# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:37:59 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: (8R,9S,13S,14S)-3-hydroxy-13-methyl-7,8,9,11,12,14,15,16-octahydro-6H-cyclopenta[a]phenanthren-17-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CC[C@H]3[C@@H](CCc4cc(O)ccc34)[C@@H]1CCC2=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
 J3Z  J3Z  (8R,9S,13S,14S)-3-hydroxy-13-methyl-7,8,9,11,12,14,15,16-octahydro-6H-cyclopenta[a]phenanthren-17-one  ligand  42  20  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_J3Z
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
 J3Z  C2    C  CH1   0  -0.262   0.2388  -0.4394  -0.5688
 J3Z  C4    C  CH2   0  -0.406  -1.9306  -1.7875  -0.3716
 J3Z  C5    C  CT    0  -0.206  -2.5940  -0.5634   0.2393
 J3Z  C6    C  CH3   0  -0.668  -2.5823  -0.6432   1.7785
 J3Z  C7    C  C     0   0.431  -4.0410  -0.3102  -0.1220
 J3Z  C8    C  CH2   0  -0.567  -4.2704   1.1944  -0.1371
 J3Z  C9    C  CH2   0  -0.460  -2.8907   1.8324   0.0859
 J3Z  C10   C  CH1   0  -0.200  -1.9335   0.7078  -0.3104
 J3Z  C12   C  CH1   0  -0.236  -0.4624   0.7814   0.0503
 J3Z  C3    C  CH2   0  -0.454  -0.4167  -1.7575  -0.1301
 J3Z  C14   C  CH2   0  -0.430   0.2209   2.0513  -0.4303
 J3Z  C15   C  CH2   0  -0.507   1.6443   2.1099   0.1007
 J3Z  C16   C  CR6   0   0.073   2.3887   0.8050  -0.0273
 J3Z  C21   C  CR6   0   0.096   1.7363  -0.3978  -0.3195
 J3Z  C17   C  CR16  0  -0.431   3.7680   0.8206   0.1758
 J3Z  C18   C  CR6   0   0.353   4.5247  -0.3388   0.0883
 J3Z  C19   C  CR16  0  -0.341   3.8891  -1.5387  -0.2165
 J3Z  C20   C  CR16  0  -0.312   2.5198  -1.5502  -0.4156
 J3Z  H2    H  HCH1  0   0.230   0.0849  -0.3537  -1.6557
 J3Z  H14   H  HCH2  0   0.235  -2.3492  -2.7103   0.0381
 J3Z  H24   H  HCH2  0   0.229  -2.1216  -1.8061  -1.4496
 J3Z  H16   H  HCH3  0   0.245  -3.0393   0.2251   2.2551
 J3Z  H26   H  HCH3  0   0.244  -3.1346  -1.5262   2.1044
 J3Z  H36   H  HCH3  0   0.249  -1.5701  -0.7284   2.1704
 J3Z  HO3   H  HOH1  0   0.472   6.1796   0.5276   0.4927
 J3Z  H18   H  HCH2  0   0.278  -4.6834   1.4663  -1.1123
 J3Z  H28   H  HCH2  0   0.278  -5.0201   1.4751   0.6056
 J3Z  H19   H  HCH2  0   0.249  -2.7548   2.7264  -0.5227
 J3Z  H29   H  HCH2  0   0.232  -2.7493   2.1299   1.1271
 J3Z  H10   H  HCH1  0   0.228  -1.9870   0.6310  -1.4081
 J3Z  H12   H  HCH1  0   0.223  -0.3598   0.7362   1.1428
 J3Z  H13   H  HCH2  0   0.243   0.0244  -2.5948  -0.6734
 J3Z  H23   H  HCH2  0   0.226  -0.1948  -1.9367   0.9259
 J3Z  H114  H  HCH2  0   0.219   0.2174   2.0736  -1.5257
 J3Z  H214  H  HCH2  0   0.241  -0.3241   2.9365  -0.0957
 J3Z  H115  H  HCH2  0   0.248   2.2065   2.9008  -0.4016
 J3Z  H215  H  HCH2  0   0.244   1.6188   2.3907   1.1590
 J3Z  H17   H  HCR6  0   0.257   4.2540   1.7643   0.4068
 J3Z  H19A  H  HCR6  0   0.255   4.4631  -2.4535  -0.2975
 J3Z  H20   H  HCR6  0   0.243   2.0584  -2.4977  -0.6611
 J3Z  O1    O  O     0  -0.401  -4.8767  -1.1496  -0.3576
 J3Z  O3    O  OH1   0  -0.639   5.8616  -0.3569   0.2809

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
 J3Z  C8   C9    single    1.536  0.020  1.536
 J3Z  C8   C7    single    1.522  0.020  1.522
 J3Z  O1   C7    double    1.208  0.020  1.208
 J3Z  C9   C10   single    1.529  0.020  1.529
 J3Z  C7   C5    single    1.513  0.020  1.513
 J3Z  C6   C5    single    1.541  0.020  1.541
 J3Z  C5   C10   single    1.534  0.020  1.534
 J3Z  C5   C4    single    1.520  0.020  1.520
 J3Z  C10  C12   single    1.516  0.020  1.516
 J3Z  C14  C12   single    1.520  0.020  1.520
 J3Z  C14  C15   single    1.520  0.020  1.520
 J3Z  C12  C2    single    1.538  0.020  1.538
 J3Z  C4   C3    single    1.533  0.020  1.533
 J3Z  C15  C16   single    1.508  0.020  1.508
 J3Z  C2   C3    single    1.536  0.020  1.536
 J3Z  C2   C21   single    1.519  0.020  1.519
 J3Z  C16  C21   aromatic  1.399  0.020  1.399
 J3Z  C16  C17   aromatic  1.394  0.020  1.394
 J3Z  C21  C20   aromatic  1.397  0.020  1.397
 J3Z  C17  C18   aromatic  1.387  0.020  1.387
 J3Z  C20  C19   aromatic  1.384  0.020  1.384
 J3Z  C18  C19   aromatic  1.392  0.020  1.392
 J3Z  C18  O3    single    1.351  0.020  1.351
 J3Z  C2   H2    single    0.970  0.020  1.090
 J3Z  C4   H14   single    0.970  0.020  1.090
 J3Z  C4   H24   single    0.970  0.020  1.090
 J3Z  C6   H16   single    0.970  0.020  1.090
 J3Z  C6   H26   single    0.970  0.020  1.090
 J3Z  C6   H36   single    0.970  0.020  1.090
 J3Z  O3   HO3   single    0.850  0.020  0.980
 J3Z  C8   H18   single    0.970  0.020  1.090
 J3Z  C8   H28   single    0.970  0.020  1.090
 J3Z  C9   H19   single    0.970  0.020  1.090
 J3Z  C9   H29   single    0.970  0.020  1.090
 J3Z  C10  H10   single    0.970  0.020  1.090
 J3Z  C12  H12   single    0.970  0.020  1.090
 J3Z  C3   H13   single    0.970  0.020  1.090
 J3Z  C3   H23   single    0.970  0.020  1.090
 J3Z  C14  H114  single    0.970  0.020  1.090
 J3Z  C14  H214  single    0.970  0.020  1.090
 J3Z  C15  H115  single    0.970  0.020  1.090
 J3Z  C15  H215  single    0.970  0.020  1.090
 J3Z  C17  H17   single    0.930  0.020  1.080
 J3Z  C19  H19A  single    0.930  0.020  1.080
 J3Z  C20  H20   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
 J3Z  H2    C2   C21   107.32  3.000
 J3Z  H2    C2   C3    106.80  3.000
 J3Z  C21   C2   C3    113.42  3.000
 J3Z  H2    C2   C12   105.78  3.000
 J3Z  C21   C2   C12   111.21  3.000
 J3Z  C3    C2   C12   111.81  3.000
 J3Z  H24   C4   H14   106.73  3.000
 J3Z  H24   C4   C3    109.12  3.000
 J3Z  H14   C4   C3    109.61  3.000
 J3Z  H24   C4   C5    109.46  3.000
 J3Z  H14   C4   C5    111.23  3.000
 J3Z  C3    C4   C5    110.59  3.000
 J3Z  C10   C5   C7    100.81  3.000
 J3Z  C10   C5   C6    113.42  3.000
 J3Z  C7    C5   C6    104.74  3.000
 J3Z  C10   C5   C4    109.59  3.000
 J3Z  C6    C5   C4    110.87  3.000
 J3Z  C7    C5   C4    117.14  3.000
 J3Z  H36   C6   H26   107.43  3.000
 J3Z  H36   C6   H16   107.13  3.000
 J3Z  H26   C6   H16   107.55  3.000
 J3Z  H36   C6   C5    111.75  3.000
 J3Z  H26   C6   C5    109.65  3.000
 J3Z  H16   C6   C5    113.08  3.000
 J3Z  C8    C7   O1    125.51  3.000
 J3Z  O1    C7   C5    126.31  3.000
 J3Z  C8    C7   C5    108.18  3.000
 J3Z  H28   C8   H18   106.46  3.000
 J3Z  H28   C8   C9    114.27  3.000
 J3Z  H18   C8   C9    111.44  3.000
 J3Z  H28   C8   C7    110.53  3.000
 J3Z  H18   C8   C7    108.15  3.000
 J3Z  C9    C8   C7    105.89  3.000
 J3Z  H29   C9   H19   107.02  3.000
 J3Z  H29   C9   C10   111.50  3.000
 J3Z  H19   C9   C10   112.37  3.000
 J3Z  H29   C9   C8    111.58  3.000
 J3Z  H19   C9   C8    111.81  3.000
 J3Z  C10   C9   C8    102.66  3.000
 J3Z  H10   C10  C12   106.71  3.000
 J3Z  H10   C10  C9    106.20  3.000
 J3Z  C12   C10  C9    120.66  3.000
 J3Z  H10   C10  C5    106.16  3.000
 J3Z  C12   C10  C5    111.88  3.000
 J3Z  C9    C10  C5    104.30  3.000
 J3Z  H12   C12  C14   107.87  3.000
 J3Z  H12   C12  C10   108.98  3.000
 J3Z  C14   C12  C10   113.67  3.000
 J3Z  H12   C12  C2    108.98  3.000
 J3Z  C14   C12  C2    109.32  3.000
 J3Z  C10   C12  C2    107.94  3.000
 J3Z  H23   C3   H13   105.84  3.000
 J3Z  H23   C3   C4    110.43  3.000
 J3Z  H13   C3   C4    107.80  3.000
 J3Z  H23   C3   C2    109.26  3.000
 J3Z  H13   C3   C2    110.10  3.000
 J3Z  C4    C3   C2    113.15  3.000
 J3Z  H214  C14  H114  106.75  3.000
 J3Z  H214  C14  C15   109.21  3.000
 J3Z  H114  C14  C15   110.57  3.000
 J3Z  H214  C14  C12   110.85  3.000
 J3Z  H114  C14  C12   109.37  3.000
 J3Z  C15   C14  C12   110.04  3.000
 J3Z  H215  C15  H115  105.69  3.000
 J3Z  H215  C15  C16   108.39  3.000
 J3Z  H115  C15  C16   109.47  3.000
 J3Z  H215  C15  C14   109.01  3.000
 J3Z  H115  C15  C14   110.43  3.000
 J3Z  C16   C15  C14   113.53  3.000
 J3Z  C17   C16  C21   120.09  3.000
 J3Z  C17   C16  C15   117.80  3.000
 J3Z  C21   C16  C15   122.10  3.000
 J3Z  C20   C21  C16   117.52  3.000
 J3Z  C20   C21  C2    121.28  3.000
 J3Z  C16   C21  C2    121.17  3.000
 J3Z  H17   C17  C18   119.69  3.000
 J3Z  H17   C17  C16   118.90  3.000
 J3Z  C18   C17  C16   121.40  3.000
 J3Z  C19   C18  C17   119.03  3.000
 J3Z  C19   C18  O3    118.14  3.000
 J3Z  C17   C18  O3    122.82  3.000
 J3Z  H19A  C19  C20   120.44  3.000
 J3Z  H19A  C19  C18   120.18  3.000
 J3Z  C20   C19  C18   119.38  3.000
 J3Z  H20   C20  C19   117.51  3.000
 J3Z  H20   C20  C21   119.92  3.000
 J3Z  C19   C20  C21   122.57  3.000
 J3Z  HO3   O3   C18   110.22  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
 J3Z  CONST_01  C19   C20  C21  C16    0.00   0.0  0
 J3Z  CONST_02  C19   C18  C17  C16    0.00   0.0  0
 J3Z  CONST_03  C18   C17  C16  C21    0.00   0.0  0
 J3Z  CONST_04  C18   C19  C20  C21    0.00   0.0  0
 J3Z  CONST_05  C20   C21  C16  C17    0.00   0.0  0
 J3Z  CONST_06  C20   C19  C18  C17    0.00   0.0  0
 J3Z  CONST_07  C16   C17  C18  O3   180.00   0.0  0
 J3Z  CONST_08  C20   C19  C18  O3   180.00   0.0  0
 J3Z  CONST_09  H20   C20  C21  C2     0.00   0.0  0
 J3Z  CONST_10  H17   C17  C16  C15    0.00   0.0  0
 J3Z  CONST_11  H19A  C19  C20  C21  180.00   0.0  0
 J3Z  Var_01    C5    C4   C3   C2   -52.14  30.0  1
 J3Z  Var_02    C9    C8   C7   C5     5.52  30.0  1
 J3Z  Var_03    C10   C9   C8   C7    20.53  30.0  1
 J3Z  Var_04    C16   C15  C14  C12   44.82  30.0  1
 J3Z  Var_05    C21   C16  C15  C14  -13.61  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
 J3Z  chir_01  C2   C12  C3   C21  positiv
 J3Z  chir_02  C5   C10  C4   C7   positiv
 J3Z  chir_03  C10  C9   C5   C12  positiv
 J3Z  chir_04  C12  C10  C14  C2   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
 J3Z  plan-1  C5    0.020
 J3Z  plan-1  C7    0.020
 J3Z  plan-1  C8    0.020
 J3Z  plan-1  O1    0.020
 J3Z  plan-2  C2    0.020
 J3Z  plan-2  C15   0.020
 J3Z  plan-2  C16   0.020
 J3Z  plan-2  C21   0.020
 J3Z  plan-2  C17   0.020
 J3Z  plan-2  C18   0.020
 J3Z  plan-2  C19   0.020
 J3Z  plan-2  C20   0.020
 J3Z  plan-2  H17   0.020
 J3Z  plan-2  H19A  0.020
 J3Z  plan-2  H20   0.020
 J3Z  plan-2  O3    0.020

