2  0   0.213   6.3049   0.3035  -1.4587
 VDZ  H242  H  HCH2  0   0.214   5.5666   1.8302  -1.0397
 VDZ  H261  H  HCH3  0   0.222   8.6466  -0.2481  -0.6202
 VDZ  H262  H  HCH3  0   0.229   9.5850   0.9877   0.2166
 VDZ  H263  H  HCH3  0   0.232   8.2897   0.1404   1.0616
 VDZ  H271  H  HCH3  0   0.221   7.4541   3.0552  -2.0146
 VDZ  H272  H  HCH3  0   0.228   9.1108   2.7188  -1.4983
 VDZ  H273  H  HCH3  0   0.231   8.2232   1.5350  -2.4594
 VDZ  HO3   H  HOH1  0   0.447   6.9211   3.2892   0.3927

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
 VDZ  O1   C1    single  1.414  0.020  1.414
 VDZ  O1   HO1   single  0.850  0.020  0.980
 VDZ  C1   C2    single  1.509  0.020  1.509
 VDZ  C1   C10   single  1.528  0.020  1.528
 VDZ  C1   H1    single  0.970  0.020  1.090
 VDZ  C2   C28   double  1.328  0.020  1.328
 VDZ  C2   C3    single  1.509  0.020  1.509
 VDZ  C28  H281  single  0.930  0.020  1.080
 VDZ  C28  H282  single  0.930  0.020  1.080
 VDZ  C3   O2    single  1.405  0.020  1.405
 VDZ  C3   C4    single  1.532  0.020  1.532
 VDZ  C3   H3    single  0.970  0.020  1.090
 VDZ  O2   HO2   single  0.850  0.020  0.980
 VDZ  C4   C5    single  1.503  0.020  1.503
 VDZ  C4   H41   single  0.970  0.020  1.090
 VDZ  C4   H42   single  0.970  0.020  1.090
 VDZ  C10  C5    single  1.500  0.020  1.500
 VDZ  C10  H101  single  0.970  0.020  1.090
 VDZ  C10  H102  single  0.970  0.020  1.090
 VDZ  C5   C6    double  1.342  0.020  1.342
 VDZ  C6   C7    single  1.452  0.020  1.452
 VDZ  C6   H6    single  0.930  0.020  1.080
 VDZ  C7   C8    double  1.342  0.020  1.342
 VDZ  C7   H7    single  0.930  0.020  1.080
 VDZ  C8   C9    single  1.505  0.020  1.505
 VDZ  C8   C14   single  1.496  0.020  1.496
 VDZ  C9   C11   single  1.532  0.020  1.532
 VDZ  C9   H91   single  0.970  0.020  1.090
 VDZ  C9   H92   single  0.970  0.020  1.090
 VDZ  C11  C12   single  1.529  0.020  1.529
 VDZ  C11  H111  single  0.970  0.020  1.090
 VDZ  C11  H112  single  0.970  0.020  1.090
 VDZ  C14  C13   single  1.552  0.020  1.552
 VDZ  C14  C15   single  1.521  0.020  1.521
 VDZ  C14  H14   single  0.970  0.020  1.090
 VDZ  C13  C12   single  1.532  0.020  1.532
 VDZ  C13  C18   single  1.530  0.020  1.530
 VDZ  C13  C17   single  1.548  0.020  1.548
 VDZ  C12  H121  single  0.970  0.020  1.090
 VDZ  C12  H122  single  0.970  0.020  1.090
 VDZ  C18  H181  single  0.970  0.020  1.090
 VDZ  C18  H182  single  0.970  0.020  1.090
 VDZ  C18  H183  single  0.970  0.020  1.090
 VDZ  C15  C16   single  1.541  0.020  1.541
 VDZ  C15  H151  single  0.970  0.020  1.090
 VDZ  C15  H152  single  0.970  0.020  1.090
 VDZ  C16  C17   single  1.551  0.020  1.551
 VDZ  C16  H161  single  0.970  0.020  1.090
 VDZ  C16  H162  single  0.970  0.020  1.090
 VDZ  C17  C20   single  1.536  0.020  1.536
 VDZ  C17  H17   single  0.970  0.020  1.090
 VDZ  C20  C21   single  1.530  0.020  1.530
 VDZ  C20  C22   single  1.533  0.020  1.533
 VDZ  C20  H20   single  0.970  0.020  1.090
 VDZ  C21  H211  single  0.970  0.020  1.090
 VDZ  C21  H212  single  0.970  0.020  1.090
 VDZ  C21  H213  single  0.970  0.020  1.090
 VDZ  C22  C23   single  1.526  0.020  1.526
 VDZ  C22  H221  single  0.970  0.020  1.090
 VDZ  C22  H222  single  0.970  0.020  1.090
 VDZ  C23  C24   single  1.524  0.020  1.524
 VDZ  C23  H231  single  0.970  0.020  1.090
 VDZ  C23  H232  single  0.970  0.020  1.090
 VDZ  C24  C25   single  1.536  0.020  1.536
 VDZ  C24  H241  single  0.970  0.020  1.090
 VDZ  C24  H242  single  0.970  0.020  1.090
 VDZ  C25  C26   single  1.524  0.020  1.524
 VDZ  C25  C27   single  1.529  0.020  1.529
 VDZ  C25  O3    single  1.422  0.020  1.422
 VDZ  C26  H261  single  0.970  0.020  1.090
 VDZ  C26  H262  single  0.970  0.020  1.090
 VDZ  C26  H263  single  0.970  0.020  1.090
 VDZ  C27  H271  single  0.970  0.020  1.090
 VDZ  C27  H272  single  0.970  0.020  1.090
 VDZ  C27  H273  single  0.970  0.020  1.090
 VDZ  O3   HO3   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
 VDZ  HO1   O1   C1    107.89  3.000
 VDZ  H1    C1   C10   108.46  3.000
 VDZ  H1    C1   C2    108.89  3.000
 VDZ  C10   C1   C2    109.59  3.000
 VDZ  H1    C1   O1    110.82  3.000
 VDZ  C10   C1   O1    107.45  3.000
 VDZ  C2    C1   O1    111.57  3.000
 VDZ  C3    C2   C28   123.97  3.000
 VDZ  C3    C2   C1    114.21  3.000
 VDZ  C28   C2   C1    121.76  3.000
 VDZ  H282  C28  H281  116.32  3.000
 VDZ  H282  C28  C2    122.77  3.000
 VDZ  H281  C28  C2    120.91  3.000
 VDZ  H3    C3   C4    107.35  3.000
 VDZ  H3    C3   O2    110.50  3.000
 VDZ  C4    C3   O2    108.14  3.000
 VDZ  H3    C3   C2    107.94  3.000
 VDZ  C4    C3   C2    108.73  3.000
 VDZ  O2    C3   C2    113.97  3.000
 VDZ  HO2   O2   C3    108.41  3.000
 VDZ  H42   C4   H41   107.71  3.000
 VDZ  H42   C4   C5    110.90  3.000
 VDZ  H41   C4   C5    109.85  3.000
 VDZ  H42   C4   C3    109.66  3.000
 VDZ  H41   C4   C3    107.94  3.000
 VDZ  C5    C4   C3    110.68  3.000
 VDZ  H102  C10  H101  106.63  3.000
 VDZ  H102  C10  C5    109.07  3.000
 VDZ  H101  C10  C5    112.87  3.000
 VDZ  H102  C10  C1    107.36  3.000
 VDZ  H101  C10  C1    109.36  3.000
 VDZ  C5    C10  C1    111.31  3.000
 VDZ  C6    C5   C10   125.28  3.000
 VDZ  C6    C5   C4    121.19  3.000
 VDZ  C10   C5   C4    113.53  3.000
 VDZ  H6    C6   C7    116.87  3.000
 VDZ  H6    C6   C5    116.58  3.000
 VDZ  C7    C6   C5    126.55  3.000
 VDZ  H7    C7   C8    117.24  3.000
 VDZ  H7    C7   C6    116.62  3.000
 VDZ  C8    C7   C6    126.14  3.000
 VDZ  C14   C8   C9    111.31  3.000
 VDZ  C14   C8   C7    123.23  3.000
 VDZ  C9    C8   C7    125.46  3.000
 VDZ  H92   C9   H91   106.22  3.000
 VDZ  H92   C9   C11   109.70  3.000
 VDZ  H91   C9   C11   108.38  3.000
 VDZ  H92   C9   C8    112.47  3.000
 VDZ  H91   C9   C8    107.76  3.000
 VDZ  C11   C9   C8    112.04  3.000
 VDZ  H112  C11  H111  106.05  3.000
 VDZ  H112  C11  C12   109.83  3.000
 VDZ  H111  C11  C12   109.41  3.000
 VDZ  H112  C11  C9    109.13  3.000
 VDZ  H111  C11  C9    109.12  3.000
 VDZ  C12   C11  C9    113.06  3.000
 VDZ  H14   C14  C15   107.23  3.000
 VDZ  H14   C14  C13   105.12  3.000
 VDZ  C15   C14  C13   104.17  3.000
 VDZ  H14   C14  C8    106.21  3.000
 VDZ  C15   C14  C8    120.73  3.000
 VDZ  C13   C14  C8    112.32  3.000
 VDZ  C17   C13  C18   110.99  3.000
 VDZ  C17   C13  C12   116.28  3.000
 VDZ  C18   C13  C12   110.80  3.000
 VDZ  C17   C13  C14    99.79  3.000
 VDZ  C18   C13  C14   110.79  3.000
 VDZ  C12   C13  C14   107.58  3.000
 VDZ  H122  C12  H121  106.23  3.000
 VDZ  H122  C12  C13   111.56  3.000
 VDZ  H121  C12  C13   108.70  3.000
 VDZ  H122  C12  C11   108.62  3.000
 VDZ  H121  C12  C11   109.51  3.000
 VDZ  C13   C12  C11   112.03  3.000
 VDZ  H183  C18  H182  107.65  3.000
 VDZ  H183  C18  H181  106.79  3.000
 VDZ  H182  C18  H181  107.43  3.000
 VDZ  H183  C18  C13   111.60  3.000
 VDZ  H182  C18  C13   111.10  3.000
 VDZ  H181  C18  C13   112.03  3.000
 VDZ  H152  C15  H151  106.75  3.000
 VDZ  H152  C15  C16   112.63  3.000
 VDZ  H151  C15  C16   110.56  3.000
 VDZ  H152  C15  C14   112.23  3.000
 VDZ  H151  C15  C14   111.01  3.000
 VDZ  C16   C15  C14   103.74  3.000
 VDZ  H162  C16  H161  106.32  3.000
 VDZ  H162  C16  C17   110.97  3.000
 VDZ  H161  C16  C17   110.37  3.000
 VDZ  H162  C16  C15   111.54  3.000
 VDZ  H161  C16  C15   110.48  3.000
 VDZ  C17   C16  C15   107.20  3.000
 VDZ  H17   C17  C20   106.85  3.000
 VDZ  H17   C17  C16   107.86  3.000
 VDZ  C20   C17  C16   112.21  3.000
 VDZ  H17   C17  C13   106.05  3.000
 VDZ  C20   C17  C13   119.81  3.000
 VDZ  C16   C17  C13   103.45  3.000
 VDZ  H20   C20  C22   107.72  3.000
 VDZ  H20   C20  C21   107.66  3.000
 VDZ  C22   C20  C21   111.05  3.000
 VDZ  H20   C20  C17   108.30  3.000
 VDZ  C22   C20  C17   112.44  3.000
 VDZ  C21   C20  C17   109.51  3.000
 VDZ  H213  C21  H212  107.68  3.000
 VDZ  H213  C21  H211  106.96  3.000
 VDZ  H212  C21  H211  107.65  3.000
 VDZ  H213  C21  C20   111.69  3.000
 VDZ  H212  C21  C20   110.72  3.000
 VDZ  H211  C21  C20   111.92  3.000
 VDZ  H222  C22  H221  105.98  3.000
 VDZ  H222  C22  C23   107.98  3.000
 VDZ  H221  C22  C23   108.69  3.000
 VDZ  H222  C22  C20   108.85  3.000
 VDZ  H221  C22  C20   109.09  3.000
 VDZ  C23   C22  C20   115.81  3.000
 VDZ  H232  C23  H231  106.51  3.000
 VDZ  H232  C23  C24   109.50  3.000
 VDZ  H231  C23  C24   109.97  3.000
 VDZ  H232  C23  C22   109.52  3.000
 VDZ  H231  C23  C22   110.05  3.000
 VDZ  C24   C23  C22   111.18  3.000
 VDZ  H242  C24  H241  105.61  3.000
 VDZ  H242  C24  C25   108.28  3.000
 VDZ  H241  C24  C25   108.25  3.000
 VDZ  H242  C24  C23   109.11  3.000
 VDZ  H241  C24  C23   109.06  3.000
 VDZ  C25   C24  C23   116.03  3.000
 VDZ  O3    C25  C27   109.99  3.000
 VDZ  O3    C25  C26   106.00  3.000
 VDZ  C27   C25  C26   109.49  3.000
 VDZ  O3    C25  C24   110.68  3.000
 VDZ  C27   C25  C24   109.02  3.000
 VDZ  C26   C25  C24   111.62  3.000
 VDZ  H263  C26  H262  107.80  3.000
 VDZ  H263  C26  H261  107.82  3.000
 VDZ  H262  C26  H261  107.77  3.000
 VDZ  H263  C26  C25   111.97  3.000
 VDZ  H262  C26  C25   110.81  3.000
 VDZ  H261  C26  C25   110.50  3.000
 VDZ  H273  C27  H272  107.86  3.000
 VDZ  H273  C27  H271  107.44  3.000
 VDZ  H272  C27  H271  107.99  3.000
 VDZ  H273  C27  C25   111.23  3.000
 VDZ  H272  C27  C25   110.99  3.000
 VDZ  H271  C27  C25   111.17  3.000
 VDZ  HO3   O3   C25   108.24  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
 VDZ  Var_01  C4    C5   C10  C1    -54.45  30.0  1
 VDZ  Var_02  C10   C5   C4   C3     55.81  30.0  1
 VDZ  Var_03  C12   C11  C9   C8     49.90  30.0  1
 VDZ  Var_04  C13   C12  C11  C9    -52.50  30.0  1
 VDZ  Var_05  C14   C8   C9   C11   -52.65  30.0  1
 VDZ  Var_06  C17   C16  C15  C14     8.45  30.0  1
 VDZ  Var_07  C7    C6   C5   C4    177.90  30.0  2
 VDZ  Var_08  C8    C7   C6   C5    176.15  30.0  2
 VDZ  Var_09  C9    C8   C7   C6     -2.73  30.0  2
 VDZ  Var_10  H281  C28  C2   C1      1.81  30.0  2
 VDZ  Var_11  C24   C23  C22  C20  -173.93  30.0  3
 VDZ  Var_12  C25   C24  C23  C22  -178.79  30.0  3
 VDZ  Var_13  C26   C25  C24  C23    60.05  30.0  3
 VDZ  Var_14  H261  C26  C25  C24    56.21  30.0  3
 VDZ  Var_15  H271  C27  C25  C24    58.94  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
 VDZ  chir_01  C1   O1   C2   C10  negativ
 VDZ  chir_02  C3   O2   C2   C4   negativ
 VDZ  chir_03  C14  C8   C13  C15  negativ
 VDZ  chir_04  C13  C17  C12  C14  negativ
 VDZ  chir_05  C17  C13  C16  C20  positiv
 VDZ  chir_06  C20  C22  C21  C17  positiv

