# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 23:46:04 2020
#   Inital geometry file: a 160 line input string
#   Ligand name: (4~{R})-4-[(3~{R},5~{R},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3-methylsulfonyloxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@@H](CC[C@]4(C)[C@H]3CC[C@]12C)O[S](C)(=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
 D0O  D0O  '(4~{R})-4-[(3~{R},5~{R},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3-methylsulfonyloxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoic acid'  ligand  72  31  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D0O
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
 D0O  C1   C  CH2    0  -0.440   2.9107   1.6329   1.5230
 D0O  C2   C  CH2    0  -0.455   3.4484   0.2131   1.6449
 D0O  C3   C  CH1    0   0.037   4.3029  -0.0825   0.4318
 D0O  C4   C  CH2    0  -0.441   3.5351   0.0953  -0.8613
 D0O  C5   C  CH1    0  -0.220   2.9362   1.5039  -0.9701
 D0O  C6   C  CH2    0  -0.433   2.1627   1.6564  -2.2795
 D0O  C7   C  CH2    0  -0.425   0.8435   0.8924  -2.2717
 D0O  C8   C  CH1    0  -0.221  -0.0215   1.2458  -1.0647
 D0O  C9   C  CH1    0  -0.192   0.7650   1.0548   0.2448
 D0O  C10  C  CT     0  -0.063   2.0746   1.8871   0.2582
 D0O  C11  C  CH2    0  -0.439  -0.1186   1.2800   1.4753
 D0O  C12  C  CH2    0  -0.407  -1.4355   0.4968   1.4498
 D0O  C13  C  CT     0  -0.055  -2.2228   0.7271   0.1606
 D0O  C14  C  CH1    0  -0.171  -1.2768   0.3893  -1.0062
 D0O  C15  C  CH2    0  -0.449  -2.1892   0.3473  -2.2261
 D0O  C16  C  CH2    0  -0.445  -3.5133  -0.2156  -1.6728
 D0O  C17  C  CH1    0  -0.158  -3.3785  -0.2647  -0.1275
 D0O  C18  C  CH3    0  -0.685  -2.7372   2.1676   0.0908
 D0O  C19  C  CH3    0  -0.666   1.7838   3.3924   0.2265
 D0O  C20  C  CH1    0  -0.229  -4.7272  -0.0724   0.5806
 D0O  C21  C  CH3    0  -0.671  -4.5959  -0.0165   2.1010
 D0O  C22  C  CH2    0  -0.397  -5.7018  -1.1883   0.1739
 D0O  C23  C  CH2    0  -0.593  -7.1520  -0.9273   0.5504
 D0O  C24  C  C      0   0.413  -8.1643  -1.9967   0.1002
 D0O  C25  C  CH3    0  -0.808   7.1530  -1.2926   1.6455
 D0O  O4A  O  O      0  -0.609  -7.7440  -2.9578  -0.5738
 D0O  O4   O  OC    -1  -0.636  -9.3489  -1.8055   0.4508
 D0O  O1   O  OC2    0  -0.594   4.7655  -1.4608   0.5369
 D0O  S    S  S      0   1.408   6.2790  -1.8249   0.1982
 D0O  OP2  O  OS     0  -0.654   6.7356  -1.0543  -0.9441
 D0O  OP1  O  OS     0  -0.649   6.2976  -3.2705   0.1274
 D0O  H1   H  HCH2   0   0.243   2.3441   1.8949   2.4185
 D0O  H2   H  HCH2   0   0.227   3.7649   2.3209   1.5044
 D0O  H3   H  HCH2   0   0.248   4.0442   0.1199   2.5565
 D0O  H4   H  HCH2   0   0.236   2.6344  -0.5139   1.7172
 D0O  H5   H  HCH1   0   0.241   5.1648   0.5952   0.4367
 D0O  H6   H  HCH2   0   0.246   4.2050  -0.0680  -1.7094
 D0O  H7   H  HCH2   0   0.233   2.7574  -0.6709  -0.9198
 D0O  H8   H  HCH1   0   0.221   3.7820   2.2049  -0.9942
 D0O  H9   H  HCH2   0   0.225   1.9636   2.7156  -2.4645
 D0O  H10  H  HCH2   0   0.226   2.7860   1.3198  -3.1131
 D0O  H11  H  HCH2   0   0.232   0.2992   1.1023  -3.1960
 D0O  H12  H  HCH2   0   0.205   1.0300  -0.1881  -2.2718
 D0O  H13  H  HCH1   0   0.206  -0.3219   2.2970  -1.1597
 D0O  H14  H  HCH1   0   0.207   1.0484  -0.0076   0.2647
 D0O  H15  H  HCH2   0   0.228   0.4245   0.9832   2.3761
 D0O  H16  H  HCH2   0   0.215  -0.3304   2.3463   1.5946
 D0O  H17  H  HCH2   0   0.206  -1.2226  -0.5751   1.5417
 D0O  H18  H  HCH2   0   0.223  -2.0123   0.7700   2.3348
 D0O  H19  H  HCH1   0   0.201  -0.9359  -0.6438  -0.8284
 D0O  H20  H  HCH2   0   0.214  -2.3284   1.3490  -2.6425
 D0O  H21  H  HCH2   0   0.227  -1.7805  -0.2681  -3.0290
 D0O  H22  H  HCH2   0   0.216  -4.3572   0.4178  -1.9593
 D0O  H23  H  HCH2   0   0.227  -3.7251  -1.2048  -2.0806
 D0O  H24  H  HCH1   0   0.199  -3.0049  -1.2608   0.1523
 D0O  H25  H  HCH3   0   0.230  -1.9386   2.9019   0.1907
 D0O  H26  H  HCH3   0   0.229  -3.2502   2.3811  -0.8487
 D0O  H27  H  HCH3   0   0.230  -3.4491   2.3626   0.8947
 D0O  H28  H  HCH3   0   0.231   1.1586   3.6988  -0.6109
 D0O  H29  H  HCH3   0   0.228   1.2857   3.7214   1.1395
 D0O  H30  H  HCH3   0   0.225   2.7194   3.9523   0.1567
 D0O  H31  H  HCH1   0   0.197  -5.1522   0.8810   0.2389
 D0O  H32  H  HCH3   0   0.209  -4.0623  -0.8922   2.4787
 D0O  H33  H  HCH3   0   0.225  -4.0569   0.8686   2.4366
 D0O  H34  H  HCH3   0   0.231  -5.5710   0.0089   2.5891
 D0O  H35  H  HCH2   0   0.221  -5.6541  -1.3458  -0.9050
 D0O  H36  H  HCH2   0   0.194  -5.3613  -2.1284   0.6233
 D0O  H37  H  HCH2   0   0.218  -7.2623  -0.8041   1.6323
 D0O  H38  H  HCH2   0   0.215  -7.4700   0.0327   0.1251
 D0O  H39  H  HCH3   0   0.304   6.7464  -1.8039   2.5145
 D0O  H40  H  HCH3   0   0.312   8.2011  -1.5545   1.5126
 D0O  H41  H  HCH3   0   0.296   7.0619  -0.2146   1.7620

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
 D0O  O4A  C24  deloc   1.247  0.020  1.247
 D0O  O4   C24  deloc   1.250  0.020  1.250
 D0O  C24  C23  single  1.540  0.020  1.540
 D0O  C23  C22  single  1.521  0.020  1.521
 D0O  C22  C20  single  1.536  0.020  1.536
 D0O  C20  C17  single  1.535  0.020  1.535
 D0O  C20  C21  single  1.527  0.020  1.527
 D0O  C16  C17  single  1.552  0.020  1.552
 D0O  C16  C15  single  1.541  0.020  1.541
 D0O  C17  C13  single  1.550  0.020  1.550
 D0O  C15  C14  single  1.524  0.020  1.524
 D0O  OP2  S    deloc   1.452  0.020  1.452
 D0O  C14  C13  single  1.540  0.020  1.540
 D0O  C14  C8   single  1.521  0.020  1.521
 D0O  C13  C12  single  1.528  0.020  1.528
 D0O  C13  C18  single  1.531  0.020  1.531
 D0O  C12  C11  single  1.532  0.020  1.532
 D0O  O1   S    single  1.593  0.020  1.593
 D0O  O1   C3   single  1.458  0.020  1.458
 D0O  S    OP1  deloc   1.447  0.020  1.447
 D0O  S    C25  single  1.773  0.020  1.773
 D0O  C7   C8   single  1.526  0.020  1.526
 D0O  C7   C6   single  1.525  0.020  1.525
 D0O  C8   C9   single  1.540  0.020  1.540
 D0O  C4   C3   single  1.514  0.020  1.514
 D0O  C4   C5   single  1.534  0.020  1.534
 D0O  C9   C11  single  1.532  0.020  1.532
 D0O  C9   C10  single  1.552  0.020  1.552
 D0O  C3   C2   single  1.513  0.020  1.513
 D0O  C6   C5   single  1.528  0.020  1.528
 D0O  C2   C1   single  1.523  0.020  1.523
 D0O  C5   C10  single  1.549  0.020  1.549
 D0O  C10  C1   single  1.537  0.020  1.537
 D0O  C10  C19  single  1.534  0.020  1.534
 D0O  C1   H1   single  0.970  0.020  1.090
 D0O  C1   H2   single  0.970  0.020  1.090
 D0O  C2   H3   single  0.970  0.020  1.090
 D0O  C2   H4   single  0.970  0.020  1.090
 D0O  C3   H5   single  0.970  0.020  1.090
 D0O  C4   H6   single  0.970  0.020  1.090
 D0O  C4   H7   single  0.970  0.020  1.090
 D0O  C5   H8   single  0.970  0.020  1.090
 D0O  C6   H9   single  0.970  0.020  1.090
 D0O  C6   H10  single  0.970  0.020  1.090
 D0O  C7   H11  single  0.970  0.020  1.090
 D0O  C7   H12  single  0.970  0.020  1.090
 D0O  C8   H13  single  0.970  0.020  1.090
 D0O  C9   H14  single  0.970  0.020  1.090
 D0O  C11  H15  single  0.970  0.020  1.090
 D0O  C11  H16  single  0.970  0.020  1.090
 D0O  C12  H17  single  0.970  0.020  1.090
 D0O  C12  H18  single  0.970  0.020  1.090
 D0O  C14  H19  single  0.970  0.020  1.090
 D0O  C15  H20  single  0.970  0.020  1.090
 D0O  C15  H21  single  0.970  0.020  1.090
 D0O  C16  H22  single  0.970  0.020  1.090
 D0O  C16  H23  single  0.970  0.020  1.090
 D0O  C17  H24  single  0.970  0.020  1.090
 D0O  C18  H25  single  0.970  0.020  1.090
 D0O  C18  H26  single  0.970  0.020  1.090
 D0O  C18  H27  single  0.970  0.020  1.090
 D0O  C19  H28  single  0.970  0.020  1.090
 D0O  C19  H29  single  0.970  0.020  1.090
 D0O  C19  H30  single  0.970  0.020  1.090
 D0O  C20  H31  single  0.970  0.020  1.090
 D0O  C21  H32  single  0.970  0.020  1.090
 D0O  C21  H33  single  0.970  0.020  1.090
 D0O  C21  H34  single  0.970  0.020  1.090
 D0O  C22  H35  single  0.970  0.020  1.090
 D0O  C22  H36  single  0.970  0.020  1.090
 D0O  C23  H37  single  0.970  0.020  1.090
 D0O  C23  H38  single  0.970  0.020  1.090
 D0O  C25  H39  single  0.970  0.020  1.090
 D0O  C25  H40  single  0.970  0.020  1.090
 D0O  C25  H41  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
 D0O  H2   C1   H1   105.52  3.000
 D0O  H2   C1   C10  107.81  3.000
 D0O  H1   C1   C10  110.67  3.000
 D0O  H2   C1   C2   108.13  3.000
 D0O  H1   C1   C2   109.95  3.000
 D0O  C10  C1   C2   114.33  3.000
 D0O  H4   C2   H3   107.09  3.000
 D0O  H4   C2   C3   110.09  3.000
 D0O  H3   C2   C3   110.14  3.000
 D0O  H4   C2   C1   111.23  3.000
 D0O  H3   C2   C1   109.80  3.000
 D0O  C3   C2   C1   108.50  3.000
 D0O  H5   C3   O1   109.55  3.000
 D0O  H5   C3   C4   109.26  3.000
 D0O  O1   C3   C4   109.48  3.000
 D0O  H5   C3   C2   108.64  3.000
 D0O  C4   C3   C2   112.05  3.000
 D0O  O1   C3   C2   107.82  3.000
 D0O  H7   C4   H6   106.84  3.000
 D0O  H7   C4   C5   111.22  3.000
 D0O  H6   C4   C5   108.74  3.000
 D0O  H7   C4   C3   108.91  3.000
 D0O  H6   C4   C3   109.52  3.000
 D0O  C5   C4   C3   111.48  3.000
 D0O  H8   C5   C10  106.73  3.000
 D0O  H8   C5   C6   107.88  3.000
 D0O  C10  C5   C6   111.91  3.000
 D0O  H8   C5   C4   106.67  3.000
 D0O  C10  C5   C4   112.83  3.000
 D0O  C6   C5   C4   110.48  3.000
 D0O  H10  C6   H9   105.84  3.000
 D0O  H10  C6   C7   110.05  3.000
 D0O  H9   C6   C7   109.20  3.000
 D0O  H10  C6   C5   109.49  3.000
 D0O  H9   C6   C5   109.50  3.000
 D0O  C7   C6   C5   112.55  3.000
 D0O  H12  C7   H11  105.89  3.000
 D0O  H12  C7   C8   108.95  3.000
 D0O  H11  C7   C8   110.00  3.000
 D0O  H12  C7   C6   110.28  3.000
 D0O  H11  C7   C6   109.29  3.000
 D0O  C8   C7   C6   112.23  3.000
 D0O  H13  C8   C14  108.48  3.000
 D0O  H13  C8   C9   109.41  3.000
 D0O  C14  C8   C9   108.61  3.000
 D0O  H13  C8   C7   107.97  3.000
 D0O  C9   C8   C7   110.75  3.000
 D0O  C14  C8   C7   111.58  3.000
 D0O  H14  C9   C11  106.03  3.000
 D0O  H14  C9   C10  107.49  3.000
 D0O  C11  C9   C10  113.65  3.000
 D0O  H14  C9   C8   105.48  3.000
 D0O  C10  C9   C8   111.84  3.000
 D0O  C11  C9   C8   111.74  3.000
 D0O  C19  C10  C9   111.49  3.000
 D0O  C19  C10  C5   109.39  3.000
 D0O  C9   C10  C5   109.27  3.000
 D0O  C19  C10  C1   106.41  3.000
 D0O  C5   C10  C1   108.00  3.000
 D0O  C9   C10  C1   112.17  3.000
 D0O  H16  C11  H15  105.73  3.000
 D0O  H16  C11  C12  109.50  3.000
 D0O  H15  C11  C12  107.57  3.000
 D0O  H16  C11  C9   110.04  3.000
 D0O  H15  C11  C9   109.60  3.000
 D0O  C12  C11  C9   114.04  3.000
 D0O  H18  C12  H17  106.22  3.000
 D0O  H18  C12  C13  111.98  3.000
 D0O  H17  C12  C13  108.54  3.000
 D0O  H18  C12  C11  108.23  3.000
 D0O  H17  C12  C11  109.35  3.000
 D0O  C13  C12  C11  112.32  3.000
 D0O  C18  C13  C17  110.06  3.000
 D0O  C18  C13  C14  112.23  3.000
 D0O  C17  C13  C14  100.19  3.000
 D0O  C18  C13  C12  110.69  3.000
 D0O  C14  C13  C12  106.84  3.000
 D0O  C17  C13  C12  116.40  3.000
 D0O  H19  C14  C15  106.76  3.000
 D0O  H19  C14  C13  105.87  3.000
 D0O  C15  C14  C13  104.17  3.000
 D0O  H19  C14  C8   106.19  3.000
 D0O  C13  C14  C8   114.38  3.000
 D0O  C15  C14  C8   118.61  3.000
 D0O  H21  C15  H20  106.51  3.000
 D0O  H21  C15  C16  112.33  3.000
 D0O  H20  C15  C16  111.21  3.000
 D0O  H21  C15  C14  112.35  3.000
 D0O  H20  C15  C14  110.83  3.000
 D0O  C16  C15  C14  103.71  3.000
 D0O  H23  C16  H22  106.11  3.000
 D0O  H23  C16  C17  111.13  3.000
 D0O  H22  C16  C17  110.26  3.000
 D0O  H23  C16  C15  111.33  3.000
 D0O  H22  C16  C15  110.94  3.000
 D0O  C17  C16  C15  107.12  3.000
 D0O  H24  C17  C20  107.12  3.000
 D0O  H24  C17  C16  108.14  3.000
 D0O  C20  C17  C16  112.27  3.000
 D0O  H24  C17  C13  106.20  3.000
 D0O  C16  C17  C13  103.28  3.000
 D0O  C20  C17  C13  119.28  3.000
 D0O  H27  C18  H26  107.01  3.000
 D0O  H27  C18  H25  106.87  3.000
 D0O  H26  C18  H25  106.95  3.000
 D0O  H27  C18  C13  110.72  3.000
 D0O  H26  C18  C13  112.40  3.000
 D0O  H25  C18  C13  112.56  3.000
 D0O  H30  C19  H29  106.85  3.000
 D0O  H30  C19  H28  107.36  3.000
 D0O  H29  C19  H28  107.26  3.000
 D0O  H30  C19  C10  110.00  3.000
 D0O  H29  C19  C10  111.43  3.000
 D0O  H28  C19  C10  113.64  3.000
 D0O  H31  C20  C22  107.62  3.000
 D0O  H31  C20  C21  108.13  3.000
 D0O  C22  C20  C21  110.17  3.000
 D0O  H31  C20  C17  107.76  3.000
 D0O  C21  C20  C17  112.84  3.000
 D0O  C22  C20  C17  110.13  3.000
 D0O  H34  C21  H33  106.60  3.000
 D0O  H34  C21  H32  107.49  3.000
 D0O  H33  C21  H32  107.64  3.000
 D0O  H34  C21  C20  111.68  3.000
 D0O  H33  C21  C20  112.28  3.000
 D0O  H32  C21  C20  110.90  3.000
 D0O  H36  C22  H35  105.54  3.000
 D0O  H36  C22  C23  109.99  3.000
 D0O  H35  C22  C23  108.13  3.000
 D0O  H36  C22  C20  108.51  3.000
 D0O  H35  C22  C20  109.80  3.000
 D0O  C23  C22  C20  114.50  3.000
 D0O  H38  C23  H37  104.80  3.000
 D0O  H38  C23  C24  107.69  3.000
 D0O  H37  C23  C24  107.52  3.000
 D0O  H38  C23  C22  109.31  3.000
 D0O  H37  C23  C22  111.10  3.000
 D0O  C24  C23  C22  115.81  3.000
 D0O  O4   C24  O4A  126.07  3.000
 D0O  O4   C24  C23  115.77  3.000
 D0O  O4A  C24  C23  118.16  3.000
 D0O  H41  C25  H40  109.40  3.000
 D0O  H41  C25  H39  110.44  3.000
 D0O  H40  C25  H39  110.15  3.000
 D0O  H41  C25  S    110.10  3.000
 D0O  H40  C25  S    107.63  3.000
 D0O  H39  C25  S    109.08  3.000
 D0O  S    O1   C3   120.15  3.000
 D0O  OP1  S    OP2  119.19  3.000
 D0O  OP1  S    O1   104.53  3.000
 D0O  OP2  S    O1   110.17  3.000
 D0O  OP1  S    C25  109.48  3.000
 D0O  O1   S    C25  103.07  3.000
 D0O  OP2  S    C25  109.15  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
 D0O  Var_01  C10  C1   C2   C3    58.55  30.0  1
 D0O  Var_02  C8   C7   C6   C5    53.16  30.0  1
 D0O  Var_03  C13  C12  C11  C9   -52.60  30.0  1
 D0O  Var_04  C17  C16  C15  C14    8.63  30.0  1
 D0O  Var_05  OP2  S    O1   C3   -38.85  30.0  3
 D0O  Var_06  C24  C23  C22  C20  177.32  30.0  1
 D0O  Var_07  O4A  C24  C23  C22   -2.71  30.0  3
 D0O  Var_08  H39  C25  S    O1    57.71  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
 D0O  chir_01  C3   O1   C4   C2   negativ
 D0O  chir_02  C5   C4   C6   C10  negativ
 D0O  chir_03  C8   C9   C7   C14  negativ
 D0O  chir_04  C9   C10  C11  C8   negativ
 D0O  chir_05  C10  C5   C1   C9   positiv
 D0O  chir_06  C13  C12  C14  C17  negativ
 D0O  chir_07  C14  C15  C13  C8   positiv
 D0O  chir_08  C17  C13  C16  C20  positiv
 D0O  chir_09  C20  C22  C17  C21  positiv

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
 D0O  plan-1  C23  0.020
 D0O  plan-1  C24  0.020
 D0O  plan-1  O4A  0.020
 D0O  plan-1  O4   0.020

