# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:06:22 2022
#   Inital geometry file: a 134 line input string
#   Ligand name: (3S,8R,9S,10R,13S,14S)-10,13-dimethyl-17-pyridin-3-yl-2,3,4,7,8,9,11,12,14,15-decahydro-1H-cyclopenta[a]phenanthren-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CC[C@H](O)CC1=CC[C@@H]3[C@@H]2CC[C@@]4(C)[C@H]3CC=C4c5cccnc5
#
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
 AER  AER  (3S,8R,9S,10R,13S,14S)-10,13-dimethyl-17-pyridin-3-yl-2,3,4,7,8,9,11,12,14,15-decahydro-1H-cyclopenta[a]phenanthren-3-ol  ligand  57  26  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AER
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
 AER  C1    C  CH2   0  -0.433  -3.2907   1.6662  -0.5558
 AER  C2    C  CH2   0  -0.467  -4.7930   1.8816  -0.4167
 AER  C3    C  CH1   0   0.090  -5.5486   0.6189  -0.7789
 AER  O3    O  OH1   0  -0.678  -6.9329   0.8674  -0.6423
 AER  C4    C  CH2   0  -0.550  -5.0828  -0.5281   0.1136
 AER  C5    C  C     0   0.208  -3.5916  -0.7276   0.0414
 AER  C6    C  C1    0  -0.329  -3.0844  -1.9316  -0.2200
 AER  C7    C  CH2   0  -0.451  -1.6271  -2.2504  -0.2713
 AER  C8    C  CH1   0  -0.248  -0.7640  -1.1439   0.3223
 AER  C9    C  CH1   0  -0.183  -1.2691   0.2245  -0.1674
 AER  C10   C  CT    0  -0.132  -2.7268   0.5000   0.2844
 AER  C11   C  CH2   0  -0.452  -0.3113   1.3812   0.1655
 AER  C12   C  CH2   0  -0.414   1.1573   1.1159  -0.1847
 AER  C13   C  CT    0  -0.145   1.6169  -0.2039   0.4283
 AER  C14   C  CH1   0  -0.199   0.6806  -1.2994  -0.1090
 AER  C15   C  CH2   0  -0.463   1.4517  -2.5958   0.1368
 AER  C16   C  C1    0  -0.293   2.8568  -2.1174  -0.1026
 AER  C17   C  C     0   0.166   2.9585  -0.7840  -0.0144
 AER  C18   C  CH3   0  -0.665   1.6101  -0.1370   1.9653
 AER  C19   C  CH3   0  -0.671  -2.7980   0.8525   1.7793
 AER  C20   C  CR6   0  -0.009   4.1884  -0.0245  -0.2568
 AER  C21   C  CR16  0  -0.121   4.4705   1.1892   0.3746
 AER  N22   N  N     0  -0.398   5.5740   1.8975   0.1721
 AER  C23   C  CR16  0  -0.076   6.4729   1.4308  -0.6848
 AER  C24   C  CR16  0  -0.313   6.3045   0.2378  -1.3732
 AER  C25   C  CR16  0  -0.209   5.1478  -0.4890  -1.1607
 AER  H1    H  HCH2  0   0.222  -3.0590   1.4785  -1.6102
 AER  H1A   H  HCH2  0   0.237  -2.7731   2.5904  -0.2894
 AER  H2    H  HCH2  0   0.220  -5.0461   2.1759   0.6075
 AER  H2A   H  HCH2  0   0.238  -5.1025   2.7050  -1.0663
 AER  H3    H  HCH1  0   0.190  -5.3071   0.3595  -1.8219
 AER  HO3   H  HOH1  0   0.446  -7.4073   0.0718  -0.9033
 AER  H4    H  HCH2  0   0.230  -5.3929  -0.3027   1.1412
 AER  H4A   H  HCH2  0   0.241  -5.5908  -1.4560  -0.1673
 AER  H6    H  H     0   0.221  -3.7692  -2.7554  -0.4043
 AER  H7    H  HCH2  0   0.238  -1.4395  -3.1940   0.2507
 AER  H7A   H  HCH2  0   0.224  -1.3306  -2.4335  -1.3130
 AER  H8    H  HCH1  0   0.222  -0.8405  -1.2007   1.4141
 AER  H9    H  HCH1  0   0.209  -1.2959   0.1485  -1.2651
 AER  H11   H  HCH2  0   0.239  -0.6362   2.2799  -0.3642
 AER  H11A  H  HCH2  0   0.225  -0.3754   1.6301   1.2267
 AER  H12   H  HCH2  0   0.220   1.2802   1.0679  -1.2718
 AER  H12A  H  HCH2  0   0.226   1.7565   1.9634   0.1594
 AER  H14   H  HCH1  0   0.222   0.6848  -1.1705  -1.2022
 AER  H15   H  HCH2  0   0.235   1.3282  -2.9760   1.1587
 AER  H15A  H  HCH2  0   0.244   1.1592  -3.4071  -0.5332
 AER  H16   H  H     0   0.240   3.6826  -2.7904  -0.3020
 AER  H18   H  HCH3  0   0.234   0.6446   0.1627   2.3716
 AER  H18A  H  HCH3  0   0.237   1.8601  -1.1031   2.4054
 AER  H18B  H  HCH3  0   0.235   2.3420   0.5839   2.3318
 AER  H19   H  HCH3  0   0.232  -2.2955   0.1002   2.3902
 AER  H19A  H  HCH3  0   0.229  -2.3396   1.8192   1.9909
 AER  H19B  H  HCH3  0   0.234  -3.8274   0.9112   2.1322
 AER  H21   H  HCR6  0   0.249   3.7746   1.6094   1.0909
 AER  H23   H  HCR6  0   0.263   7.3629   2.0319  -0.8347
 AER  H24   H  HCR6  0   0.270   7.0583  -0.1045  -2.0689
 AER  H25   H  HCR6  0   0.263   4.9779  -1.4099  -1.7043

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
 AER  C1   H1    single    0.970  0.020  1.090
 AER  C1   H1A   single    0.970  0.020  1.090
 AER  C2   C1    single    1.524  0.020  1.524
 AER  C2   H2    single    0.970  0.020  1.090
 AER  C2   H2A   single    0.970  0.020  1.090
 AER  C3   C2    single    1.515  0.020  1.515
 AER  C3   H3    single    0.970  0.020  1.090
 AER  O3   C3    single    1.413  0.020  1.413
 AER  O3   HO3   single    0.850  0.020  0.980
 AER  C4   C3    single    1.526  0.020  1.526
 AER  C4   C5    single    1.506  0.020  1.506
 AER  C4   H4    single    0.970  0.020  1.090
 AER  C4   H4A   single    0.970  0.020  1.090
 AER  C5   C10   single    1.521  0.020  1.521
 AER  C6   C5    double    1.332  0.020  1.332
 AER  C6   C7    single    1.493  0.020  1.493
 AER  C6   H6    single    0.930  0.020  1.080
 AER  C7   C8    single    1.524  0.020  1.524
 AER  C7   H7    single    0.970  0.020  1.090
 AER  C7   H7A   single    0.970  0.020  1.090
 AER  C8   C14   single    1.516  0.020  1.516
 AER  C8   C9    single    1.539  0.020  1.539
 AER  C8   H8    single    0.970  0.020  1.090
 AER  C9   C11   single    1.538  0.020  1.538
 AER  C9   H9    single    0.970  0.020  1.090
 AER  C10  C1    single    1.544  0.020  1.544
 AER  C10  C9    single    1.551  0.020  1.551
 AER  C11  C12   single    1.533  0.020  1.533
 AER  C11  H11   single    0.970  0.020  1.090
 AER  C11  H11A  single    0.970  0.020  1.090
 AER  C12  H12   single    0.970  0.020  1.090
 AER  C12  H12A  single    0.970  0.020  1.090
 AER  C13  C12   single    1.526  0.020  1.526
 AER  C13  C17   single    1.527  0.020  1.527
 AER  C14  C13   single    1.538  0.020  1.538
 AER  C14  H14   single    0.970  0.020  1.090
 AER  C15  C14   single    1.528  0.020  1.528
 AER  C15  C16   single    1.503  0.020  1.503
 AER  C15  H15   single    0.970  0.020  1.090
 AER  C15  H15A  single    0.970  0.020  1.090
 AER  C16  C17   double    1.340  0.020  1.340
 AER  C16  H16   single    0.930  0.020  1.080
 AER  C17  C20   single    1.466  0.020  1.466
 AER  C18  C13   single    1.538  0.020  1.538
 AER  C18  H18   single    0.970  0.020  1.090
 AER  C18  H18A  single    0.970  0.020  1.090
 AER  C18  H18B  single    0.970  0.020  1.090
 AER  C19  C10   single    1.538  0.020  1.538
 AER  C19  H19   single    0.970  0.020  1.090
 AER  C19  H19A  single    0.970  0.020  1.090
 AER  C19  H19B  single    0.970  0.020  1.090
 AER  C20  C25   aromatic  1.398  0.020  1.398
 AER  C20  C21   aromatic  1.397  0.020  1.397
 AER  C21  N22   aromatic  1.327  0.020  1.327
 AER  C21  H21   single    0.930  0.020  1.080
 AER  N22  C23   aromatic  1.327  0.020  1.327
 AER  C23  H23   single    0.930  0.020  1.080
 AER  C24  C23   aromatic  1.388  0.020  1.388
 AER  C24  H24   single    0.930  0.020  1.080
 AER  C25  C24   aromatic  1.382  0.020  1.382
 AER  C25  H25   single    0.930  0.020  1.080

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
 AER  H1A   C1   H1    106.22  3.000
 AER  H1A   C1   C10   109.47  3.000
 AER  H1    C1   C10   108.48  3.000
 AER  C10   C1   C2    114.66  3.000
 AER  H1A   C1   C2    108.98  3.000
 AER  H1    C1   C2    108.69  3.000
 AER  H2A   C2   H2    106.73  3.000
 AER  H2A   C2   C3    110.14  3.000
 AER  H2    C2   C3    109.40  3.000
 AER  C3    C2   C1    110.60  3.000
 AER  H2A   C2   C1    109.34  3.000
 AER  H2    C2   C1    110.55  3.000
 AER  H3    C3   C4    108.05  3.000
 AER  C4    C3   O3    112.00  3.000
 AER  H3    C3   O3    110.35  3.000
 AER  C4    C3   C2    109.53  3.000
 AER  O3    C3   C2    108.59  3.000
 AER  H3    C3   C2    108.25  3.000
 AER  HO3   O3   C3    108.14  3.000
 AER  H4A   C4   H4    106.47  3.000
 AER  H4A   C4   C5    109.57  3.000
 AER  H4    C4   C5    110.61  3.000
 AER  H4A   C4   C3    110.21  3.000
 AER  H4    C4   C3    107.89  3.000
 AER  C5    C4   C3    111.94  3.000
 AER  C10   C5   C6    122.97  3.000
 AER  C6    C5   C4    120.39  3.000
 AER  C10   C5   C4    116.64  3.000
 AER  H6    C6   C7    116.58  3.000
 AER  H6    C6   C5    118.58  3.000
 AER  C7    C6   C5    124.85  3.000
 AER  H7A   C7   H7    105.20  3.000
 AER  H7A   C7   C8    109.74  3.000
 AER  H7    C7   C8    110.07  3.000
 AER  H7A   C7   C6    109.38  3.000
 AER  H7    C7   C6    109.57  3.000
 AER  C8    C7   C6    112.62  3.000
 AER  H8    C8   C14   110.17  3.000
 AER  H8    C8   C9    109.89  3.000
 AER  C14   C8   C9    108.28  3.000
 AER  H8    C8   C7    108.12  3.000
 AER  C9    C8   C7    109.62  3.000
 AER  C14   C8   C7    110.76  3.000
 AER  H9    C9   C11   106.43  3.000
 AER  H9    C9   C10   106.26  3.000
 AER  C11   C9   C10   112.87  3.000
 AER  C10   C9   C8    111.96  3.000
 AER  H9    C9   C8    105.31  3.000
 AER  C11   C9   C8    113.29  3.000
 AER  C19   C10  C9    111.56  3.000
 AER  C19   C10  C5    108.30  3.000
 AER  C9    C10  C5    110.15  3.000
 AER  C19   C10  C1    109.81  3.000
 AER  C9    C10  C1    108.60  3.000
 AER  C5    C10  C1    108.35  3.000
 AER  H11A  C11  H11   105.44  3.000
 AER  H11A  C11  C12   108.53  3.000
 AER  H11   C11  C12   108.45  3.000
 AER  H11A  C11  C9    110.19  3.000
 AER  H11   C11  C9    109.17  3.000
 AER  C12   C11  C9    114.64  3.000
 AER  H12A  C12  H12   106.55  3.000
 AER  H12A  C12  C13   112.26  3.000
 AER  H12   C12  C13   109.09  3.000
 AER  C13   C12  C11   110.27  3.000
 AER  H12A  C12  C11   108.60  3.000
 AER  H12   C12  C11   109.99  3.000
 AER  C18   C13  C17   108.06  3.000
 AER  C18   C13  C14   112.17  3.000
 AER  C17   C13  C14    99.38  3.000
 AER  C18   C13  C12   111.25  3.000
 AER  C14   C13  C12   106.99  3.000
 AER  C17   C13  C12   118.47  3.000
 AER  H14   C14  C15   104.90  3.000
 AER  C15   C14  C13   103.93  3.000
 AER  H14   C14  C13   105.14  3.000
 AER  C15   C14  C8    121.48  3.000
 AER  H14   C14  C8    105.92  3.000
 AER  C13   C14  C8    114.06  3.000
 AER  H15A  C15  H15   106.49  3.000
 AER  H15A  C15  C16   112.89  3.000
 AER  H15   C15  C16   111.33  3.000
 AER  H15A  C15  C14   113.35  3.000
 AER  H15   C15  C14   112.76  3.000
 AER  C16   C15  C14   100.14  3.000
 AER  H16   C16  C17   124.90  3.000
 AER  H16   C16  C15   122.94  3.000
 AER  C17   C16  C15   112.14  3.000
 AER  C20   C17  C16   124.63  3.000
 AER  C20   C17  C13   126.03  3.000
 AER  C16   C17  C13   109.29  3.000
 AER  H18B  C18  H18A  107.22  3.000
 AER  H18B  C18  H18   106.70  3.000
 AER  H18A  C18  H18   107.24  3.000
 AER  H18B  C18  C13   111.19  3.000
 AER  H18A  C18  C13   111.32  3.000
 AER  H18   C18  C13   112.86  3.000
 AER  H19B  C19  H19A  106.65  3.000
 AER  H19B  C19  H19   106.90  3.000
 AER  H19A  C19  H19   107.99  3.000
 AER  H19B  C19  C10   111.77  3.000
 AER  H19A  C19  C10   111.86  3.000
 AER  H19   C19  C10   111.39  3.000
 AER  C25   C20  C21   116.26  3.000
 AER  C21   C20  C17   123.02  3.000
 AER  C25   C20  C17   120.72  3.000
 AER  H21   C21  N22   115.35  3.000
 AER  H21   C21  C20   120.40  3.000
 AER  N22   C21  C20   124.25  3.000
 AER  C23   N22  C21   118.31  3.000
 AER  H23   C23  C24   120.51  3.000
 AER  C24   C23  N22   122.72  3.000
 AER  H23   C23  N22   116.76  3.000
 AER  H24   C24  C25   121.05  3.000
 AER  C25   C24  C23   118.51  3.000
 AER  H24   C24  C23   120.44  3.000
 AER  H25   C25  C24   120.08  3.000
 AER  H25   C25  C20   119.98  3.000
 AER  C24   C25  C20   119.94  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
 AER  CONST_01  C23  C24  C25  C20     0.00   0.0  0
 AER  CONST_02  C23  N22  C21  C20     0.00   0.0  0
 AER  CONST_03  C24  C25  C20  C21     0.00   0.0  0
 AER  CONST_04  C24  C23  N22  C21     0.00   0.0  0
 AER  CONST_05  C25  C20  C21  N22     0.00   0.0  0
 AER  CONST_06  C25  C24  C23  N22     0.00   0.0  0
 AER  CONST_07  C24  C25  C20  C17   180.00   0.0  0
 AER  CONST_08  N22  C21  C20  C17   180.00   0.0  0
 AER  CONST_09  H25  C25  C20  C17     0.00   0.0  0
 AER  CONST_10  H21  C21  C20  C17     0.00   0.0  0
 AER  CONST_11  H24  C24  C25  C20   180.00   0.0  0
 AER  CONST_12  H23  C23  N22  C21   180.00   0.0  0
 AER  Var_01    C7   C6   C5   C4   -177.94   0.0  0
 AER  Var_02    C10  C1   C2   C3    -56.95  30.0  1
 AER  Var_03    C8   C7   C6   C5     13.46  30.0  1
 AER  Var_04    C13  C12  C11  C9    -52.39  30.0  1
 AER  Var_05    C15  C16  C17  C13     5.05  30.0  1
 AER  Var_06    C25  C20  C17  C13  -152.43  30.0  2
 AER  Var_07    C17  C16  C15  C14    19.12  30.0  1

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
 AER  chir_01  C3   C2   O3   C4   positiv
 AER  chir_02  C8   C7   C14  C9   negativ
 AER  chir_03  C9   C10  C11  C8   negativ
 AER  chir_04  C10  C1   C9   C5   positiv
 AER  chir_05  C13  C14  C17  C12  negativ
 AER  chir_06  C14  C15  C13  C8   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
 AER  plan-1  C17  0.020
 AER  plan-1  C20  0.020
 AER  plan-1  C21  0.020
 AER  plan-1  N22  0.020
 AER  plan-1  C23  0.020
 AER  plan-1  C24  0.020
 AER  plan-1  C25  0.020
 AER  plan-1  H21  0.020
 AER  plan-1  H23  0.020
 AER  plan-1  H24  0.020
 AER  plan-1  H25  0.020
 AER  plan-2  C4   0.020
 AER  plan-2  C5   0.020
 AER  plan-2  C6   0.020
 AER  plan-2  C7   0.020
 AER  plan-2  C10  0.020
 AER  plan-2  H6   0.020

