# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jul  4 16:55:43 2020
#   Inital geometry file: a 167 line input string
#   Ligand name: (1R,3R,7E,17E)-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: C\C(CCCC(C)(C)O)=C/1CC[C@H]2C(\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
 VD5  VD5  (1R,3R,7E,17E)-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_VD5
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
 VD5  O2    O  OH1   0  -0.666  4.8059    0.8835   2.1706
 VD5  C3    C  CH1   0  -0.004  3.8482    1.8041   2.6542
 VD5  C2    C  C     0   0.105  4.5363    3.1349   2.8176
 VD5  C28   C  C2    0  -0.599  4.6489    3.7117   4.0087
 VD5  C1    C  CH1   0   0.045  5.0043    3.7552   1.5303
 VD5  O1    O  OH1   0  -0.666  5.5802    5.0099   1.7865
 VD5  C10   C  CH2   0  -0.528  3.8135    3.8601   0.5586
 VD5  C4    C  CH2   0  -0.566  2.6695    1.9458   1.6814
 VD5  C5    C  C     0   0.130  3.1421    2.5299   0.3851
 VD5  C6    C  C1    0  -0.319  3.0618    1.9354  -0.8153
 VD5  C7    C  C1    0  -0.362  2.4828    0.6374  -1.1073
 VD5  C8    C  C     0   0.160  2.4875    0.0578  -2.3172
 VD5  C9    C  CH2   0  -0.513  3.0992    0.6858  -3.5517
 VD5  C11   C  CH2   0  -0.457  2.7320   -0.0776  -4.8221
 VD5  C12   C  CH2   0  -0.421  3.1014   -1.5683  -4.7726
 VD5  C14   C  CH1   0  -0.272  1.9206   -1.3003  -2.5742
 VD5  C13   C  CT    0  -0.124  2.9231   -2.1793  -3.3638
 VD5  C18   C  CH3   0  -0.649  4.2754   -2.2480  -2.6361
 VD5  C15   C  CH2   0  -0.458  1.4587   -2.1816  -1.4285
 VD5  C16   C  CH2   0  -0.502  1.2706   -3.5361  -2.1211
 VD5  C17   C  C     0   0.148  2.2639   -3.5507  -3.2740
 VD5  C20   C  C     0   0.001  2.5050   -4.6266  -4.0284
 VD5  C21   C  CH3   0  -0.744  3.5258   -4.6890  -5.1293
 VD5  C22   C  CH2   0  -0.497  1.7642   -5.9198  -3.7981
 VD5  C23   C  CH2   0  -0.419  2.5288   -6.8943  -2.8983
 VD5  C24   C  CH2   0  -0.434  1.7440   -8.1792  -2.6648
 VD5  C25   C  CT    0   0.202  2.4580   -9.2605  -1.8418
 VD5  C27   C  CH3   0  -0.664  1.5385  -10.4753  -1.7111
 VD5  C26   C  CH3   0  -0.667  2.8364   -8.7517  -0.4562
 VD5  O3    O  OH1   0  -0.678  3.6781   -9.6404  -2.4687
 VD5  HO2   H  HOH1  0   0.451  4.3450    0.0877   1.8857
 VD5  H3    H  HCH1  0   0.226  3.4581    1.4844   3.6295
 VD5  H281  H  H     0   0.238  4.2745    3.2200   4.8980
 VD5  H282  H  H     0   0.245  5.1093    4.6792   4.1507
 VD5  H1    H  HCH1  0   0.222  5.7412    3.0788   1.0736
 VD5  HO1   H  HOH1  0   0.455  5.9431    5.3450   0.9608
 VD5  H101  H  HCH2  0   0.248  4.1577    4.2507  -0.4026
 VD5  H102  H  HCH2  0   0.239  3.1049    4.5846   0.9780
 VD5  H41   H  HCH2  0   0.253  1.9327    2.6140   2.1402
 VD5  H42   H  HCH2  0   0.260  2.1742    0.9801   1.5608
 VD5  H6    H  H     0   0.234  3.4852    2.4760  -1.6573
 VD5  H7    H  H     0   0.230  2.0257    0.0950  -0.2869
 VD5  H91   H  HCH2  0   0.248  2.7837    1.7275  -3.6539
 VD5  H92   H  HCH2  0   0.239  4.1893    0.7176  -3.4459
 VD5  H111  H  HCH2  0   0.225  1.6585    0.0295  -4.9976
 VD5  H112  H  HCH2  0   0.237  3.2206    0.3890  -5.6795
 VD5  H121  H  HCH2  0   0.234  2.4855   -2.1029  -5.4986
 VD5  H122  H  HCH2  0   0.222  4.1367   -1.6909  -5.1012
 VD5  H14   H  HCH1  0   0.248  1.0465   -1.1750  -3.2330
 VD5  H181  H  HCH3  0   0.229  4.7736   -1.2775  -2.5897
 VD5  H182  H  HCH3  0   0.227  4.1722   -2.6129  -1.6130
 VD5  H183  H  HCH3  0   0.231  4.9449   -2.9338  -3.1579
 VD5  H151  H  HCH2  0   0.237  0.5418   -1.8226  -0.9585
 VD5  H152  H  HCH2  0   0.224  2.2183   -2.2448  -0.6456
 VD5  H161  H  HCH2  0   0.237  0.2463   -3.6182  -2.5004
 VD5  H162  H  HCH2  0   0.240  1.4099   -4.3740  -1.4348
 VD5  H211  H  HCH3  0   0.233  3.0458   -4.7253  -6.1115
 VD5  H212  H  HCH3  0   0.240  4.2180   -3.8522  -5.1289
 VD5  H213  H  HCH3  0   0.235  4.1203   -5.6024  -5.0456
 VD5  H221  H  HCH2  0   0.230  0.7792   -5.7316  -3.3629
 VD5  H222  H  HCH2  0   0.226  1.5779   -6.4064  -4.7624
 VD5  H231  H  HCH2  0   0.223  2.7420   -6.4018  -1.9456
 VD5  H232  H  HCH2  0   0.217  3.4970   -7.1284  -3.3491
 VD5  H241  H  HCH2  0   0.217  0.7961   -7.9376  -2.1730
 VD5  H242  H  HCH2  0   0.218  1.4706   -8.6117  -3.6365
 VD5  H271  H  HCH3  0   0.224  1.2594  -10.8647  -2.6934
 VD5  H272  H  HCH3  0   0.221  0.6163  -10.2151  -1.1893
 VD5  H273  H  HCH3  0   0.230  2.0255  -11.2768  -1.1530
 VD5  H261  H  HCH3  0   0.234  3.5582   -7.9359  -0.5045
 VD5  H262  H  HCH3  0   0.223  1.9536   -8.3853   0.0692
 VD5  H263  H  HCH3  0   0.230  3.2730   -9.5513   0.1452
 VD5  HO3   H  HOH1  0   0.440  3.4728   -9.9477  -3.3582

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
 VD5  C21  C20   single  1.503  0.020  1.503
 VD5  O3   C25   single  1.423  0.020  1.423
 VD5  C22  C20   single  1.508  0.020  1.508
 VD5  C22  C23   single  1.531  0.020  1.531
 VD5  C26  C25   single  1.524  0.020  1.524
 VD5  C20  C17   double  1.336  0.020  1.336
 VD5  C24  C25   single  1.535  0.020  1.535
 VD5  C24  C23   single  1.524  0.020  1.524
 VD5  C25  C27   single  1.529  0.020  1.529
 VD5  C12  C11   single  1.537  0.020  1.537
 VD5  C12  C13   single  1.546  0.020  1.546
 VD5  C17  C13   single  1.524  0.020  1.524
 VD5  C17  C16   single  1.522  0.020  1.522
 VD5  C11  C9    single  1.527  0.020  1.527
 VD5  C13  C14   single  1.550  0.020  1.550
 VD5  C13  C18   single  1.537  0.020  1.537
 VD5  C16  C15   single  1.533  0.020  1.533
 VD5  C9   C8    single  1.514  0.020  1.514
 VD5  C14  C15   single  1.518  0.020  1.518
 VD5  C14  C8    single  1.494  0.020  1.494
 VD5  C8   C7    double  1.342  0.020  1.342
 VD5  C7   C6    single  1.451  0.020  1.451
 VD5  C6   C5    double  1.342  0.020  1.342
 VD5  C5   C4    single  1.498  0.020  1.498
 VD5  C5   C10   single  1.500  0.020  1.500
 VD5  C4   C3    single  1.535  0.020  1.535
 VD5  C10  C1    single  1.541  0.020  1.541
 VD5  O2   C3    single  1.414  0.020  1.414
 VD5  C3   C2    single  1.507  0.020  1.507
 VD5  C1   C2    single  1.504  0.020  1.504
 VD5  C1   O1    single  1.404  0.020  1.404
 VD5  C2   C28   double  1.328  0.020  1.328
 VD5  O2   HO2   single  0.850  0.020  0.980
 VD5  C3   H3    single  0.970  0.020  1.090
 VD5  C28  H281  single  0.930  0.020  1.080
 VD5  C28  H282  single  0.930  0.020  1.080
 VD5  C1   H1    single  0.970  0.020  1.090
 VD5  O1   HO1   single  0.850  0.020  0.980
 VD5  C10  H101  single  0.970  0.020  1.090
 VD5  C10  H102  single  0.970  0.020  1.090
 VD5  C4   H41   single  0.970  0.020  1.090
 VD5  C4   H42   single  0.970  0.020  1.090
 VD5  C6   H6    single  0.930  0.020  1.080
 VD5  C7   H7    single  0.930  0.020  1.080
 VD5  C9   H91   single  0.970  0.020  1.090
 VD5  C9   H92   single  0.970  0.020  1.090
 VD5  C11  H111  single  0.970  0.020  1.090
 VD5  C11  H112  single  0.970  0.020  1.090
 VD5  C12  H121  single  0.970  0.020  1.090
 VD5  C12  H122  single  0.970  0.020  1.090
 VD5  C14  H14   single  0.970  0.020  1.090
 VD5  C18  H181  single  0.970  0.020  1.090
 VD5  C18  H182  single  0.970  0.020  1.090
 VD5  C18  H183  single  0.970  0.020  1.090
 VD5  C15  H151  single  0.970  0.020  1.090
 VD5  C15  H152  single  0.970  0.020  1.090
 VD5  C16  H161  single  0.970  0.020  1.090
 VD5  C16  H162  single  0.970  0.020  1.090
 VD5  C21  H211  single  0.970  0.020  1.090
 VD5  C21  H212  single  0.970  0.020  1.090
 VD5  C21  H213  single  0.970  0.020  1.090
 VD5  C22  H221  single  0.970  0.020  1.090
 VD5  C22  H222  single  0.970  0.020  1.090
 VD5  C23  H231  single  0.970  0.020  1.090
 VD5  C23  H232  single  0.970  0.020  1.090
 VD5  C24  H241  single  0.970  0.020  1.090
 VD5  C24  H242  single  0.970  0.020  1.090
 VD5  C27  H271  single  0.970  0.020  1.090
 VD5  C27  H272  single  0.970  0.020  1.090
 VD5  C27  H273  single  0.970  0.020  1.090
 VD5  C26  H261  single  0.970  0.020  1.090
 VD5  C26  H262  single  0.970  0.020  1.090
 VD5  C26  H263  single  0.970  0.020  1.090
 VD5  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
 VD5  HO2   O2   C3    108.37  3.000
 VD5  H3    C3   C4    108.49  3.000
 VD5  H3    C3   C2    108.85  3.000
 VD5  C4    C3   C2    109.75  3.000
 VD5  H3    C3   O2    110.78  3.000
 VD5  C2    C3   O2    107.63  3.000
 VD5  C4    C3   O2    111.31  3.000
 VD5  C1    C2   C28   124.21  3.000
 VD5  C28   C2   C3    121.29  3.000
 VD5  C1    C2   C3    114.43  3.000
 VD5  H282  C28  H281  116.47  3.000
 VD5  H282  C28  C2    122.87  3.000
 VD5  H281  C28  C2    120.66  3.000
 VD5  H1    C1   C10   107.33  3.000
 VD5  H1    C1   O1    110.52  3.000
 VD5  C10   C1   O1    111.79  3.000
 VD5  H1    C1   C2    108.08  3.000
 VD5  O1    C1   C2    109.88  3.000
 VD5  C10   C1   C2    109.12  3.000
 VD5  HO1   O1   C1    108.02  3.000
 VD5  H102  C10  H101  107.68  3.000
 VD5  H102  C10  C5    109.93  3.000
 VD5  H101  C10  C5    110.86  3.000
 VD5  H102  C10  C1    107.65  3.000
 VD5  H101  C10  C1    109.61  3.000
 VD5  C5    C10  C1    111.01  3.000
 VD5  H42   C4   H41   106.30  3.000
 VD5  H42   C4   C5    113.10  3.000
 VD5  H41   C4   C5    109.68  3.000
 VD5  H42   C4   C3    109.68  3.000
 VD5  H41   C4   C3    107.90  3.000
 VD5  C5    C4   C3    110.01  3.000
 VD5  C6    C5   C4    125.61  3.000
 VD5  C4    C5   C10   112.76  3.000
 VD5  C6    C5   C10   121.54  3.000
 VD5  H6    C6   C7    116.40  3.000
 VD5  H6    C6   C5    116.71  3.000
 VD5  C7    C6   C5    126.88  3.000
 VD5  H7    C7   C8    117.89  3.000
 VD5  H7    C7   C6    117.60  3.000
 VD5  C8    C7   C6    124.51  3.000
 VD5  C14   C8   C9    112.96  3.000
 VD5  C14   C8   C7    123.13  3.000
 VD5  C9    C8   C7    123.89  3.000
 VD5  H92   C9   H91   105.58  3.000
 VD5  H92   C9   C11   109.52  3.000
 VD5  H91   C9   C11   109.23  3.000
 VD5  H92   C9   C8    109.59  3.000
 VD5  H91   C9   C8    110.78  3.000
 VD5  C11   C9   C8    111.95  3.000
 VD5  H112  C11  H111  105.76  3.000
 VD5  H112  C11  C12   109.42  3.000
 VD5  H111  C11  C12   109.65  3.000
 VD5  H112  C11  C9    109.40  3.000
 VD5  H111  C11  C9    108.71  3.000
 VD5  C12   C11  C9    113.60  3.000
 VD5  H122  C12  H121  106.22  3.000
 VD5  H122  C12  C13   109.81  3.000
 VD5  H121  C12  C13   110.32  3.000
 VD5  H122  C12  C11   109.08  3.000
 VD5  H121  C12  C11   108.54  3.000
 VD5  C13   C12  C11   112.65  3.000
 VD5  H14   C14  C15   106.03  3.000
 VD5  H14   C14  C13   105.84  3.000
 VD5  C15   C14  C13   104.61  3.000
 VD5  H14   C14  C8    107.49  3.000
 VD5  C15   C14  C8    120.91  3.000
 VD5  C13   C14  C8    110.97  3.000
 VD5  C17   C13  C18   108.20  3.000
 VD5  C18   C13  C14   110.68  3.000
 VD5  C17   C13  C14   101.57  3.000
 VD5  C18   C13  C12   110.34  3.000
 VD5  C14   C13  C12   108.35  3.000
 VD5  C17   C13  C12   117.34  3.000
 VD5  H183  C18  H182  107.23  3.000
 VD5  H183  C18  H181  107.39  3.000
 VD5  H182  C18  H181  107.49  3.000
 VD5  H183  C18  C13   109.97  3.000
 VD5  H182  C18  C13   112.07  3.000
 VD5  H181  C18  C13   112.44  3.000
 VD5  H152  C15  H151  107.13  3.000
 VD5  H152  C15  C16   110.98  3.000
 VD5  H151  C15  C16   112.47  3.000
 VD5  H152  C15  C14   111.28  3.000
 VD5  H151  C15  C14   112.94  3.000
 VD5  C16   C15  C14   102.09  3.000
 VD5  H162  C16  H161  106.22  3.000
 VD5  H162  C16  C17   112.67  3.000
 VD5  H161  C16  C17   110.32  3.000
 VD5  H162  C16  C15   112.23  3.000
 VD5  H161  C16  C15   109.72  3.000
 VD5  C17   C16  C15   105.70  3.000
 VD5  C20   C17  C16   123.59  3.000
 VD5  C16   C17  C13   108.56  3.000
 VD5  C20   C17  C13   127.82  3.000
 VD5  C22   C20  C21   114.20  3.000
 VD5  C22   C20  C17   121.04  3.000
 VD5  C21   C20  C17   124.74  3.000
 VD5  H213  C21  H212  107.29  3.000
 VD5  H213  C21  H211  106.24  3.000
 VD5  H212  C21  H211  107.79  3.000
 VD5  H213  C21  C20   110.37  3.000
 VD5  H212  C21  C20   113.63  3.000
 VD5  H211  C21  C20   111.18  3.000
 VD5  H222  C22  H221  105.87  3.000
 VD5  H222  C22  C23   108.63  3.000
 VD5  H221  C22  C23   109.01  3.000
 VD5  H222  C22  C20   109.26  3.000
 VD5  H221  C22  C20   110.84  3.000
 VD5  C23   C22  C20   112.97  3.000
 VD5  H232  C23  H231  106.44  3.000
 VD5  H232  C23  C24   109.80  3.000
 VD5  H231  C23  C24   110.29  3.000
 VD5  H232  C23  C22   109.65  3.000
 VD5  H231  C23  C22   108.83  3.000
 VD5  C24   C23  C22   111.69  3.000
 VD5  H242  C24  H241  105.59  3.000
 VD5  H242  C24  C25   108.23  3.000
 VD5  H241  C24  C25   108.50  3.000
 VD5  H242  C24  C23   108.96  3.000
 VD5  H241  C24  C23   109.19  3.000
 VD5  C25   C24  C23   115.89  3.000
 VD5  O3    C25  C26   106.07  3.000
 VD5  C26   C25  C27   109.68  3.000
 VD5  O3    C25  C27   109.94  3.000
 VD5  C27   C25  C24   109.01  3.000
 VD5  C26   C25  C24   111.58  3.000
 VD5  O3    C25  C24   110.52  3.000
 VD5  H273  C27  H272  107.93  3.000
 VD5  H273  C27  H271  108.17  3.000
 VD5  H272  C27  H271  107.40  3.000
 VD5  H273  C27  C25   111.03  3.000
 VD5  H272  C27  C25   111.08  3.000
 VD5  H271  C27  C25   111.09  3.000
 VD5  H263  C26  H262  107.73  3.000
 VD5  H263  C26  H261  107.92  3.000
 VD5  H262  C26  H261  107.81  3.000
 VD5  H263  C26  C25   110.83  3.000
 VD5  H262  C26  C25   110.44  3.000
 VD5  H261  C26  C25   111.95  3.000
 VD5  HO3   O3   C25   108.01  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
 VD5  Var_01  C10   C5   C4   C3    -57.35  30.0  1
 VD5  Var_02  C4    C5   C10  C1     57.14  30.0  1
 VD5  Var_03  C12   C11  C9   C8    -55.51  30.0  1
 VD5  Var_04  C13   C12  C11  C9     35.67  30.0  1
 VD5  Var_05  C14   C8   C9   C11    12.21  30.0  1
 VD5  Var_06  C17   C16  C15  C14    29.20  30.0  1
 VD5  Var_07  C15   C16  C17  C13    -6.00  30.0  1
 VD5  Var_08  C7    C6   C5   C10   177.76  30.0  2
 VD5  Var_09  C8    C7   C6   C5   -176.49  30.0  2
 VD5  Var_10  C9    C8   C7   C6     -0.15  30.0  2
 VD5  Var_11  C21   C20  C17  C13     1.14  30.0  2
 VD5  Var_12  H281  C28  C2   C3      2.00  30.0  2
 VD5  Var_13  C23   C22  C20  C17   -95.07  30.0  1
 VD5  Var_14  H211  C21  C20  C17  -108.95  30.0  3
 VD5  Var_15  C24   C23  C22  C20   178.98  30.0  3
 VD5  Var_16  C25   C24  C23  C22   176.52  30.0  1
 VD5  Var_17  O3    C25  C24  C23   -58.76  30.0  3
 VD5  Var_18  H261  C26  C25  C24   -63.83  30.0  3
 VD5  Var_19  H271  C27  C25  C24    58.04  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
 VD5  chir_01  C3   C4   O2   C2   negativ
 VD5  chir_02  C1   O1   C10  C2   positiv
 VD5  chir_03  C14  C13  C15  C8   negativ
 VD5  chir_04  C13  C14  C17  C12  negativ

