# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:54:34 2021
#   Inital geometry file: a 105 line input string
#   Ligand name: 3-[(~{E},2~{S},4~{S})-2,4-dimethyloct-6-enoyl]-4-oxidanyl-1~{H}-pyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C\C=C\C[C@H](C)C[C@H](C)C(=O)C1=C(O)C=CNC1=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
 F56  F56  3-[(~{E},2~{S},4~{S})-2,4-dimethyloct-6-enoyl]-4-oxidanyl-1~{H}-pyridin-2-one  ligand  40  19  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F56
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
 F56  C1   C  CR16  0  -0.469  -25.1532  30.4801  -23.7240
 F56  C2   C  CR16  0   0.082  -24.8670  31.8010  -23.8031
 F56  C4   C  CR6   0   0.539  -27.1765  32.4336  -24.1924
 F56  C5   C  CR6   0  -0.448  -27.5270  31.0321  -24.0837
 F56  C6   C  CR6   0   0.514  -26.5019  30.0823  -23.8695
 F56  C7   C  C     0   0.494  -28.8968  30.5403  -24.1777
 F56  C8   C  CH1   0  -0.374  -30.0872  31.4456  -24.3942
 F56  C9   C  CH2   0  -0.382  -31.3602  30.8762  -23.7706
 F56  C10  C  CH1   0  -0.242  -31.3727  30.8569  -22.2403
 F56  C11  C  CH2   0  -0.468  -32.5293  29.9906  -21.7204
 F56  C12  C  C1    0  -0.185  -32.3769  28.5402  -22.0521
 F56  C13  C  C1    0  -0.232  -33.2416  27.8148  -22.7554
 F56  C14  C  CH3   0  -0.707  -33.0796  26.3662  -23.0852
 F56  C18  C  CH3   0  -0.656  -30.2506  31.6312  -25.9092
 F56  C19  C  CH3   0  -0.661  -31.4689  32.2644  -21.6586
 F56  N3   N  NR16  0  -0.671  -25.8274  32.7134  -24.0202
 F56  O15  O  OH1   0  -0.595  -26.7533  28.8027  -23.7910
 F56  O16  O  O     0  -0.501  -29.1036  29.3187  -24.1111
 F56  O17  O  O     0  -0.477  -27.9295  33.3722  -24.4217
 F56  H1   H  HCR6  0   0.291  -24.3768  29.7497  -23.5537
 F56  H2   H  HCR6  0   0.327  -23.8625  32.1847  -23.6988
 F56  H4   H  HCH1  0   0.266  -29.8751  32.4233  -23.9696
 F56  H5   H  HCH2  0   0.218  -32.2009  31.4897  -24.1146
 F56  H6   H  HCH2  0   0.236  -31.5436  29.8713  -24.1555
 F56  H7   H  HCH1  0   0.219  -30.4411  30.4032  -21.8810
 F56  H8   H  HCH2  0   0.220  -33.4773  30.3714  -22.1158
 F56  H9   H  HCH2  0   0.231  -32.5798  30.1050  -20.6315
 F56  H10  H  H     0   0.221  -31.4708  28.0626  -21.6825
 F56  H11  H  H     0   0.224  -34.1416  28.2960  -23.1319
 F56  H12  H  HCH3  0   0.232  -33.9154  25.7756  -22.7029
 F56  H13  H  HCH3  0   0.233  -33.0584  26.2083  -24.1659
 F56  H14  H  HCH3  0   0.232  -32.1594  25.9574  -22.6670
 F56  H15  H  HCH3  0   0.241  -31.0517  32.3434  -26.1079
 F56  H16  H  HCH3  0   0.241  -29.3443  32.0155  -26.3762
 F56  H17  H  HCH3  0   0.227  -30.5101  30.6883  -26.3932
 F56  H18  H  HCH3  0   0.227  -31.4316  32.2445  -20.5680
 F56  H19  H  HCH3  0   0.228  -30.6558  32.9074  -21.9987
 F56  H20  H  HCH3  0   0.214  -32.4084  32.7411  -21.9497
 F56  H21  H  HOH1  0   0.486  -27.7551  28.7098  -23.9107
 F56  H3   H  HNR6  0   0.427  -25.5671  33.6883  -24.0828

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
 F56  C18  C8   single  1.535  0.020  1.535
 F56  O17  C4   double  1.225  0.020  1.225
 F56  N3   C4   single  1.389  0.020  1.389
 F56  N3   C2   single  1.342  0.020  1.342
 F56  C4   C5   single  1.449  0.020  1.449
 F56  C2   C1   double  1.354  0.020  1.354
 F56  C8   C7   single  1.511  0.020  1.511
 F56  C8   C9   single  1.528  0.020  1.528
 F56  C5   C6   double  1.414  0.020  1.414
 F56  C5   C7   single  1.458  0.020  1.458
 F56  C1   C6   single  1.414  0.020  1.414
 F56  C6   O15  single  1.306  0.020  1.306
 F56  C7   O16  double  1.241  0.020  1.241
 F56  C9   C10  single  1.530  0.020  1.530
 F56  C14  C13  single  1.494  0.020  1.494
 F56  C13  C12  double  1.330  0.020  1.330
 F56  C12  C11  single  1.496  0.020  1.496
 F56  C10  C11  single  1.536  0.020  1.536
 F56  C10  C19  single  1.526  0.020  1.526
 F56  C1   H1   single  0.930  0.020  1.080
 F56  C2   H2   single  0.930  0.020  1.080
 F56  C8   H4   single  0.970  0.020  1.090
 F56  C9   H5   single  0.970  0.020  1.090
 F56  C9   H6   single  0.970  0.020  1.090
 F56  C10  H7   single  0.970  0.020  1.090
 F56  C11  H8   single  0.970  0.020  1.090
 F56  C11  H9   single  0.970  0.020  1.090
 F56  C12  H10  single  0.930  0.020  1.080
 F56  C13  H11  single  0.930  0.020  1.080
 F56  C14  H12  single  0.970  0.020  1.090
 F56  C14  H13  single  0.970  0.020  1.090
 F56  C14  H14  single  0.970  0.020  1.090
 F56  C18  H15  single  0.970  0.020  1.090
 F56  C18  H16  single  0.970  0.020  1.090
 F56  C18  H17  single  0.970  0.020  1.090
 F56  C19  H18  single  0.970  0.020  1.090
 F56  C19  H19  single  0.970  0.020  1.090
 F56  C19  H20  single  0.970  0.020  1.090
 F56  O15  H21  single  0.850  0.020  0.980
 F56  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
 F56  H1   C1   C6   120.80  3.000
 F56  H1   C1   C2   121.15  3.000
 F56  C6   C1   C2   118.05  3.000
 F56  H2   C2   N3   116.07  3.000
 F56  H2   C2   C1   122.51  3.000
 F56  N3   C2   C1   121.42  3.000
 F56  O17  C4   N3   117.78  3.000
 F56  N3   C4   C5   114.88  3.000
 F56  O17  C4   C5   127.34  3.000
 F56  C7   C5   C6   117.66  3.000
 F56  C7   C5   C4   123.27  3.000
 F56  C6   C5   C4   119.07  3.000
 F56  O15  C6   C5   121.84  3.000
 F56  O15  C6   C1   116.93  3.000
 F56  C5   C6   C1   121.22  3.000
 F56  O16  C7   C8   117.80  3.000
 F56  O16  C7   C5   119.01  3.000
 F56  C8   C7   C5   123.17  3.000
 F56  H4   C8   C18  107.31  3.000
 F56  H4   C8   C9   109.78  3.000
 F56  C18  C8   C9   111.05  3.000
 F56  H4   C8   C7   109.23  3.000
 F56  C9   C8   C7   112.00  3.000
 F56  C18  C8   C7   107.32  3.000
 F56  H6   C9   H5   106.01  3.000
 F56  H6   C9   C10  109.85  3.000
 F56  H5   C9   C10  108.34  3.000
 F56  H6   C9   C8   109.83  3.000
 F56  H5   C9   C8   107.60  3.000
 F56  C10  C9   C8   114.81  3.000
 F56  H7   C10  C19  108.07  3.000
 F56  H7   C10  C11  107.18  3.000
 F56  C19  C10  C11  110.11  3.000
 F56  H7   C10  C9   109.02  3.000
 F56  C19  C10  C9   111.72  3.000
 F56  C11  C10  C9   110.60  3.000
 F56  H9   C11  H8   106.40  3.000
 F56  H9   C11  C12  109.04  3.000
 F56  H8   C11  C12  110.19  3.000
 F56  H9   C11  C10  108.19  3.000
 F56  H8   C11  C10  109.48  3.000
 F56  C12  C11  C10  113.28  3.000
 F56  H10  C12  C13  118.77  3.000
 F56  H10  C12  C11  115.78  3.000
 F56  C13  C12  C11  125.45  3.000
 F56  H11  C13  C14  116.23  3.000
 F56  H11  C13  C12  118.67  3.000
 F56  C14  C13  C12  125.10  3.000
 F56  H14  C14  H13  107.99  3.000
 F56  H14  C14  H12  107.98  3.000
 F56  H13  C14  H12  106.43  3.000
 F56  H14  C14  C13  111.73  3.000
 F56  H13  C14  C13  111.13  3.000
 F56  H12  C14  C13  111.34  3.000
 F56  H17  C18  H16  108.21  3.000
 F56  H17  C18  H15  107.99  3.000
 F56  H16  C18  H15  107.62  3.000
 F56  H17  C18  C8   111.01  3.000
 F56  H16  C18  C8   112.15  3.000
 F56  H15  C18  C8   109.70  3.000
 F56  H20  C19  H19  107.49  3.000
 F56  H20  C19  H18  107.67  3.000
 F56  H19  C19  H18  107.26  3.000
 F56  H20  C19  C10  110.79  3.000
 F56  H19  C19  C10  112.19  3.000
 F56  H18  C19  C10  111.22  3.000
 F56  H3   N3   C4   115.90  3.000
 F56  H3   N3   C2   118.77  3.000
 F56  C4   N3   C2   125.33  3.000
 F56  H21  O15  C6   105.84  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
 F56  CONST_01  C5   C4   N3   C2      0.00   0.0  0
 F56  CONST_02  O17  C4   N3   C2    180.00   0.0  0
 F56  CONST_03  H3   N3   C4   C5    180.00   0.0  0
 F56  Var_01    C8   C7   C5   C4     -0.17  30.0  2
 F56  Var_02    C14  C13  C12  C11   179.84   0.0  2
 F56  Var_03    C13  C12  C11  C10  -121.33  30.0  1
 F56  Var_04    H12  C14  C13  C12   121.48  30.0  3

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
 F56  chir_01  C8   C18  C7   C9   positiv
 F56  chir_02  C10  C9   C11  C19  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
 F56  plan-1  C1   0.020
 F56  plan-1  C2   0.020
 F56  plan-1  C4   0.020
 F56  plan-1  C5   0.020
 F56  plan-1  C6   0.020
 F56  plan-1  C7   0.020
 F56  plan-1  N3   0.020
 F56  plan-1  O15  0.020
 F56  plan-1  O17  0.020
 F56  plan-1  H1   0.020
 F56  plan-1  H2   0.020
 F56  plan-1  H3   0.020
 F56  plan-2  C5   0.020
 F56  plan-2  C7   0.020
 F56  plan-2  C8   0.020
 F56  plan-2  O16  0.020
 F56  plan-3  C11  0.020
 F56  plan-3  C12  0.020
 F56  plan-3  C13  0.020
 F56  plan-3  C14  0.020
 F56  plan-3  H10  0.020
 F56  plan-3  H11  0.020

