# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 18:24:56 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: 5-fluoranyl-2-oxidanylidene-pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(=O)CCCF
#
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
 6Y5  6Y5  '5-fluoranyl-2-oxidanylidene-pentanoic acid'  ligand  15  9  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6Y5
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
 6Y5  O10  O  O      0  -0.396  -0.8012  -1.6509  -0.0104
 6Y5  C5   C  C      0   0.242  -0.8789  -0.4452   0.0203
 6Y5  C6   C  C      0   0.347  -2.2673   0.2619   0.0427
 6Y5  O8   O  O      0  -0.577  -2.2346   1.5009   0.1306
 6Y5  O7   O  OC    -1  -0.582  -3.2501  -0.4875  -0.0287
 6Y5  C4   C  CH2    0  -0.567   0.3424   0.4354   0.0375
 6Y5  C3   C  CH2    0  -0.491   1.6574  -0.3252  -0.0235
 6Y5  C2   C  CH2    0   0.004   2.8197   0.6380  -0.0126
 6Y5  F1   F  F      0  -0.385   4.0265  -0.0604  -0.0924
 6Y5  H2   H  HCH2   0   0.263   0.2597   1.1401  -0.7970
 6Y5  H3   H  HCH2   0   0.265   0.2932   1.0633   0.9335
 6Y5  H4   H  HCH2   0   0.237   1.7398  -1.0058   0.8270
 6Y5  H5   H  HCH2   0   0.237   1.6988  -0.9332  -0.9306
 6Y5  H6   H  HCH2   0   0.202   2.7728   1.3212  -0.8633
 6Y5  H7   H  HCH2   0   0.202   2.8349   1.2293   0.9057

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
 6Y5  C2   F1  single  1.397  0.020  1.397
 6Y5  C2   C3  single  1.510  0.020  1.510
 6Y5  O10  C5  double  1.209  0.020  1.209
 6Y5  C3   C4  single  1.520  0.020  1.520
 6Y5  C5   C4  single  1.506  0.020  1.506
 6Y5  C5   C6  single  1.558  0.020  1.558
 6Y5  O8   C6  deloc   1.243  0.020  1.243
 6Y5  C6   O7  deloc   1.238  0.020  1.238
 6Y5  C4   H2  single  0.970  0.020  1.090
 6Y5  C4   H3  single  0.970  0.020  1.090
 6Y5  C3   H4  single  0.970  0.020  1.090
 6Y5  C3   H5  single  0.970  0.020  1.090
 6Y5  C2   H6  single  0.970  0.020  1.090
 6Y5  C2   H7  single  0.970  0.020  1.090

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
 6Y5  C4  C5  C6   117.20  3.000
 6Y5  C6  C5  O10  120.68  3.000
 6Y5  C4  C5  O10  122.11  3.000
 6Y5  O7  C6  O8   128.95  3.000
 6Y5  O7  C6  C5   115.58  3.000
 6Y5  O8  C6  C5   115.47  3.000
 6Y5  H3  C4  H2   104.54  3.000
 6Y5  H3  C4  C3   111.01  3.000
 6Y5  H2  C4  C3   110.89  3.000
 6Y5  H3  C4  C5   107.95  3.000
 6Y5  H2  C4  C5   107.84  3.000
 6Y5  C3  C4  C5   114.11  3.000
 6Y5  H5  C3  H4   107.27  3.000
 6Y5  H5  C3  C2   109.38  3.000
 6Y5  H4  C3  C2   109.50  3.000
 6Y5  H5  C3  C4   110.15  3.000
 6Y5  H4  C3  C4   110.22  3.000
 6Y5  C2  C3  C4   110.27  3.000
 6Y5  H7  C2  H6   108.47  3.000
 6Y5  H7  C2  F1   107.86  3.000
 6Y5  H6  C2  F1   107.79  3.000
 6Y5  H7  C2  C3   111.23  3.000
 6Y5  H6  C2  C3   111.13  3.000
 6Y5  F1  C2  C3   110.23  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
 6Y5  Var_01  C3  C4  C5  O10     1.51  30.0  3
 6Y5  Var_02  O8  C6  C5  O10   177.10  30.0  2
 6Y5  Var_03  C2  C3  C4  C5    179.54  30.0  1
 6Y5  Var_04  F1  C2  C3  C4   -178.96  30.0  3

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
 6Y5  plan-1  O10  0.020
 6Y5  plan-1  C5   0.020
 6Y5  plan-1  C6   0.020
 6Y5  plan-1  C4   0.020
 6Y5  plan-2  C5   0.020
 6Y5  plan-2  C6   0.020
 6Y5  plan-2  O8   0.020
 6Y5  plan-2  O7   0.020

