# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun  3 20:32:42 2020
#   Inital geometry file: a 161 line input string
#   Ligand name: (3beta,7alpha,9beta,14beta)-cholest-5-ene-3,7-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3[C@H](O)C=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
#
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
 5JK  5JK  (3beta,7alpha,9beta,14beta)-cholest-5-ene-3,7-diol  ligand  75  29  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5JK
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
 5JK  C18  C  CH3   0  -0.685   0.7090   1.0165   1.5583
 5JK  C13  C  CT    0  -0.057   0.6471   0.3826   0.1650
 5JK  C12  C  CH2   0  -0.404   0.0150   1.3366  -0.8490
 5JK  C11  C  CH2   0  -0.447  -1.4512   1.6107  -0.5145
 5JK  C9   C  CH1   0  -0.182  -2.3135   0.3470  -0.3787
 5JK  C10  C  CT    0  -0.133  -3.7789   0.6628   0.0243
 5JK  C19  C  CH3   0  -0.680  -3.8409   1.6526   1.2003
 5JK  C1   C  CH2   0  -0.429  -4.5007   1.2674  -1.1998
 5JK  C2   C  CH2   0  -0.483  -6.0029   1.4373  -1.0140
 5JK  C3   C  CH1   0   0.088  -6.6505   0.1005  -0.6879
 5JK  O1   O  OH1   0  -0.677  -8.0400   0.2092  -0.4554
 5JK  C4   C  CH2   0  -0.532  -6.0161  -0.4915   0.5626
 5JK  C5   C  C     0   0.218  -4.5197  -0.6005   0.4253
 5JK  C6   C  C1    0  -0.367  -3.9125  -1.7643   0.6481
 5JK  C7   C  CH1   0   0.044  -2.4398  -2.0021   0.5205
 5JK  O2   O  OH1   0  -0.671  -2.1574  -2.6999  -0.6862
 5JK  C8   C  CH1   0  -0.285  -1.6588  -0.6930   0.5427
 5JK  C14  C  CH1   0  -0.164  -0.2039  -0.8974   0.1440
 5JK  C15  C  CH2   0  -0.450   0.6253  -1.9131   0.9171
 5JK  C16  C  CH2   0  -0.445   2.0761  -1.5526   0.5399
 5JK  C17  C  CH1   0  -0.161   2.0322  -0.1978  -0.2175
 5JK  C20  C  CH1   0  -0.223   3.2883   0.6488   0.0294
 5JK  C21  C  CH3   0  -0.697   3.2102   2.0342  -0.6104
 5JK  C22  C  CH2   0  -0.432   4.5361  -0.0861  -0.4841
 5JK  C23  C  CH2   0  -0.454   5.8526   0.4332   0.0870
 5JK  C24  C  CH2   0  -0.423   7.0624  -0.2380  -0.5550
 5JK  C25  C  CH1   0  -0.238   8.4154   0.2620  -0.0456
 5JK  C27  C  CH3   0  -0.676   8.6394  -0.0883   1.4233
 5JK  C26  C  CH3   0  -0.663   9.5468  -0.3036  -0.8994
 5JK  H1   H  HCH3  0   0.227  -0.2747   1.2804   1.9462
 5JK  H2   H  HCH3  0   0.229   1.1760   0.3554   2.2905
 5JK  H3   H  HCH3  0   0.228   1.2981   1.9352   1.5407
 5JK  H4   H  HCH2  0   0.225   0.5465   2.2885  -0.8987
 5JK  H5   H  HCH2  0   0.205   0.0927   0.8893  -1.8467
 5JK  H6   H  HCH2  0   0.221  -1.4846   2.1909   0.4097
 5JK  H7   H  HCH2  0   0.230  -1.8779   2.2607  -1.2826
 5JK  H8   H  HCH1  0   0.211  -2.3598  -0.1153  -1.3743
 5JK  H9   H  HCH3  0   0.232  -3.5232   2.6502   0.8952
 5JK  H10  H  HCH3  0   0.236  -4.8488   1.7543   1.6009
 5JK  H11  H  HCH3  0   0.233  -3.2005   1.3336   2.0246
 5JK  H12  H  HCH2  0   0.237  -4.0490   2.2310  -1.4469
 5JK  H13  H  HCH2  0   0.223  -4.3269   0.6132  -2.0612
 5JK  H14  H  HCH2  0   0.222  -6.2195   2.1513  -0.2130
 5JK  H15  H  HCH2  0   0.236  -6.4373   1.8512  -1.9295
 5JK  H16  H  HCH1  0   0.192  -6.4545  -0.5866  -1.5263
 5JK  H17  H  HOH1  0   0.446  -8.4507   0.5591  -1.2524
 5JK  H18  H  HCH2  0   0.233  -6.2791   0.1455   1.4154
 5JK  H19  H  HCH2  0   0.247  -6.4388  -1.4779   0.7699
 5JK  H21  H  H     0   0.230  -4.5175  -2.6288   0.9141
 5JK  H23  H  HCH1  0   0.206  -2.1103  -2.6088   1.3762
 5JK  H24  H  HOH1  0   0.445  -2.6829  -3.5057  -0.6940
 5JK  H25  H  HCH1  0   0.221  -1.7010  -0.3369   1.5803
 5JK  H26  H  HCH1  0   0.212  -0.2031  -1.2236  -0.9044
 5JK  H27  H  HCH2  0   0.211   0.4605  -1.8150   1.9937
 5JK  H28  H  HCH2  0   0.228   0.3699  -2.9394   0.6509
 5JK  H29  H  HCH2  0   0.215   2.7057  -1.4719   1.4302
 5JK  H30  H  HCH2  0   0.224   2.5267  -2.3315  -0.0765
 5JK  H31  H  HCH1  0   0.200   1.9920  -0.4057  -1.2964
 5JK  H32  H  HCH1  0   0.193   3.4021   0.7740   1.1143
 5JK  H33  H  HCH3  0   0.214   2.4679   2.6719  -0.1298
 5JK  H34  H  HCH3  0   0.248   4.1640   2.5593  -0.5454
 5JK  H35  H  HCH3  0   0.234   2.9467   1.9597  -1.6679
 5JK  H36  H  HCH2  0   0.235   4.4703  -1.1529  -0.2533
 5JK  H37  H  HCH2  0   0.225   4.5563  -0.0164  -1.5785
 5JK  H38  H  HCH2  0   0.226   5.9368   1.5151  -0.0560
 5JK  H39  H  HCH2  0   0.228   5.8561   0.2689   1.1691
 5JK  H40  H  HCH2  0   0.216   7.0028  -1.3240  -0.4098
 5JK  H41  H  HCH2  0   0.232   7.0120  -0.0761  -1.6378
 5JK  H42  H  HCH1  0   0.229   8.4284   1.3538  -0.1443
 5JK  H43  H  HCH3  0   0.251   7.8677   0.3293   2.0704
 5JK  H44  H  HCH3  0   0.207   8.6373  -1.1732   1.5607
 5JK  H45  H  HCH3  0   0.213   9.6037   0.2856   1.7749
 5JK  H46  H  HCH3  0   0.223   9.4235  -0.0395  -1.9517
 5JK  H47  H  HCH3  0   0.216  10.5203   0.0695  -0.5742
 5JK  H48  H  HCH3  0   0.212   9.5731  -1.3947  -0.8341

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
 5JK  O2   C7   single  1.422  0.020  1.422
 5JK  O1   C3   single  1.413  0.020  1.413
 5JK  C4   C3   single  1.522  0.020  1.522
 5JK  C4   C5   single  1.507  0.020  1.507
 5JK  C6   C7   single  1.497  0.020  1.497
 5JK  C6   C5   double  1.332  0.020  1.332
 5JK  C7   C8   single  1.525  0.020  1.525
 5JK  C3   C2   single  1.521  0.020  1.521
 5JK  C5   C10  single  1.518  0.020  1.518
 5JK  C15  C14  single  1.522  0.020  1.522
 5JK  C15  C16  single  1.542  0.020  1.542
 5JK  C8   C14  single  1.522  0.020  1.522
 5JK  C8   C9   single  1.536  0.020  1.536
 5JK  C14  C13  single  1.537  0.020  1.537
 5JK  C2   C1   single  1.523  0.020  1.523
 5JK  C9   C10  single  1.552  0.020  1.552
 5JK  C9   C11  single  1.536  0.020  1.536
 5JK  C16  C17  single  1.553  0.020  1.553
 5JK  C10  C1   single  1.544  0.020  1.544
 5JK  C10  C19  single  1.538  0.020  1.538
 5JK  C17  C13  single  1.550  0.020  1.550
 5JK  C17  C20  single  1.535  0.020  1.535
 5JK  C13  C12  single  1.529  0.020  1.529
 5JK  C13  C18  single  1.532  0.020  1.532
 5JK  C11  C12  single  1.529  0.020  1.529
 5JK  C22  C20  single  1.536  0.020  1.536
 5JK  C22  C23  single  1.526  0.020  1.526
 5JK  C24  C23  single  1.525  0.020  1.525
 5JK  C24  C25  single  1.530  0.020  1.530
 5JK  C27  C25  single  1.527  0.020  1.527
 5JK  C20  C21  single  1.528  0.020  1.528
 5JK  C25  C26  single  1.526  0.020  1.526
 5JK  C18  H1   single  0.970  0.020  1.090
 5JK  C18  H2   single  0.970  0.020  1.090
 5JK  C18  H3   single  0.970  0.020  1.090
 5JK  C12  H4   single  0.970  0.020  1.090
 5JK  C12  H5   single  0.970  0.020  1.090
 5JK  C11  H6   single  0.970  0.020  1.090
 5JK  C11  H7   single  0.970  0.020  1.090
 5JK  C9   H8   single  0.970  0.020  1.090
 5JK  C19  H9   single  0.970  0.020  1.090
 5JK  C19  H10  single  0.970  0.020  1.090
 5JK  C19  H11  single  0.970  0.020  1.090
 5JK  C1   H12  single  0.970  0.020  1.090
 5JK  C1   H13  single  0.970  0.020  1.090
 5JK  C2   H14  single  0.970  0.020  1.090
 5JK  C2   H15  single  0.970  0.020  1.090
 5JK  C3   H16  single  0.970  0.020  1.090
 5JK  O1   H17  single  0.850  0.020  0.980
 5JK  C4   H18  single  0.970  0.020  1.090
 5JK  C4   H19  single  0.970  0.020  1.090
 5JK  C6   H21  single  0.930  0.020  1.080
 5JK  C7   H23  single  0.970  0.020  1.090
 5JK  O2   H24  single  0.850  0.020  0.980
 5JK  C8   H25  single  0.970  0.020  1.090
 5JK  C14  H26  single  0.970  0.020  1.090
 5JK  C15  H27  single  0.970  0.020  1.090
 5JK  C15  H28  single  0.970  0.020  1.090
 5JK  C16  H29  single  0.970  0.020  1.090
 5JK  C16  H30  single  0.970  0.020  1.090
 5JK  C17  H31  single  0.970  0.020  1.090
 5JK  C20  H32  single  0.970  0.020  1.090
 5JK  C21  H33  single  0.970  0.020  1.090
 5JK  C21  H34  single  0.970  0.020  1.090
 5JK  C21  H35  single  0.970  0.020  1.090
 5JK  C22  H36  single  0.970  0.020  1.090
 5JK  C22  H37  single  0.970  0.020  1.090
 5JK  C23  H38  single  0.970  0.020  1.090
 5JK  C23  H39  single  0.970  0.020  1.090
 5JK  C24  H40  single  0.970  0.020  1.090
 5JK  C24  H41  single  0.970  0.020  1.090
 5JK  C25  H42  single  0.970  0.020  1.090
 5JK  C27  H43  single  0.970  0.020  1.090
 5JK  C27  H44  single  0.970  0.020  1.090
 5JK  C27  H45  single  0.970  0.020  1.090
 5JK  C26  H46  single  0.970  0.020  1.090
 5JK  C26  H47  single  0.970  0.020  1.090
 5JK  C26  H48  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
 5JK  H3   C18  H2   106.84  3.000
 5JK  H3   C18  H1   106.81  3.000
 5JK  H2   C18  H1   107.10  3.000
 5JK  H3   C18  C13  110.82  3.000
 5JK  H2   C18  C13  112.13  3.000
 5JK  H1   C18  C13  112.79  3.000
 5JK  C17  C13  C14  100.34  3.000
 5JK  C17  C13  C12  116.07  3.000
 5JK  C14  C13  C12  106.36  3.000
 5JK  C12  C13  C18  111.21  3.000
 5JK  C17  C13  C18  110.08  3.000
 5JK  C14  C13  C18  112.29  3.000
 5JK  H5   C12  H4   106.26  3.000
 5JK  H5   C12  C11  109.90  3.000
 5JK  H4   C12  C11  108.70  3.000
 5JK  H5   C12  C13  108.65  3.000
 5JK  H4   C12  C13  111.90  3.000
 5JK  C11  C12  C13  111.30  3.000
 5JK  H7   C11  H6   105.49  3.000
 5JK  H7   C11  C9   109.41  3.000
 5JK  H6   C11  C9   110.20  3.000
 5JK  H7   C11  C12  109.11  3.000
 5JK  H6   C11  C12  108.05  3.000
 5JK  C9   C11  C12  114.22  3.000
 5JK  H8   C9   C8   106.06  3.000
 5JK  H8   C9   C10  106.32  3.000
 5JK  C8   C9   C10  112.61  3.000
 5JK  H8   C9   C11  106.84  3.000
 5JK  C10  C9   C11  112.68  3.000
 5JK  C8   C9   C11  111.77  3.000
 5JK  C5   C10  C1   107.88  3.000
 5JK  C1   C10  C19  109.58  3.000
 5JK  C5   C10  C19  108.28  3.000
 5JK  C19  C10  C9   111.56  3.000
 5JK  C1   C10  C9   108.37  3.000
 5JK  C5   C10  C9   111.10  3.000
 5JK  H11  C19  H10  107.00  3.000
 5JK  H11  C19  H9   107.92  3.000
 5JK  H10  C19  H9   106.68  3.000
 5JK  H11  C19  C10  111.44  3.000
 5JK  H10  C19  C10  112.25  3.000
 5JK  H9   C19  C10  111.28  3.000
 5JK  H13  C1   H12  106.45  3.000
 5JK  H13  C1   C2   108.60  3.000
 5JK  H12  C1   C2   109.69  3.000
 5JK  H13  C1   C10  108.38  3.000
 5JK  H12  C1   C10  109.35  3.000
 5JK  C2   C1   C10  114.08  3.000
 5JK  H15  C2   H14  106.67  3.000
 5JK  H15  C2   C3   110.04  3.000
 5JK  H14  C2   C3   109.40  3.000
 5JK  H15  C2   C1   109.36  3.000
 5JK  H14  C2   C1   110.93  3.000
 5JK  C3   C2   C1   110.37  3.000
 5JK  H16  C3   C4   107.98  3.000
 5JK  H16  C3   O1   110.37  3.000
 5JK  C4   C3   O1   107.74  3.000
 5JK  H16  C3   C2   108.02  3.000
 5JK  C4   C3   C2   109.91  3.000
 5JK  O1   C3   C2   112.73  3.000
 5JK  H17  O1   C3   108.15  3.000
 5JK  H19  C4   H18  106.50  3.000
 5JK  H19  C4   C5   109.64  3.000
 5JK  H18  C4   C5   110.55  3.000
 5JK  H19  C4   C3   110.22  3.000
 5JK  H18  C4   C3   108.25  3.000
 5JK  C5   C4   C3   111.54  3.000
 5JK  C6   C5   C4   120.06  3.000
 5JK  C6   C5   C10  123.29  3.000
 5JK  C4   C5   C10  116.65  3.000
 5JK  H21  C6   C7   116.21  3.000
 5JK  H21  C6   C5   118.80  3.000
 5JK  C7   C6   C5   124.97  3.000
 5JK  H23  C7   C8   107.99  3.000
 5JK  H23  C7   O2   109.28  3.000
 5JK  C8   C7   O2   109.38  3.000
 5JK  H23  C7   C6   108.43  3.000
 5JK  C8   C7   C6   111.49  3.000
 5JK  O2   C7   C6   110.22  3.000
 5JK  H24  O2   C7   108.02  3.000
 5JK  H25  C8   C14  109.14  3.000
 5JK  H25  C8   C7   105.82  3.000
 5JK  C14  C8   C7   111.75  3.000
 5JK  H25  C8   C9   109.33  3.000
 5JK  C14  C8   C9   109.95  3.000
 5JK  C7   C8   C9   110.75  3.000
 5JK  H26  C14  C15  106.64  3.000
 5JK  H26  C14  C8   106.90  3.000
 5JK  C15  C14  C8   118.50  3.000
 5JK  H26  C14  C13  105.07  3.000
 5JK  C8   C14  C13  114.44  3.000
 5JK  C15  C14  C13  104.31  3.000
 5JK  H28  C15  H27  106.83  3.000
 5JK  H28  C15  C16  112.37  3.000
 5JK  H27  C15  C16  111.21  3.000
 5JK  H28  C15  C14  112.11  3.000
 5JK  H27  C15  C14  110.98  3.000
 5JK  C16  C15  C14  103.43  3.000
 5JK  H30  C16  H29  105.97  3.000
 5JK  H30  C16  C17  111.04  3.000
 5JK  H29  C16  C17  110.43  3.000
 5JK  H30  C16  C15  111.10  3.000
 5JK  H29  C16  C15  111.09  3.000
 5JK  C17  C16  C15  107.26  3.000
 5JK  H31  C17  C20  106.98  3.000
 5JK  H31  C17  C16  108.35  3.000
 5JK  C20  C17  C16  112.31  3.000
 5JK  H31  C17  C13  106.28  3.000
 5JK  C20  C17  C13  119.02  3.000
 5JK  C16  C17  C13  103.40  3.000
 5JK  H32  C20  C22  107.49  3.000
 5JK  H32  C20  C21  108.40  3.000
 5JK  C22  C20  C21  109.59  3.000
 5JK  H32  C20  C17  107.86  3.000
 5JK  C21  C20  C17  113.02  3.000
 5JK  C22  C20  C17  110.31  3.000
 5JK  H35  C21  H34  107.55  3.000
 5JK  H35  C21  H33  107.60  3.000
 5JK  H34  C21  H33  106.71  3.000
 5JK  H35  C21  C20  110.84  3.000
 5JK  H34  C21  C20  111.52  3.000
 5JK  H33  C21  C20  112.37  3.000
 5JK  H37  C22  H36  105.88  3.000
 5JK  H37  C22  C23  109.63  3.000
 5JK  H36  C22  C23  107.76  3.000
 5JK  H37  C22  C20  108.54  3.000
 5JK  H36  C22  C20  110.32  3.000
 5JK  C23  C22  C20  114.38  3.000
 5JK  H39  C23  H38  106.10  3.000
 5JK  H39  C23  C24  110.33  3.000
 5JK  H38  C23  C24  108.60  3.000
 5JK  H39  C23  C22  108.76  3.000
 5JK  H38  C23  C22  110.73  3.000
 5JK  C24  C23  C22  112.15  3.000
 5JK  H41  C24  H40  105.93  3.000
 5JK  H41  C24  C25  108.75  3.000
 5JK  H40  C24  C25  109.11  3.000
 5JK  H41  C24  C23  108.32  3.000
 5JK  H40  C24  C23  109.68  3.000
 5JK  C25  C24  C23  114.68  3.000
 5JK  H42  C25  C26  108.05  3.000
 5JK  H42  C25  C27  108.27  3.000
 5JK  C26  C25  C27  110.15  3.000
 5JK  H42  C25  C24  107.82  3.000
 5JK  C26  C25  C24  110.38  3.000
 5JK  C27  C25  C24  112.04  3.000
 5JK  H45  C27  H44  107.51  3.000
 5JK  H45  C27  H43  107.62  3.000
 5JK  H44  C27  H43  107.70  3.000
 5JK  H45  C27  C25  111.15  3.000
 5JK  H44  C27  C25  110.38  3.000
 5JK  H43  C27  C25  112.29  3.000
 5JK  H48  C26  H47  107.56  3.000
 5JK  H48  C26  H46  107.56  3.000
 5JK  H47  C26  H46  107.75  3.000
 5JK  H48  C26  C25  110.75  3.000
 5JK  H47  C26  C25  111.57  3.000
 5JK  H46  C26  C25  111.46  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
 5JK  Var_01  C9   C11  C12  C13   -54.87  30.0  1
 5JK  Var_02  C3   C4   C5   C10    52.86  30.0  1
 5JK  Var_03  C7   C6   C5   C10    -0.89  30.0  1
 5JK  Var_04  C3   C2   C1   C10   -57.72  30.0  1
 5JK  Var_05  C17  C16  C15  C14    10.15  30.0  1
 5JK  Var_06  C24  C23  C22  C20  -174.48  30.0  3
 5JK  Var_07  C25  C24  C23  C22   178.75  30.0  1
 5JK  Var_08  C27  C25  C24  C23    65.88  30.0  3
 5JK  Var_09  H43  C27  C25  C24   -58.70  30.0  3
 5JK  Var_10  H46  C26  C25  C24    57.47  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
 5JK  chir_01  C13  C17  C12  C14  negativ
 5JK  chir_02  C9   C11  C10  C8   positiv
 5JK  chir_03  C10  C1   C9   C5   positiv
 5JK  chir_04  C3   O1   C2   C4   negativ
 5JK  chir_05  C7   O2   C6   C8   positiv
 5JK  chir_06  C8   C7   C14  C9   negativ
 5JK  chir_07  C14  C15  C8   C13  negativ
 5JK  chir_08  C17  C16  C13  C20  negativ
 5JK  chir_09  C20  C17  C22  C21  negativ

