# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:20:00 2021
#   Inital geometry file: a 100 line input string
#   Ligand name: 3-[(1~{R},2~{S},4~{R},6~{S})-2-ethenyl-4,6-dimethyl-cyclohexyl]-4-oxidanyl-1~{H}-pyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@H](C)[C@H]([C@@H](C1)C=C)C2=C(O)C=CNC2=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
 F5F  F5F  3-[(1~{R},2~{S},4~{R},6~{S})-2-ethenyl-4,6-dimethyl-cyclohexyl]-4-oxidanyl-1~{H}-pyridin-2-one  ligand  39  18  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_F5F
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
 F5F  C1   C  CR16  0  -0.505  -24.0674  30.1751  -23.0141
 F5F  C2   C  CR16  0   0.049  -23.6085  31.2566  -23.6820
 F5F  C4   C  CR6   0   0.522  -25.8376  32.1735  -23.9390
 F5F  C5   C  CR6   0  -0.185  -26.3481  31.0372  -23.2217
 F5F  C6   C  CR6   0   0.428  -25.4675  30.0753  -22.7833
 F5F  C7   C  CH1   0  -0.253  -27.8266  30.9355  -22.9428
 F5F  C10  C  CH1   0  -0.215  -28.6915  30.7748  -24.2060
 F5F  C11  C  CH2   0  -0.389  -30.1507  30.5638  -23.8059
 F5F  C12  C  CH1   0  -0.236  -30.6951  31.6754  -22.9151
 F5F  C13  C  CH2   0  -0.390  -29.8038  31.8537  -21.6896
 F5F  C14  C  CH1   0  -0.292  -28.3378  32.0958  -22.0616
 F5F  C15  C  CH3   0  -0.654  -28.2076  29.6246  -25.0800
 F5F  C16  C  CH3   0  -0.653  -32.1393  31.4056  -22.5127
 F5F  C17  C  C1    0  -0.104  -27.5080  32.2277  -20.8240
 F5F  C18  C  C2    0  -0.549  -26.8291  33.3109  -20.4653
 F5F  N3   N  NR16  0  -0.665  -24.4635  32.2021  -24.1160
 F5F  O8   O  OH1   0  -0.611  -25.9414  29.0130  -22.1177
 F5F  O9   O  O     0  -0.512  -26.5081  33.1001  -24.3993
 F5F  H1   H  HCR6  0   0.286  -23.3807  29.4149  -22.6674
 F5F  H2   H  HCR6  0   0.312  -22.5628  31.4163  -23.8985
 F5F  H4   H  HCH1  0   0.226  -27.9823  30.0241  -22.3552
 F5F  H5   H  HCH1  0   0.216  -28.6320  31.6997  -24.7876
 F5F  H6   H  HCH2  0   0.220  -30.7661  30.4832  -24.7078
 F5F  H7   H  HCH2  0   0.197  -30.2449  29.6030  -23.2820
 F5F  H8   H  HCH1  0   0.208  -30.6690  32.6109  -23.4895
 F5F  H9   H  HCH2  0   0.226  -30.1683  32.6885  -21.0838
 F5F  H10  H  HCH2  0   0.202  -29.8748  30.9576  -21.0596
 F5F  H11  H  HCH1  0   0.229  -28.2773  33.0256  -22.6332
 F5F  H12  H  HCH3  0   0.227  -27.2012  29.7974  -25.4627
 F5F  H13  H  HCH3  0   0.211  -28.1912  28.6859  -24.5205
 F5F  H14  H  HCH3  0   0.223  -28.8671  29.4864  -25.9390
 F5F  H15  H  HCH3  0   0.223  -32.5439  32.2176  -21.9056
 F5F  H16  H  HCH3  0   0.223  -32.7824  31.2958  -23.3876
 F5F  H17  H  HCH3  0   0.211  -32.2138  30.4856  -21.9277
 F5F  H18  H  H     0   0.228  -27.4899  31.3530  -20.1759
 F5F  H19  H  H     0   0.228  -26.2583  33.3471  -19.5460
 F5F  H20  H  H     0   0.225  -26.8126  34.2007  -21.0846
 F5F  H21  H  HOH1  0   0.481  -25.2234  28.4201  -21.8695
 F5F  H3   H  HNR6  0   0.415  -24.0936  32.9998  -24.6130

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
 F5F  C15  C10  single  1.523  0.020  1.523
 F5F  O9   C4   double  1.233  0.020  1.233
 F5F  N3   C4   single  1.386  0.020  1.386
 F5F  N3   C2   single  1.347  0.020  1.347
 F5F  C10  C11  single  1.528  0.020  1.528
 F5F  C10  C7   single  1.539  0.020  1.539
 F5F  C4   C5   single  1.437  0.020  1.437
 F5F  C2   C1   double  1.351  0.020  1.351
 F5F  C11  C12  single  1.525  0.020  1.525
 F5F  C5   C7   single  1.508  0.020  1.508
 F5F  C5   C6   double  1.376  0.020  1.376
 F5F  C1   C6   single  1.423  0.020  1.423
 F5F  C12  C16  single  1.523  0.020  1.523
 F5F  C12  C13  single  1.526  0.020  1.526
 F5F  C7   C14  single  1.544  0.020  1.544
 F5F  C6   O8   single  1.340  0.020  1.340
 F5F  C14  C13  single  1.532  0.020  1.532
 F5F  C14  C17  single  1.496  0.020  1.496
 F5F  C17  C18  double  1.328  0.020  1.328
 F5F  C1   H1   single  0.930  0.020  1.080
 F5F  C2   H2   single  0.930  0.020  1.080
 F5F  C7   H4   single  0.970  0.020  1.090
 F5F  C10  H5   single  0.970  0.020  1.090
 F5F  C11  H6   single  0.970  0.020  1.090
 F5F  C11  H7   single  0.970  0.020  1.090
 F5F  C12  H8   single  0.970  0.020  1.090
 F5F  C13  H9   single  0.970  0.020  1.090
 F5F  C13  H10  single  0.970  0.020  1.090
 F5F  C14  H11  single  0.970  0.020  1.090
 F5F  C15  H12  single  0.970  0.020  1.090
 F5F  C15  H13  single  0.970  0.020  1.090
 F5F  C15  H14  single  0.970  0.020  1.090
 F5F  C16  H15  single  0.970  0.020  1.090
 F5F  C16  H16  single  0.970  0.020  1.090
 F5F  C16  H17  single  0.970  0.020  1.090
 F5F  C17  H18  single  0.930  0.020  1.080
 F5F  C18  H19  single  0.930  0.020  1.080
 F5F  C18  H20  single  0.930  0.020  1.080
 F5F  O8   H21  single  0.850  0.020  0.980
 F5F  N3   H3   single  0.860  0.020  1.020

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
 F5F  H1   C1   C6   121.57  3.000
 F5F  H1   C1   C2   120.36  3.000
 F5F  C6   C1   C2   118.07  3.000
 F5F  H2   C2   N3   116.52  3.000
 F5F  H2   C2   C1   123.11  3.000
 F5F  N3   C2   C1   120.37  3.000
 F5F  O9   C4   N3   118.43  3.000
 F5F  N3   C4   C5   115.61  3.000
 F5F  O9   C4   C5   125.96  3.000
 F5F  C7   C5   C6   121.43  3.000
 F5F  C6   C5   C4   118.97  3.000
 F5F  C7   C5   C4   119.59  3.000
 F5F  O8   C6   C5   119.08  3.000
 F5F  O8   C6   C1   118.96  3.000
 F5F  C5   C6   C1   121.95  3.000
 F5F  H4   C7   C14  105.79  3.000
 F5F  H4   C7   C10  105.87  3.000
 F5F  C14  C7   C10  111.15  3.000
 F5F  H4   C7   C5   107.13  3.000
 F5F  C14  C7   C5   112.30  3.000
 F5F  C10  C7   C5   113.96  3.000
 F5F  H5   C10  C15  108.42  3.000
 F5F  H5   C10  C11  107.93  3.000
 F5F  C15  C10  C11  110.45  3.000
 F5F  H5   C10  C7   108.50  3.000
 F5F  C11  C10  C7   109.64  3.000
 F5F  C15  C10  C7   111.78  3.000
 F5F  H7   C11  H6   106.28  3.000
 F5F  H7   C11  C12  109.17  3.000
 F5F  H6   C11  C12  109.52  3.000
 F5F  H7   C11  C10  109.13  3.000
 F5F  H6   C11  C10  109.35  3.000
 F5F  C12  C11  C10  113.16  3.000
 F5F  H8   C12  C16  108.16  3.000
 F5F  H8   C12  C13  107.86  3.000
 F5F  C16  C12  C13  111.24  3.000
 F5F  H8   C12  C11  107.88  3.000
 F5F  C13  C12  C11  110.23  3.000
 F5F  C16  C12  C11  111.33  3.000
 F5F  H10  C13  H9   106.47  3.000
 F5F  H10  C13  C14  109.29  3.000
 F5F  H9   C13  C14  109.44  3.000
 F5F  H10  C13  C12  109.14  3.000
 F5F  H9   C13  C12  109.84  3.000
 F5F  C14  C13  C12  112.49  3.000
 F5F  H11  C14  C17  109.08  3.000
 F5F  H11  C14  C13  108.33  3.000
 F5F  C17  C14  C13  110.12  3.000
 F5F  H11  C14  C7   108.81  3.000
 F5F  C17  C14  C7   110.78  3.000
 F5F  C13  C14  C7   109.67  3.000
 F5F  H14  C15  H13  107.65  3.000
 F5F  H14  C15  H12  107.54  3.000
 F5F  H13  C15  H12  107.57  3.000
 F5F  H14  C15  C10  110.80  3.000
 F5F  H13  C15  C10  111.07  3.000
 F5F  H12  C15  C10  112.02  3.000
 F5F  H17  C16  H16  107.71  3.000
 F5F  H17  C16  H15  107.65  3.000
 F5F  H16  C16  H15  107.60  3.000
 F5F  H17  C16  C12  110.80  3.000
 F5F  H16  C16  C12  111.39  3.000
 F5F  H15  C16  C12  111.51  3.000
 F5F  H18  C17  C18  119.09  3.000
 F5F  H18  C17  C14  115.52  3.000
 F5F  C18  C17  C14  125.38  3.000
 F5F  H20  C18  H19  116.71  3.000
 F5F  H20  C18  C17  121.54  3.000
 F5F  H19  C18  C17  121.75  3.000
 F5F  H3   N3   C4   116.25  3.000
 F5F  H3   N3   C2   118.72  3.000
 F5F  C4   N3   C2   125.03  3.000
 F5F  H21  O8   C6   110.62  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
 F5F  CONST_01  C5   C4   N3   C2     0.00  0.0  0
 F5F  CONST_02  O9   C4   N3   C2   180.00  0.0  0
 F5F  CONST_03  H3   N3   C4   C5   180.00  0.0  0
 F5F  Var_01    H19  C18  C17  C14  179.02  0.0  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
 F5F  chir_01  C7   C10  C5   C14  negativ
 F5F  chir_02  C10  C7   C11  C15  positiv
 F5F  chir_03  C12  C11  C16  C13  negativ
 F5F  chir_04  C14  C17  C13  C7   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
 F5F  plan-1  C1   0.020
 F5F  plan-1  C2   0.020
 F5F  plan-1  C4   0.020
 F5F  plan-1  C5   0.020
 F5F  plan-1  C6   0.020
 F5F  plan-1  C7   0.020
 F5F  plan-1  N3   0.020
 F5F  plan-1  O8   0.020
 F5F  plan-1  O9   0.020
 F5F  plan-1  H1   0.020
 F5F  plan-1  H2   0.020
 F5F  plan-1  H3   0.020
 F5F  plan-2  C14  0.020
 F5F  plan-2  C17  0.020
 F5F  plan-2  C18  0.020
 F5F  plan-2  H18  0.020
 F5F  plan-2  H19  0.020
 F5F  plan-2  H20  0.020

