# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 20:20:16 2021
#   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  73  31  .  2021-08-08  2022-11-17
;
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  10.3256   2.5437  28.5244
 D0O  C2   C  CH2   0  -0.458   9.3508   1.9332  27.5261
 D0O  C3   C  CH1   0   0.037   9.6309   0.4509  27.4083
 D0O  C4   C  CH2   0  -0.441  11.0654   0.1777  27.0074
 D0O  C5   C  CH1   0  -0.221  12.0585   0.8312  27.9787
 D0O  C6   C  CH2   0  -0.432  13.4941   0.5372  27.5444
 D0O  C7   C  CH2   0  -0.430  13.8859   1.3041  26.2880
 D0O  C8   C  CH1   0  -0.217  13.6523   2.8052  26.4376
 D0O  C9   C  CH1   0  -0.192  12.2057   3.1036  26.8767
 D0O  C10  C  CT    0  -0.062  11.8101   2.3465  28.1711
 D0O  C11  C  CH2   0  -0.441  11.9538   4.6136  26.9443
 D0O  C12  C  CH2   0  -0.408  12.3202   5.3541  25.6554
 D0O  C13  C  CT    0  -0.057  13.7604   5.0736  25.2230
 D0O  C14  C  CH1   0  -0.172  13.9127   3.5440  25.1341
 D0O  C15  C  CH2   0  -0.448  15.2460   3.3424  24.4260
 D0O  C16  C  CH2   0  -0.448  15.2991   4.5088  23.4201
 D0O  C17  C  CH1   0  -0.160  14.1292   5.4684  23.7705
 D0O  C18  C  CH3   0  -0.686  14.7535   5.7035  26.2040
 D0O  C19  C  CH3   0  -0.667  12.6133   2.8484  29.3771
 D0O  C20  C  CH1   0  -0.240  14.4601   6.9346  23.4515
 D0O  C21  C  CH3   0  -0.674  13.3441   7.8986  23.8470
 D0O  C22  C  CH2   0  -0.410  14.7871   7.0642  21.9570
 D0O  C23  C  CH2   0  -0.596  15.2510   8.4539  21.5487
 D0O  C24  C  C     0   0.555  15.7409   8.5334  20.1295
 D0O  C25  C  CH3   0  -0.808   6.8038  -1.2141  27.8154
 D0O  O4A  O  O     0  -0.446  15.7691   7.6181  19.3445
 D0O  O4   O  OH1   0  -0.599  16.1505   9.7611  19.8177
 D0O  O1   O  OC2   0  -0.594   8.7211  -0.0778  26.3980
 D0O  S    S  S     0   1.409   8.0459  -1.5084  26.5858
 D0O  OP2  O  OS    0  -0.650   7.4087  -1.7760  25.3138
 D0O  OP1  O  OS    0  -0.654   9.0134  -2.4575  27.1054
 D0O  H1   H  HCH2  0   0.242  10.1001   3.6038  28.6554
 D0O  H2   H  HCH2  0   0.227  10.1462   2.0861  29.5046
 D0O  H3   H  HCH2  0   0.236   9.4436   2.4098  26.5464
 D0O  H4   H  HCH2  0   0.250   8.3239   2.0961  27.8628
 D0O  H5   H  HCH1  0   0.241   9.4197  -0.0238  28.3741
 D0O  H6   H  HCH2  0   0.247  11.2481  -0.8993  26.9927
 D0O  H7   H  HCH2  0   0.233  11.2150   0.5335  25.9850
 D0O  H8   H  HCH1  0   0.221  11.8995   0.3567  28.9565
 D0O  H9   H  HCH2  0   0.226  13.6119  -0.5383  27.3810
 D0O  H10  H  HCH2  0   0.225  14.1838   0.7937  28.3541
 D0O  H11  H  HCH2  0   0.207  13.3180   0.9374  25.4252
 D0O  H12  H  HCH2  0   0.233  14.9372   1.1150  26.0554
 D0O  H13  H  HCH1  0   0.205  14.3472   3.1753  27.2021
 D0O  H14  H  HCH1  0   0.207  11.5719   2.7253  26.0620
 D0O  H15  H  HCH2  0   0.217  12.5119   5.0442  27.7801
 D0O  H16  H  HCH2  0   0.229  10.8997   4.8025  27.1611
 D0O  H17  H  HCH2  0   0.224  12.1416   6.4197  25.8085
 D0O  H18  H  HCH2  0   0.207  11.6447   5.0409  24.8500
 D0O  H19  H  HCH1  0   0.202  13.1311   3.2075  24.4339
 D0O  H20  H  HCH2  0   0.228  15.3129   2.3701  23.9352
 D0O  H21  H  HCH2  0   0.215  16.0771   3.3922  25.1348
 D0O  H22  H  HCH2  0   0.229  15.2116   4.1473  22.3947
 D0O  H23  H  HCH2  0   0.219  16.2574   5.0331  23.4749
 D0O  H24  H  HCH1  0   0.204  13.2649   5.1954  23.1473
 D0O  H25  H  HCH3  0   0.232  14.6020   5.3684  27.2299
 D0O  H26  H  HCH3  0   0.231  15.7901   5.4816  25.9457
 D0O  H27  H  HCH3  0   0.230  14.6486   6.7898  26.2116
 D0O  H28  H  HCH3  0   0.225  12.4054   2.2271  30.2515
 D0O  H29  H  HCH3  0   0.231  13.6906   2.8338  29.2159
 D0O  H30  H  HCH3  0   0.229  12.3375   3.8718  29.6372
 D0O  H31  H  HCH1  0   0.209  15.3643   7.2122  24.0094
 D0O  H32  H  HCH3  0   0.232  13.1936   7.9320  24.9245
 D0O  H33  H  HCH3  0   0.235  13.5639   8.9204  23.5366
 D0O  H34  H  HCH3  0   0.214  12.3958   7.6101  23.3872
 D0O  H35  H  HCH2  0   0.219  13.9055   6.7793  21.3733
 D0O  H36  H  HCH2  0   0.244  15.5697   6.3492  21.6986
 D0O  H37  H  HCH2  0   0.274  16.0586   8.7966  22.2049
 D0O  H38  H  HCH2  0   0.278  14.4546   9.1947  21.6586
 D0O  H39  H  HCH3  0   0.296   7.2662  -0.8992  28.7482
 D0O  H40  H  HCH3  0   0.303   6.1161  -0.4537  27.4537
 D0O  H41  H  HCH3  0   0.312   6.2735  -2.1517  27.9733
 D0O  H42  H  HOH1  0   0.477  16.4565   9.7824  18.8989

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  double  1.206  0.020  1.206
 D0O  O4   C24  single  1.331  0.020  1.331
 D0O  C24  C23  single  1.503  0.020  1.503
 D0O  C23  C22  single  1.521  0.020  1.521
 D0O  C22  C20  single  1.535  0.020  1.535
 D0O  C20  C17  single  1.536  0.020  1.536
 D0O  C20  C21  single  1.527  0.020  1.527
 D0O  C16  C17  single  1.553  0.020  1.553
 D0O  C16  C15  single  1.541  0.020  1.541
 D0O  C17  C13  single  1.550  0.020  1.550
 D0O  C15  C14  single  1.523  0.020  1.523
 D0O  OP2  S    double  1.448  0.020  1.448
 D0O  C14  C13  single  1.540  0.020  1.540
 D0O  C14  C8   single  1.521  0.020  1.521
 D0O  C13  C12  single  1.530  0.020  1.530
 D0O  C13  C18  single  1.532  0.020  1.532
 D0O  C12  C11  single  1.531  0.020  1.531
 D0O  O1   S    single  1.593  0.020  1.593
 D0O  O1   C3   single  1.459  0.020  1.459
 D0O  S    OP1  double  1.451  0.020  1.451
 D0O  S    C25  single  1.772  0.020  1.772
 D0O  C7   C8   single  1.526  0.020  1.526
 D0O  C7   C6   single  1.523  0.020  1.523
 D0O  C8   C9   single  1.541  0.020  1.541
 D0O  C4   C3   single  1.514  0.020  1.514
 D0O  C4   C5   single  1.535  0.020  1.535
 D0O  C9   C11  single  1.532  0.020  1.532
 D0O  C9   C10  single  1.551  0.020  1.551
 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  1.548  0.020  1.548
 D0O  C10  C1   single  1.539  0.020  1.539
 D0O  C10  C19  single  1.533  0.020  1.533
 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
 D0O  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
 D0O  H2   C1   H1   105.32  3.000
 D0O  H2   C1   C10  108.04  3.000
 D0O  H1   C1   C10  110.56  3.000
 D0O  H2   C1   C2   108.29  3.000
 D0O  H1   C1   C2   109.62  3.000
 D0O  C10  C1   C2   114.56  3.000
 D0O  H4   C2   H3   106.91  3.000
 D0O  H4   C2   C3   110.12  3.000
 D0O  H3   C2   C3   109.97  3.000
 D0O  H4   C2   C1   109.85  3.000
 D0O  H3   C2   C1   110.99  3.000
 D0O  C3   C2   C1   108.98  3.000
 D0O  H5   C3   O1   109.45  3.000
 D0O  H5   C3   C4   109.72  3.000
 D0O  O1   C3   C4   110.00  3.000
 D0O  H5   C3   C2   108.65  3.000
 D0O  C4   C3   C2   111.88  3.000
 D0O  O1   C3   C2   107.07  3.000
 D0O  H7   C4   H6   106.59  3.000
 D0O  H7   C4   C5   111.39  3.000
 D0O  H6   C4   C5   108.65  3.000
 D0O  H7   C4   C3   108.58  3.000
 D0O  H6   C4   C3   109.87  3.000
 D0O  C5   C4   C3   111.62  3.000
 D0O  H8   C5   C10  106.80  3.000
 D0O  H8   C5   C6   107.81  3.000
 D0O  C10  C5   C6   111.99  3.000
 D0O  H8   C5   C4   106.60  3.000
 D0O  C10  C5   C4   113.06  3.000
 D0O  C6   C5   C4   110.24  3.000
 D0O  H10  C6   H9   105.85  3.000
 D0O  H10  C6   C7   109.28  3.000
 D0O  H9   C6   C7   110.12  3.000
 D0O  H10  C6   C5   109.68  3.000
 D0O  H9   C6   C5   109.43  3.000
 D0O  C7   C6   C5   112.28  3.000
 D0O  H12  C7   H11  105.84  3.000
 D0O  H12  C7   C8   109.76  3.000
 D0O  H11  C7   C8   109.08  3.000
 D0O  H12  C7   C6   109.61  3.000
 D0O  H11  C7   C6   110.34  3.000
 D0O  C8   C7   C6   112.02  3.000
 D0O  H13  C8   C14  108.96  3.000
 D0O  H13  C8   C9   109.30  3.000
 D0O  C14  C8   C9   108.12  3.000
 D0O  H13  C8   C7   107.64  3.000
 D0O  C9   C8   C7   111.22  3.000
 D0O  C14  C8   C7   111.56  3.000
 D0O  H14  C9   C11  106.09  3.000
 D0O  H14  C9   C10  107.67  3.000
 D0O  C11  C9   C10  113.72  3.000
 D0O  H14  C9   C8   105.27  3.000
 D0O  C10  C9   C8   112.51  3.000
 D0O  C11  C9   C8   110.96  3.000
 D0O  C19  C10  C9   111.29  3.000
 D0O  C19  C10  C5   109.52  3.000
 D0O  C9   C10  C5   109.47  3.000
 D0O  C19  C10  C1   106.43  3.000
 D0O  C5   C10  C1   107.99  3.000
 D0O  C9   C10  C1   112.04  3.000
 D0O  H16  C11  H15  105.83  3.000
 D0O  H16  C11  C12  108.31  3.000
 D0O  H15  C11  C12  109.32  3.000
 D0O  H16  C11  C9   109.74  3.000
 D0O  H15  C11  C9   109.75  3.000
 D0O  C12  C11  C9   113.59  3.000
 D0O  H18  C12  H17  106.33  3.000
 D0O  H18  C12  C13  108.65  3.000
 D0O  H17  C12  C13  111.89  3.000
 D0O  H18  C12  C11  109.43  3.000
 D0O  H17  C12  C11  108.37  3.000
 D0O  C13  C12  C11  112.00  3.000
 D0O  C18  C13  C17  109.95  3.000
 D0O  C18  C13  C14  112.42  3.000
 D0O  C17  C13  C14  100.11  3.000
 D0O  C18  C13  C12  110.74  3.000
 D0O  C14  C13  C12  106.96  3.000
 D0O  C17  C13  C12  116.25  3.000
 D0O  H19  C14  C15  106.56  3.000
 D0O  H19  C14  C13  105.66  3.000
 D0O  C15  C14  C13  104.18  3.000
 D0O  H19  C14  C8   105.95  3.000
 D0O  C13  C14  C8   114.60  3.000
 D0O  C15  C14  C8   118.95  3.000
 D0O  H21  C15  H20  106.60  3.000
 D0O  H21  C15  C16  111.24  3.000
 D0O  H20  C15  C16  112.25  3.000
 D0O  H21  C15  C14  110.98  3.000
 D0O  H20  C15  C14  112.38  3.000
 D0O  C16  C15  C14  103.50  3.000
 D0O  H23  C16  H22  106.04  3.000
 D0O  H23  C16  C17  110.64  3.000
 D0O  H22  C16  C17  110.88  3.000
 D0O  H23  C16  C15  111.12  3.000
 D0O  H22  C16  C15  111.09  3.000
 D0O  C17  C16  C15  107.12  3.000
 D0O  H24  C17  C20  106.77  3.000
 D0O  H24  C17  C16  108.10  3.000
 D0O  C20  C17  C16  112.36  3.000
 D0O  H24  C17  C13  106.30  3.000
 D0O  C16  C17  C13  103.49  3.000
 D0O  C20  C17  C13  119.27  3.000
 D0O  H27  C18  H26  107.18  3.000
 D0O  H27  C18  H25  106.63  3.000
 D0O  H26  C18  H25  107.00  3.000
 D0O  H27  C18  C13  110.58  3.000
 D0O  H26  C18  C13  112.38  3.000
 D0O  H25  C18  C13  112.73  3.000
 D0O  H30  C19  H29  107.33  3.000
 D0O  H30  C19  H28  107.13  3.000
 D0O  H29  C19  H28  107.40  3.000
 D0O  H30  C19  C10  111.22  3.000
 D0O  H29  C19  C10  113.40  3.000
 D0O  H28  C19  C10  110.09  3.000
 D0O  H31  C20  C22  107.33  3.000
 D0O  H31  C20  C21  108.10  3.000
 D0O  C22  C20  C21  110.76  3.000
 D0O  H31  C20  C17  108.24  3.000
 D0O  C21  C20  C17  113.03  3.000
 D0O  C22  C20  C17  109.18  3.000
 D0O  H34  C21  H33  107.61  3.000
 D0O  H34  C21  H32  107.74  3.000
 D0O  H33  C21  H32  106.31  3.000
 D0O  H34  C21  C20  111.02  3.000
 D0O  H33  C21  C20  111.75  3.000
 D0O  H32  C21  C20  112.14  3.000
 D0O  H36  C22  H35  106.31  3.000
 D0O  H36  C22  C23  108.45  3.000
 D0O  H35  C22  C23  109.89  3.000
 D0O  H36  C22  C20  109.15  3.000
 D0O  H35  C22  C20  108.99  3.000
 D0O  C23  C22  C20  113.79  3.000
 D0O  H38  C23  H37  105.36  3.000
 D0O  H38  C23  C24  107.25  3.000
 D0O  H37  C23  C24  107.98  3.000
 D0O  H38  C23  C22  111.71  3.000
 D0O  H37  C23  C22  110.48  3.000
 D0O  C24  C23  C22  113.65  3.000
 D0O  O4   C24  O4A  122.70  3.000
 D0O  O4   C24  C23  111.72  3.000
 D0O  O4A  C24  C23  125.58  3.000
 D0O  H41  C25  H40  110.03  3.000
 D0O  H41  C25  H39  109.39  3.000
 D0O  H40  C25  H39  110.59  3.000
 D0O  H41  C25  S    107.40  3.000
 D0O  H40  C25  S    109.19  3.000
 D0O  H39  C25  S    110.19  3.000
 D0O  H42  O4   C24  109.85  3.000
 D0O  S    O1   C3   120.54  3.000
 D0O  OP1  S    OP2  119.15  3.000
 D0O  OP1  S    O1   110.30  3.000
 D0O  OP2  S    O1   104.42  3.000
 D0O  OP1  S    C25  109.11  3.000
 D0O  O1   S    C25  103.28  3.000
 D0O  OP2  S    C25  109.38  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  CONST_01  H42  O4   C24  C23   180.00   0.0  0
 D0O  Var_01    C10  C1   C2   C3     57.89  30.0  1
 D0O  Var_02    C8   C7   C6   C5     54.12  30.0  1
 D0O  Var_03    C13  C12  C11  C9    -54.14  30.0  1
 D0O  Var_04    C17  C16  C15  C14    10.13  30.0  1
 D0O  Var_05    OP2  S    O1   C3   -170.86  30.0  3
 D0O  Var_06    C24  C23  C22  C20   172.43  30.0  2
 D0O  Var_07    O4A  C24  C23  C22     0.88  30.0  2
 D0O  Var_08    H39  C25  S    O1    -62.75  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
 D0O  plan-1  H42  0.020

