# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:38:07 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: (3E,5E)-6-(4-nitrophenyl)-2-oxohexa-3,5-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(=O)/C=C/C=C/c1ccc(cc1)[N+]([O-])=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
 J6S  J6S  '(3E,5E)-6-(4-nitrophenyl)-2-oxohexa-3,5-dienoic acid'  ligand  26  18  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J6S
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
 J6S  C1   C  C      0   0.350   5.8725  -0.5784   0.0419
 J6S  C10  C  CR6    0   0.239  -4.2532  -0.0598  -0.0032
 J6S  C2   C  C      0   0.185   4.7079   0.4519   0.0116
 J6S  C3   C  C1     0  -0.378   3.3342  -0.0812   0.0253
 J6S  C4   C  C1     0  -0.162   2.2564   0.7211   0.0072
 J6S  C5   C  C1     0  -0.233   0.9059   0.2202   0.0186
 J6S  C6   C  C1     0  -0.290  -0.1635   1.0347  -0.0068
 J6S  C7   C  CR6    0   0.172  -1.5599   0.6210  -0.0036
 J6S  C8A  C  CR16   0  -0.303  -2.5514   1.6074  -0.0308
 J6S  C8B  C  CR16   0  -0.318  -1.9591  -0.7212   0.0243
 J6S  C9A  C  CR16   0  -0.253  -3.8937   1.2795  -0.0308
 J6S  C9B  C  CR16   0  -0.243  -3.2945  -1.0662   0.0241
 J6S  O11  O  OC    -1  -0.582   7.0107  -0.0958   0.1001
 J6S  O12  O  O      0  -0.573   5.5350  -1.7748   0.0008
 J6S  O13  O  O     -1  -0.380  -5.9462  -1.5942   0.0124
 J6S  O14  O  O      0  -0.381  -6.4758   0.4722  -0.0221
 J6S  H3   H  H      0   0.265   3.2117  -1.1556   0.0517
 J6S  H4   H  H      0   0.268   2.3841   1.7997  -0.0189
 J6S  H5   H  H      0   0.272   0.7861  -0.8572   0.0448
 J6S  H6   H  H      0   0.267   0.0049   2.1070  -0.0327
 J6S  H7   H  HCR6   0   0.276  -2.2665   2.6513  -0.0532
 J6S  H8   H  HCR6   0   0.276  -1.2233  -1.5131   0.0453
 J6S  H9   H  HCR6   0   0.300  -4.6374   2.0621  -0.0525
 J6S  H10  H  HCR6   0   0.299  -3.5770  -2.1082   0.0478
 J6S  O1   O  O      0  -0.401   4.9375   1.6444  -0.0253
 J6S  N11  N  N      1   0.329  -5.6591  -0.4196  -0.0045

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
 J6S  O12  C1   deloc     1.244  0.020  1.244
 J6S  O11  C1   deloc     1.238  0.020  1.238
 J6S  C1   C2   single    1.555  0.020  1.555
 J6S  C2   C3   single    1.474  0.020  1.474
 J6S  C4   C3   double    1.344  0.020  1.344
 J6S  C4   C5   single    1.440  0.020  1.440
 J6S  C5   C6   double    1.345  0.020  1.345
 J6S  C6   C7   single    1.456  0.020  1.456
 J6S  C8B  C7   aromatic  1.401  0.020  1.401
 J6S  C8B  C9B  aromatic  1.379  0.020  1.379
 J6S  C7   C8A  aromatic  1.399  0.020  1.399
 J6S  C9B  C10  aromatic  1.390  0.020  1.390
 J6S  C8A  C9A  aromatic  1.382  0.020  1.382
 J6S  C10  C9A  aromatic  1.387  0.020  1.387
 J6S  C10  N11  single    1.451  0.020  1.451
 J6S  O13  N11  single    1.209  0.020  1.209
 J6S  N11  O14  double    1.209  0.020  1.209
 J6S  C3   H3   single    0.930  0.020  1.080
 J6S  C4   H4   single    0.930  0.020  1.080
 J6S  C5   H5   single    0.930  0.020  1.080
 J6S  C6   H6   single    0.930  0.020  1.080
 J6S  C8A  H7   single    0.930  0.020  1.080
 J6S  C8B  H8   single    0.930  0.020  1.080
 J6S  C9A  H9   single    0.930  0.020  1.080
 J6S  C9B  H10  single    0.930  0.020  1.080
 J6S  C2   O1   double    1.215  0.020  1.215

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
 J6S  O12  C1   O11  128.77  3.000
 J6S  O11  C1   C2   115.55  3.000
 J6S  O12  C1   C2   115.68  3.000
 J6S  N11  C10  C9B  119.25  3.000
 J6S  N11  C10  C9A  119.37  3.000
 J6S  C9B  C10  C9A  121.38  3.000
 J6S  O1   C2   C3   122.10  3.000
 J6S  O1   C2   C1   120.62  3.000
 J6S  C3   C2   C1   117.28  3.000
 J6S  H3   C3   C4   120.17  3.000
 J6S  H3   C3   C2   117.72  3.000
 J6S  C4   C3   C2   122.12  3.000
 J6S  H4   C4   C5   117.11  3.000
 J6S  H4   C4   C3   119.92  3.000
 J6S  C5   C4   C3   122.97  3.000
 J6S  H5   C5   C6   120.96  3.000
 J6S  H5   C5   C4   116.70  3.000
 J6S  C6   C5   C4   122.34  3.000
 J6S  H6   C6   C7   115.42  3.000
 J6S  H6   C6   C5   118.38  3.000
 J6S  C7   C6   C5   126.19  3.000
 J6S  C8B  C7   C8A  118.30  3.000
 J6S  C8A  C7   C6   118.64  3.000
 J6S  C8B  C7   C6   123.07  3.000
 J6S  H7   C8A  C9A  118.99  3.000
 J6S  H7   C8A  C7   119.60  3.000
 J6S  C9A  C8A  C7   121.42  3.000
 J6S  H8   C8B  C9B  118.41  3.000
 J6S  H8   C8B  C7   120.55  3.000
 J6S  C9B  C8B  C7   121.04  3.000
 J6S  H9   C9A  C8A  119.80  3.000
 J6S  H9   C9A  C10  121.45  3.000
 J6S  C8A  C9A  C10  118.75  3.000
 J6S  H10  C9B  C8B  119.65  3.000
 J6S  H10  C9B  C10  121.24  3.000
 J6S  C8B  C9B  C10  119.12  3.000
 J6S  O14  N11  O13  123.79  3.000
 J6S  O14  N11  C10  118.12  3.000
 J6S  O13  N11  C10  118.09  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
 J6S  CONST_01  C7   C8B  C9B  C10     0.00   0.0  0
 J6S  CONST_02  C7   C8A  C9A  C10     0.00   0.0  0
 J6S  CONST_03  C9B  C8B  C7   C8A     0.00   0.0  0
 J6S  CONST_04  C9B  C10  C9A  C8A     0.00   0.0  0
 J6S  CONST_05  C9A  C8A  C7   C8B     0.00   0.0  0
 J6S  CONST_06  C9A  C10  C9B  C8B     0.00   0.0  0
 J6S  CONST_07  C9B  C8B  C7   C6    180.00   0.0  0
 J6S  CONST_08  C9A  C8A  C7   C6    180.00   0.0  0
 J6S  CONST_09  N11  C10  C9A  C8A   180.00   0.0  0
 J6S  CONST_10  N11  C10  C9B  C8B   180.00   0.0  0
 J6S  CONST_11  H8   C8B  C9B  C10   180.00   0.0  0
 J6S  CONST_12  H7   C8A  C9A  C10   180.00   0.0  0
 J6S  CONST_13  H10  C9B  C8B  C7    180.00   0.0  0
 J6S  CONST_14  H9   C9A  C8A  C7    180.00   0.0  0
 J6S  CONST_15  O13  N11  C10  C9A   180.00   0.0  0
 J6S  CONST_16  O14  N11  C10  C9A     0.00   0.0  0
 J6S  CONST_17  O13  N11  C10  C9B     0.00   0.0  0
 J6S  CONST_18  O14  N11  C10  C9B   180.00   0.0  0
 J6S  Var_01    C8B  C7   C6   C5     -0.16  30.0  2
 J6S  Var_02    C7   C6   C5   C4    179.73   0.0  2
 J6S  Var_03    C5   C4   C3   C2    179.93   0.0  2
 J6S  Var_04    C4   C3   C2   C1    179.71  30.0  2
 J6S  Var_05    O12  C1   C2   C3      3.81  30.0  3
 J6S  Var_06    C6   C5   C4   C3   -179.64  30.0  2

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
 J6S  plan-1  C10  0.020
 J6S  plan-1  C6   0.020
 J6S  plan-1  C7   0.020
 J6S  plan-1  C8A  0.020
 J6S  plan-1  C8B  0.020
 J6S  plan-1  C9A  0.020
 J6S  plan-1  C9B  0.020
 J6S  plan-1  H7   0.020
 J6S  plan-1  H8   0.020
 J6S  plan-1  H9   0.020
 J6S  plan-1  H10  0.020
 J6S  plan-1  N11  0.020
 J6S  plan-2  C10  0.020
 J6S  plan-2  O13  0.020
 J6S  plan-2  O14  0.020
 J6S  plan-2  N11  0.020
 J6S  plan-3  C1   0.020
 J6S  plan-3  C2   0.020
 J6S  plan-3  C3   0.020
 J6S  plan-3  O1   0.020
 J6S  plan-4  C1   0.020
 J6S  plan-4  C2   0.020
 J6S  plan-4  O11  0.020
 J6S  plan-4  O12  0.020
 J6S  plan-5  C2   0.020
 J6S  plan-5  C3   0.020
 J6S  plan-5  C4   0.020
 J6S  plan-5  C5   0.020
 J6S  plan-5  H3   0.020
 J6S  plan-5  H4   0.020
 J6S  plan-6  C4   0.020
 J6S  plan-6  C5   0.020
 J6S  plan-6  C6   0.020
 J6S  plan-6  C7   0.020
 J6S  plan-6  H5   0.020
 J6S  plan-6  H6   0.020

