# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 10:13:19 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: (8R,9S,13S,14S,16R)-3,16-dihydroxy-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]1C[C@@H](O)C2=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
 J2Z  J2Z  (8R,9S,13S,14S,16R)-3,16-dihydroxy-13-methyl-7,8,9,11,12,14,15,16-octahydro-6H-cyclopenta[a]phenanthren-17-one  ligand  43  21  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J2Z
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
 J2Z  O1    O  O     0  -0.384  -4.4661  -1.4715  -0.4480
 J2Z  C7    C  C     0   0.397  -3.7098  -0.6369  -0.0168
 J2Z  C8    C  CH1   0  -0.035  -4.0864   0.8425   0.1841
 J2Z  O2    O  OH1   0  -0.665  -4.8452   1.3205  -0.8984
 J2Z  C9    C  CH2   0  -0.484  -2.7359   1.5699   0.2754
 J2Z  C10   C  CH1   0  -0.209  -1.7121   0.5281  -0.1840
 J2Z  C5    C  CT    0  -0.215  -2.2583  -0.8082   0.3452
 J2Z  C6    C  CH3   0  -0.669  -2.2105  -0.9248   1.8807
 J2Z  C12   C  CH1   0  -0.239  -0.2444   0.7057   0.1515
 J2Z  C2    C  CH1   0  -0.261   0.5380  -0.4438  -0.5067
 J2Z  C3    C  CH2   0  -0.456  -0.0052  -1.8183  -0.0863
 J2Z  C4    C  CH2   0  -0.406  -1.5148  -1.9603  -0.3096
 J2Z  C14   C  CH2   0  -0.431   0.3278   2.0355  -0.3119
 J2Z  C15   C  CH2   0  -0.507   1.7527   2.1939   0.1938
 J2Z  C16   C  CR6   0   0.073   2.5959   0.9551   0.0232
 J2Z  C21   C  CR6   0   0.098   2.0322  -0.2907  -0.2828
 J2Z  C17   C  CR16  0  -0.383   3.9716   1.0756   0.1990
 J2Z  C18   C  CR6   0   0.346   4.8153  -0.0191   0.0712
 J2Z  O3    O  OH1   0  -0.638   6.1392   0.1735   0.2590
 J2Z  C19   C  CR16  0  -0.386   4.2692  -1.2585  -0.2457
 J2Z  C20   C  CR16  0  -0.312   2.8995  -1.3748  -0.4181
 J2Z  H8    H  HCH1  0   0.248  -4.6457   0.9266   1.1272
 J2Z  HO2   H  HOH1  0   0.451  -5.6455   0.7881  -0.9626
 J2Z  H19   H  HCH2  0   0.260  -2.7363   2.4609  -0.3532
 J2Z  H29   H  HCH2  0   0.244  -2.5381   1.8999   1.2967
 J2Z  H10   H  HCH1  0   0.235  -1.7857   0.4784  -1.2817
 J2Z  H16   H  HCH3  0   0.248  -2.7064  -1.8444   2.1955
 J2Z  H26   H  HCH3  0   0.252  -1.1848  -0.9661   2.2431
 J2Z  H36   H  HCH3  0   0.245  -2.6989  -0.0945   2.3923
 J2Z  H12   H  HCH1  0   0.226  -0.1212   0.6455   1.2415
 J2Z  H2    H  HCH1  0   0.231   0.3589  -0.3482  -1.5889
 J2Z  H13   H  HCH2  0   0.245   0.4912  -2.6084  -0.6520
 J2Z  H23   H  HCH2  0   0.227   0.2447  -2.0001   0.9630
 J2Z  H14   H  HCH2  0   0.238  -1.8556  -2.9226   0.0808
 J2Z  H24   H  HCH2  0   0.231  -1.7200  -1.9656  -1.3850
 J2Z  H114  H  HCH2  0   0.220   0.2994   2.0812  -1.4061
 J2Z  H214  H  HCH2  0   0.243  -0.2759   2.8694   0.0535
 J2Z  H115  H  HCH2  0   0.249   2.2414   3.0368  -0.3005
 J2Z  H215  H  HCH2  0   0.244   1.7270   2.4498   1.2583
 J2Z  H17   H  HCR6  0   0.249   4.3953   2.0449   0.4402
 J2Z  HO3   H  HOH1  0   0.472   6.6187  -0.6497   0.1167
 J2Z  H19A  H  HCR6  0   0.264   4.9045  -2.1298  -0.3595
 J2Z  H20   H  HCR6  0   0.245   2.5097  -2.3511  -0.6740

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
 J2Z  O2   C8    single    1.406  0.020  1.406
 J2Z  C8   C9    single    1.537  0.020  1.537
 J2Z  C8   C7    single    1.540  0.020  1.540
 J2Z  O1   C7    double    1.206  0.020  1.206
 J2Z  C9   C10   single    1.531  0.020  1.531
 J2Z  C7   C5    single    1.506  0.020  1.506
 J2Z  C6   C5    single    1.541  0.020  1.541
 J2Z  C10  C5    single    1.537  0.020  1.537
 J2Z  C10  C12   single    1.516  0.020  1.516
 J2Z  C5   C4    single    1.520  0.020  1.520
 J2Z  C14  C12   single    1.520  0.020  1.520
 J2Z  C14  C15   single    1.520  0.020  1.520
 J2Z  C12  C2    single    1.538  0.020  1.538
 J2Z  C4   C3    single    1.533  0.020  1.533
 J2Z  C15  C16   single    1.508  0.020  1.508
 J2Z  C2   C3    single    1.537  0.020  1.537
 J2Z  C2   C21   single    1.519  0.020  1.519
 J2Z  C16  C21   aromatic  1.401  0.020  1.401
 J2Z  C16  C17   aromatic  1.392  0.020  1.392
 J2Z  C21  C20   aromatic  1.395  0.020  1.395
 J2Z  C17  C18   aromatic  1.388  0.020  1.388
 J2Z  C20  C19   aromatic  1.385  0.020  1.385
 J2Z  C18  C19   aromatic  1.391  0.020  1.391
 J2Z  C18  O3    single    1.351  0.020  1.351
 J2Z  C8   H8    single    0.970  0.020  1.090
 J2Z  O2   HO2   single    0.850  0.020  0.980
 J2Z  C9   H19   single    0.970  0.020  1.090
 J2Z  C9   H29   single    0.970  0.020  1.090
 J2Z  C10  H10   single    0.970  0.020  1.090
 J2Z  C6   H16   single    0.970  0.020  1.090
 J2Z  C6   H26   single    0.970  0.020  1.090
 J2Z  C6   H36   single    0.970  0.020  1.090
 J2Z  C12  H12   single    0.970  0.020  1.090
 J2Z  C2   H2    single    0.970  0.020  1.090
 J2Z  C3   H13   single    0.970  0.020  1.090
 J2Z  C3   H23   single    0.970  0.020  1.090
 J2Z  C4   H14   single    0.970  0.020  1.090
 J2Z  C4   H24   single    0.970  0.020  1.090
 J2Z  C14  H114  single    0.970  0.020  1.090
 J2Z  C14  H214  single    0.970  0.020  1.090
 J2Z  C15  H115  single    0.970  0.020  1.090
 J2Z  C15  H215  single    0.970  0.020  1.090
 J2Z  C17  H17   single    0.930  0.020  1.080
 J2Z  O3   HO3   single    0.850  0.020  0.980
 J2Z  C19  H19A  single    0.930  0.020  1.080
 J2Z  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
 J2Z  C5    C7   C8    108.28  3.000
 J2Z  C5    C7   O1    127.72  3.000
 J2Z  C8    C7   O1    123.93  3.000
 J2Z  H8    C8   C9    111.09  3.000
 J2Z  H8    C8   O2    111.09  3.000
 J2Z  C9    C8   O2    111.05  3.000
 J2Z  H8    C8   C7    108.05  3.000
 J2Z  C9    C8   C7    104.34  3.000
 J2Z  O2    C8   C7    110.99  3.000
 J2Z  HO2   O2   C8    108.17  3.000
 J2Z  H29   C9   H19   107.01  3.000
 J2Z  H29   C9   C10   111.43  3.000
 J2Z  H19   C9   C10   112.53  3.000
 J2Z  H29   C9   C8    110.98  3.000
 J2Z  H19   C9   C8    110.62  3.000
 J2Z  C10   C9   C8    104.34  3.000
 J2Z  H10   C10  C12   106.89  3.000
 J2Z  H10   C10  C5    106.27  3.000
 J2Z  C12   C10  C5    111.69  3.000
 J2Z  H10   C10  C9    106.56  3.000
 J2Z  C12   C10  C9    120.08  3.000
 J2Z  C5    C10  C9    104.51  3.000
 J2Z  C4    C5   C6    110.91  3.000
 J2Z  C4    C5   C10   109.68  3.000
 J2Z  C6    C5   C10   113.44  3.000
 J2Z  C4    C5   C7    117.02  3.000
 J2Z  C10   C5   C7     99.26  3.000
 J2Z  C6    C5   C7    106.15  3.000
 J2Z  H36   C6   H26   107.13  3.000
 J2Z  H36   C6   H16   107.62  3.000
 J2Z  H26   C6   H16   107.47  3.000
 J2Z  H36   C6   C5    113.33  3.000
 J2Z  H26   C6   C5    111.34  3.000
 J2Z  H16   C6   C5    109.71  3.000
 J2Z  H12   C12  C14   107.95  3.000
 J2Z  H12   C12  C2    109.06  3.000
 J2Z  C14   C12  C2    109.37  3.000
 J2Z  H12   C12  C10   108.77  3.000
 J2Z  C2    C12  C10   108.07  3.000
 J2Z  C14   C12  C10   113.55  3.000
 J2Z  H2    C2   C21   107.23  3.000
 J2Z  H2    C2   C3    106.80  3.000
 J2Z  C21   C2   C3    113.43  3.000
 J2Z  H2    C2   C12   105.84  3.000
 J2Z  C21   C2   C12   111.22  3.000
 J2Z  C3    C2   C12   111.81  3.000
 J2Z  H23   C3   H13   105.84  3.000
 J2Z  H23   C3   C4    110.45  3.000
 J2Z  H13   C3   C4    107.79  3.000
 J2Z  H23   C3   C2    109.29  3.000
 J2Z  H13   C3   C2    110.19  3.000
 J2Z  C4    C3   C2    113.03  3.000
 J2Z  H24   C4   H14   106.75  3.000
 J2Z  H24   C4   C3    109.16  3.000
 J2Z  H14   C4   C3    109.67  3.000
 J2Z  H24   C4   C5    109.59  3.000
 J2Z  H14   C4   C5    111.17  3.000
 J2Z  C3    C4   C5    110.42  3.000
 J2Z  H214  C14  H114  106.73  3.000
 J2Z  H214  C14  C15   109.10  3.000
 J2Z  H114  C14  C15   110.62  3.000
 J2Z  H214  C14  C12   110.96  3.000
 J2Z  H114  C14  C12   109.35  3.000
 J2Z  C15   C14  C12   110.04  3.000
 J2Z  H215  C15  H115  105.66  3.000
 J2Z  H215  C15  C16   108.37  3.000
 J2Z  H115  C15  C16   109.42  3.000
 J2Z  H215  C15  C14   109.01  3.000
 J2Z  H115  C15  C14   110.43  3.000
 J2Z  C16   C15  C14   113.63  3.000
 J2Z  C17   C16  C21   120.14  3.000
 J2Z  C17   C16  C15   117.85  3.000
 J2Z  C21   C16  C15   122.01  3.000
 J2Z  C20   C21  C16   117.52  3.000
 J2Z  C20   C21  C2    121.27  3.000
 J2Z  C16   C21  C2    121.17  3.000
 J2Z  H17   C17  C18   119.19  3.000
 J2Z  H17   C17  C16   119.42  3.000
 J2Z  C18   C17  C16   121.38  3.000
 J2Z  C19   C18  O3    122.92  3.000
 J2Z  O3    C18  C17   118.06  3.000
 J2Z  C19   C18  C17   119.02  3.000
 J2Z  HO3   O3   C18   110.21  3.000
 J2Z  H19A  C19  C20   119.91  3.000
 J2Z  H19A  C19  C18   120.66  3.000
 J2Z  C20   C19  C18   119.42  3.000
 J2Z  H20   C20  C19   117.47  3.000
 J2Z  H20   C20  C21   120.02  3.000
 J2Z  C19   C20  C21   122.51  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
 J2Z  CONST_01  C19   C20  C21  C16    0.00   0.0  0
 J2Z  CONST_02  C19   C18  C17  C16    0.00   0.0  0
 J2Z  CONST_03  C18   C17  C16  C21    0.00   0.0  0
 J2Z  CONST_04  C18   C19  C20  C21    0.00   0.0  0
 J2Z  CONST_05  C20   C21  C16  C17    0.00   0.0  0
 J2Z  CONST_06  C20   C19  C18  C17    0.00   0.0  0
 J2Z  CONST_07  O3    C18  C17  C16  180.00   0.0  0
 J2Z  CONST_08  C20   C19  C18  O3   180.00   0.0  0
 J2Z  CONST_09  H20   C20  C21  C2     0.00   0.0  0
 J2Z  CONST_10  H17   C17  C16  C15    0.00   0.0  0
 J2Z  CONST_11  H19A  C19  C20  C21  180.00   0.0  0
 J2Z  Var_01    C2    C3   C4   C5   -52.60  30.0  1
 J2Z  Var_02    C16   C15  C14  C12   44.79  30.0  1
 J2Z  Var_03    C21   C16  C15  C14  -13.71  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
 J2Z  chir_01  C8   O2   C9   C7   positiv
 J2Z  chir_02  C10  C9   C5   C12  positiv
 J2Z  chir_03  C5   C7   C10  C4   positiv
 J2Z  chir_04  C12  C10  C14  C2   positiv
 J2Z  chir_05  C2   C12  C3   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
 J2Z  plan-1  O1    0.020
 J2Z  plan-1  C7    0.020
 J2Z  plan-1  C8    0.020
 J2Z  plan-1  C5    0.020
 J2Z  plan-2  C2    0.020
 J2Z  plan-2  C15   0.020
 J2Z  plan-2  C16   0.020
 J2Z  plan-2  C21   0.020
 J2Z  plan-2  C17   0.020
 J2Z  plan-2  C18   0.020
 J2Z  plan-2  O3    0.020
 J2Z  plan-2  C19   0.020
 J2Z  plan-2  C20   0.020
 J2Z  plan-2  H17   0.020
 J2Z  plan-2  H19A  0.020
 J2Z  plan-2  H20   0.020

