# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 14:31:58 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: (6S)-4-fluoro-6-hydroperoxy-6-hydroxycyclohexa-2,4-dien-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OO[C@@]1(O)C=C(F)C=CC1=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
 3N9  3N9  (6S)-4-fluoro-6-hydroperoxy-6-hydroxycyclohexa-2,4-dien-1-one  ligand  16  11  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3N9
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
 3N9  C1  C  C     0   0.410  -0.5834   1.3416  -0.0240
 3N9  C2  C  CT    0   0.337  -0.8074  -0.1561   0.3110
 3N9  C3  C  C1    0  -0.438   0.4315  -1.0038   0.2946
 3N9  C4  C  C     0   0.538   1.6051  -0.4603   0.0073
 3N9  C5  C  C1    0  -0.329   1.7989   0.9401  -0.3162
 3N9  C6  C  C1    0  -0.346   0.7688   1.7942  -0.3321
 3N9  O2  O  OH1   0  -0.638  -1.4085  -0.1656   1.5539
 3N9  O3  O  O2    0  -0.302  -1.6948  -0.5346  -0.7234
 3N9  O4  O  OH1   0  -0.442  -2.0556  -1.8840  -0.5524
 3N9  O1  O  O     0  -0.375  -1.5377   2.0819  -0.0109
 3N9  F4  F  F     0  -0.305   2.7230  -1.1955   0.0027
 3N9  H1  H  H     0   0.321   0.3537  -2.0562   0.5411
 3N9  H2  H  H     0   0.314   2.8027   1.2776  -0.5419
 3N9  H3  H  H     0   0.300   0.9094   2.8412  -0.5646
 3N9  H4  H  HOH1  0   0.474  -1.3674  -1.0499   1.9389
 3N9  H5  H  HOH1  0   0.481  -1.5496  -2.3285  -1.2483

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
 3N9  O4  O3  single  1.407  0.020  1.407
 3N9  O3  C2  single  1.414  0.020  1.414
 3N9  F4  C4  single  1.338  0.020  1.338
 3N9  C3  C2  single  1.501  0.020  1.501
 3N9  C3  C4  double  1.325  0.020  1.325
 3N9  C2  O2  single  1.381  0.020  1.381
 3N9  C2  C1  single  1.551  0.020  1.551
 3N9  C4  C5  single  1.450  0.020  1.450
 3N9  C1  O1  double  1.208  0.020  1.208
 3N9  C1  C6  single  1.459  0.020  1.459
 3N9  C5  C6  double  1.338  0.020  1.338
 3N9  C3  H1  single  0.930  0.020  1.080
 3N9  C5  H2  single  0.930  0.020  1.080
 3N9  C6  H3  single  0.930  0.020  1.080
 3N9  O2  H4  single  0.850  0.020  0.980
 3N9  O4  H5  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
 3N9  O1  C1  C6  122.98  3.000
 3N9  C6  C1  C2  118.62  3.000
 3N9  O1  C1  C2  118.39  3.000
 3N9  O3  C2  O2  112.54  3.000
 3N9  O2  C2  C3  111.42  3.000
 3N9  O3  C2  C3  111.02  3.000
 3N9  O2  C2  C1  105.31  3.000
 3N9  C3  C2  C1  115.07  3.000
 3N9  O3  C2  C1  101.02  3.000
 3N9  H1  C3  C4  120.75  3.000
 3N9  H1  C3  C2  119.12  3.000
 3N9  C4  C3  C2  120.12  3.000
 3N9  F4  C4  C5  114.72  3.000
 3N9  C5  C4  C3  124.25  3.000
 3N9  F4  C4  C3  121.03  3.000
 3N9  H2  C5  C6  120.81  3.000
 3N9  H2  C5  C4  118.12  3.000
 3N9  C6  C5  C4  121.07  3.000
 3N9  H3  C6  C5  121.35  3.000
 3N9  H3  C6  C1  117.79  3.000
 3N9  C5  C6  C1  120.86  3.000
 3N9  H4  O2  C2  110.29  3.000
 3N9  O4  O3  C2  109.19  3.000
 3N9  H5  O4  O3  102.64  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
 3N9  Var_01  C4  C5  C6  C1  -0.01  30.0  1
 3N9  Var_02  C5  C6  C1  C2  -0.55  30.0  1
 3N9  Var_03  C6  C5  C4  C3   0.60  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
 3N9  chir_01  C2  C3  O2  C1  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
 3N9  plan-1  C1  0.020
 3N9  plan-1  C2  0.020
 3N9  plan-1  C6  0.020
 3N9  plan-1  O1  0.020

