# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 20:09:49 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: [(8~{S},9~{R},13~{S},14~{S})-13-methyl-17-oxidanylidene-7,8,9,11,12,14,15,16-octahydro-6~{H}-cyclopenta[a]phenanthren-3-yl] hydrogen sulfate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CC[C@@H]3[C@H](CCc4cc(O[S](O)(=O)=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
 FY5  FY5  '[(8~{S},9~{R},13~{S},14~{S})-13-methyl-17-oxidanylidene-7,8,9,11,12,14,15,16-octahydro-6~{H}-cyclopenta[a]phenanthren-3-yl] hydrogen sulfate'  ligand  45  24  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FY5
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
 FY5  C10  C  C      0   0.422  -5.4964   0.3633   0.3752
 FY5  C13  C  CH2    0  -0.501  -0.0275  -2.0902  -0.7702
 FY5  C15  C  CR6    0   0.119   0.1889   0.4419  -0.4707
 FY5  C17  C  CR16   0  -0.316   2.3953   1.4576  -0.4348
 FY5  C02  C  CT     0  -0.192  -4.1095   0.4964  -0.2281
 FY5  C03  C  CH2    0  -0.414  -3.4478   1.8752  -0.0957
 FY5  C04  C  CH2    0  -0.458  -1.9341   1.7771   0.1978
 FY5  C05  C  CH1    0  -0.292  -1.3188   0.5349  -0.4420
 FY5  C06  C  CH1    0  -0.214  -1.8838  -0.7477   0.1950
 FY5  C07  C  CH1    0  -0.220  -3.3424  -0.5391   0.6027
 FY5  C08  C  CH2    0  -0.460  -4.2957  -1.7274   0.7118
 FY5  C09  C  CH2    0  -0.563  -5.6506  -1.0435   0.9328
 FY5  C12  C  CH2    0  -0.447  -1.5472  -1.9088  -0.7281
 FY5  C14  C  CR6    0   0.072   0.7800  -0.8135  -0.6719
 FY5  C16  C  CR16   0  -0.339   1.0149   1.5576  -0.3541
 FY5  C18  C  CR6    0   0.336   2.9690   0.2129  -0.6440
 FY5  C19  C  CR16   0  -0.355   2.1665  -0.9114  -0.7491
 FY5  O11  O  O      0  -0.401  -6.3442   1.2230   0.4036
 FY5  O20  O  OC2    0  -0.637   4.3280   0.0943  -0.7912
 FY5  S21  S  S      0   1.557   5.2359  -0.1134   0.5984
 FY5  H1   H  HCH2   0   0.247   0.2723  -2.7334   0.0631
 FY5  H2   H  HCH2   0   0.251   0.2639  -2.6307  -1.6740
 FY5  H3   H  HCR6   0   0.257   3.0162   2.3395  -0.3506
 FY5  H7   H  HCH2   0   0.235  -3.5999   2.4455  -1.0150
 FY5  H8   H  HCH2   0   0.238  -3.9239   2.4525   0.7003
 FY5  H9   H  HCH2   0   0.243  -1.4615   2.6875  -0.1734
 FY5  H10  H  HCH2   0   0.227  -1.7515   1.7588   1.2765
 FY5  H11  H  HCH1   0   0.242  -1.6282   0.5394  -1.4943
 FY5  H12  H  HCH1   0   0.227  -1.3313  -0.9172   1.1290
 FY5  H13  H  HCH1   0   0.244  -3.3005  -0.1039   1.6117
 FY5  H14  H  HCH2   0   0.235  -4.3003  -2.3223  -0.2035
 FY5  H15  H  HCH2   0   0.248  -4.0356  -2.4004   1.5291
 FY5  H16  H  HCH2   0   0.279  -5.8824  -0.9594   1.9985
 FY5  H17  H  HCH2   0   0.278  -6.4969  -1.5540   0.4688
 FY5  H18  H  HCH2   0   0.226  -1.9379  -1.7187  -1.7319
 FY5  H19  H  HCH2   0   0.241  -2.0050  -2.8396  -0.3872
 FY5  H20  H  HCR6   0   0.243   0.5830   2.5368  -0.1953
 FY5  H21  H  HCR6   0   0.249   2.6272  -1.8798  -0.9081
 FY5  C01  C  CH3    0  -0.675  -4.3114   0.1022  -1.7043
 FY5  H4   H  HCH3   0   0.245  -5.0110   0.7938  -2.1777
 FY5  O22  O  OS    -1  -0.723   4.7089  -1.3271   1.2181
 FY5  O23  O  OS     0  -0.725   6.5658  -0.2384   0.0132
 FY5  O24  O  OS     0  -0.723   5.0154   1.1006   1.3822
 FY5  H5   H  HCH3   0   0.252  -3.3842   0.1531  -2.2724
 FY5  H6   H  HCH3   0   0.241  -4.7125  -0.9052  -1.8265

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
 FY5  O24  S21  deloc     1.462  0.020  1.462
 FY5  O23  S21  deloc     1.458  0.020  1.458
 FY5  O22  S21  deloc     1.461  0.020  1.461
 FY5  S21  O20  single    1.673  0.020  1.673
 FY5  C17  C16  aromatic  1.386  0.020  1.386
 FY5  C17  C18  aromatic  1.386  0.020  1.386
 FY5  O20  C18  single    1.372  0.020  1.372
 FY5  C16  C15  aromatic  1.393  0.020  1.393
 FY5  C18  C19  aromatic  1.385  0.020  1.385
 FY5  C04  C03  single    1.545  0.020  1.545
 FY5  C04  C05  single    1.527  0.020  1.527
 FY5  C03  C02  single    1.535  0.020  1.535
 FY5  C15  C05  single    1.511  0.020  1.511
 FY5  C15  C14  aromatic  1.402  0.020  1.402
 FY5  C19  C14  aromatic  1.392  0.020  1.392
 FY5  C05  C06  single    1.539  0.020  1.539
 FY5  C14  C13  single    1.514  0.020  1.514
 FY5  O11  C10  double    1.208  0.020  1.208
 FY5  C01  C02  single    1.541  0.020  1.541
 FY5  C02  C10  single    1.518  0.020  1.518
 FY5  C02  C07  single    1.533  0.020  1.533
 FY5  C06  C07  single    1.529  0.020  1.529
 FY5  C06  C12  single    1.521  0.020  1.521
 FY5  C10  C09  single    1.521  0.020  1.521
 FY5  C07  C08  single    1.527  0.020  1.527
 FY5  C13  C12  single    1.531  0.020  1.531
 FY5  C09  C08  single    1.534  0.020  1.534
 FY5  C13  H1   single    0.970  0.020  1.090
 FY5  C13  H2   single    0.970  0.020  1.090
 FY5  C17  H3   single    0.930  0.020  1.080
 FY5  C01  H4   single    0.970  0.020  1.090
 FY5  C01  H5   single    0.970  0.020  1.090
 FY5  C01  H6   single    0.970  0.020  1.090
 FY5  C03  H7   single    0.970  0.020  1.090
 FY5  C03  H8   single    0.970  0.020  1.090
 FY5  C04  H9   single    0.970  0.020  1.090
 FY5  C04  H10  single    0.970  0.020  1.090
 FY5  C05  H11  single    0.970  0.020  1.090
 FY5  C06  H12  single    0.970  0.020  1.090
 FY5  C07  H13  single    0.970  0.020  1.090
 FY5  C08  H14  single    0.970  0.020  1.090
 FY5  C08  H15  single    0.970  0.020  1.090
 FY5  C09  H16  single    0.970  0.020  1.090
 FY5  C09  H17  single    0.970  0.020  1.090
 FY5  C12  H18  single    0.970  0.020  1.090
 FY5  C12  H19  single    0.970  0.020  1.090
 FY5  C16  H20  single    0.930  0.020  1.080
 FY5  C19  H21  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
 FY5  O11  C10  C09  125.35  3.000
 FY5  C09  C10  C02  108.62  3.000
 FY5  O11  C10  C02  126.03  3.000
 FY5  H2   C13  H1   105.42  3.000
 FY5  H2   C13  C14  109.18  3.000
 FY5  H1   C13  C14  107.46  3.000
 FY5  H2   C13  C12  110.24  3.000
 FY5  H1   C13  C12  108.71  3.000
 FY5  C14  C13  C12  115.33  3.000
 FY5  C16  C15  C14  118.63  3.000
 FY5  C14  C15  C05  118.59  3.000
 FY5  C16  C15  C05  122.74  3.000
 FY5  H3   C17  C18  120.40  3.000
 FY5  H3   C17  C16  120.54  3.000
 FY5  C18  C17  C16  119.05  3.000
 FY5  C07  C02  C03  110.13  3.000
 FY5  C07  C02  C01  114.32  3.000
 FY5  C03  C02  C01  111.64  3.000
 FY5  C07  C02  C10  100.52  3.000
 FY5  C01  C02  C10  103.80  3.000
 FY5  C03  C02  C10  115.99  3.000
 FY5  H8   C03  H7   106.05  3.000
 FY5  H8   C03  C04  108.79  3.000
 FY5  H7   C03  C04  109.23  3.000
 FY5  H8   C03  C02  110.46  3.000
 FY5  H7   C03  C02  109.65  3.000
 FY5  C04  C03  C02  112.44  3.000
 FY5  H10  C04  H9   106.09  3.000
 FY5  H10  C04  C05  109.40  3.000
 FY5  H9   C04  C05  111.22  3.000
 FY5  H10  C04  C03  110.60  3.000
 FY5  H9   C04  C03  107.87  3.000
 FY5  C05  C04  C03  111.52  3.000
 FY5  H11  C05  C06  107.27  3.000
 FY5  H11  C05  C04  106.56  3.000
 FY5  C06  C05  C04  110.89  3.000
 FY5  H11  C05  C15  105.28  3.000
 FY5  C06  C05  C15  108.83  3.000
 FY5  C04  C05  C15  117.40  3.000
 FY5  H12  C06  C12  106.68  3.000
 FY5  H12  C06  C07  105.91  3.000
 FY5  C12  C06  C07  118.50  3.000
 FY5  H12  C06  C05  107.21  3.000
 FY5  C12  C06  C05  107.68  3.000
 FY5  C07  C06  C05  110.29  3.000
 FY5  H13  C07  C08  105.44  3.000
 FY5  H13  C07  C06  105.21  3.000
 FY5  C08  C07  C06  120.56  3.000
 FY5  H13  C07  C02  104.42  3.000
 FY5  C08  C07  C02  104.59  3.000
 FY5  C06  C07  C02  115.15  3.000
 FY5  H15  C08  H14  107.04  3.000
 FY5  H15  C08  C09  112.21  3.000
 FY5  H14  C08  C09  111.11  3.000
 FY5  H15  C08  C07  112.64  3.000
 FY5  H14  C08  C07  111.51  3.000
 FY5  C09  C08  C07  102.40  3.000
 FY5  H17  C09  H16  106.60  3.000
 FY5  H17  C09  C08  114.52  3.000
 FY5  H16  C09  C08  111.22  3.000
 FY5  H17  C09  C10  110.81  3.000
 FY5  H16  C09  C10  107.91  3.000
 FY5  C08  C09  C10  105.66  3.000
 FY5  H19  C12  H18  106.56  3.000
 FY5  H19  C12  C06  111.62  3.000
 FY5  H18  C12  C06  110.20  3.000
 FY5  H19  C12  C13  108.89  3.000
 FY5  H18  C12  C13  110.49  3.000
 FY5  C06  C12  C13  109.07  3.000
 FY5  C19  C14  C15  119.39  3.000
 FY5  C19  C14  C13  117.93  3.000
 FY5  C15  C14  C13  122.65  3.000
 FY5  H20  C16  C17  118.12  3.000
 FY5  H20  C16  C15  120.03  3.000
 FY5  C17  C16  C15  121.85  3.000
 FY5  O20  C18  C19  119.71  3.000
 FY5  C19  C18  C17  120.02  3.000
 FY5  O20  C18  C17  120.24  3.000
 FY5  H21  C19  C18  119.33  3.000
 FY5  H21  C19  C14  119.62  3.000
 FY5  C18  C19  C14  121.05  3.000
 FY5  S21  O20  C18  117.33  3.000
 FY5  O24  S21  O23  115.08  3.000
 FY5  O23  S21  O22  115.34  3.000
 FY5  O24  S21  O22  114.08  3.000
 FY5  O22  S21  O20  105.05  3.000
 FY5  O23  S21  O20   99.92  3.000
 FY5  O24  S21  O20  105.10  3.000
 FY5  H6   C01  H5   107.32  3.000
 FY5  H6   C01  H4   107.51  3.000
 FY5  H5   C01  H4   106.86  3.000
 FY5  H6   C01  C02  113.05  3.000
 FY5  H5   C01  C02  112.10  3.000
 FY5  H4   C01  C02  109.71  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
 FY5  CONST_01  C18  C17  C16  C15    0.00   0.0  0
 FY5  CONST_02  C18  C19  C14  C15    0.00   0.0  0
 FY5  CONST_03  C14  C15  C16  C17    0.00   0.0  0
 FY5  CONST_04  C14  C19  C18  C17    0.00   0.0  0
 FY5  CONST_05  C19  C18  C17  C16    0.00   0.0  0
 FY5  CONST_06  C19  C14  C15  C16    0.00   0.0  0
 FY5  CONST_07  O20  C18  C19  C14  180.00   0.0  0
 FY5  CONST_08  O20  C18  C17  C16  180.00   0.0  0
 FY5  CONST_09  H21  C19  C14  C13    0.00   0.0  0
 FY5  CONST_10  H3   C17  C16  C15  180.00   0.0  0
 FY5  CONST_11  H20  C16  C15  C05    0.00   0.0  0
 FY5  Var_01    C07  C08  C09  C10   22.79  30.0  1
 FY5  Var_02    C12  C13  C14  C15    3.91  30.0  1
 FY5  Var_03    C05  C04  C03  C02   31.48  30.0  1
 FY5  Var_04    C08  C09  C10  C02    2.79  30.0  1
 FY5  Var_05    C14  C13  C12  C06  -34.40  30.0  1
 FY5  Var_06    O24  S21  O20  C18  -62.33  30.0  2

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
 FY5  chir_01  C02  C03  C10  C07  positiv
 FY5  chir_02  C05  C06  C15  C04  positiv
 FY5  chir_03  C06  C12  C07  C05  positiv
 FY5  chir_04  C07  C08  C06  C02  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
 FY5  plan-1  C10  0.020
 FY5  plan-1  C02  0.020
 FY5  plan-1  C09  0.020
 FY5  plan-1  O11  0.020
 FY5  plan-2  C13  0.020
 FY5  plan-2  C15  0.020
 FY5  plan-2  C17  0.020
 FY5  plan-2  C05  0.020
 FY5  plan-2  C14  0.020
 FY5  plan-2  C16  0.020
 FY5  plan-2  C18  0.020
 FY5  plan-2  C19  0.020
 FY5  plan-2  O20  0.020
 FY5  plan-2  H3   0.020
 FY5  plan-2  H20  0.020
 FY5  plan-2  H21  0.020

