# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 03:06:33 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: (5S,8R,9S,10S,13R,14S,17S)-13-{2-[(3,5-difluorobenzyl)oxy]ethyl}-17-hydroxy-10-methylhexadecahydro-3H-cyclopenta[a]phenanthren-3-one (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CCC(=O)C[C@@H]1CC[C@@H]3[C@@H]2CC[C@]4(CCOCc5cc(F)cc(F)c5)[C@@H](O)CC[C@@H]34
#
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
 ENM  ENM  '(5S,8R,9S,10S,13R,14S,17S)-13-{2-[(3,5-difluorobenzyl)oxy]ethyl}-17-hydroxy-10-methylhexadecahydro-3H-cyclopenta[a]phenanthren-3-one (non-preferred name)'  ligand  68  32  .  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_ENM
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
 ENM  C23   C  CR16  0  -0.461   5.7004  -0.5978   0.1383
 ENM  C24   C  CR6   0   0.557   6.6641   0.0562   0.8798
 ENM  F2    F  F     0  -0.309   7.5837  -0.6677   1.5309
 ENM  C25   C  CR16  0  -0.565   6.7237   1.4333   0.9804
 ENM  C26   C  CR6   0   0.558   5.7614   2.1499   0.2961
 ENM  F1    F  F     0  -0.309   5.7920   3.4868   0.3725
 ENM  C27   C  CR16  0  -0.466   4.7753   1.5456  -0.4591
 ENM  C22   C  CR6   0   0.111   4.7499   0.1578  -0.5409
 ENM  C21   C  CH2   0  -0.201   3.6641  -0.5309  -1.3161
 ENM  O03   O  O2    0  -0.489   2.6154  -0.8295  -0.4289
 ENM  C20   C  CH2   0  -0.129   1.5388  -1.4825  -1.0750
 ENM  C19   C  CH2   0  -0.481   0.4569  -1.7373  -0.0404
 ENM  C12   C  CT    0  -0.112  -0.8241  -2.4288  -0.5578
 ENM  C13   C  CH2   0  -0.432  -1.3502  -1.7866  -1.8379
 ENM  C14   C  CH2   0  -0.447  -1.7967  -0.3467  -1.5781
 ENM  C10   C  CH1   0  -0.170  -2.8625  -0.2480  -0.4778
 ENM  C05   C  CT    0  -0.059  -3.3729   1.1937  -0.2204
 ENM  C18   C  CH3   0  -0.694  -2.2392   2.1002   0.2715
 ENM  C06   C  CH2   0  -0.432  -3.9678   1.7754  -1.5117
 ENM  C01   C  CH2   0  -0.566  -4.6663   3.1249  -1.3179
 ENM  C02   C  C     0   0.420  -5.6676   3.1064  -0.1954
 ENM  O02   O  O     0  -0.411  -6.7765   3.5859  -0.3022
 ENM  C03   C  CH2   0  -0.559  -5.1833   2.4619   1.0744
 ENM  C04   C  CH1   0  -0.220  -4.5198   1.1054   0.8117
 ENM  C07   C  CH2   0  -0.417  -4.0831   0.4443   2.1129
 ENM  C08   C  CH2   0  -0.417  -3.5342  -0.9515   1.8533
 ENM  C09   C  CH1   0  -0.232  -2.4089  -0.9438   0.8230
 ENM  C11   C  CH1   0  -0.183  -1.9537  -2.3549   0.4870
 ENM  C15   C  CH2   0  -0.449  -1.4878  -3.2810   1.6140
 ENM  C16   C  CH2   0  -0.493  -0.6882  -4.3796   0.8785
 ENM  C17   C  CH1   0   0.108  -0.6598  -3.9524  -0.6048
 ENM  O01   O  OH1   0  -0.671   0.4870  -4.3630  -1.3088
 ENM  H23   H  HCR6  0   0.281   5.6946  -1.6792   0.0836
 ENM  H25   H  HCR6  0   0.304   7.4906   1.9268   1.5627
 ENM  H27   H  HCR6  0   0.281   4.0422   2.1470  -0.9812
 ENM  H211  H  HCH2  0   0.220   3.3152   0.1153  -2.1329
 ENM  H212  H  HCH2  0   0.218   4.0569  -1.4460  -1.7793
 ENM  H201  H  HCH2  0   0.195   1.1581  -0.8473  -1.8862
 ENM  H202  H  HCH2  0   0.211   1.8825  -2.4148  -1.5339
 ENM  H191  H  HCH2  0   0.242   0.8891  -2.3226   0.7762
 ENM  H192  H  HCH2  0   0.234   0.1971  -0.7687   0.3934
 ENM  H131  H  HCH2  0   0.231  -0.6175  -1.8135  -2.6486
 ENM  H132  H  HCH2  0   0.218  -2.2102  -2.3701  -2.1871
 ENM  H141  H  HCH2  0   0.217  -0.9269   0.2628  -1.3161
 ENM  H142  H  HCH2  0   0.237  -2.1844   0.0691  -2.5101
 ENM  H10   H  HCH1  0   0.201  -3.7333  -0.8217  -0.8352
 ENM  H181  H  HCH3  0   0.237  -1.4520   2.1855  -0.4789
 ENM  H182  H  HCH3  0   0.235  -2.5834   3.1132   0.4815
 ENM  H183  H  HCH3  0   0.237  -1.7741   1.7330   1.1862
 ENM  H061  H  HCH2  0   0.245  -3.1935   1.9046  -2.2699
 ENM  H062  H  HCH2  0   0.231  -4.6879   1.0613  -1.9260
 ENM  H011  H  HCH2  0   0.263  -3.9225   3.8930  -1.0769
 ENM  H012  H  HCH2  0   0.262  -5.1526   3.4425  -2.2415
 ENM  H031  H  HCH2  0   0.259  -4.4651   3.1423   1.5479
 ENM  H032  H  HCH2  0   0.258  -6.0177   2.3517   1.7701
 ENM  H04   H  HCH1  0   0.226  -5.2855   0.4542   0.3649
 ENM  H071  H  HCH2  0   0.216  -3.3322   1.0643   2.6139
 ENM  H072  H  HCH2  0   0.230  -4.9343   0.3883   2.7976
 ENM  H081  H  HCH2  0   0.233  -3.1831  -1.3944   2.7888
 ENM  H082  H  HCH2  0   0.205  -4.3481  -1.5914   1.4896
 ENM  H09   H  HCH1  0   0.214  -1.5687  -0.3885   1.2582
 ENM  H11   H  HCH1  0   0.213  -2.8228  -2.8458   0.0208
 ENM  H151  H  HCH2  0   0.223  -0.8600  -2.7444   2.3299
 ENM  H152  H  HCH2  0   0.234  -2.3281  -3.6886   2.1766
 ENM  H161  H  HCH2  0   0.229   0.3331  -4.4509   1.2595
 ENM  H162  H  HCH2  0   0.236  -1.1367  -5.3674   0.9972
 ENM  H17   H  HCH1  0   0.195  -1.5584  -4.3538  -1.0988
 ENM  HO01  H  HOH1  0   0.449   0.5289  -5.3237  -1.2771

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
 ENM  C23  C22   aromatic  1.391  0.020  1.391
 ENM  C23  C24   aromatic  1.381  0.020  1.381
 ENM  C23  H23   single    0.930  0.020  1.080
 ENM  C24  C25   aromatic  1.382  0.020  1.382
 ENM  C24  F2    single    1.339  0.020  1.339
 ENM  C25  C26   aromatic  1.381  0.020  1.381
 ENM  C25  H25   single    0.930  0.020  1.080
 ENM  C26  C27   aromatic  1.381  0.020  1.381
 ENM  C26  F1    single    1.339  0.020  1.339
 ENM  C27  C22   aromatic  1.390  0.020  1.390
 ENM  C27  H27   single    0.930  0.020  1.080
 ENM  C22  C21   single    1.501  0.020  1.501
 ENM  C21  O03   single    1.406  0.020  1.406
 ENM  C21  H211  single    0.970  0.020  1.090
 ENM  C21  H212  single    0.970  0.020  1.090
 ENM  O03  C20   single    1.415  0.020  1.415
 ENM  C20  C19   single    1.518  0.020  1.518
 ENM  C20  H201  single    0.970  0.020  1.090
 ENM  C20  H202  single    0.970  0.020  1.090
 ENM  C19  C12   single    1.545  0.020  1.545
 ENM  C19  H191  single    0.970  0.020  1.090
 ENM  C19  H192  single    0.970  0.020  1.090
 ENM  C12  C17   single    1.533  0.020  1.533
 ENM  C12  C11   single    1.540  0.020  1.540
 ENM  C12  C13   single    1.526  0.020  1.526
 ENM  C13  C14   single    1.530  0.020  1.530
 ENM  C13  H131  single    0.970  0.020  1.090
 ENM  C13  H132  single    0.970  0.020  1.090
 ENM  C14  C10   single    1.535  0.020  1.535
 ENM  C14  H141  single    0.970  0.020  1.090
 ENM  C14  H142  single    0.970  0.020  1.090
 ENM  C10  C09   single    1.543  0.020  1.543
 ENM  C10  C05   single    1.551  0.020  1.551
 ENM  C10  H10   single    0.970  0.020  1.090
 ENM  C05  C04   single    1.545  0.020  1.545
 ENM  C05  C06   single    1.536  0.020  1.536
 ENM  C05  C18   single    1.533  0.020  1.533
 ENM  C18  H181  single    0.970  0.020  1.090
 ENM  C18  H182  single    0.970  0.020  1.090
 ENM  C18  H183  single    0.970  0.020  1.090
 ENM  C06  C01   single    1.532  0.020  1.532
 ENM  C06  H061  single    0.970  0.020  1.090
 ENM  C06  H062  single    0.970  0.020  1.090
 ENM  C01  C02   single    1.504  0.020  1.504
 ENM  C01  H011  single    0.970  0.020  1.090
 ENM  C01  H012  single    0.970  0.020  1.090
 ENM  C02  O02   double    1.213  0.020  1.213
 ENM  C02  C03   single    1.504  0.020  1.504
 ENM  C03  C04   single    1.533  0.020  1.533
 ENM  C03  H031  single    0.970  0.020  1.090
 ENM  C03  H032  single    0.970  0.020  1.090
 ENM  C04  C07   single    1.523  0.020  1.523
 ENM  C04  H04   single    0.970  0.020  1.090
 ENM  C07  C08   single    1.522  0.020  1.522
 ENM  C07  H071  single    0.970  0.020  1.090
 ENM  C07  H072  single    0.970  0.020  1.090
 ENM  C08  C09   single    1.526  0.020  1.526
 ENM  C08  H081  single    0.970  0.020  1.090
 ENM  C08  H082  single    0.970  0.020  1.090
 ENM  C09  C11   single    1.520  0.020  1.520
 ENM  C09  H09   single    0.970  0.020  1.090
 ENM  C11  C15   single    1.531  0.020  1.531
 ENM  C11  H11   single    0.970  0.020  1.090
 ENM  C15  C16   single    1.545  0.020  1.545
 ENM  C15  H151  single    0.970  0.020  1.090
 ENM  C15  H152  single    0.970  0.020  1.090
 ENM  C16  C17   single    1.544  0.020  1.544
 ENM  C16  H161  single    0.970  0.020  1.090
 ENM  C16  H162  single    0.970  0.020  1.090
 ENM  C17  O01   single    1.407  0.020  1.407
 ENM  C17  H17   single    0.970  0.020  1.090
 ENM  O01  HO01  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
 ENM  H23   C23  C22   120.93  3.000
 ENM  H23   C23  C24   120.26  3.000
 ENM  C22   C23  C24   118.81  3.000
 ENM  C25   C24  F2    118.26  3.000
 ENM  F2    C24  C23   118.98  3.000
 ENM  C25   C24  C23   122.76  3.000
 ENM  H25   C25  C26   121.58  3.000
 ENM  H25   C25  C24   121.62  3.000
 ENM  C26   C25  C24   116.80  3.000
 ENM  C27   C26  F1    118.96  3.000
 ENM  F1    C26  C25   118.27  3.000
 ENM  C27   C26  C25   122.77  3.000
 ENM  H27   C27  C22   120.91  3.000
 ENM  H27   C27  C26   120.27  3.000
 ENM  C22   C27  C26   118.81  3.000
 ENM  C21   C22  C27   120.10  3.000
 ENM  C21   C22  C23   119.81  3.000
 ENM  C27   C22  C23   120.05  3.000
 ENM  H212  C21  H211  106.87  3.000
 ENM  H212  C21  O03   110.85  3.000
 ENM  H211  C21  O03   110.94  3.000
 ENM  H212  C21  C22   109.96  3.000
 ENM  H211  C21  C22   110.11  3.000
 ENM  O03   C21  C22   108.12  3.000
 ENM  C20   O03  C21   112.17  3.000
 ENM  H202  C20  H201  106.96  3.000
 ENM  H202  C20  C19   111.50  3.000
 ENM  H201  C20  C19   110.69  3.000
 ENM  H202  C20  O03   110.22  3.000
 ENM  H201  C20  O03   109.51  3.000
 ENM  C19   C20  O03   107.96  3.000
 ENM  H192  C19  H191  105.78  3.000
 ENM  H192  C19  C12   109.42  3.000
 ENM  H191  C19  C12   109.77  3.000
 ENM  H192  C19  C20   106.93  3.000
 ENM  H191  C19  C20   108.48  3.000
 ENM  C12   C19  C20   115.96  3.000
 ENM  C17   C12  C11    98.46  3.000
 ENM  C11   C12  C13   107.22  3.000
 ENM  C17   C12  C13   115.44  3.000
 ENM  C13   C12  C19   112.24  3.000
 ENM  C11   C12  C19   111.07  3.000
 ENM  C17   C12  C19   111.48  3.000
 ENM  H132  C13  H131  106.05  3.000
 ENM  H132  C13  C14   109.03  3.000
 ENM  H131  C13  C14   110.17  3.000
 ENM  H132  C13  C12   108.28  3.000
 ENM  H131  C13  C12   112.38  3.000
 ENM  C14   C13  C12   110.76  3.000
 ENM  H142  C14  H141  105.94  3.000
 ENM  H142  C14  C10   109.93  3.000
 ENM  H141  C14  C10   110.15  3.000
 ENM  H142  C14  C13   108.49  3.000
 ENM  H141  C14  C13   109.45  3.000
 ENM  C10   C14  C13   112.64  3.000
 ENM  H10   C10  C09   105.71  3.000
 ENM  H10   C10  C05   106.12  3.000
 ENM  C09   C10  C05   112.08  3.000
 ENM  H10   C10  C14   106.41  3.000
 ENM  C05   C10  C14   114.03  3.000
 ENM  C09   C10  C14   111.78  3.000
 ENM  C04   C05  C06   107.20  3.000
 ENM  C06   C05  C18   109.41  3.000
 ENM  C04   C05  C18   111.62  3.000
 ENM  C18   C05  C10   111.08  3.000
 ENM  C06   C05  C10   109.87  3.000
 ENM  C04   C05  C10   107.58  3.000
 ENM  H183  C18  H182  106.63  3.000
 ENM  H183  C18  H181  107.20  3.000
 ENM  H182  C18  H181  106.72  3.000
 ENM  H183  C18  C05   112.69  3.000
 ENM  H182  C18  C05   112.19  3.000
 ENM  H181  C18  C05   111.05  3.000
 ENM  H062  C06  H061  106.31  3.000
 ENM  H062  C06  C01   108.81  3.000
 ENM  H061  C06  C01   107.89  3.000
 ENM  H062  C06  C05   109.00  3.000
 ENM  H061  C06  C05   110.74  3.000
 ENM  C01   C06  C05   113.82  3.000
 ENM  H012  C01  H011  106.54  3.000
 ENM  H012  C01  C02   109.79  3.000
 ENM  H011  C01  C02   107.23  3.000
 ENM  H012  C01  C06   110.65  3.000
 ENM  H011  C01  C06   109.62  3.000
 ENM  C02   C01  C06   112.77  3.000
 ENM  C03   C02  O02   122.55  3.000
 ENM  C03   C02  C01   114.89  3.000
 ENM  O02   C02  C01   122.55  3.000
 ENM  H032  C03  H031  106.73  3.000
 ENM  H032  C03  C04   110.53  3.000
 ENM  H031  C03  C04   109.85  3.000
 ENM  H032  C03  C02   109.58  3.000
 ENM  H031  C03  C02   108.03  3.000
 ENM  C04   C03  C02   111.96  3.000
 ENM  H04   C04  C07   106.83  3.000
 ENM  H04   C04  C03   106.99  3.000
 ENM  C07   C04  C03   111.21  3.000
 ENM  H04   C04  C05   106.21  3.000
 ENM  C07   C04  C05   112.49  3.000
 ENM  C03   C04  C05   112.65  3.000
 ENM  H072  C07  H071  106.04  3.000
 ENM  H072  C07  C08   109.91  3.000
 ENM  H071  C07  C08   110.48  3.000
 ENM  H072  C07  C04   109.50  3.000
 ENM  H071  C07  C04   109.97  3.000
 ENM  C08   C07  C04   110.83  3.000
 ENM  H082  C08  H081  106.60  3.000
 ENM  H082  C08  C09   109.04  3.000
 ENM  H081  C08  C09   110.06  3.000
 ENM  H082  C08  C07   108.89  3.000
 ENM  H081  C08  C07   109.96  3.000
 ENM  C09   C08  C07   112.12  3.000
 ENM  H09   C09  C11   109.15  3.000
 ENM  H09   C09  C08   107.43  3.000
 ENM  C11   C09  C08   111.43  3.000
 ENM  H09   C09  C10   109.34  3.000
 ENM  C11   C09  C10   108.67  3.000
 ENM  C08   C09  C10   110.77  3.000
 ENM  H11   C11  C15   106.38  3.000
 ENM  H11   C11  C09   105.72  3.000
 ENM  C15   C11  C09   119.32  3.000
 ENM  H11   C11  C12   105.67  3.000
 ENM  C15   C11  C12   104.30  3.000
 ENM  C09   C11  C12   114.46  3.000
 ENM  H152  C15  H151  106.75  3.000
 ENM  H152  C15  C16   112.25  3.000
 ENM  H151  C15  C16   111.33  3.000
 ENM  H152  C15  C11   111.80  3.000
 ENM  H151  C15  C11   111.10  3.000
 ENM  C16   C15  C11   103.71  3.000
 ENM  H162  C16  H161  106.69  3.000
 ENM  H162  C16  C17   111.26  3.000
 ENM  H161  C16  C17   109.64  3.000
 ENM  H162  C16  C15   112.28  3.000
 ENM  H161  C16  C15   111.36  3.000
 ENM  C17   C16  C15   105.67  3.000
 ENM  H17   C17  O01   109.53  3.000
 ENM  H17   C17  C16   108.37  3.000
 ENM  O01   C17  C16   114.52  3.000
 ENM  H17   C17  C12   106.77  3.000
 ENM  O01   C17  C12   113.12  3.000
 ENM  C16   C17  C12   104.10  3.000
 ENM  HO01  O01  C17   108.09  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
 ENM  CONST_01  C26  C27  C22  C23     0.00   0.0  0
 ENM  CONST_02  C26  C25  C24  C23     0.00   0.0  0
 ENM  CONST_03  C27  C22  C23  C24     0.00   0.0  0
 ENM  CONST_04  C27  C26  C25  C24     0.00   0.0  0
 ENM  CONST_05  C22  C23  C24  C25     0.00   0.0  0
 ENM  CONST_06  C22  C27  C26  C25     0.00   0.0  0
 ENM  CONST_07  C21  C22  C23  C24   180.00   0.0  0
 ENM  CONST_08  F1   C26  C25  C24   180.00   0.0  0
 ENM  CONST_09  C22  C23  C24  F2    180.00   0.0  0
 ENM  CONST_10  C26  C25  C24  F2    180.00   0.0  0
 ENM  CONST_11  C21  C22  C27  C26   180.00   0.0  0
 ENM  CONST_12  C22  C27  C26  F1    180.00   0.0  0
 ENM  CONST_13  H27  C27  C22  C23   180.00   0.0  0
 ENM  CONST_14  H25  C25  C24  C23   180.00   0.0  0
 ENM  CONST_15  H23  C23  C24  C25   180.00   0.0  0
 ENM  Var_01    C10  C14  C13  C12   -56.90  30.0  1
 ENM  Var_02    C02  C01  C06  C05   -51.03  30.0  1
 ENM  Var_03    C03  C02  C01  C06    46.05  30.0  1
 ENM  Var_04    C04  C03  C02  C01   -48.04  30.0  1
 ENM  Var_05    C09  C08  C07  C04    54.61  30.0  1
 ENM  Var_06    C17  C16  C15  C11     4.14  30.0  1
 ENM  Var_07    O03  C21  C22  C23    85.24  30.0  2
 ENM  Var_08    C12  C19  C20  O03   179.07  30.0  3
 ENM  Var_09    C19  C20  O03  C21  -179.06  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
 ENM  chir_01  C12  C17  C11  C13  positiv
 ENM  chir_02  C10  C05  C09  C14  positiv
 ENM  chir_03  C05  C06  C04  C10  negativ
 ENM  chir_04  C04  C07  C03  C05  negativ
 ENM  chir_05  C09  C10  C08  C11  negativ
 ENM  chir_06  C11  C15  C09  C12  negativ
 ENM  chir_07  C17  O01  C16  C12  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
 ENM  plan-1  C23  0.020
 ENM  plan-1  C24  0.020
 ENM  plan-1  F2   0.020
 ENM  plan-1  C25  0.020
 ENM  plan-1  C26  0.020
 ENM  plan-1  F1   0.020
 ENM  plan-1  C27  0.020
 ENM  plan-1  C22  0.020
 ENM  plan-1  C21  0.020
 ENM  plan-1  H23  0.020
 ENM  plan-1  H25  0.020
 ENM  plan-1  H27  0.020
 ENM  plan-2  C01  0.020
 ENM  plan-2  C02  0.020
 ENM  plan-2  O02  0.020
 ENM  plan-2  C03  0.020

