# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jul  4 19:36:26 2020
#   Inital geometry file: a 167 line input string
#   Ligand name: (1R,3R,7E,17Z)-17-(5-hydroxy-1,5-dimethylhexylidene)-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(/CCCC(C)(C)O)=C/1CC[C@H]2C(/CCC[C@]/12C)=C/C=C3\C[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
 VD4  VD4  (1R,3R,7E,17Z)-17-(5-hydroxy-1,5-dimethylhexylidene)-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol  ligand  72  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_VD4
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
 VD4  O3    O  OH1   0  -0.678   4.7169   8.5502   4.3860
 VD4  C25   C  CT    0   0.202   5.9384   8.5407   3.6558
 VD4  C26   C  CH3   0  -0.664   5.9491   9.6887   2.6459
 VD4  C27   C  CH3   0  -0.665   7.0451   8.7497   4.6818
 VD4  C24   C  CH2   0  -0.436   6.1133   7.2131   2.9038
 VD4  C23   C  CH2   0  -0.417   5.9803   5.9482   3.7422
 VD4  C22   C  CH2   0  -0.507   6.1965   4.6950   2.8896
 VD4  C20   C  C     0   0.011   6.0176   3.4174   3.6637
 VD4  C21   C  CH3   0  -0.738   6.9785   3.2617   4.8158
 VD4  C17   C  CR5   0   0.144   5.0764   2.4973   3.4247
 VD4  C13   C  CR5   0  -0.133   4.0011   2.4779   2.3380
 VD4  C18   C  CH3   0  -0.647   2.8780   3.4342   2.7651
 VD4  C12   C  CH2   0  -0.427   4.4164   2.7429   0.8841
 VD4  C11   C  CH2   0  -0.434   3.2803   2.4254  -0.0932
 VD4  C9    C  CH2   0  -0.505   2.6820   1.0248   0.0868
 VD4  C16   C  CH2   0  -0.500   4.8648   1.2888   4.3283
 VD4  C15   C  CH2   0  -0.455   3.5488   0.6521   3.8718
 VD4  C14   C  CR15  0  -0.253   3.5452   0.9935   2.3950
 VD4  C8    C  C     0   0.157   2.3576   0.7364   1.5269
 VD4  C7    C  C1    0  -0.363   1.1807   0.2987   2.0005
 VD4  C6    C  C1    0  -0.331  -0.0097   0.0368   1.2121
 VD4  C5    C  C     0   0.132  -1.1808  -0.4427   1.6583
 VD4  C10   C  CH2   0  -0.529  -2.3381  -0.6571   0.7275
 VD4  C1    C  CH1   0   0.045  -3.5840   0.1219   1.1868
 VD4  O1    O  OH1   0  -0.667  -4.7014  -0.1659   0.3858
 VD4  C4    C  CH2   0  -0.567  -1.5004  -0.7856   3.0813
 VD4  C3    C  CH1   0  -0.003  -2.7258   0.0020   3.5626
 VD4  O2    O  OH1   0  -0.665  -2.4649   1.3912   3.5944
 VD4  C2    C  C     0   0.106  -3.8792  -0.2218   2.6197
 VD4  C28   C  C2    0  -0.601  -5.0286  -0.7347   3.0435
 VD4  HO3   H  HOH1  0   0.439   3.9939   8.4233   3.7621
 VD4  H261  H  HCH3  0   0.225   5.1291   9.5858   1.9310
 VD4  H262  H  HCH3  0   0.222   6.8803   9.7049   2.0774
 VD4  H263  H  HCH3  0   0.230   5.8451  10.6533   3.1459
 VD4  H271  H  HCH3  0   0.233   7.0433   7.9781   5.4526
 VD4  H272  H  HCH3  0   0.223   8.0206   8.7332   4.1950
 VD4  H273  H  HCH3  0   0.230   6.9387   9.7169   5.1764
 VD4  H241  H  HCH2  0   0.217   7.0926   7.2216   2.4128
 VD4  H242  H  HCH2  0   0.217   5.3767   7.1753   2.0906
 VD4  H231  H  HCH2  0   0.226   6.6968   5.9630   4.5675
 VD4  H232  H  HCH2  0   0.217   4.9860   5.9034   4.1950
 VD4  H221  H  HCH2  0   0.222   7.2095   4.7273   2.4698
 VD4  H222  H  HCH2  0   0.227   5.5150   4.7403   2.0432
 VD4  H211  H  HCH3  0   0.236   6.6375   3.7999   5.7053
 VD4  H212  H  HCH3  0   0.244   7.1289   2.2232   5.1076
 VD4  H213  H  HCH3  0   0.233   7.9562   3.6749   4.5587
 VD4  H181  H  HCH3  0   0.229   2.5039   3.2020   3.7631
 VD4  H182  H  HCH3  0   0.230   3.2521   4.4595   2.7910
 VD4  H183  H  HCH3  0   0.229   2.0233   3.4095   2.0880
 VD4  H121  H  HCH2  0   0.219   5.2907   2.1264   0.6482
 VD4  H122  H  HCH2  0   0.235   4.7152   3.7786   0.7200
 VD4  H111  H  HCH2  0   0.236   3.6493   2.5259  -1.1164
 VD4  H112  H  HCH2  0   0.223   2.4878   3.1697   0.0147
 VD4  H91   H  HCH2  0   0.233   3.4252   0.2876  -0.2409
 VD4  H92   H  HCH2  0   0.245   1.8212   0.9101  -0.5711
 VD4  H161  H  HCH2  0   0.237   5.6815   0.5695   4.2012
 VD4  H162  H  HCH2  0   0.240   4.8532   1.5576   5.3860
 VD4  H151  H  HCH2  0   0.237   3.5144  -0.4225   4.0568
 VD4  H152  H  HCH2  0   0.224   2.6968   1.0962   4.3921
 VD4  H14   H  HCR5  0   0.237   4.3771   0.4240   1.9486
 VD4  H7    H  H     0   0.228   1.1121   0.1169   3.0679
 VD4  H6    H  H     0   0.231   0.0534   0.2450   0.1485
 VD4  H101  H  HCH2  0   0.247  -2.0757  -0.3597  -0.2914
 VD4  H102  H  HCH2  0   0.239  -2.6029  -1.7214   0.7022
 VD4  H1    H  HCH1  0   0.223  -3.3404   1.1929   1.1340
 VD4  HO1   H  HOH1  0   0.455  -4.5176   0.1503  -0.5041
 VD4  H41   H  HCH2  0   0.254  -1.7364  -1.8528   3.1597
 VD4  H42   H  HCH2  0   0.260  -0.6635  -0.6097   3.7603
 VD4  H3    H  HCH1  0   0.226  -3.0044  -0.3659   4.5589
 VD4  HO2   H  HOH1  0   0.449  -1.6268   1.5309   4.0471
 VD4  H281  H  H     0   0.238  -5.1730  -0.9762   4.0894
 VD4  H282  H  H     0   0.244  -5.8610  -0.9320   2.3827

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
 VD4  O3   C25   single  1.423  0.020  1.423
 VD4  C26  C25   single  1.529  0.020  1.529
 VD4  C22  C20   single  1.505  0.020  1.505
 VD4  C22  C23   single  1.531  0.020  1.531
 VD4  C21  C20   single  1.508  0.020  1.508
 VD4  C24  C25   single  1.536  0.020  1.536
 VD4  C24  C23   single  1.523  0.020  1.523
 VD4  C25  C27   single  1.523  0.020  1.523
 VD4  C20  C17   double  1.338  0.020  1.338
 VD4  C12  C11   single  1.532  0.020  1.532
 VD4  C12  C13   single  1.535  0.020  1.535
 VD4  C17  C16   single  1.524  0.020  1.524
 VD4  C17  C13   single  1.529  0.020  1.529
 VD4  C11  C9    single  1.534  0.020  1.534
 VD4  C16  C15   single  1.532  0.020  1.532
 VD4  C13  C14   single  1.554  0.020  1.554
 VD4  C13  C18   single  1.536  0.020  1.536
 VD4  C9   C8    single  1.504  0.020  1.504
 VD4  C14  C15   single  1.516  0.020  1.516
 VD4  C14  C8    single  1.493  0.020  1.493
 VD4  C8   C7    double  1.342  0.020  1.342
 VD4  C7   C6    single  1.452  0.020  1.452
 VD4  C6   C5    double  1.342  0.020  1.342
 VD4  C5   C4    single  1.498  0.020  1.498
 VD4  C5   C10   single  1.501  0.020  1.501
 VD4  C4   C3    single  1.534  0.020  1.534
 VD4  C10  C1    single  1.539  0.020  1.539
 VD4  O2   C3    single  1.414  0.020  1.414
 VD4  C3   C2    single  1.507  0.020  1.507
 VD4  C1   C2    single  1.503  0.020  1.503
 VD4  C1   O1    single  1.405  0.020  1.405
 VD4  C2   C28   double  1.328  0.020  1.328
 VD4  O3   HO3   single  0.850  0.020  0.980
 VD4  C26  H261  single  0.970  0.020  1.090
 VD4  C26  H262  single  0.970  0.020  1.090
 VD4  C26  H263  single  0.970  0.020  1.090
 VD4  C27  H271  single  0.970  0.020  1.090
 VD4  C27  H272  single  0.970  0.020  1.090
 VD4  C27  H273  single  0.970  0.020  1.090
 VD4  C24  H241  single  0.970  0.020  1.090
 VD4  C24  H242  single  0.970  0.020  1.090
 VD4  C23  H231  single  0.970  0.020  1.090
 VD4  C23  H232  single  0.970  0.020  1.090
 VD4  C22  H221  single  0.970  0.020  1.090
 VD4  C22  H222  single  0.970  0.020  1.090
 VD4  C21  H211  single  0.970  0.020  1.090
 VD4  C21  H212  single  0.970  0.020  1.090
 VD4  C21  H213  single  0.970  0.020  1.090
 VD4  C18  H181  single  0.970  0.020  1.090
 VD4  C18  H182  single  0.970  0.020  1.090
 VD4  C18  H183  single  0.970  0.020  1.090
 VD4  C12  H121  single  0.970  0.020  1.090
 VD4  C12  H122  single  0.970  0.020  1.090
 VD4  C11  H111  single  0.970  0.020  1.090
 VD4  C11  H112  single  0.970  0.020  1.090
 VD4  C9   H91   single  0.970  0.020  1.090
 VD4  C9   H92   single  0.970  0.020  1.090
 VD4  C16  H161  single  0.970  0.020  1.090
 VD4  C16  H162  single  0.970  0.020  1.090
 VD4  C15  H151  single  0.970  0.020  1.090
 VD4  C15  H152  single  0.970  0.020  1.090
 VD4  C14  H14   single  0.970  0.020  1.090
 VD4  C7   H7    single  0.930  0.020  1.080
 VD4  C6   H6    single  0.930  0.020  1.080
 VD4  C10  H101  single  0.970  0.020  1.090
 VD4  C10  H102  single  0.970  0.020  1.090
 VD4  C1   H1    single  0.970  0.020  1.090
 VD4  O1   HO1   single  0.850  0.020  0.980
 VD4  C4   H41   single  0.970  0.020  1.090
 VD4  C4   H42   single  0.970  0.020  1.090
 VD4  C3   H3    single  0.970  0.020  1.090
 VD4  O2   HO2   single  0.850  0.020  0.980
 VD4  C28  H281  single  0.930  0.020  1.080
 VD4  C28  H282  single  0.930  0.020  1.080

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
 VD4  HO3   O3   C25   108.12  3.000
 VD4  C24   C25  C27   111.45  3.000
 VD4  C27   C25  C26   109.68  3.000
 VD4  C24   C25  C26   108.95  3.000
 VD4  C27   C25  O3    106.09  3.000
 VD4  C24   C25  O3    110.78  3.000
 VD4  C26   C25  O3    109.87  3.000
 VD4  H263  C26  H262  107.88  3.000
 VD4  H263  C26  H261  108.15  3.000
 VD4  H262  C26  H261  107.52  3.000
 VD4  H263  C26  C25   111.11  3.000
 VD4  H262  C26  C25   111.17  3.000
 VD4  H261  C26  C25   110.86  3.000
 VD4  H273  C27  H272  107.63  3.000
 VD4  H273  C27  H271  107.85  3.000
 VD4  H272  C27  H271  107.83  3.000
 VD4  H273  C27  C25   110.85  3.000
 VD4  H272  C27  C25   110.31  3.000
 VD4  H271  C27  C25   112.19  3.000
 VD4  H242  C24  H241  105.55  3.000
 VD4  H242  C24  C23   108.70  3.000
 VD4  H241  C24  C23   109.34  3.000
 VD4  H242  C24  C25   108.42  3.000
 VD4  H241  C24  C25   108.33  3.000
 VD4  C23   C24  C25   116.00  3.000
 VD4  H232  C23  H231  106.50  3.000
 VD4  H232  C23  C22   108.99  3.000
 VD4  H231  C23  C22   109.81  3.000
 VD4  H232  C23  C24   109.96  3.000
 VD4  H231  C23  C24   110.31  3.000
 VD4  C22   C23  C24   111.15  3.000
 VD4  H222  C22  H221  106.24  3.000
 VD4  H222  C22  C20   111.18  3.000
 VD4  H221  C22  C20   109.38  3.000
 VD4  H222  C22  C23   108.11  3.000
 VD4  H221  C22  C23   108.62  3.000
 VD4  C20   C22  C23   113.06  3.000
 VD4  C17   C20  C21   120.91  3.000
 VD4  C17   C20  C22   125.15  3.000
 VD4  C21   C20  C22   113.89  3.000
 VD4  H213  C21  H212  107.46  3.000
 VD4  H213  C21  H211  106.52  3.000
 VD4  H212  C21  H211  107.12  3.000
 VD4  H213  C21  C20   110.57  3.000
 VD4  H212  C21  C20   113.02  3.000
 VD4  H211  C21  C20   111.82  3.000
 VD4  C16   C17  C13   108.29  3.000
 VD4  C13   C17  C20   129.09  3.000
 VD4  C16   C17  C20   122.50  3.000
 VD4  C14   C13  C12   106.20  3.000
 VD4  C14   C13  C18   111.72  3.000
 VD4  C12   C13  C18   110.72  3.000
 VD4  C18   C13  C17   107.99  3.000
 VD4  C14   C13  C17   101.10  3.000
 VD4  C12   C13  C17   118.73  3.000
 VD4  H183  C18  H182  107.73  3.000
 VD4  H183  C18  H181  107.12  3.000
 VD4  H182  C18  H181  107.20  3.000
 VD4  H183  C18  C13   112.73  3.000
 VD4  H182  C18  C13   109.92  3.000
 VD4  H181  C18  C13   111.88  3.000
 VD4  H122  C12  H121  106.47  3.000
 VD4  H122  C12  C11   107.70  3.000
 VD4  H121  C12  C11   109.75  3.000
 VD4  H122  C12  C13   112.37  3.000
 VD4  H121  C12  C13   108.82  3.000
 VD4  C11   C12  C13   111.58  3.000
 VD4  H112  C11  H111  105.95  3.000
 VD4  H112  C11  C9    109.12  3.000
 VD4  H111  C11  C9    109.01  3.000
 VD4  H112  C11  C12   109.50  3.000
 VD4  H111  C11  C12   109.15  3.000
 VD4  C9    C11  C12   113.81  3.000
 VD4  H92   C9   H91   106.52  3.000
 VD4  H92   C9   C8    112.80  3.000
 VD4  H91   C9   C8    107.66  3.000
 VD4  H92   C9   C11   109.48  3.000
 VD4  H91   C9   C11   108.32  3.000
 VD4  C8    C9   C11   111.81  3.000
 VD4  H162  C16  H161  106.38  3.000
 VD4  H162  C16  C15   112.46  3.000
 VD4  H161  C16  C15   109.45  3.000
 VD4  H162  C16  C17   112.38  3.000
 VD4  H161  C16  C17   110.39  3.000
 VD4  C15   C16  C17   105.80  3.000
 VD4  H152  C15  H151  107.16  3.000
 VD4  H152  C15  C14   111.75  3.000
 VD4  H151  C15  C14   112.77  3.000
 VD4  H152  C15  C16   111.05  3.000
 VD4  H151  C15  C16   112.71  3.000
 VD4  C14   C15  C16   101.47  3.000
 VD4  H14   C14  C8    106.00  3.000
 VD4  H14   C14  C15   106.04  3.000
 VD4  C8    C14  C15   121.97  3.000
 VD4  H14   C14  C13   104.90  3.000
 VD4  C8    C14  C13   112.12  3.000
 VD4  C15   C14  C13   104.49  3.000
 VD4  C7    C8   C14   123.25  3.000
 VD4  C7    C8   C9    126.13  3.000
 VD4  C14   C8   C9    110.61  3.000
 VD4  H7    C7   C6    116.89  3.000
 VD4  H7    C7   C8    117.22  3.000
 VD4  C6    C7   C8    125.89  3.000
 VD4  H6    C6   C5    116.43  3.000
 VD4  H6    C6   C7    116.73  3.000
 VD4  C5    C6   C7    126.84  3.000
 VD4  C4    C5   C10   113.08  3.000
 VD4  C10   C5   C6    121.19  3.000
 VD4  C4    C5   C6    125.72  3.000
 VD4  H102  C10  H101  107.48  3.000
 VD4  H102  C10  C1    107.61  3.000
 VD4  H101  C10  C1    109.55  3.000
 VD4  H102  C10  C5    109.82  3.000
 VD4  H101  C10  C5    110.73  3.000
 VD4  C1    C10  C5    111.52  3.000
 VD4  H1    C1   C2    108.18  3.000
 VD4  H1    C1   O1    110.38  3.000
 VD4  C2    C1   O1    109.91  3.000
 VD4  H1    C1   C10   107.41  3.000
 VD4  O1    C1   C10   111.72  3.000
 VD4  C2    C1   C10   109.13  3.000
 VD4  HO1   O1   C1    107.94  3.000
 VD4  H42   C4   H41   106.11  3.000
 VD4  H42   C4   C3    109.54  3.000
 VD4  H41   C4   C3    107.79  3.000
 VD4  H42   C4   C5    112.97  3.000
 VD4  H41   C4   C5    109.67  3.000
 VD4  C3    C4   C5    110.54  3.000
 VD4  H3    C3   C2    108.90  3.000
 VD4  H3    C3   O2    110.83  3.000
 VD4  C2    C3   O2    107.54  3.000
 VD4  H3    C3   C4    108.38  3.000
 VD4  C2    C3   C4    109.81  3.000
 VD4  O2    C3   C4    111.35  3.000
 VD4  HO2   O2   C3    108.29  3.000
 VD4  C28   C2   C3    121.35  3.000
 VD4  C28   C2   C1    124.24  3.000
 VD4  C3    C2   C1    114.36  3.000
 VD4  H282  C28  H281  116.55  3.000
 VD4  H282  C28  C2    122.81  3.000
 VD4  H281  C28  C2    120.64  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
 VD4  Var_01  C14   C15  C16  C17    30.78  30.0  1
 VD4  Var_02  C9    C11  C12  C13   -52.08  30.0  1
 VD4  Var_03  C15   C16  C17  C13    -6.96  30.0  1
 VD4  Var_04  C8    C9   C11  C12    48.65  30.0  1
 VD4  Var_05  C14   C8   C9   C11   -52.41  30.0  1
 VD4  Var_06  C3    C4   C5   C10   -55.69  30.0  1
 VD4  Var_07  C4    C5   C10  C1     55.56  30.0  1
 VD4  Var_08  C16   C17  C20  C22  -174.01  30.0  2
 VD4  Var_09  C6    C7   C8   C9     -0.85  30.0  2
 VD4  Var_10  C5    C6   C7   C8    177.60  30.0  2
 VD4  Var_11  H281  C28  C2   C1    178.97  30.0  2
 VD4  Var_12  C17   C20  C22  C23   116.66  30.0  3
 VD4  Var_13  H211  C21  C20  C17   -95.29  30.0  3
 VD4  Var_14  C23   C24  C25  O3    -52.88  30.0  3
 VD4  Var_15  C22   C23  C24  C25  -179.07  30.0  3
 VD4  Var_16  C20   C22  C23  C24  -177.58  30.0  1
 VD4  Var_17  H261  C26  C25  O3    -60.79  30.0  3
 VD4  Var_18  H271  C27  C25  O3     58.57  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
 VD4  chir_01  C13  C17  C14  C12  positiv
 VD4  chir_02  C14  C13  C15  C8   negativ
 VD4  chir_03  C1   O1   C10  C2   positiv
 VD4  chir_04  C3   O2   C2   C4   negativ

