# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 24 09:45:31 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: 4-oxo-4-{[(3alpha,5beta,8alpha,14beta,17alpha)-20-oxopregnan-3-yl]oxy}butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@H]1CC[C@H]2[C@@H]3CC[C@H]4C[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)OC(=O)CCC(O)=O
#
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
 S5H  S5H  '4-oxo-4-{[(3alpha,5beta,8alpha,14beta,17alpha)-20-oxopregnan-3-yl]oxy}butanoic acid'  ligand  67  30  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_S5H
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
 S5H  C1    C  CH2    0  -0.434   1.2818  -0.0195  -0.5995
 S5H  C2    C  CH2    0  -0.466   1.1380   0.3054  -2.0860
 S5H  C3    C  CH1    0   0.067  -0.1646  -0.2523  -2.6314
 S5H  O3    O  O2     0  -0.483  -0.3674   0.1399  -4.0010
 S5H  C4    C  CH2    0  -0.454  -1.3542   0.2540  -1.8387
 S5H  C5    C  CH1    0  -0.214  -1.1927  -0.0903  -0.3598
 S5H  C6    C  CH2    0  -0.419  -2.4276   0.2836   0.4480
 S5H  C7    C  CH2    0  -0.418  -2.3138  -0.2212   1.8789
 S5H  C8    C  CH1    0  -0.228  -1.0238   0.2370   2.5551
 S5H  C9    C  CH1    0  -0.175   0.2133  -0.0952   1.6963
 S5H  C10   C  CT     0  -0.046   0.1064   0.4787   0.2592
 S5H  C11   C  CH2    0  -0.444   1.5142   0.2783   2.4186
 S5H  C12   C  CH2    0  -0.411   1.6193  -0.3017   3.8321
 S5H  C13   C  CT     0  -0.058   0.4004   0.0538   4.6752
 S5H  C14   C  CH1    0  -0.174  -0.8544  -0.4124   3.9191
 S5H  C15   C  CH2    0  -0.449  -1.9755  -0.2911   4.9469
 S5H  C16   C  CH2    0  -0.431  -1.2940  -0.6494   6.2862
 S5H  C17   C  CH1    0  -0.347   0.2144  -0.7660   5.9855
 S5H  C18   C  CH3    0  -0.677   0.3834   1.5542   4.9823
 S5H  C19   C  CH3    0  -0.693   0.1151   2.0121   0.2783
 S5H  C20   C  C      0   0.406   1.1245  -0.3558   7.1167
 S5H  O20   O  O      0  -0.409   0.7971   0.4568   7.9553
 S5H  C21   C  CH3    0  -0.778   2.4658  -1.0346   7.1686
 S5H  CH1   C  C      0   0.603   0.1906  -0.5710  -4.9773
 S5H  OH1   O  O      0  -0.460   0.8958  -1.5312  -4.7833
 S5H  CH2   C  CH2    0  -0.581  -0.1926  -0.0329  -6.3298
 S5H  CH3   C  CH2    0  -0.586   0.5104  -0.7228  -7.4829
 S5H  CH4   C  C      0   0.421   0.1073  -0.2126  -8.8787
 S5H  OH4   O  O      0  -0.607  -0.7501   0.6900  -8.9439
 S5H  OH5   O  OC    -1  -0.629   0.6843  -0.7584  -9.8416
 S5H  H11   H  HCH2   0   0.220   1.3772  -1.1055  -0.4792
 S5H  H12   H  HCH2   0   0.236   2.2210   0.4105  -0.2453
 S5H  H21   H  HCH2   0   0.244   1.9876  -0.1144  -2.6287
 S5H  H22   H  HCH2   0   0.227   1.1660   1.3873  -2.2446
 S5H  H3    H  HCH1   0   0.226  -0.1411  -1.3453  -2.5713
 S5H  H41   H  HCH2   0   0.239  -2.2706  -0.2102  -2.2152
 S5H  H42   H  HCH2   0   0.225  -1.4700   1.3339  -1.9740
 S5H  H5    H  HCH1   0   0.211  -1.0969  -1.1853  -0.2976
 S5H  H61   H  HCH2   0   0.224  -3.3169  -0.1426  -0.0259
 S5H  H62   H  HCH2   0   0.214  -2.5690   1.3696   0.4396
 S5H  H71   H  HCH2   0   0.203  -2.3497  -1.3178   1.8789
 S5H  H72   H  HCH2   0   0.230  -3.1759   0.1138   2.4622
 S5H  H8    H  HCH1   0   0.211  -1.0901   1.3237   2.6878
 S5H  H9    H  HCH1   0   0.199   0.2206  -1.1909   1.5796
 S5H  H111  H  HCH2   0   0.236   2.3709  -0.0812   1.8445
 S5H  H112  H  HCH2   0   0.220   1.6200   1.3655   2.4627
 S5H  H121  H  HCH2   0   0.216   1.7072  -1.3928   3.7730
 S5H  H122  H  HCH2   0   0.225   2.5423   0.0607   4.2941
 S5H  H14   H  HCH1   0   0.211  -0.7085  -1.4880   3.7340
 S5H  H151  H  HCH2   0   0.235  -2.8134  -0.9517   4.7218
 S5H  H152  H  HCH2   0   0.220  -2.3738   0.7267   4.9705
 S5H  H161  H  HCH2   0   0.239  -1.6688  -1.5900   6.6913
 S5H  H162  H  HCH2   0   0.234  -1.4845   0.1134   7.0405
 S5H  H17   H  HCH1   0   0.252   0.4572  -1.8051   5.7331
 S5H  H181  H  HCH3   0   0.237   0.2866   2.1566   4.0802
 S5H  H182  H  HCH3   0   0.238  -0.4305   1.8379   5.6497
 S5H  H183  H  HCH3   0   0.230   1.3156   1.8575   5.4631
 S5H  H191  H  HCH3   0   0.234  -0.1230   2.4420  -0.6949
 S5H  H192  H  HCH3   0   0.233  -0.5990   2.4296   0.9871
 S5H  H193  H  HCH3   0   0.231   1.1011   2.3925   0.5510
 S5H  H211  H  HCH3   0   0.256   3.1632  -0.5061   7.8156
 S5H  H212  H  HCH3   0   0.271   2.3226  -2.0443   7.5636
 S5H  H213  H  HCH3   0   0.260   2.9014  -1.1553   6.1772
 S5H  HH21  H  HCH2   0   0.266  -1.2780  -0.1288  -6.4271
 S5H  HH22  H  HCH2   0   0.262  -0.0006   1.0426  -6.3417
 S5H  HH31  H  HCH2   0   0.231   1.5945  -0.6157  -7.3806
 S5H  HH32  H  HCH2   0   0.232   0.3243  -1.8001  -7.4469

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
 S5H  C1   C2    single  1.528  0.020  1.528
 S5H  C1   C10   single  1.539  0.020  1.539
 S5H  C1   H11   single  0.970  0.020  1.090
 S5H  C1   H12   single  0.970  0.020  1.090
 S5H  C2   C3    single  1.518  0.020  1.518
 S5H  C2   H21   single  0.970  0.020  1.090
 S5H  C2   H22   single  0.970  0.020  1.090
 S5H  C3   O3    single  1.439  0.020  1.439
 S5H  C3   C4    single  1.517  0.020  1.517
 S5H  C3   H3    single  0.970  0.020  1.090
 S5H  O3   CH1   single  1.330  0.020  1.330
 S5H  C4   C5    single  1.527  0.020  1.527
 S5H  C4   H41   single  0.970  0.020  1.090
 S5H  C4   H42   single  0.970  0.020  1.090
 S5H  C5   C6    single  1.522  0.020  1.522
 S5H  C5   C10   single  1.547  0.020  1.547
 S5H  C5   H5    single  0.970  0.020  1.090
 S5H  C6   C7    single  1.522  0.020  1.522
 S5H  C6   H61   single  0.970  0.020  1.090
 S5H  C6   H62   single  0.970  0.020  1.090
 S5H  C7   C8    single  1.527  0.020  1.527
 S5H  C7   H71   single  0.970  0.020  1.090
 S5H  C7   H72   single  0.970  0.020  1.090
 S5H  C8   C9    single  1.542  0.020  1.542
 S5H  C8   C14   single  1.520  0.020  1.520
 S5H  C8   H8    single  0.970  0.020  1.090
 S5H  C9   C10   single  1.551  0.020  1.551
 S5H  C9   C11   single  1.534  0.020  1.534
 S5H  C9   H9    single  0.970  0.020  1.090
 S5H  C10  C19   single  1.534  0.020  1.534
 S5H  C11  C12   single  1.531  0.020  1.531
 S5H  C11  H111  single  0.970  0.020  1.090
 S5H  C11  H112  single  0.970  0.020  1.090
 S5H  C12  C13   single  1.524  0.020  1.524
 S5H  C12  H121  single  0.970  0.020  1.090
 S5H  C12  H122  single  0.970  0.020  1.090
 S5H  C13  C14   single  1.537  0.020  1.537
 S5H  C13  C17   single  1.557  0.020  1.557
 S5H  C13  C18   single  1.532  0.020  1.532
 S5H  C14  C15   single  1.526  0.020  1.526
 S5H  C14  H14   single  0.970  0.020  1.090
 S5H  C15  C16   single  1.545  0.020  1.545
 S5H  C15  H151  single  0.970  0.020  1.090
 S5H  C15  H152  single  0.970  0.020  1.090
 S5H  C16  C17   single  1.542  0.020  1.542
 S5H  C16  H161  single  0.970  0.020  1.090
 S5H  C16  H162  single  0.970  0.020  1.090
 S5H  C17  C20   single  1.509  0.020  1.509
 S5H  C17  H17   single  0.970  0.020  1.090
 S5H  C18  H181  single  0.970  0.020  1.090
 S5H  C18  H182  single  0.970  0.020  1.090
 S5H  C18  H183  single  0.970  0.020  1.090
 S5H  C19  H191  single  0.970  0.020  1.090
 S5H  C19  H192  single  0.970  0.020  1.090
 S5H  C19  H193  single  0.970  0.020  1.090
 S5H  C20  O20   double  1.213  0.020  1.213
 S5H  C20  C21   single  1.504  0.020  1.504
 S5H  C21  H211  single  0.970  0.020  1.090
 S5H  C21  H212  single  0.970  0.020  1.090
 S5H  C21  H213  single  0.970  0.020  1.090
 S5H  CH1  OH1   double  1.207  0.020  1.207
 S5H  CH1  CH2   single  1.505  0.020  1.505
 S5H  CH2  CH3   single  1.517  0.020  1.517
 S5H  CH2  HH21  single  0.970  0.020  1.090
 S5H  CH2  HH22  single  0.970  0.020  1.090
 S5H  CH3  CH4   single  1.540  0.020  1.540
 S5H  CH3  HH31  single  0.970  0.020  1.090
 S5H  CH3  HH32  single  0.970  0.020  1.090
 S5H  CH4  OH4   deloc   1.247  0.020  1.247
 S5H  CH4  OH5   deloc   1.248  0.020  1.248

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
 S5H  H12   C1   H11   106.23  3.000
 S5H  H12   C1   C10   110.40  3.000
 S5H  H11   C1   C10   109.02  3.000
 S5H  H12   C1   C2    108.22  3.000
 S5H  H11   C1   C2    108.99  3.000
 S5H  C10   C1   C2    113.71  3.000
 S5H  H22   C2   H21   106.75  3.000
 S5H  H22   C2   C3    109.46  3.000
 S5H  H21   C2   C3    110.35  3.000
 S5H  H22   C2   C1    110.42  3.000
 S5H  H21   C2   C1    109.17  3.000
 S5H  C3    C2   C1    110.61  3.000
 S5H  H3    C3   C4    108.75  3.000
 S5H  H3    C3   O3    109.11  3.000
 S5H  C4    C3   O3    107.21  3.000
 S5H  H3    C3   C2    109.18  3.000
 S5H  C4    C3   C2    111.26  3.000
 S5H  O3    C3   C2    111.27  3.000
 S5H  CH1   O3   C3    119.58  3.000
 S5H  H42   C4   H41   106.71  3.000
 S5H  H42   C4   C5    110.69  3.000
 S5H  H41   C4   C5    109.04  3.000
 S5H  H42   C4   C3    110.34  3.000
 S5H  H41   C4   C3    109.60  3.000
 S5H  C5    C4   C3    110.37  3.000
 S5H  H5    C5   C10   105.67  3.000
 S5H  H5    C5   C6    106.55  3.000
 S5H  C10   C5   C6    112.24  3.000
 S5H  H5    C5   C4    106.74  3.000
 S5H  C10   C5   C4    113.16  3.000
 S5H  C6    C5   C4    111.89  3.000
 S5H  H62   C6   H61   106.14  3.000
 S5H  H62   C6   C7    110.23  3.000
 S5H  H61   C6   C7    109.80  3.000
 S5H  H62   C6   C5    110.13  3.000
 S5H  H61   C6   C5    109.51  3.000
 S5H  C7    C6   C5    110.91  3.000
 S5H  H72   C7   H71   106.29  3.000
 S5H  H72   C7   C8    109.75  3.000
 S5H  H71   C7   C8    109.12  3.000
 S5H  H72   C7   C6    109.94  3.000
 S5H  H71   C7   C6    109.22  3.000
 S5H  C8    C7   C6    112.34  3.000
 S5H  H8    C8   C14   108.75  3.000
 S5H  H8    C8   C9    109.22  3.000
 S5H  C14   C8   C9    108.56  3.000
 S5H  H8    C8   C7    107.44  3.000
 S5H  C14   C8   C7    111.30  3.000
 S5H  C9    C8   C7    111.50  3.000
 S5H  H9    C9   C11   106.64  3.000
 S5H  H9    C9   C10   105.68  3.000
 S5H  C11   C9   C10   113.86  3.000
 S5H  H9    C9   C8    106.17  3.000
 S5H  C11   C9   C8    111.44  3.000
 S5H  C10   C9   C8    112.39  3.000
 S5H  C19   C10  C9    110.98  3.000
 S5H  C19   C10  C5    112.17  3.000
 S5H  C9    C10  C5    107.00  3.000
 S5H  C19   C10  C1    109.05  3.000
 S5H  C9    C10  C1    110.16  3.000
 S5H  C5    C10  C1    107.40  3.000
 S5H  H112  C11  H111  105.82  3.000
 S5H  H112  C11  C12   109.44  3.000
 S5H  H111  C11  C12   107.86  3.000
 S5H  H112  C11  C9    110.07  3.000
 S5H  H111  C11  C9    109.72  3.000
 S5H  C12   C11  C9    113.61  3.000
 S5H  H122  C12  H121  106.55  3.000
 S5H  H122  C12  C13   111.34  3.000
 S5H  H121  C12  C13   109.04  3.000
 S5H  H122  C12  C11   108.80  3.000
 S5H  H121  C12  C11   109.43  3.000
 S5H  C13   C12  C11   111.55  3.000
 S5H  C18   C13  C17   110.23  3.000
 S5H  C18   C13  C14   112.74  3.000
 S5H  C17   C13  C14    99.02  3.000
 S5H  C18   C13  C12   110.38  3.000
 S5H  C17   C13  C12   116.00  3.000
 S5H  C14   C13  C12   108.06  3.000
 S5H  H14   C14  C15   106.75  3.000
 S5H  H14   C14  C13   105.70  3.000
 S5H  C15   C14  C13   104.14  3.000
 S5H  H14   C14  C8    106.33  3.000
 S5H  C15   C14  C8    119.25  3.000
 S5H  C13   C14  C8    113.75  3.000
 S5H  H152  C15  H151  106.77  3.000
 S5H  H152  C15  C16   110.97  3.000
 S5H  H151  C15  C16   112.18  3.000
 S5H  H152  C15  C14   110.87  3.000
 S5H  H151  C15  C14   112.17  3.000
 S5H  C16   C15  C14   103.97  3.000
 S5H  H162  C16  H161  106.65  3.000
 S5H  H162  C16  C17   111.03  3.000
 S5H  H161  C16  C17   110.08  3.000
 S5H  H162  C16  C15   111.14  3.000
 S5H  H161  C16  C15   111.75  3.000
 S5H  C17   C16  C15   106.26  3.000
 S5H  H17   C17  C20   107.26  3.000
 S5H  H17   C17  C16   109.46  3.000
 S5H  C20   C17  C16   115.04  3.000
 S5H  H17   C17  C13   106.19  3.000
 S5H  C20   C17  C13   114.57  3.000
 S5H  C16   C17  C13   103.95  3.000
 S5H  H183  C18  H182  107.19  3.000
 S5H  H183  C18  H181  106.68  3.000
 S5H  H182  C18  H181  107.26  3.000
 S5H  H183  C18  C13   110.54  3.000
 S5H  H182  C18  C13   112.70  3.000
 S5H  H181  C18  C13   112.14  3.000
 S5H  H193  C19  H192  107.22  3.000
 S5H  H193  C19  H191  106.43  3.000
 S5H  H192  C19  H191  106.65  3.000
 S5H  H193  C19  C10   110.90  3.000
 S5H  H192  C19  C10   112.80  3.000
 S5H  H191  C19  C10   112.45  3.000
 S5H  C21   C20  O20   121.28  3.000
 S5H  C21   C20  C17   116.17  3.000
 S5H  O20   C20  C17   122.53  3.000
 S5H  H213  C21  H212  106.19  3.000
 S5H  H213  C21  H211  109.79  3.000
 S5H  H212  C21  H211  108.51  3.000
 S5H  H213  C21  C20   112.04  3.000
 S5H  H212  C21  C20   108.20  3.000
 S5H  H211  C21  C20   111.89  3.000
 S5H  CH2   CH1  OH1   125.28  3.000
 S5H  CH2   CH1  O3    111.20  3.000
 S5H  OH1   CH1  O3    123.52  3.000
 S5H  HH22  CH2  HH21  105.05  3.000
 S5H  HH22  CH2  CH3   110.99  3.000
 S5H  HH21  CH2  CH3   110.64  3.000
 S5H  HH22  CH2  CH1   108.48  3.000
 S5H  HH21  CH2  CH1   107.52  3.000
 S5H  CH3   CH2  CH1   113.74  3.000
 S5H  HH32  CH3  HH31  105.18  3.000
 S5H  HH32  CH3  CH4   108.16  3.000
 S5H  HH31  CH3  CH4   108.16  3.000
 S5H  HH32  CH3  CH2   110.13  3.000
 S5H  HH31  CH3  CH2   110.10  3.000
 S5H  CH4   CH3  CH2   114.65  3.000
 S5H  OH5   CH4  OH4   126.46  3.000
 S5H  OH5   CH4  CH3   115.68  3.000
 S5H  OH4   CH4  CH3   117.87  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
 S5H  Var_01  C10   C1   C2   C3   -56.13  30.0  1
 S5H  Var_02  C8    C7   C6   C5    53.63  30.0  1
 S5H  Var_03  C13   C12  C11  C9   -53.41  30.0  1
 S5H  Var_04  C17   C16  C15  C14    7.60  30.0  1
 S5H  Var_05  OH1   CH1  O3   C3    -1.61  30.0  3
 S5H  Var_06  H211  C21  C20  C17  163.86  30.0  3
 S5H  Var_07  CH3   CH2  CH1  O3   174.81  30.0  3
 S5H  Var_08  CH4   CH3  CH2  CH1  178.53  30.0  3
 S5H  Var_09  OH4   CH4  CH3  CH2   -0.74  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
 S5H  chir_01  C3   C2   O3   C4   positiv
 S5H  chir_02  C5   C4   C6   C10  positiv
 S5H  chir_03  C8   C14  C9   C7   negativ
 S5H  chir_04  C9   C11  C10  C8   positiv
 S5H  chir_05  C10  C5   C9   C1   negativ
 S5H  chir_06  C13  C17  C14  C12  positiv
 S5H  chir_07  C14  C15  C13  C8   positiv
 S5H  chir_08  C17  C20  C16  C13  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
 S5H  plan-1  C17  0.020
 S5H  plan-1  C20  0.020
 S5H  plan-1  O20  0.020
 S5H  plan-1  C21  0.020
 S5H  plan-2  CH3  0.020
 S5H  plan-2  CH4  0.020
 S5H  plan-2  OH4  0.020
 S5H  plan-2  OH5  0.020
 S5H  plan-3  O3   0.020
 S5H  plan-3  CH1  0.020
 S5H  plan-3  OH1  0.020
 S5H  plan-3  CH2  0.020

