# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 23:57:14 2022
#   Inital geometry file: a 165 line input string
#   Ligand name: (3S,5Z,14beta,17alpha)-9,10-secocholesta-5,7,10-triene-3,25-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=C3/C[C@@H](O)CCC3=C
#
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
 VDY  VDY  (3S,5Z,14beta,17alpha)-9,10-secocholesta-5,7,10-triene-3,25-diol  ligand  73  29  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VDY
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
 VDY  O1    O  OH1   0  -0.674  -0.9356   1.4176  -8.4153
 VDY  O2    O  OH1   0  -0.679  -2.6627   0.3749   7.3405
 VDY  C1    C  CH2   0  -0.509  -2.6197  -0.3560  -5.5929
 VDY  C2    C  CH2   0  -0.463  -2.3869   0.1748  -7.0073
 VDY  C3    C  CH1   0   0.075  -1.0914   0.9649  -7.0874
 VDY  C4    C  CH2   0  -0.534   0.0855   0.0921  -6.6411
 VDY  C5    C  C     0   0.074  -0.1417  -0.4535  -5.2562
 VDY  C6    C  C1    0  -0.297   0.7462  -0.2464  -4.2672
 VDY  C7    C  C1    0  -0.362   0.5934  -0.6314  -2.8779
 VDY  C8    C  C     0   0.155   1.5048  -0.4735  -1.9043
 VDY  C9    C  CH2   0  -0.505   2.8845   0.1007  -2.0723
 VDY  C10   C  C     0   0.110  -1.4367  -1.1452  -5.0947
 VDY  C11   C  CH2   0  -0.436   3.1459   1.2465  -1.0865
 VDY  C12   C  CH2   0  -0.417   2.8003   0.8825   0.3580
 VDY  C13   C  CT    0  -0.064   1.3755   0.3360   0.4886
 VDY  C14   C  CH1   0  -0.244   1.2493  -0.8638  -0.4826
 VDY  C15   C  CH2   0  -0.455  -0.0520  -1.5372  -0.0781
 VDY  C16   C  CH2   0  -0.445  -0.0838  -1.3664   1.4527
 VDY  C17   C  CH1   0  -0.165   1.0377  -0.3602   1.8298
 VDY  C18   C  CH3   0  -0.675   0.3423   1.4157   0.1593
 VDY  C19   C  C2    0  -0.590  -1.5534  -2.3784  -4.6037
 VDY  C20   C  CH1   0  -0.231   0.6577   0.5094   3.0367
 VDY  C21   C  CH3   0  -0.673   1.7171   1.5558   3.3769
 VDY  C22   C  CH2   0  -0.412   0.3871  -0.3756   4.2631
 VDY  C23   C  CH2   0  -0.428  -0.3586   0.3240   5.3956
 VDY  C24   C  CH2   0  -0.429  -0.5593  -0.5952   6.5942
 VDY  C25   C  CT    0   0.202  -1.3588  -0.0063   7.7658
 VDY  C26   C  CH3   0  -0.664  -1.4585  -1.0529   8.8758
 VDY  C27   C  CH3   0  -0.668  -0.7103   1.2595   8.3122
 VDY  HO1   H  HOH1  0   0.448  -0.1444   1.9638  -8.4577
 VDY  HO2   H  HOH1  0   0.439  -3.0984  -0.4040   6.9783
 VDY  H11   H  HCH2  0   0.248  -3.5244  -0.9658  -5.5617
 VDY  H12   H  HCH2  0   0.239  -2.7864   0.4917  -4.9184
 VDY  H21   H  HCH2  0   0.244  -3.2283   0.8034  -7.3086
 VDY  H22   H  HCH2  0   0.226  -2.3400  -0.6647  -7.7090
 VDY  H31   H  HCH1  0   0.197  -1.1603   1.8179  -6.3947
 VDY  H41   H  HCH2  0   0.244   1.0164   0.6655  -6.6724
 VDY  H42   H  HCH2  0   0.236   0.1846  -0.7327  -7.3578
 VDY  H61   H  H     0   0.231   1.6478   0.2945  -4.5375
 VDY  H71   H  H     0   0.234  -0.3585  -1.0740  -2.6077
 VDY  H91   H  HCH2  0   0.231   3.6101  -0.6985  -1.8766
 VDY  H92   H  HCH2  0   0.244   3.0745   0.4414  -3.0902
 VDY  H111  H  HCH2  0   0.233   4.1977   1.5360  -1.1469
 VDY  H112  H  HCH2  0   0.221   2.5743   2.1245  -1.3990
 VDY  H121  H  HCH2  0   0.211   3.4983   0.1157   0.7141
 VDY  H122  H  HCH2  0   0.231   2.9550   1.7557   0.9932
 VDY  H141  H  HCH1  0   0.230   2.0662  -1.5499  -0.2054
 VDY  H151  H  HCH2  0   0.234  -0.0884  -2.5832  -0.3869
 VDY  H152  H  HCH2  0   0.221  -0.9110  -1.0452  -0.5389
 VDY  H161  H  HCH2  0   0.231   0.0656  -2.3209   1.9583
 VDY  H162  H  HCH2  0   0.221  -1.0581  -0.9947   1.7803
 VDY  H171  H  HCH1  0   0.206   1.9313  -0.9329   2.1155
 VDY  H181  H  HCH3  0   0.235   0.4507   1.7841  -0.8611
 VDY  H182  H  HCH3  0   0.231  -0.6815   1.0508   0.2572
 VDY  H183  H  HCH3  0   0.229   0.4413   2.2717   0.8293
 VDY  H191  H  H     0   0.238  -0.6925  -2.9480  -4.2770
 VDY  H192  H  H     0   0.236  -2.5197  -2.8616  -4.5203
 VDY  H201  H  HCH1  0   0.204  -0.2773   1.0305   2.7944
 VDY  H211  H  HCH3  0   0.213   2.7031   1.0950   3.4708
 VDY  H212  H  HCH3  0   0.227   1.7901   2.3405   2.6249
 VDY  H213  H  HCH3  0   0.231   1.4967   2.0494   4.3237
 VDY  H221  H  HCH2  0   0.231  -0.1954  -1.2535   3.9708
 VDY  H222  H  HCH2  0   0.204   1.3426  -0.7642   4.6367
 VDY  H231  H  HCH2  0   0.218   0.1865   1.2180   5.7082
 VDY  H232  H  HCH2  0   0.211  -1.3281   0.6703   5.0255
 VDY  H241  H  HCH2  0   0.216  -1.0633  -1.5131   6.2639
 VDY  H242  H  HCH2  0   0.215   0.4188  -0.9150   6.9687
 VDY  H261  H  HCH3  0   0.229  -2.0375  -0.6757   9.7209
 VDY  H262  H  HCH3  0   0.224  -1.9421  -1.9650   8.5162
 VDY  H263  H  HCH3  0   0.222  -0.4702  -1.3312   9.2442
 VDY  H271  H  HCH3  0   0.223   0.3229   1.0665   8.6025
 VDY  H272  H  HCH3  0   0.234  -0.7058   2.0648   7.5772
 VDY  H273  H  HCH3  0   0.231  -1.2435   1.6156   9.1957

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
 VDY  O1   C3    single  1.412  0.020  1.412
 VDY  O1   HO1   single  0.850  0.020  0.980
 VDY  O2   C25   single  1.423  0.020  1.423
 VDY  O2   HO2   single  0.850  0.020  0.980
 VDY  C1   C2    single  1.529  0.020  1.529
 VDY  C1   C10   single  1.507  0.020  1.507
 VDY  C1   H11   single  0.970  0.020  1.090
 VDY  C1   H12   single  0.970  0.020  1.090
 VDY  C2   C3    single  1.520  0.020  1.520
 VDY  C2   H21   single  0.970  0.020  1.090
 VDY  C2   H22   single  0.970  0.020  1.090
 VDY  C3   C4    single  1.532  0.020  1.532
 VDY  C3   H31   single  0.970  0.020  1.090
 VDY  C4   C5    single  1.506  0.020  1.506
 VDY  C4   H41   single  0.970  0.020  1.090
 VDY  C4   H42   single  0.970  0.020  1.090
 VDY  C5   C6    double  1.345  0.020  1.345
 VDY  C5   C10   single  1.477  0.020  1.477
 VDY  C6   C7    single  1.450  0.020  1.450
 VDY  C6   H61   single  0.930  0.020  1.080
 VDY  C7   C8    double  1.343  0.020  1.343
 VDY  C7   H71   single  0.930  0.020  1.080
 VDY  C8   C9    single  1.504  0.020  1.504
 VDY  C8   C14   single  1.496  0.020  1.496
 VDY  C9   C11   single  1.534  0.020  1.534
 VDY  C9   H91   single  0.970  0.020  1.090
 VDY  C9   H92   single  0.970  0.020  1.090
 VDY  C10  C19   double  1.333  0.020  1.333
 VDY  C11  C12   single  1.529  0.020  1.529
 VDY  C11  H111  single  0.970  0.020  1.090
 VDY  C11  H112  single  0.970  0.020  1.090
 VDY  C12  C13   single  1.532  0.020  1.532
 VDY  C12  H121  single  0.970  0.020  1.090
 VDY  C12  H122  single  0.970  0.020  1.090
 VDY  C13  C14   single  1.549  0.020  1.549
 VDY  C13  C17   single  1.548  0.020  1.548
 VDY  C13  C18   single  1.530  0.020  1.530
 VDY  C14  C15   single  1.520  0.020  1.520
 VDY  C14  H141  single  0.970  0.020  1.090
 VDY  C15  C16   single  1.541  0.020  1.541
 VDY  C15  H151  single  0.970  0.020  1.090
 VDY  C15  H152  single  0.970  0.020  1.090
 VDY  C16  C17   single  1.553  0.020  1.553
 VDY  C16  H161  single  0.970  0.020  1.090
 VDY  C16  H162  single  0.970  0.020  1.090
 VDY  C17  C20   single  1.535  0.020  1.535
 VDY  C17  H171  single  0.970  0.020  1.090
 VDY  C18  H181  single  0.970  0.020  1.090
 VDY  C18  H182  single  0.970  0.020  1.090
 VDY  C18  H183  single  0.970  0.020  1.090
 VDY  C19  H191  single  0.930  0.020  1.080
 VDY  C19  H192  single  0.930  0.020  1.080
 VDY  C20  C21   single  1.527  0.020  1.527
 VDY  C20  C22   single  1.536  0.020  1.536
 VDY  C20  H201  single  0.970  0.020  1.090
 VDY  C21  H211  single  0.970  0.020  1.090
 VDY  C21  H212  single  0.970  0.020  1.090
 VDY  C21  H213  single  0.970  0.020  1.090
 VDY  C22  C23   single  1.526  0.020  1.526
 VDY  C22  H221  single  0.970  0.020  1.090
 VDY  C22  H222  single  0.970  0.020  1.090
 VDY  C23  C24   single  1.524  0.020  1.524
 VDY  C23  H231  single  0.970  0.020  1.090
 VDY  C23  H232  single  0.970  0.020  1.090
 VDY  C24  C25   single  1.536  0.020  1.536
 VDY  C24  H241  single  0.970  0.020  1.090
 VDY  C24  H242  single  0.970  0.020  1.090
 VDY  C25  C26   single  1.529  0.020  1.529
 VDY  C25  C27   single  1.524  0.020  1.524
 VDY  C26  H261  single  0.970  0.020  1.090
 VDY  C26  H262  single  0.970  0.020  1.090
 VDY  C26  H263  single  0.970  0.020  1.090
 VDY  C27  H271  single  0.970  0.020  1.090
 VDY  C27  H272  single  0.970  0.020  1.090
 VDY  C27  H273  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
 VDY  HO1   O1   C3    108.31  3.000
 VDY  HO2   O2   C25   108.07  3.000
 VDY  H12   C1   H11   106.77  3.000
 VDY  H12   C1   C10   108.72  3.000
 VDY  H11   C1   C10   110.41  3.000
 VDY  H12   C1   C2    108.91  3.000
 VDY  H11   C1   C2    110.29  3.000
 VDY  C10   C1   C2    111.60  3.000
 VDY  H22   C2   H21   107.30  3.000
 VDY  H22   C2   C3    109.17  3.000
 VDY  H21   C2   C3    110.05  3.000
 VDY  H22   C2   C1    109.46  3.000
 VDY  H21   C2   C1    109.73  3.000
 VDY  C3    C2   C1    111.05  3.000
 VDY  H31   C3   C4    107.83  3.000
 VDY  H31   C3   C2    108.44  3.000
 VDY  C4    C3   C2    110.09  3.000
 VDY  H31   C3   O1    110.50  3.000
 VDY  C4    C3   O1    111.84  3.000
 VDY  C2    C3   O1    108.08  3.000
 VDY  H42   C4   H41   107.37  3.000
 VDY  H42   C4   C5    110.01  3.000
 VDY  H41   C4   C5    110.17  3.000
 VDY  H42   C4   C3    107.90  3.000
 VDY  H41   C4   C3    110.30  3.000
 VDY  C5    C4   C3    111.01  3.000
 VDY  C10   C5   C6    124.78  3.000
 VDY  C10   C5   C4    113.74  3.000
 VDY  C6    C5   C4    121.39  3.000
 VDY  H61   C6   C7    117.29  3.000
 VDY  H61   C6   C5    116.22  3.000
 VDY  C7    C6   C5    126.45  3.000
 VDY  H71   C7   C8    117.59  3.000
 VDY  H71   C7   C6    116.10  3.000
 VDY  C8    C7   C6    126.30  3.000
 VDY  C14   C8   C9    111.25  3.000
 VDY  C14   C8   C7    122.84  3.000
 VDY  C9    C8   C7    125.91  3.000
 VDY  H92   C9   H91   106.20  3.000
 VDY  H92   C9   C11   109.69  3.000
 VDY  H91   C9   C11   108.47  3.000
 VDY  H92   C9   C8    112.55  3.000
 VDY  H91   C9   C8    107.98  3.000
 VDY  C11   C9   C8    111.70  3.000
 VDY  C19   C10  C5    123.40  3.000
 VDY  C19   C10  C1    122.53  3.000
 VDY  C5    C10  C1    114.01  3.000
 VDY  H112  C11  H111  105.95  3.000
 VDY  H112  C11  C12   110.06  3.000
 VDY  H111  C11  C12   109.44  3.000
 VDY  H112  C11  C9    109.10  3.000
 VDY  H111  C11  C9    109.05  3.000
 VDY  C12   C11  C9    113.00  3.000
 VDY  H122  C12  H121  106.28  3.000
 VDY  H122  C12  C13   111.58  3.000
 VDY  H121  C12  C13   108.37  3.000
 VDY  H122  C12  C11   109.12  3.000
 VDY  H121  C12  C11   109.23  3.000
 VDY  C13   C12  C11   112.07  3.000
 VDY  C18   C13  C17   110.88  3.000
 VDY  C18   C13  C14   110.89  3.000
 VDY  C17   C13  C14   100.20  3.000
 VDY  C18   C13  C12   110.98  3.000
 VDY  C17   C13  C12   115.93  3.000
 VDY  C14   C13  C12   107.38  3.000
 VDY  H141  C14  C15   106.96  3.000
 VDY  H141  C14  C13   105.32  3.000
 VDY  C15   C14  C13   104.25  3.000
 VDY  H141  C14  C8    105.95  3.000
 VDY  C15   C14  C8    120.97  3.000
 VDY  C13   C14  C8    112.32  3.000
 VDY  H152  C15  H151  106.63  3.000
 VDY  H152  C15  C16   110.68  3.000
 VDY  H151  C15  C16   112.75  3.000
 VDY  H152  C15  C14   111.20  3.000
 VDY  H151  C15  C14   112.21  3.000
 VDY  C16   C15  C14   103.47  3.000
 VDY  H162  C16  H161  106.31  3.000
 VDY  H162  C16  C17   110.52  3.000
 VDY  H161  C16  C17   110.83  3.000
 VDY  H162  C16  C15   110.73  3.000
 VDY  H161  C16  C15   111.15  3.000
 VDY  C17   C16  C15   107.35  3.000
 VDY  H171  C17  C20   106.98  3.000
 VDY  H171  C17  C16   108.22  3.000
 VDY  C20   C17  C16   112.27  3.000
 VDY  H171  C17  C13   106.38  3.000
 VDY  C20   C17  C13   118.70  3.000
 VDY  C16   C17  C13   103.79  3.000
 VDY  H183  C18  H182  107.00  3.000
 VDY  H183  C18  H181  107.48  3.000
 VDY  H182  C18  H181  106.87  3.000
 VDY  H183  C18  C13   111.10  3.000
 VDY  H182  C18  C13   112.22  3.000
 VDY  H181  C18  C13   111.88  3.000
 VDY  H192  C19  H191  116.82  3.000
 VDY  H192  C19  C10   121.28  3.000
 VDY  H191  C19  C10   121.90  3.000
 VDY  H201  C20  C22   107.44  3.000
 VDY  H201  C20  C21   108.35  3.000
 VDY  C22   C20  C21   109.81  3.000
 VDY  H201  C20  C17   107.83  3.000
 VDY  C22   C20  C17   110.17  3.000
 VDY  C21   C20  C17   113.04  3.000
 VDY  H213  C21  H212  106.68  3.000
 VDY  H213  C21  H211  107.39  3.000
 VDY  H212  C21  H211  107.63  3.000
 VDY  H213  C21  C20   111.31  3.000
 VDY  H212  C21  C20   112.71  3.000
 VDY  H211  C21  C20   110.86  3.000
 VDY  H222  C22  H221  105.70  3.000
 VDY  H222  C22  C23   109.59  3.000
 VDY  H221  C22  C23   107.83  3.000
 VDY  H222  C22  C20   108.81  3.000
 VDY  H221  C22  C20   110.05  3.000
 VDY  C23   C22  C20   114.49  3.000
 VDY  H232  C23  H231  106.25  3.000
 VDY  H232  C23  C24   109.90  3.000
 VDY  H231  C23  C24   109.52  3.000
 VDY  H232  C23  C22   109.10  3.000
 VDY  H231  C23  C22   110.10  3.000
 VDY  C24   C23  C22   111.82  3.000
 VDY  H242  C24  H241  105.59  3.000
 VDY  H242  C24  C25   108.43  3.000
 VDY  H241  C24  C25   108.12  3.000
 VDY  H242  C24  C23   109.12  3.000
 VDY  H241  C24  C23   109.15  3.000
 VDY  C25   C24  C23   115.93  3.000
 VDY  C27   C25  C26   109.64  3.000
 VDY  C27   C25  C24   111.75  3.000
 VDY  C26   C25  C24   108.98  3.000
 VDY  C27   C25  O2    105.93  3.000
 VDY  C26   C25  O2    109.91  3.000
 VDY  C24   C25  O2    110.59  3.000
 VDY  H263  C26  H262  107.40  3.000
 VDY  H263  C26  H261  107.89  3.000
 VDY  H262  C26  H261  107.96  3.000
 VDY  H263  C26  C25   111.15  3.000
 VDY  H262  C26  C25   111.17  3.000
 VDY  H261  C26  C25   111.10  3.000
 VDY  H273  C27  H272  107.85  3.000
 VDY  H273  C27  H271  107.76  3.000
 VDY  H272  C27  H271  107.84  3.000
 VDY  H273  C27  C25   110.69  3.000
 VDY  H272  C27  C25   111.94  3.000
 VDY  H271  C27  C25   110.59  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
 VDY  Var_01  C4    C5   C10  C1    -49.85  30.0  1
 VDY  Var_02  C5    C10  C1   C2     49.89  30.0  1
 VDY  Var_03  C10   C1   C2   C3    -53.85  30.0  1
 VDY  Var_04  C12   C11  C9   C8     50.13  30.0  1
 VDY  Var_05  C13   C12  C11  C9    -52.69  30.0  1
 VDY  Var_06  C14   C8   C9   C11   -53.04  30.0  1
 VDY  Var_07  C17   C16  C15  C14    11.37  30.0  1
 VDY  Var_08  C7    C6   C5   C4    175.05   0.0  2
 VDY  Var_09  C9    C8   C7   C6     -1.87   0.0  2
 VDY  Var_10  C8    C7   C6   C5    177.01  30.0  2
 VDY  Var_11  H191  C19  C10  C1    178.06   0.0  2
 VDY  Var_12  C23   C24  C25  O2     59.30  30.0  1
 VDY  Var_13  C24   C23  C22  C20  -178.37  30.0  3
 VDY  Var_14  C25   C24  C23  C22  -177.26  30.0  3
 VDY  Var_15  H261  C26  C25  O2    -57.63  30.0  3
 VDY  Var_16  H271  C27  C25  O2   -176.33  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
 VDY  chir_01  C3   O1   C2   C4   negativ
 VDY  chir_02  C13  C14  C17  C12  negativ
 VDY  chir_03  C14  C8   C13  C15  negativ
 VDY  chir_04  C17  C13  C16  C20  positiv
 VDY  chir_05  C20  C22  C21  C17  negativ

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
 VDY  plan-1  C4    0.020
 VDY  plan-1  C5    0.020
 VDY  plan-1  C6    0.020
 VDY  plan-1  C7    0.020
 VDY  plan-1  C10   0.020
 VDY  plan-1  H61   0.020
 VDY  plan-2  C6    0.020
 VDY  plan-2  C7    0.020
 VDY  plan-2  C8    0.020
 VDY  plan-2  C9    0.020
 VDY  plan-2  C14   0.020
 VDY  plan-2  H71   0.020
 VDY  plan-3  C1    0.020
 VDY  plan-3  C5    0.020
 VDY  plan-3  C10   0.020
 VDY  plan-3  C19   0.020
 VDY  plan-3  H191  0.020
 VDY  plan-3  H192  0.020

