# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 09:22:39 2021
#   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  46  24  .  2021-08-09  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  CR5   0   0.423  151.5999  152.9859  149.9678
 FY5  C13  C  CH2   0  -0.502  157.3396  155.0182  149.7606
 FY5  C15  C  CR6   0   0.135  156.2345  155.2794  147.4667
 FY5  C17  C  CR16  0  -0.291  157.4243  156.4157  145.6805
 FY5  C02  C  CR5   0  -0.196  152.8808  153.2083  149.1844
 FY5  C03  C  CH2   0  -0.412  152.7049  153.5917  147.7073
 FY5  C04  C  CH2   0  -0.458  153.7195  154.6611  147.2492
 FY5  C05  C  CH1   0  -0.296  155.0449  154.5128  147.9923
 FY5  C06  C  CH1   0  -0.219  154.8723  154.8233  149.4915
 FY5  C07  C  CR15  0  -0.220  153.4862  154.3820  149.9626
 FY5  C08  C  CH2   0  -0.460  153.2351  154.0419  151.4299
 FY5  C09  C  CH2   0  -0.565  151.8125  153.4691  151.3945
 FY5  C12  C  CH2   0  -0.448  156.0867  154.2701  150.2215
 FY5  C14  C  CR6   0   0.074  157.3397  155.4556  148.3124
 FY5  C16  C  CR16  0  -0.342  156.2942  155.7770  146.1671
 FY5  C18  C  CR6   0   0.296  158.5069  156.5591  146.5260
 FY5  C19  C  CR16  0  -0.330  158.4762  156.0959  147.8266
 FY5  O11  O  O     0  -0.400  150.5803  152.5016  149.5389
 FY5  O20  O  OC2   0  -0.601  159.6448  157.2282  146.0668
 FY5  S21  S  S     0   1.643  160.8081  156.3024  145.4476
 FY5  H1   H  HCH2  0   0.257  158.2316  154.4184  149.9566
 FY5  H2   H  HCH2  0   0.253  157.4515  155.9201  150.3701
 FY5  H3   H  HCR6  0   0.276  157.4533  156.7980  144.6688
 FY5  H7   H  HCH2  0   0.239  151.6931  153.9630  147.5284
 FY5  H8   H  HCH2  0   0.235  152.8117  152.7028  147.0813
 FY5  H9   H  HCH2  0   0.244  153.8549  154.5549  146.1719
 FY5  H10  H  HCH2  0   0.230  153.3241  155.6684  147.4104
 FY5  H11  H  HCH1  0   0.249  155.3304  153.4572  147.9038
 FY5  H12  H  HCH1  0   0.231  154.9027  155.9154  149.6043
 FY5  H13  H  HCR5  0   0.246  152.8199  155.2281  149.7419
 FY5  H14  H  HCH2  0   0.235  153.9439  153.2972  151.7976
 FY5  H15  H  HCH2  0   0.249  153.3159  154.9128  152.0807
 FY5  H16  H  HCH2  0   0.279  151.0672  154.2427  151.6021
 FY5  H17  H  HCH2  0   0.279  151.6326  152.6638  152.1096
 FY5  H18  H  HCH2  0   0.244  155.9888  154.3846  151.3026
 FY5  H19  H  HCH2  0   0.229  156.1836  153.1981  150.0299
 FY5  H20  H  HCR6  0   0.254  155.4475  155.6655  145.5037
 FY5  H21  H  HCR6  0   0.270  159.3313  156.2424  148.4761
 FY5  H22  H  H     0   0.521  161.5058  157.8771  144.1615
 FY5  C01  C  CH3   0  -0.673  153.6513  151.8825  149.3493
 FY5  H4   H  HCH3  0   0.242  153.7840  151.5985  150.3946
 FY5  O22  O  OS    0  -0.688  161.7749  157.4558  144.9969
 FY5  O23  O  OS    0  -0.615  160.2790  155.5758  144.3239
 FY5  O24  O  OS    0  -0.615  161.4801  155.6105  146.5116
 FY5  H5   H  HCH3  0   0.246  153.1086  151.0758  148.8545
 FY5  H6   H  HCH3  0   0.251  154.6421  151.9282  148.9009

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  double    1.436  0.020  1.436
 FY5  O23  S21  double    1.439  0.020  1.439
 FY5  O22  S21  single    1.571  0.020  1.571
 FY5  S21  O20  single    1.611  0.020  1.611
 FY5  C17  C16  aromatic  1.386  0.020  1.386
 FY5  C17  C18  aromatic  1.381  0.020  1.381
 FY5  O20  C18  single    1.398  0.020  1.398
 FY5  C16  C15  aromatic  1.393  0.020  1.393
 FY5  C18  C19  aromatic  1.381  0.020  1.381
 FY5  C04  C03  single    1.544  0.020  1.544
 FY5  C04  C05  single    1.527  0.020  1.527
 FY5  C03  C02  single    1.536  0.020  1.536
 FY5  C15  C05  single    1.510  0.020  1.510
 FY5  C15  C14  aromatic  1.403  0.020  1.403
 FY5  C19  C14  aromatic  1.392  0.020  1.392
 FY5  C05  C06  single    1.541  0.020  1.541
 FY5  C14  C13  single    1.513  0.020  1.513
 FY5  O11  C10  double    1.207  0.020  1.207
 FY5  C01  C02  single    1.542  0.020  1.542
 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    1.530  0.020  1.530
 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
 FY5  O22  H22  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
 FY5  O11  C10  C09  125.35  3.000
 FY5  C09  C10  C02  108.64  3.000
 FY5  O11  C10  C02  126.01  3.000
 FY5  H2   C13  H1   105.61  3.000
 FY5  H2   C13  C14  107.15  3.000
 FY5  H1   C13  C14  109.29  3.000
 FY5  H2   C13  C12  108.60  3.000
 FY5  H1   C13  C12  110.25  3.000
 FY5  C14  C13  C12  115.45  3.000
 FY5  C16  C15  C14  118.94  3.000
 FY5  C14  C15  C05  118.34  3.000
 FY5  C16  C15  C05  122.68  3.000
 FY5  H3   C17  C18  120.98  3.000
 FY5  H3   C17  C16  120.86  3.000
 FY5  C18  C17  C16  118.16  3.000
 FY5  C07  C02  C03  110.02  3.000
 FY5  C07  C02  C01  113.99  3.000
 FY5  C03  C02  C01  112.00  3.000
 FY5  C07  C02  C10  100.57  3.000
 FY5  C01  C02  C10  103.91  3.000
 FY5  C03  C02  C10  115.86  3.000
 FY5  H8   C03  H7   105.86  3.000
 FY5  H8   C03  C04  109.23  3.000
 FY5  H7   C03  C04  108.95  3.000
 FY5  H8   C03  C02  109.67  3.000
 FY5  H7   C03  C02  110.39  3.000
 FY5  C04  C03  C02  112.52  3.000
 FY5  H10  C04  H9   106.26  3.000
 FY5  H10  C04  C05  109.36  3.000
 FY5  H9   C04  C05  111.31  3.000
 FY5  H10  C04  C03  110.89  3.000
 FY5  H9   C04  C03  107.89  3.000
 FY5  C05  C04  C03  111.03  3.000
 FY5  H11  C05  C06  107.56  3.000
 FY5  H11  C05  C04  106.27  3.000
 FY5  C06  C05  C04  110.90  3.000
 FY5  H11  C05  C15  104.80  3.000
 FY5  C06  C05  C15  108.94  3.000
 FY5  C04  C05  C15  117.73  3.000
 FY5  H12  C06  C12  106.87  3.000
 FY5  H12  C06  C07  106.29  3.000
 FY5  C12  C06  C07  118.09  3.000
 FY5  H12  C06  C05  107.30  3.000
 FY5  C12  C06  C05  107.71  3.000
 FY5  C07  C06  C05  110.07  3.000
 FY5  H13  C07  C08  105.35  3.000
 FY5  H13  C07  C06  105.39  3.000
 FY5  C08  C07  C06  120.63  3.000
 FY5  H13  C07  C02  104.36  3.000
 FY5  C08  C07  C02  104.62  3.000
 FY5  C06  C07  C02  115.00  3.000
 FY5  H15  C08  H14  107.20  3.000
 FY5  H15  C08  C09  112.39  3.000
 FY5  H14  C08  C09  110.80  3.000
 FY5  H15  C08  C07  112.55  3.000
 FY5  H14  C08  C07  111.63  3.000
 FY5  C09  C08  C07  102.33  3.000
 FY5  H17  C09  H16  106.56  3.000
 FY5  H17  C09  C08  114.40  3.000
 FY5  H16  C09  C08  111.31  3.000
 FY5  H17  C09  C10  110.91  3.000
 FY5  H16  C09  C10  107.90  3.000
 FY5  C08  C09  C10  105.66  3.000
 FY5  H19  C12  H18  106.52  3.000
 FY5  H19  C12  C06  110.08  3.000
 FY5  H18  C12  C06  111.45  3.000
 FY5  H19  C12  C13  110.73  3.000
 FY5  H18  C12  C13  108.68  3.000
 FY5  C06  C12  C13  109.35  3.000
 FY5  C19  C14  C15  119.39  3.000
 FY5  C19  C14  C13  117.85  3.000
 FY5  C15  C14  C13  122.74  3.000
 FY5  H20  C16  C17  118.06  3.000
 FY5  H20  C16  C15  120.14  3.000
 FY5  C17  C16  C15  121.80  3.000
 FY5  O20  C18  C19  119.22  3.000
 FY5  C19  C18  C17  121.62  3.000
 FY5  O20  C18  C17  119.13  3.000
 FY5  H21  C19  C18  120.10  3.000
 FY5  H21  C19  C14  119.82  3.000
 FY5  C18  C19  C14  120.08  3.000
 FY5  S21  O20  C18  116.05  3.000
 FY5  O24  S21  O23  120.49  3.000
 FY5  O23  S21  O22  111.90  3.000
 FY5  O24  S21  O22  106.16  3.000
 FY5  O22  S21  O20   97.63  3.000
 FY5  O23  S21  O20  108.96  3.000
 FY5  O24  S21  O20  109.27  3.000
 FY5  H6   C01  H5   107.27  3.000
 FY5  H6   C01  H4   107.15  3.000
 FY5  H5   C01  H4   107.61  3.000
 FY5  H6   C01  C02  112.00  3.000
 FY5  H5   C01  C02  109.80  3.000
 FY5  H4   C01  C02  112.77  3.000
 FY5  H22  O22  S21  113.19  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   23.13  30.0  1
 FY5  Var_02    C12  C13  C14  C15    4.45  30.0  1
 FY5  Var_03    C05  C04  C03  C02   32.26  30.0  1
 FY5  Var_04    C08  C09  C10  C02    2.34  30.0  1
 FY5  Var_05    C14  C13  C12  C06  -33.93  30.0  1
 FY5  Var_06    O24  S21  O20  C18  -73.70  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
 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

