# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun May 31 18:48:11 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: (3~{R},5~{S},7~{R},8~{R},9~{S},10~{S},12~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-17-[(2~{R})-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthrene-3,7,12-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3[C@H](O)C[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[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
 4QM  4QM  (3~{R},5~{S},7~{R},8~{R},9~{S},10~{S},12~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-17-[(2~{R})-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthrene-3,7,12-triol  ligand  69  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4QM
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
 4QM  C1   C  CH2   0  -0.433   3.6093   1.7151  -0.8125
 4QM  C2   C  CT    0  -0.051   2.8563   0.4045  -1.1050
 4QM  C3   C  CH2   0  -0.494   0.5458   1.5072  -0.9039
 4QM  C4   C  CH1   0   0.095  -0.8580   1.5011  -0.2885
 4QM  C5   C  CT    0  -0.086  -1.5487   0.1526  -0.5302
 4QM  C6   C  CH1   0  -0.171  -0.6233  -0.9605   0.0016
 4QM  C7   C  CH2   0  -0.447  -1.4849  -2.2120  -0.0882
 4QM  C8   C  CH2   0  -0.450  -2.9026  -1.7057   0.2418
 4QM  C9   C  CH1   0  -0.166  -2.8441  -0.1541   0.2692
 4QM  C10  C  CH3   0  -0.695  -1.8363   0.0122  -2.0307
 4QM  C11  C  CH3   0  -0.680   2.7501   0.3082  -2.6344
 4QM  C12  C  CH2   0  -0.473   4.0344   1.8985   0.6373
 4QM  C13  C  CH1   0   0.084   4.9204   0.7368   1.0611
 4QM  C14  C  CH2   0  -0.454   4.1704  -0.5691   0.8795
 4QM  C15  C  CH1   0  -0.211   3.7090  -0.7708  -0.5695
 4QM  C16  C  CH2   0  -0.478   3.0012  -2.1106  -0.7716
 4QM  C17  C  CH1   0   0.071   1.5917  -2.1790  -0.1887
 4QM  C18  C  CH1   0  -0.263   0.7526  -0.9900  -0.6509
 4QM  C19  C  CH1   0  -0.188   1.4559   0.3658  -0.4391
 4QM  C20  C  CH1   0  -0.234  -4.1664   0.4841  -0.1866
 4QM  C21  C  CH3   0  -0.672  -4.1225   2.0101  -0.1742
 4QM  C22  C  CH2   0  -0.398  -5.3238  -0.0241   0.6848
 4QM  C23  C  CH2   0  -0.428  -6.7145   0.4245   0.2440
 4QM  C24  C  CH3   0  -0.662  -7.8185  -0.2779   1.0236
 4QM  O2   O  OH1   0  -0.682   5.3269   0.8247   2.4141
 4QM  O3   O  OH1   0  -0.671   1.5820  -2.2273   1.2268
 4QM  O4   O  OH1   0  -0.674  -0.8120   1.7559   1.1021
 4QM  H1   H  HCH2  0   0.220   4.5120   1.7185  -1.4353
 4QM  H2   H  HCH2  0   0.232   3.0227   2.5728  -1.1486
 4QM  H3   H  HCH2  0   0.230   0.4426   1.4902  -1.9916
 4QM  H4   H  HCH2  0   0.235   1.0005   2.4760  -0.6728
 4QM  H5   H  HCH1  0   0.198  -1.4239   2.2971  -0.7908
 4QM  H6   H  HCH1  0   0.219  -0.4749  -0.7461   1.0663
 4QM  H7   H  HCH2  0   0.212  -1.4464  -2.6360  -1.0957
 4QM  H8   H  HCH2  0   0.228  -1.1526  -2.9965   0.5932
 4QM  H9   H  HCH2  0   0.216  -3.6204  -2.0494  -0.5076
 4QM  H10  H  HCH2  0   0.228  -3.2503  -2.1001   1.1975
 4QM  H11  H  HCH1  0   0.213  -2.6746   0.1613   1.3047
 4QM  H12  H  HCH3  0   0.234  -0.9334  -0.0480  -2.6374
 4QM  H13  H  HCH3  0   0.237  -2.4312  -0.8743  -2.2547
 4QM  H14  H  HCH3  0   0.231  -2.4006   0.8727  -2.3968
 4QM  H15  H  HCH3  0   0.227   3.7330   0.1067  -3.0665
 4QM  H16  H  HCH3  0   0.230   2.0788  -0.4764  -2.9812
 4QM  H17  H  HCH3  0   0.229   2.3998   1.2461  -3.0695
 4QM  H18  H  HCH2  0   0.229   4.5734   2.8460   0.7409
 4QM  H19  H  HCH2  0   0.216   3.1661   1.9539   1.3020
 4QM  H20  H  HCH1  0   0.177   5.8028   0.7283   0.3997
 4QM  H21  H  HCH2  0   0.223   4.8178  -1.4073   1.1574
 4QM  H22  H  HCH2  0   0.228   3.3232  -0.5849   1.5666
 4QM  H23  H  HCH1  0   0.213   4.6209  -0.7939  -1.1817
 4QM  H24  H  HCH2  0   0.234   2.9274  -2.3217  -1.8426
 4QM  H25  H  HCH2  0   0.230   3.6117  -2.9227  -0.3593
 4QM  H26  H  HCH1  0   0.205   1.1189  -3.0909  -0.5836
 4QM  H27  H  HCH1  0   0.214   0.6151  -1.1461  -1.7275
 4QM  H28  H  HCH1  0   0.218   1.5990   0.4922   0.6402
 4QM  H29  H  HCH1  0   0.201  -4.3660   0.1525  -1.2145
 4QM  H30  H  HCH3  0   0.210  -3.8483   2.3863   0.8144
 4QM  H31  H  HCH3  0   0.227  -3.4035   2.4077  -0.8876
 4QM  H32  H  HCH3  0   0.232  -5.0889   2.4426  -0.4354
 4QM  H33  H  HCH2  0   0.224  -5.3183  -1.1174   0.6900
 4QM  H34  H  HCH2  0   0.200  -5.1538   0.2823   1.7245
 4QM  H35  H  HCH2  0   0.215  -6.8284   1.5045   0.3628
 4QM  H36  H  HCH2  0   0.208  -6.8352   0.2209  -0.8250
 4QM  H37  H  HCH3  0   0.215  -7.7328  -0.0799   2.0939
 4QM  H38  H  HCH3  0   0.225  -8.8081   0.0526   0.7061
 4QM  H39  H  HCH3  0   0.215  -7.7705  -1.3601   0.8870
 4QM  H40  H  HOH1  0   0.444   5.8126   1.6478   2.5255
 4QM  H41  H  HOH1  0   0.444   2.1891  -2.9197   1.5050
 4QM  H42  H  HOH1  0   0.443  -0.2714   2.5394   1.2405

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
 4QM  C24  C23  single  1.523  0.020  1.523
 4QM  C23  C22  single  1.526  0.020  1.526
 4QM  C22  C20  single  1.535  0.020  1.535
 4QM  C21  C20  single  1.527  0.020  1.527
 4QM  C20  C9   single  1.537  0.020  1.537
 4QM  O4   C4   single  1.414  0.020  1.414
 4QM  C9   C8   single  1.553  0.020  1.553
 4QM  C9   C5   single  1.553  0.020  1.553
 4QM  C8   C7   single  1.541  0.020  1.541
 4QM  C4   C5   single  1.534  0.020  1.534
 4QM  C4   C3   single  1.533  0.020  1.533
 4QM  C5   C6   single  1.542  0.020  1.542
 4QM  C5   C10  single  1.534  0.020  1.534
 4QM  O2   C13  single  1.416  0.020  1.416
 4QM  C6   C7   single  1.522  0.020  1.522
 4QM  C6   C18  single  1.523  0.020  1.523
 4QM  C3   C19  single  1.532  0.020  1.532
 4QM  O3   C17  single  1.416  0.020  1.416
 4QM  C12  C13  single  1.521  0.020  1.521
 4QM  C12  C1   single  1.522  0.020  1.522
 4QM  C19  C18  single  1.542  0.020  1.542
 4QM  C19  C2   single  1.551  0.020  1.551
 4QM  C13  C14  single  1.517  0.020  1.517
 4QM  C18  C17  single  1.527  0.020  1.527
 4QM  C14  C15  single  1.534  0.020  1.534
 4QM  C17  C16  single  1.527  0.020  1.527
 4QM  C1   C2   single  1.540  0.020  1.540
 4QM  C2   C15  single  1.548  0.020  1.548
 4QM  C2   C11  single  1.536  0.020  1.536
 4QM  C15  C16  single  1.529  0.020  1.529
 4QM  C1   H1   single  0.970  0.020  1.090
 4QM  C1   H2   single  0.970  0.020  1.090
 4QM  C3   H3   single  0.970  0.020  1.090
 4QM  C3   H4   single  0.970  0.020  1.090
 4QM  C4   H5   single  0.970  0.020  1.090
 4QM  C6   H6   single  0.970  0.020  1.090
 4QM  C7   H7   single  0.970  0.020  1.090
 4QM  C7   H8   single  0.970  0.020  1.090
 4QM  C8   H9   single  0.970  0.020  1.090
 4QM  C8   H10  single  0.970  0.020  1.090
 4QM  C9   H11  single  0.970  0.020  1.090
 4QM  C10  H12  single  0.970  0.020  1.090
 4QM  C10  H13  single  0.970  0.020  1.090
 4QM  C10  H14  single  0.970  0.020  1.090
 4QM  C11  H15  single  0.970  0.020  1.090
 4QM  C11  H16  single  0.970  0.020  1.090
 4QM  C11  H17  single  0.970  0.020  1.090
 4QM  C12  H18  single  0.970  0.020  1.090
 4QM  C12  H19  single  0.970  0.020  1.090
 4QM  C13  H20  single  0.970  0.020  1.090
 4QM  C14  H21  single  0.970  0.020  1.090
 4QM  C14  H22  single  0.970  0.020  1.090
 4QM  C15  H23  single  0.970  0.020  1.090
 4QM  C16  H24  single  0.970  0.020  1.090
 4QM  C16  H25  single  0.970  0.020  1.090
 4QM  C17  H26  single  0.970  0.020  1.090
 4QM  C18  H27  single  0.970  0.020  1.090
 4QM  C19  H28  single  0.970  0.020  1.090
 4QM  C20  H29  single  0.970  0.020  1.090
 4QM  C21  H30  single  0.970  0.020  1.090
 4QM  C21  H31  single  0.970  0.020  1.090
 4QM  C21  H32  single  0.970  0.020  1.090
 4QM  C22  H33  single  0.970  0.020  1.090
 4QM  C22  H34  single  0.970  0.020  1.090
 4QM  C23  H35  single  0.970  0.020  1.090
 4QM  C23  H36  single  0.970  0.020  1.090
 4QM  C24  H37  single  0.970  0.020  1.090
 4QM  C24  H38  single  0.970  0.020  1.090
 4QM  C24  H39  single  0.970  0.020  1.090
 4QM  O2   H40  single  0.850  0.020  0.980
 4QM  O3   H41  single  0.850  0.020  0.980
 4QM  O4   H42  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
 4QM  H2   C1   H1   105.36  3.000
 4QM  H2   C1   C12  110.40  3.000
 4QM  H1   C1   C12  108.10  3.000
 4QM  H2   C1   C2   110.32  3.000
 4QM  H1   C1   C2   107.30  3.000
 4QM  C12  C1   C2   114.85  3.000
 4QM  C19  C2   C15  109.26  3.000
 4QM  C15  C2   C11  109.57  3.000
 4QM  C19  C2   C11  111.32  3.000
 4QM  C11  C2   C1   106.04  3.000
 4QM  C15  C2   C1   108.13  3.000
 4QM  C19  C2   C1   112.41  3.000
 4QM  H4   C3   H3   105.25  3.000
 4QM  H4   C3   C19  110.40  3.000
 4QM  H3   C3   C19  110.27  3.000
 4QM  H4   C3   C4   107.40  3.000
 4QM  H3   C3   C4   108.25  3.000
 4QM  C19  C3   C4   114.79  3.000
 4QM  H5   C4   O4   109.62  3.000
 4QM  H5   C4   C5   109.45  3.000
 4QM  O4   C4   C5   109.14  3.000
 4QM  H5   C4   C3   106.58  3.000
 4QM  C5   C4   C3   110.64  3.000
 4QM  O4   C4   C3   111.36  3.000
 4QM  C10  C5   C9   109.21  3.000
 4QM  C10  C5   C6   112.56  3.000
 4QM  C9   C5   C6   100.40  3.000
 4QM  C10  C5   C4   108.60  3.000
 4QM  C6   C5   C4   108.06  3.000
 4QM  C9   C5   C4   117.91  3.000
 4QM  H6   C6   C18  107.32  3.000
 4QM  H6   C6   C7   107.14  3.000
 4QM  C18  C6   C7   118.05  3.000
 4QM  H6   C6   C5   105.96  3.000
 4QM  C18  C6   C5   114.10  3.000
 4QM  C7   C6   C5   103.50  3.000
 4QM  H8   C7   H7   106.62  3.000
 4QM  H8   C7   C8   112.50  3.000
 4QM  H7   C7   C8   110.92  3.000
 4QM  H8   C7   C6   112.46  3.000
 4QM  H7   C7   C6   110.68  3.000
 4QM  C8   C7   C6   103.77  3.000
 4QM  H10  C8   H9   106.12  3.000
 4QM  H10  C8   C9   110.97  3.000
 4QM  H9   C8   C9   110.55  3.000
 4QM  H10  C8   C7   111.23  3.000
 4QM  H9   C8   C7   110.73  3.000
 4QM  C9   C8   C7   107.30  3.000
 4QM  H11  C9   C20  107.08  3.000
 4QM  H11  C9   C8   108.07  3.000
 4QM  C20  C9   C8   112.16  3.000
 4QM  H11  C9   C5   107.49  3.000
 4QM  C8   C9   C5   102.69  3.000
 4QM  C20  C9   C5   118.88  3.000
 4QM  H14  C10  H13  106.84  3.000
 4QM  H14  C10  H12  106.57  3.000
 4QM  H13  C10  H12  107.02  3.000
 4QM  H14  C10  C5   110.64  3.000
 4QM  H13  C10  C5   112.17  3.000
 4QM  H12  C10  C5   113.23  3.000
 4QM  H17  C11  H16  107.11  3.000
 4QM  H17  C11  H15  106.84  3.000
 4QM  H16  C11  H15  107.20  3.000
 4QM  H17  C11  C2   111.42  3.000
 4QM  H16  C11  C2   113.87  3.000
 4QM  H15  C11  C2   110.07  3.000
 4QM  H19  C12  H18  106.80  3.000
 4QM  H19  C12  C13  109.36  3.000
 4QM  H18  C12  C13  110.35  3.000
 4QM  H19  C12  C1   111.27  3.000
 4QM  H18  C12  C1   109.38  3.000
 4QM  C13  C12  C1   109.64  3.000
 4QM  H20  C13  O2   110.12  3.000
 4QM  H20  C13  C14  108.49  3.000
 4QM  O2   C13  C14  108.05  3.000
 4QM  H20  C13  C12  107.75  3.000
 4QM  C14  C13  C12  109.64  3.000
 4QM  O2   C13  C12  112.71  3.000
 4QM  H22  C14  H21  106.75  3.000
 4QM  H22  C14  C15  111.07  3.000
 4QM  H21  C14  C15  108.48  3.000
 4QM  H22  C14  C13  108.73  3.000
 4QM  H21  C14  C13  109.65  3.000
 4QM  C15  C14  C13  112.03  3.000
 4QM  H23  C15  C16  107.00  3.000
 4QM  H23  C15  C14  106.23  3.000
 4QM  C16  C15  C14  112.29  3.000
 4QM  H23  C15  C2   106.29  3.000
 4QM  C16  C15  C2   111.39  3.000
 4QM  C14  C15  C2   113.12  3.000
 4QM  H25  C16  H24  105.23  3.000
 4QM  H25  C16  C17  109.72  3.000
 4QM  H24  C16  C17  107.63  3.000
 4QM  H25  C16  C15  109.98  3.000
 4QM  H24  C16  C15  109.25  3.000
 4QM  C17  C16  C15  114.60  3.000
 4QM  H26  C17  O3   109.11  3.000
 4QM  H26  C17  C18  107.49  3.000
 4QM  O3   C17  C18  108.99  3.000
 4QM  H26  C17  C16  107.26  3.000
 4QM  C18  C17  C16  110.91  3.000
 4QM  O3   C17  C16  112.92  3.000
 4QM  H27  C18  C19  108.50  3.000
 4QM  H27  C18  C17  104.79  3.000
 4QM  C19  C18  C17  113.11  3.000
 4QM  H27  C18  C6   108.06  3.000
 4QM  C17  C18  C6   112.45  3.000
 4QM  C19  C18  C6   109.64  3.000
 4QM  H28  C19  C18  107.23  3.000
 4QM  H28  C19  C3   106.88  3.000
 4QM  C18  C19  C3   110.03  3.000
 4QM  H28  C19  C2   107.58  3.000
 4QM  C18  C19  C2   112.01  3.000
 4QM  C3   C19  C2   112.79  3.000
 4QM  H29  C20  C22  107.11  3.000
 4QM  H29  C20  C21  108.34  3.000
 4QM  C22  C20  C21  110.36  3.000
 4QM  H29  C20  C9   107.96  3.000
 4QM  C21  C20  C9   112.82  3.000
 4QM  C22  C20  C9   110.04  3.000
 4QM  H32  C21  H31  106.48  3.000
 4QM  H32  C21  H30  107.62  3.000
 4QM  H31  C21  H30  107.55  3.000
 4QM  H32  C21  C20  111.65  3.000
 4QM  H31  C21  C20  112.27  3.000
 4QM  H30  C21  C20  111.02  3.000
 4QM  H34  C22  H33  105.90  3.000
 4QM  H34  C22  C23  109.44  3.000
 4QM  H33  C22  C23  107.45  3.000
 4QM  H34  C22  C20  109.18  3.000
 4QM  H33  C22  C20  109.26  3.000
 4QM  C23  C22  C20  115.19  3.000
 4QM  H36  C23  H35  106.17  3.000
 4QM  H36  C23  C24  109.52  3.000
 4QM  H35  C23  C24  108.94  3.000
 4QM  H36  C23  C22  109.13  3.000
 4QM  H35  C23  C22  110.74  3.000
 4QM  C24  C23  C22  112.15  3.000
 4QM  H39  C24  H38  107.69  3.000
 4QM  H39  C24  H37  107.39  3.000
 4QM  H38  C24  H37  107.56  3.000
 4QM  H39  C24  C23  111.17  3.000
 4QM  H38  C24  C23  111.65  3.000
 4QM  H37  C24  C23  111.18  3.000
 4QM  H40  O2   C13  107.98  3.000
 4QM  H41  O3   C17  108.02  3.000
 4QM  H42  O4   C4   107.84  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
 4QM  Var_01  C13  C12  C1   C2    57.95  30.0  1
 4QM  Var_02  C9   C8   C7   C6     9.49  30.0  1
 4QM  Var_03  C24  C23  C22  C20  171.58  30.0  1
 4QM  Var_04  H37  C24  C23  C22   59.56  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
 4QM  chir_01  C2   C1   C15  C19  negativ
 4QM  chir_02  C4   O4   C5   C3   positiv
 4QM  chir_03  C5   C6   C4   C9   positiv
 4QM  chir_04  C6   C5   C7   C18  negativ
 4QM  chir_05  C9   C5   C8   C20  positiv
 4QM  chir_06  C13  O2   C12  C14  positiv
 4QM  chir_07  C15  C16  C2   C14  negativ
 4QM  chir_08  C17  O3   C18  C16  negativ
 4QM  chir_09  C18  C17  C19  C6   positiv
 4QM  chir_10  C19  C2   C18  C3   positiv
 4QM  chir_11  C20  C22  C21  C9   negativ

