# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 19:44:00 2020
#   Inital geometry file: a 161 line input string
#   Ligand name: (3S,8S,9S,10R,13S,14S,17R)-17-[(2S,3R)-3-hydroxy-6-methyl-heptan-2-yl]-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CC[C@@H](O)[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=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
 HC9  HC9  (3S,8S,9S,10R,13S,14S,17R)-17-[(2S,3R)-3-hydroxy-6-methyl-heptan-2-yl]-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol  ligand  75  29  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HC9
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
 HC9  C1    C  CH2   0  -0.433  -4.5856   1.5446  -0.9664
 HC9  O1    O  OH1   0  -0.678  -8.1584   0.5144  -1.2522
 HC9  C2    C  CH2   0  -0.465  -6.1027   1.6838  -0.9898
 HC9  O2    O  OH1   0  -0.658   4.4968  -1.6719   0.1122
 HC9  C3    C  CH1   0   0.089  -6.7563   0.3383  -1.2306
 HC9  C4    C  CH2   0  -0.547  -6.3222  -0.6432  -0.1458
 HC9  C5    C  C     0   0.204  -4.8234  -0.7563  -0.0476
 HC9  C6    C  C1    0  -0.327  -4.2360  -1.9521  -0.0540
 HC9  C7    C  CH2   0  -0.452  -2.7693  -2.1889   0.0846
 HC9  C8    C  CH1   0  -0.236  -1.9970  -0.9428   0.5046
 HC9  C9    C  CH1   0  -0.183  -2.5437   0.2899  -0.2260
 HC9  C10   C  CT    0  -0.126  -4.0433   0.5429   0.0749
 HC9  C11   C  CH2   0  -0.444  -1.6596   1.5188   0.0094
 HC9  C12   C  CH2   0  -0.409  -0.1712   1.2770  -0.2585
 HC9  C13   C  CT    0  -0.065   0.3724   0.0938   0.5491
 HC9  C14   C  CH1   0  -0.180  -0.5193  -1.1086   0.1924
 HC9  C15   C  CH2   0  -0.448   0.2052  -2.3013   0.7960
 HC9  C16   C  CH2   0  -0.421   1.6929  -1.9477   0.6161
 HC9  C17   C  CH1   0  -0.162   1.7612  -0.4727   0.1279
 HC9  C18   C  CH3   0  -0.685   0.3497   0.3861   2.0537
 HC9  C19   C  CH3   0  -0.672  -4.2538   1.0993   1.4919
 HC9  C20   C  CH1   0  -0.266   3.0446   0.2694   0.5643
 HC9  C21   C  CH3   0  -0.687   2.9566   1.7767   0.3231
 HC9  C22   C  CH1   0   0.090   4.2948  -0.2965  -0.1540
 HC9  C23   C  CH2   0  -0.478   5.5834   0.4825   0.1316
 HC9  C24   C  CH2   0  -0.388   6.8147  -0.1085  -0.5468
 HC9  C25   C  CH1   0  -0.228   8.1245   0.6050  -0.2042
 HC9  C26   C  CH3   0  -0.652   9.3011  -0.1146  -0.8566
 HC9  C27   C  CH3   0  -0.660   8.1160   2.0769  -0.6063
 HC9  H1    H  HCH2  0   0.221  -4.2468   1.2295  -1.9600
 HC9  H1A   H  HCH2  0   0.236  -4.1448   2.5279  -0.7892
 HC9  HO1   H  HOH1  0   0.446  -8.5635  -0.3329  -1.4618
 HC9  H2    H  HCH2  0   0.220  -6.4665   2.1052  -0.0464
 HC9  H2A   H  HCH2  0   0.237  -6.3875   2.3870  -1.7772
 HC9  H3    H  HCH1  0   0.190  -6.4054  -0.0468  -2.2014
 HC9  H4    H  HCH2  0   0.229  -6.7431  -0.2990   0.8068
 HC9  H4A   H  HCH2  0   0.239  -6.7522  -1.6312  -0.3375
 HC9  H6    H  H     0   0.219  -4.8597  -2.8359  -0.1630
 HC9  H7    H  HCH2  0   0.236  -2.6004  -2.9955   0.8050
 HC9  H7A   H  HCH2  0   0.222  -2.3743  -2.5679  -0.8681
 HC9  H8    H  HCH1  0   0.213  -2.1241  -0.8097   1.5860
 HC9  H9    H  HCH1  0   0.202  -2.4809   0.0573  -1.3000
 HC9  H11   H  HCH2  0   0.232  -1.9918   2.3419  -0.6286
 HC9  H11A  H  HCH2  0   0.219  -1.7805   1.8750   1.0355
 HC9  H12   H  HCH2  0   0.207  -0.0204   1.0712  -1.3251
 HC9  H12A  H  HCH2  0   0.224   0.3632   2.2037  -0.0486
 HC9  H14   H  HCH1  0   0.204  -0.4510  -1.2138  -0.9026
 HC9  H15   H  HCH2  0   0.213  -0.0547  -2.4156   1.8524
 HC9  H15A  H  HCH2  0   0.227  -0.0605  -3.2411   0.3082
 HC9  H16   H  HCH2  0   0.206   2.2341  -2.0644   1.5576
 HC9  H16A  H  HCH2  0   0.228   2.1711  -2.6169  -0.0948
 HC9  H17   H  HCH1  0   0.201   1.7588  -0.4742  -0.9716
 HC9  H18   H  HCH3  0   0.231  -0.6539   0.5911   2.4263
 HC9  H18A  H  HCH3  0   0.232   0.7354  -0.4499   2.6390
 HC9  H18B  H  HCH3  0   0.230   0.9590   1.2564   2.3031
 HC9  H19   H  HCH3  0   0.233  -5.3083   1.1152   1.7692
 HC9  H19A  H  HCH3  0   0.232  -3.7397   0.4901   2.2370
 HC9  H19B  H  HCH3  0   0.228  -3.8882   2.1229   1.5862
 HC9  H20   H  HCH1  0   0.206   3.1854   0.1143   1.6443
 HC9  H21   H  HCH3  0   0.237   2.1096   2.2158   0.8412
 HC9  H21A  H  HCH3  0   0.239   3.8395   2.2994   0.6863
 HC9  H21B  H  HCH3  0   0.215   2.8479   2.0062  -0.7400
 HC9  H22   H  HCH1  0   0.202   4.1036  -0.2421  -1.2337
 HC9  H23   H  HCH2  0   0.230   5.4625   1.5116  -0.2060
 HC9  H23A  H  HCH2  0   0.208   5.7445   0.5330   1.2170
 HC9  H24   H  HCH2  0   0.216   6.9181  -1.1622  -0.2772
 HC9  H24A  H  HCH2  0   0.199   6.6734  -0.0852  -1.6350
 HC9  H25   H  HCH1  0   0.207   8.2574   0.5512   0.8836
 HC9  H26   H  HCH3  0   0.211   9.2378  -0.0567  -1.9463
 HC9  H26A  H  HCH3  0   0.223  10.2537   0.3259  -0.5577
 HC9  H26B  H  HCH3  0   0.221   9.3233  -1.1715  -0.5842
 HC9  H27   H  HCH3  0   0.224   9.0819   2.5438  -0.4044
 HC9  H27A  H  HCH3  0   0.211   7.9123   2.1862  -1.6748
 HC9  H27B  H  HCH3  0   0.226   7.3617   2.6501  -0.0662
 HC9  HO2   H  HOH1  0   0.437   4.6573  -1.7691   1.0570

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
 HC9  C1   C2    single  1.524  0.020  1.524
 HC9  C1   C10   single  1.543  0.020  1.543
 HC9  O1   C3    single  1.413  0.020  1.413
 HC9  C2   C3    single  1.515  0.020  1.515
 HC9  O2   C22   single  1.415  0.020  1.415
 HC9  C3   C4    single  1.526  0.020  1.526
 HC9  C4   C5    single  1.506  0.020  1.506
 HC9  C5   C6    double  1.332  0.020  1.332
 HC9  C5   C10   single  1.520  0.020  1.520
 HC9  C6   C7    single  1.492  0.020  1.492
 HC9  C7   C8    single  1.525  0.020  1.525
 HC9  C8   C9    single  1.534  0.020  1.534
 HC9  C8   C14   single  1.519  0.020  1.519
 HC9  C9   C10   single  1.550  0.020  1.550
 HC9  C9   C11   single  1.532  0.020  1.532
 HC9  C10  C19   single  1.537  0.020  1.537
 HC9  C11  C12   single  1.532  0.020  1.532
 HC9  C12  C13   single  1.532  0.020  1.532
 HC9  C13  C14   single  1.539  0.020  1.539
 HC9  C13  C17   single  1.558  0.020  1.558
 HC9  C13  C18   single  1.533  0.020  1.533
 HC9  C14  C15   single  1.520  0.020  1.520
 HC9  C15  C16   single  1.540  0.020  1.540
 HC9  C16  C17   single  1.555  0.020  1.555
 HC9  C17  C20   single  1.545  0.020  1.545
 HC9  C20  C21   single  1.529  0.020  1.529
 HC9  C20  C22   single  1.549  0.020  1.549
 HC9  C22  C23   single  1.533  0.020  1.533
 HC9  C23  C24   single  1.525  0.020  1.525
 HC9  C24  C25   single  1.530  0.020  1.530
 HC9  C25  C26   single  1.526  0.020  1.526
 HC9  C25  C27   single  1.526  0.020  1.526
 HC9  C1   H1    single  0.970  0.020  1.090
 HC9  C1   H1A   single  0.970  0.020  1.090
 HC9  O1   HO1   single  0.850  0.020  0.980
 HC9  C2   H2    single  0.970  0.020  1.090
 HC9  C2   H2A   single  0.970  0.020  1.090
 HC9  O2   HO2   single  0.850  0.020  0.980
 HC9  C3   H3    single  0.970  0.020  1.090
 HC9  C4   H4    single  0.970  0.020  1.090
 HC9  C4   H4A   single  0.970  0.020  1.090
 HC9  C6   H6    single  0.930  0.020  1.080
 HC9  C7   H7    single  0.970  0.020  1.090
 HC9  C7   H7A   single  0.970  0.020  1.090
 HC9  C8   H8    single  0.970  0.020  1.090
 HC9  C9   H9    single  0.970  0.020  1.090
 HC9  C11  H11   single  0.970  0.020  1.090
 HC9  C11  H11A  single  0.970  0.020  1.090
 HC9  C12  H12   single  0.970  0.020  1.090
 HC9  C12  H12A  single  0.970  0.020  1.090
 HC9  C14  H14   single  0.970  0.020  1.090
 HC9  C15  H15   single  0.970  0.020  1.090
 HC9  C15  H15A  single  0.970  0.020  1.090
 HC9  C16  H16   single  0.970  0.020  1.090
 HC9  C16  H16A  single  0.970  0.020  1.090
 HC9  C17  H17   single  0.970  0.020  1.090
 HC9  C18  H18   single  0.970  0.020  1.090
 HC9  C18  H18A  single  0.970  0.020  1.090
 HC9  C18  H18B  single  0.970  0.020  1.090
 HC9  C19  H19   single  0.970  0.020  1.090
 HC9  C19  H19A  single  0.970  0.020  1.090
 HC9  C19  H19B  single  0.970  0.020  1.090
 HC9  C20  H20   single  0.970  0.020  1.090
 HC9  C21  H21   single  0.970  0.020  1.090
 HC9  C21  H21A  single  0.970  0.020  1.090
 HC9  C21  H21B  single  0.970  0.020  1.090
 HC9  C22  H22   single  0.970  0.020  1.090
 HC9  C23  H23   single  0.970  0.020  1.090
 HC9  C23  H23A  single  0.970  0.020  1.090
 HC9  C24  H24   single  0.970  0.020  1.090
 HC9  C24  H24A  single  0.970  0.020  1.090
 HC9  C25  H25   single  0.970  0.020  1.090
 HC9  C26  H26   single  0.970  0.020  1.090
 HC9  C26  H26A  single  0.970  0.020  1.090
 HC9  C26  H26B  single  0.970  0.020  1.090
 HC9  C27  H27   single  0.970  0.020  1.090
 HC9  C27  H27A  single  0.970  0.020  1.090
 HC9  C27  H27B  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
 HC9  H1A   C1   H1    106.33  3.000
 HC9  H1A   C1   C10   109.45  3.000
 HC9  H1    C1   C10   108.45  3.000
 HC9  H1A   C1   C2    108.80  3.000
 HC9  H1    C1   C2    108.67  3.000
 HC9  C10   C1   C2    114.81  3.000
 HC9  HO1   O1   C3    108.13  3.000
 HC9  H2A   C2   H2    106.64  3.000
 HC9  H2A   C2   C3    110.14  3.000
 HC9  H2    C2   C3    109.59  3.000
 HC9  H2A   C2   C1    109.22  3.000
 HC9  H2    C2   C1    110.65  3.000
 HC9  C3    C2   C1    110.54  3.000
 HC9  HO2   O2   C22   107.84  3.000
 HC9  H3    C3   C4    108.12  3.000
 HC9  H3    C3   C2    108.24  3.000
 HC9  C4    C3   C2    109.60  3.000
 HC9  H3    C3   O1    110.24  3.000
 HC9  C4    C3   O1    111.92  3.000
 HC9  C2    C3   O1    108.65  3.000
 HC9  H4A   C4   H4    106.54  3.000
 HC9  H4A   C4   C5    109.55  3.000
 HC9  H4    C4   C5    110.41  3.000
 HC9  H4A   C4   C3    110.14  3.000
 HC9  H4    C4   C3    107.84  3.000
 HC9  C5    C4   C3    112.19  3.000
 HC9  C10   C5   C6    122.76  3.000
 HC9  C10   C5   C4    116.85  3.000
 HC9  C6    C5   C4    120.38  3.000
 HC9  H6    C6   C7    116.37  3.000
 HC9  H6    C6   C5    118.50  3.000
 HC9  C7    C6   C5    125.13  3.000
 HC9  H7A   C7   H7    105.13  3.000
 HC9  H7A   C7   C8    109.79  3.000
 HC9  H7    C7   C8    110.05  3.000
 HC9  H7A   C7   C6    109.12  3.000
 HC9  H7    C7   C6    109.25  3.000
 HC9  C8    C7   C6    113.18  3.000
 HC9  H8    C8   C14   109.18  3.000
 HC9  H8    C8   C9    109.32  3.000
 HC9  C14   C8   C9    109.66  3.000
 HC9  H8    C8   C7    108.18  3.000
 HC9  C14   C8   C7    110.29  3.000
 HC9  C9    C8   C7    110.19  3.000
 HC9  H9    C9   C11   106.65  3.000
 HC9  H9    C9   C10   106.20  3.000
 HC9  C11   C9   C10   113.42  3.000
 HC9  H9    C9   C8    105.94  3.000
 HC9  C11   C9   C8    111.46  3.000
 HC9  C10   C9   C8    112.55  3.000
 HC9  C19   C10  C9    111.75  3.000
 HC9  C19   C10  C5    108.26  3.000
 HC9  C9    C10  C5    109.95  3.000
 HC9  C19   C10  C1    109.82  3.000
 HC9  C9    C10  C1    108.36  3.000
 HC9  C5    C10  C1    108.66  3.000
 HC9  H11A  C11  H11   105.60  3.000
 HC9  H11A  C11  C12   108.85  3.000
 HC9  H11   C11  C12   108.18  3.000
 HC9  H11A  C11  C9    110.00  3.000
 HC9  H11   C11  C9    109.81  3.000
 HC9  C12   C11  C9    114.04  3.000
 HC9  H12A  C12  H12   106.22  3.000
 HC9  H12A  C12  C13   112.40  3.000
 HC9  H12   C12  C13   108.60  3.000
 HC9  H12A  C12  C11   107.97  3.000
 HC9  H12   C12  C11   109.48  3.000
 HC9  C13   C12  C11   111.99  3.000
 HC9  C18   C13  C17   110.36  3.000
 HC9  C18   C13  C14   111.59  3.000
 HC9  C17   C13  C14    99.78  3.000
 HC9  C18   C13  C12   111.40  3.000
 HC9  C17   C13  C12   117.04  3.000
 HC9  C14   C13  C12   106.00  3.000
 HC9  H14   C14  C15   106.86  3.000
 HC9  H14   C14  C13   105.60  3.000
 HC9  C15   C14  C13   104.17  3.000
 HC9  H14   C14  C8    105.95  3.000
 HC9  C15   C14  C8    117.87  3.000
 HC9  C13   C14  C8    115.51  3.000
 HC9  H15A  C15  H15   106.48  3.000
 HC9  H15A  C15  C16   112.38  3.000
 HC9  H15   C15  C16   111.49  3.000
 HC9  H15A  C15  C14   112.45  3.000
 HC9  H15   C15  C14   110.62  3.000
 HC9  C16   C15  C14   103.53  3.000
 HC9  H16A  C16  H16   106.26  3.000
 HC9  H16A  C16  C17   111.05  3.000
 HC9  H16   C16  C17   110.50  3.000
 HC9  H16A  C16  C15   111.10  3.000
 HC9  H16   C16  C15   110.70  3.000
 HC9  C17   C16  C15   107.28  3.000
 HC9  H17   C17  C20   106.55  3.000
 HC9  H17   C17  C16   108.22  3.000
 HC9  C20   C17  C16   113.78  3.000
 HC9  H17   C17  C13   105.60  3.000
 HC9  C20   C17  C13   119.30  3.000
 HC9  C16   C17  C13   102.76  3.000
 HC9  H18B  C18  H18A  106.92  3.000
 HC9  H18B  C18  H18   106.62  3.000
 HC9  H18A  C18  H18   106.63  3.000
 HC9  H18B  C18  C13   111.60  3.000
 HC9  H18A  C18  C13   112.04  3.000
 HC9  H18   C18  C13   112.65  3.000
 HC9  H19B  C19  H19A  107.88  3.000
 HC9  H19B  C19  H19   106.76  3.000
 HC9  H19A  C19  H19   106.87  3.000
 HC9  H19B  C19  C10   111.93  3.000
 HC9  H19A  C19  C10   111.28  3.000
 HC9  H19   C19  C10   111.85  3.000
 HC9  H20   C20  C22   107.49  3.000
 HC9  H20   C20  C21   107.53  3.000
 HC9  C22   C20  C21   109.48  3.000
 HC9  H20   C20  C17   108.41  3.000
 HC9  C22   C20  C17   111.34  3.000
 HC9  C21   C20  C17   112.40  3.000
 HC9  H21B  C21  H21A  107.72  3.000
 HC9  H21B  C21  H21   107.55  3.000
 HC9  H21A  C21  H21   106.22  3.000
 HC9  H21B  C21  C20   111.48  3.000
 HC9  H21A  C21  C20   111.97  3.000
 HC9  H21   C21  C20   111.62  3.000
 HC9  H22   C22  C23   107.73  3.000
 HC9  H22   C22  C20   107.30  3.000
 HC9  C23   C22  C20   113.98  3.000
 HC9  H22   C22  O2    104.95  3.000
 HC9  C23   C22  O2    109.81  3.000
 HC9  C20   C22  O2    112.52  3.000
 HC9  H23A  C23  H23   106.21  3.000
 HC9  H23A  C23  C24   109.81  3.000
 HC9  H23   C23  C24   108.53  3.000
 HC9  H23A  C23  C22   109.32  3.000
 HC9  H23   C23  C22   109.20  3.000
 HC9  C24   C23  C22   113.51  3.000
 HC9  H24A  C24  H24   106.11  3.000
 HC9  H24A  C24  C25   108.80  3.000
 HC9  H24   C24  C25   108.27  3.000
 HC9  H24A  C24  C23   109.20  3.000
 HC9  H24   C24  C23   109.90  3.000
 HC9  C25   C24  C23   114.25  3.000
 HC9  H25   C25  C27   108.02  3.000
 HC9  H25   C25  C26   107.90  3.000
 HC9  C27   C25  C26   110.28  3.000
 HC9  H25   C25  C24   107.62  3.000
 HC9  C27   C25  C24   112.70  3.000
 HC9  C26   C25  C24   110.14  3.000
 HC9  H26B  C26  H26A  107.74  3.000
 HC9  H26B  C26  H26   107.53  3.000
 HC9  H26A  C26  H26   107.59  3.000
 HC9  H26B  C26  C25   111.45  3.000
 HC9  H26A  C26  C25   111.44  3.000
 HC9  H26   C26  C25   110.90  3.000
 HC9  H27B  C27  H27A  107.62  3.000
 HC9  H27B  C27  H27   107.19  3.000
 HC9  H27A  C27  H27   107.63  3.000
 HC9  H27B  C27  C25   112.36  3.000
 HC9  H27A  C27  C25   110.80  3.000
 HC9  H27   C27  C25   111.03  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
 HC9  Var_01  C10  C1   C2   C3    -56.85  30.0  1
 HC9  Var_02  C6   C5   C4   C3   -129.52  30.0  1
 HC9  Var_03  C7   C6   C5   C4   -177.78  30.0  1
 HC9  Var_04  C8   C7   C6   C5     11.02  30.0  1
 HC9  Var_05  C13  C12  C11  C9    -54.96  30.0  1
 HC9  Var_06  C17  C16  C15  C14     8.94  30.0  1
 HC9  Var_07  C25  C24  C23  C22  -176.43  30.0  3
 HC9  Var_08  C26  C25  C24  C23   176.31  30.0  3
 HC9  Var_09  H26  C26  C25  C24    64.99  30.0  3
 HC9  Var_10  H27  C27  C25  C24  -176.63  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
 HC9  chir_01  C3   O1   C2   C4   negativ
 HC9  chir_02  C8   C7   C9   C14  positiv
 HC9  chir_03  C9   C11  C10  C8   positiv
 HC9  chir_04  C10  C9   C5   C1   positiv
 HC9  chir_05  C13  C17  C14  C12  positiv
 HC9  chir_06  C14  C8   C13  C15  negativ
 HC9  chir_07  C17  C20  C16  C13  negativ
 HC9  chir_08  C20  C17  C21  C22  positiv
 HC9  chir_09  C22  O2   C20  C23  negativ

