# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jul  4 13:48:04 2020
#   Inital geometry file: a 167 line input string
#   Ligand name: (1R,2R,3R,5E,7E,17beta)-17-[(1R)-5-hydroxy-1,5-dimethylhexyl]-2-methyl-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]2\C(CCC[C@]12C)=C\C=C/3C[C@@H](O)[C@H](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
 VD2  VD2  (1R,2R,3R,5E,7E,17beta)-17-[(1R)-5-hydroxy-1,5-dimethylhexyl]-2-methyl-9,10-secoestra-5,7-diene-1,3-diol  ligand  76  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 GRAND
;

data_comp_VD2
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
 VD2  O3    O  OH1   0  -0.679  -2.7504   0.3483   7.7367
 VD2  C25   C  CT    0   0.202  -1.4467  -0.0561   8.1410
 VD2  C27   C  CH3   0  -0.665  -1.5471  -1.1253   9.2290
 VD2  C26   C  CH3   0  -0.669  -0.7789   1.1901   8.7090
 VD2  C24   C  CH2   0  -0.428  -0.6658  -0.6280   6.9483
 VD2  C23   C  CH2   0  -0.429  -0.4691   0.3149   5.7677
 VD2  C22   C  CH2   0  -0.409   0.2784  -0.3598   4.6210
 VD2  C20   C  CH1   0  -0.233   0.5215   0.5350   3.3962
 VD2  C21   C  CH3   0  -0.673   1.4816   1.6666   3.7553
 VD2  C17   C  CR15  0  -0.163   1.0086  -0.3174   2.2151
 VD2  C16   C  CH2   0  -0.444  -0.0319  -1.3898   1.7956
 VD2  C13   C  CR5   0  -0.066   1.3686   0.3859   0.8841
 VD2  C18   C  CH3   0  -0.675   0.2840   1.3881   0.4852
 VD2  C14   C  CR15  0  -0.242   1.3736  -0.8304  -0.0755
 VD2  C15   C  CH2   0  -0.456   0.1042  -1.5904   0.2739
 VD2  C12   C  CH2   0  -0.417   2.7598   1.0241   0.8211
 VD2  C11   C  CH2   0  -0.436   3.1557   1.4014  -0.6060
 VD2  C9    C  CH2   0  -0.504   3.0142   0.2381  -1.5937
 VD2  C8    C  C     0   0.156   1.6736  -0.4377  -1.4882
 VD2  C7    C  C1    0  -0.366   0.8441  -0.6886  -2.5140
 VD2  C6    C  C1    0  -0.343   1.0645  -0.3231  -3.9023
 VD2  C5    C  C     0   0.154   0.3058  -0.6676  -4.9544
 VD2  C10   C  CH2   0  -0.561  -0.9325  -1.5087  -4.9066
 VD2  C4    C  CH2   0  -0.532   0.6482  -0.2118  -6.3422
 VD2  C3    C  CH1   0   0.100  -0.5228   0.5177  -7.0072
 VD2  O2    O  OH1   0  -0.676  -0.2285   0.8206  -8.3565
 VD2  C2    C  CH1   0  -0.286  -1.7861  -0.3407  -6.9813
 VD2  C28   C  CH3   0  -0.655  -2.9737   0.3468  -7.6467
 VD2  C1    C  CH1   0   0.059  -2.1133  -0.7803  -5.5532
 VD2  O1    O  OH1   0  -0.668  -2.4732   0.3664  -4.8111
 VD2  HO3   H  HOH1  0   0.440  -3.1998  -0.4201   7.3685
 VD2  H271  H  HCH3  0   0.229  -2.1134  -0.7599  10.0879
 VD2  H272  H  HCH3  0   0.224  -2.0441  -2.0242   8.8550
 VD2  H273  H  HCH3  0   0.222  -0.5583  -1.4215   9.5818
 VD2  H261  H  HCH3  0   0.223   0.2549   0.9793   8.9840
 VD2  H262  H  HCH3  0   0.233  -0.7735   2.0123   7.9928
 VD2  H263  H  HCH3  0   0.231  -1.2990   1.5315   9.6060
 VD2  H241  H  HCH2  0   0.216  -1.1821  -1.5344   6.6054
 VD2  H242  H  HCH2  0   0.214   0.3135  -0.9643   7.3048
 VD2  H231  H  HCH2  0   0.219   0.0777   1.2011   6.0976
 VD2  H232  H  HCH2  0   0.210  -1.4393   0.6685   5.4062
 VD2  H221  H  HCH2  0   0.230  -0.2880  -1.2475   4.3255
 VD2  H222  H  HCH2  0   0.203   1.2456  -0.7300   4.9837
 VD2  H20   H  HCH1  0   0.203  -0.4423   0.9797   3.1150
 VD2  H211  H  HCH3  0   0.212   2.4868   1.2828   3.9458
 VD2  H212  H  HCH3  0   0.230   1.5564   2.4148   2.9679
 VD2  H213  H  HCH3  0   0.232   1.1575   2.1907   4.6544
 VD2  H17   H  HCR5  0   0.205   1.9199  -0.8348   2.5470
 VD2  H161  H  HCH2  0   0.231   0.1334  -2.3232   2.3345
 VD2  H162  H  HCH2  0   0.221  -1.0415  -1.0599   2.0540
 VD2  H181  H  HCH3  0   0.234   0.4276   1.7601  -0.5295
 VD2  H182  H  HCH3  0   0.231  -0.7144   0.9491   0.5209
 VD2  H183  H  HCH3  0   0.230   0.2784   2.2511   1.1534
 VD2  H14   H  HCR5  0   0.228   2.2216  -1.4523   0.2540
 VD2  H151  H  HCH2  0   0.234   0.1680  -2.6427  -0.0079
 VD2  H152  H  HCH2  0   0.221  -0.7612  -1.1788  -0.2500
 VD2  H121  H  HCH2  0   0.210   3.4873   0.3078   1.2215
 VD2  H122  H  HCH2  0   0.231   2.8237   1.9090   1.4553
 VD2  H111  H  HCH2  0   0.233   4.1897   1.7540  -0.6151
 VD2  H112  H  HCH2  0   0.221   2.5498   2.2432  -0.9524
 VD2  H91   H  HCH2  0   0.230   3.7835  -0.5098  -1.3636
 VD2  H92   H  HCH2  0   0.244   3.2266   0.5881  -2.6037
 VD2  H7    H  H     0   0.225  -0.0760  -1.2174  -2.2886
 VD2  H6    H  H     0   0.227   1.9339   0.2904  -4.1171
 VD2  H101  H  HCH2  0   0.244  -0.7600  -2.4363  -5.4654
 VD2  H102  H  HCH2  0   0.254  -1.2009  -1.8127  -3.8927
 VD2  H41   H  HCH2  0   0.241   1.5287   0.4371  -6.3267
 VD2  H42   H  HCH2  0   0.230   0.8991  -1.0823  -6.9633
 VD2  H3    H  HCH1  0   0.198  -0.7153   1.4430  -6.4458
 VD2  HO2   H  HOH1  0   0.448   0.5146   1.4316  -8.3703
 VD2  H2    H  HCH1  0   0.227  -1.5666  -1.2627  -7.5359
 VD2  H281  H  HCH3  0   0.222  -3.8635  -0.2836  -7.5947
 VD2  H282  H  HCH3  0   0.221  -3.2096   1.2967  -7.1657
 VD2  H283  H  HCH3  0   0.230  -2.7794   0.5448  -8.6997
 VD2  H1    H  HCH1  0   0.214  -2.9571  -1.4838  -5.6047
 VD2  HO1   H  HOH1  0   0.447  -2.6286   0.1007  -3.8996

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
 VD2  O3   C25   single  1.424  0.020  1.424
 VD2  O3   HO3   single  0.850  0.020  0.980
 VD2  C25  C27   single  1.529  0.020  1.529
 VD2  C25  C26   single  1.524  0.020  1.524
 VD2  C25  C24   single  1.536  0.020  1.536
 VD2  C27  H271  single  0.970  0.020  1.090
 VD2  C27  H272  single  0.970  0.020  1.090
 VD2  C27  H273  single  0.970  0.020  1.090
 VD2  C26  H261  single  0.970  0.020  1.090
 VD2  C26  H262  single  0.970  0.020  1.090
 VD2  C26  H263  single  0.970  0.020  1.090
 VD2  C24  C23   single  1.524  0.020  1.524
 VD2  C24  H241  single  0.970  0.020  1.090
 VD2  C24  H242  single  0.970  0.020  1.090
 VD2  C23  C22   single  1.526  0.020  1.526
 VD2  C23  H231  single  0.970  0.020  1.090
 VD2  C23  H232  single  0.970  0.020  1.090
 VD2  C22  C20   single  1.536  0.020  1.536
 VD2  C22  H221  single  0.970  0.020  1.090
 VD2  C22  H222  single  0.970  0.020  1.090
 VD2  C20  C21   single  1.527  0.020  1.527
 VD2  C20  C17   single  1.536  0.020  1.536
 VD2  C20  H20   single  0.970  0.020  1.090
 VD2  C21  H211  single  0.970  0.020  1.090
 VD2  C21  H212  single  0.970  0.020  1.090
 VD2  C21  H213  single  0.970  0.020  1.090
 VD2  C17  C16   single  1.552  0.020  1.552
 VD2  C17  C13   single  1.548  0.020  1.548
 VD2  C17  H17   single  0.970  0.020  1.090
 VD2  C16  C15   single  1.541  0.020  1.541
 VD2  C16  H161  single  0.970  0.020  1.090
 VD2  C16  H162  single  0.970  0.020  1.090
 VD2  C13  C18   single  1.530  0.020  1.530
 VD2  C13  C14   single  1.549  0.020  1.549
 VD2  C13  C12   single  1.532  0.020  1.532
 VD2  C18  H181  single  0.970  0.020  1.090
 VD2  C18  H182  single  0.970  0.020  1.090
 VD2  C18  H183  single  0.970  0.020  1.090
 VD2  C14  C15   single  1.520  0.020  1.520
 VD2  C14  C8    single  1.497  0.020  1.497
 VD2  C14  H14   single  0.970  0.020  1.090
 VD2  C15  H151  single  0.970  0.020  1.090
 VD2  C15  H152  single  0.970  0.020  1.090
 VD2  C12  C11   single  1.528  0.020  1.528
 VD2  C12  H121  single  0.970  0.020  1.090
 VD2  C12  H122  single  0.970  0.020  1.090
 VD2  C11  C9    single  1.533  0.020  1.533
 VD2  C11  H111  single  0.970  0.020  1.090
 VD2  C11  H112  single  0.970  0.020  1.090
 VD2  C9   C8    single  1.505  0.020  1.505
 VD2  C9   H91   single  0.970  0.020  1.090
 VD2  C9   H92   single  0.970  0.020  1.090
 VD2  C8   C7    double  1.343  0.020  1.343
 VD2  C7   C6    single  1.452  0.020  1.452
 VD2  C7   H7    single  0.930  0.020  1.080
 VD2  C6   C5    double  1.342  0.020  1.342
 VD2  C6   H6    single  0.930  0.020  1.080
 VD2  C5   C10   single  1.498  0.020  1.498
 VD2  C5   C4    single  1.500  0.020  1.500
 VD2  C10  C1    single  1.531  0.020  1.531
 VD2  C10  H101  single  0.970  0.020  1.090
 VD2  C10  H102  single  0.970  0.020  1.090
 VD2  C4   C3    single  1.532  0.020  1.532
 VD2  C4   H41   single  0.970  0.020  1.090
 VD2  C4   H42   single  0.970  0.020  1.090
 VD2  C3   O2    single  1.414  0.020  1.414
 VD2  C3   C2    single  1.528  0.020  1.528
 VD2  C3   H3    single  0.970  0.020  1.090
 VD2  O2   HO2   single  0.850  0.020  0.980
 VD2  C2   C28   single  1.525  0.020  1.525
 VD2  C2   C1    single  1.530  0.020  1.530
 VD2  C2   H2    single  0.970  0.020  1.090
 VD2  C28  H281  single  0.970  0.020  1.090
 VD2  C28  H282  single  0.970  0.020  1.090
 VD2  C28  H283  single  0.970  0.020  1.090
 VD2  C1   O1    single  1.413  0.020  1.413
 VD2  C1   H1    single  0.970  0.020  1.090
 VD2  O1   HO1   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
 VD2  HO3   O3   C25   108.01  3.000
 VD2  C24   C25  C26   111.79  3.000
 VD2  C24   C25  C27   109.00  3.000
 VD2  C26   C25  C27   109.60  3.000
 VD2  C24   C25  O3    110.54  3.000
 VD2  C26   C25  O3    105.95  3.000
 VD2  C27   C25  O3    109.92  3.000
 VD2  H273  C27  H272  107.43  3.000
 VD2  H273  C27  H271  107.86  3.000
 VD2  H272  C27  H271  107.97  3.000
 VD2  H273  C27  C25   111.13  3.000
 VD2  H272  C27  C25   111.19  3.000
 VD2  H271  C27  C25   111.09  3.000
 VD2  H263  C26  H262  107.84  3.000
 VD2  H263  C26  H261  107.75  3.000
 VD2  H262  C26  H261  107.86  3.000
 VD2  H263  C26  C25   110.69  3.000
 VD2  H262  C26  C25   111.97  3.000
 VD2  H261  C26  C25   110.57  3.000
 VD2  H242  C24  H241  105.58  3.000
 VD2  H242  C24  C23   109.08  3.000
 VD2  H241  C24  C23   109.24  3.000
 VD2  H242  C24  C25   108.43  3.000
 VD2  H241  C24  C25   108.11  3.000
 VD2  C23   C24  C25   115.91  3.000
 VD2  H232  C23  H231  106.35  3.000
 VD2  H232  C23  C22   109.21  3.000
 VD2  H231  C23  C22   109.90  3.000
 VD2  H232  C23  C24   109.97  3.000
 VD2  H231  C23  C24   109.43  3.000
 VD2  C22   C23  C24   111.83  3.000
 VD2  H222  C22  H221  105.78  3.000
 VD2  H222  C22  C20   108.70  3.000
 VD2  H221  C22  C20   109.83  3.000
 VD2  H222  C22  C23   109.42  3.000
 VD2  H221  C22  C23   107.95  3.000
 VD2  C20   C22  C23   114.78  3.000
 VD2  H20   C20  C17   107.83  3.000
 VD2  H20   C20  C21   108.18  3.000
 VD2  C17   C20  C21   113.12  3.000
 VD2  H20   C20  C22   107.53  3.000
 VD2  C17   C20  C22   109.88  3.000
 VD2  C21   C20  C22   110.10  3.000
 VD2  H213  C21  H212  106.65  3.000
 VD2  H213  C21  H211  107.37  3.000
 VD2  H212  C21  H211  107.71  3.000
 VD2  H213  C21  C20   111.31  3.000
 VD2  H212  C21  C20   112.49  3.000
 VD2  H211  C21  C20   111.05  3.000
 VD2  H17   C17  C13   106.30  3.000
 VD2  H17   C17  C16   108.19  3.000
 VD2  C13   C17  C16   103.74  3.000
 VD2  H17   C17  C20   106.98  3.000
 VD2  C13   C17  C20   118.87  3.000
 VD2  C16   C17  C20   112.25  3.000
 VD2  H162  C16  H161  106.35  3.000
 VD2  H162  C16  C15   110.75  3.000
 VD2  H161  C16  C15   111.30  3.000
 VD2  H162  C16  C17   110.29  3.000
 VD2  H161  C16  C17   110.87  3.000
 VD2  C15   C16  C17   107.32  3.000
 VD2  C12   C13  C14   107.38  3.000
 VD2  C12   C13  C18   111.11  3.000
 VD2  C14   C13  C18   110.80  3.000
 VD2  C12   C13  C17   115.84  3.000
 VD2  C14   C13  C17   100.18  3.000
 VD2  C18   C13  C17   110.92  3.000
 VD2  H183  C18  H182  107.06  3.000
 VD2  H183  C18  H181  107.50  3.000
 VD2  H182  C18  H181  106.75  3.000
 VD2  H183  C18  C13   111.23  3.000
 VD2  H182  C18  C13   112.12  3.000
 VD2  H181  C18  C13   111.89  3.000
 VD2  H14   C14  C8    106.03  3.000
 VD2  H14   C14  C15   106.96  3.000
 VD2  C8    C14  C15   121.03  3.000
 VD2  H14   C14  C13   105.09  3.000
 VD2  C8    C14  C13   112.29  3.000
 VD2  C15   C14  C13   104.33  3.000
 VD2  H152  C15  H151  106.62  3.000
 VD2  H152  C15  C14   111.28  3.000
 VD2  H151  C15  C14   111.96  3.000
 VD2  H152  C15  C16   110.77  3.000
 VD2  H151  C15  C16   112.69  3.000
 VD2  C14   C15  C16   103.63  3.000
 VD2  H122  C12  H121  106.18  3.000
 VD2  H122  C12  C11   109.12  3.000
 VD2  H121  C12  C11   109.30  3.000
 VD2  H122  C12  C13   111.55  3.000
 VD2  H121  C12  C13   108.38  3.000
 VD2  C11   C12  C13   112.12  3.000
 VD2  H112  C11  H111  105.86  3.000
 VD2  H112  C11  C9    109.21  3.000
 VD2  H111  C11  C9    109.09  3.000
 VD2  H112  C11  C12   110.02  3.000
 VD2  H111  C11  C12   109.43  3.000
 VD2  C9    C11  C12   112.98  3.000
 VD2  H92   C9   H91   106.06  3.000
 VD2  H92   C9   C8    112.51  3.000
 VD2  H91   C9   C8    107.68  3.000
 VD2  H92   C9   C11   109.60  3.000
 VD2  H91   C9   C11   108.51  3.000
 VD2  C8    C9   C11   112.20  3.000
 VD2  C7    C8   C9    125.49  3.000
 VD2  C7    C8   C14   123.25  3.000
 VD2  C9    C8   C14   111.26  3.000
 VD2  H7    C7   C6    116.74  3.000
 VD2  H7    C7   C8    117.14  3.000
 VD2  C6    C7   C8    126.12  3.000
 VD2  H6    C6   C5    116.28  3.000
 VD2  H6    C6   C7    116.93  3.000
 VD2  C5    C6   C7    126.80  3.000
 VD2  C4    C5   C10   112.88  3.000
 VD2  C4    C5   C6    121.21  3.000
 VD2  C10   C5   C6    125.91  3.000
 VD2  H102  C10  H101  106.04  3.000
 VD2  H102  C10  C1    109.58  3.000
 VD2  H101  C10  C1    107.98  3.000
 VD2  H102  C10  C5    112.90  3.000
 VD2  H101  C10  C5    109.19  3.000
 VD2  C1    C10  C5    110.92  3.000
 VD2  H42   C4   H41   107.12  3.000
 VD2  H42   C4   C3    107.86  3.000
 VD2  H41   C4   C3    109.82  3.000
 VD2  H42   C4   C5    109.54  3.000
 VD2  H41   C4   C5    110.53  3.000
 VD2  C3    C4   C5    111.83  3.000
 VD2  H3    C3   C2    108.64  3.000
 VD2  H3    C3   O2    110.09  3.000
 VD2  C2    C3   O2    107.98  3.000
 VD2  H3    C3   C4    108.25  3.000
 VD2  C2    C3   C4    110.94  3.000
 VD2  O2    C3   C4    110.93  3.000
 VD2  HO2   O2   C3    108.09  3.000
 VD2  H2    C2   C1    105.84  3.000
 VD2  H2    C2   C28   108.29  3.000
 VD2  C1    C2   C28   111.74  3.000
 VD2  H2    C2   C3    107.34  3.000
 VD2  C1    C2   C3    110.74  3.000
 VD2  C28   C2   C3    112.54  3.000
 VD2  H283  C28  H282  107.86  3.000
 VD2  H283  C28  H281  107.25  3.000
 VD2  H282  C28  H281  107.80  3.000
 VD2  H283  C28  C2    111.40  3.000
 VD2  H282  C28  C2    111.64  3.000
 VD2  H281  C28  C2    110.70  3.000
 VD2  H1    C1   O1    110.39  3.000
 VD2  H1    C1   C2    107.71  3.000
 VD2  O1    C1   C2    108.16  3.000
 VD2  H1    C1   C10   107.90  3.000
 VD2  O1    C1   C10   111.16  3.000
 VD2  C2    C1   C10   111.48  3.000
 VD2  HO1   O1   C1    108.34  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
 VD2  Var_01  C14   C15  C16  C17    10.14  30.0  1
 VD2  Var_02  C9    C11  C12  C13   -52.38  30.0  1
 VD2  Var_03  C8    C9   C11  C12    49.41  30.0  1
 VD2  Var_04  C3    C4   C5   C10    54.61  30.0  1
 VD2  Var_05  C1    C10  C5   C4    -54.64  30.0  1
 VD2  Var_06  C6    C7   C8   C14   179.24  30.0  2
 VD2  Var_07  C5    C6   C7   C8    173.67  30.0  2
 VD2  Var_08  C10   C5   C6   C7     -0.09  30.0  2
 VD2  Var_09  C23   C24  C25  O3     59.23  30.0  3
 VD2  Var_10  C22   C23  C24  C25  -178.24  30.0  3
 VD2  Var_11  C20   C22  C23  C24  -179.65  30.0  3
 VD2  Var_12  H271  C27  C25  O3    -57.66  30.0  3
 VD2  Var_13  H261  C26  C25  O3   -176.28  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
 VD2  chir_01  C20  C22  C21  C17  negativ
 VD2  chir_02  C17  C20  C16  C13  negativ
 VD2  chir_03  C13  C17  C14  C12  positiv
 VD2  chir_04  C14  C8   C15  C13  positiv
 VD2  chir_05  C3   O2   C2   C4   negativ
 VD2  chir_06  C2   C3   C28  C1   positiv
 VD2  chir_07  C1   O1   C2   C10  negativ

