# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 21:02:09 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (3Z,5E)-6-hydroxy-5-nitro-2-oxohexa-3,5-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O\C=C(/C=C\C(=O)C(O)=O)[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
 XXP  XXP  '(3Z,5E)-6-hydroxy-5-nitro-2-oxohexa-3,5-dienoic acid'  ligand  17  13  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XXP
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
 XXP  O8    O  O      0  -0.422   3.1082   3.8700  -0.1310
 XXP  N7    N  N      1   0.360   3.0040   2.6847  -0.3784
 XXP  O9    O  O     -1  -0.404   3.6888   2.1185  -1.2064
 XXP  C5    C  C      0   0.102   2.0379   1.8895   0.3111
 XXP  C6    C  C1     0   0.054   1.2665   2.5104   1.2294
 XXP  O10   O  OH1    0  -0.545   0.3760   1.8427   1.9252
 XXP  C4    C  C1     0  -0.224   2.0479   0.4545   0.0306
 XXP  C3    C  C1     0  -0.281   0.9684  -0.3091  -0.1428
 XXP  C2    C  C      0   0.180  -0.4238   0.1909  -0.2707
 XXP  O11   O  O      0  -0.383  -0.6908   1.1645  -0.9361
 XXP  C1    C  C      0   0.343  -1.5126  -0.6092   0.4856
 XXP  O12   O  O      0  -0.571  -1.0723  -1.4737   1.2629
 XXP  O13   O  OC    -1  -0.581  -2.6851  -0.2950   0.2465
 XXP  H6    H  H      0   0.301   1.3660   3.5728   1.4204
 XXP  HO10  H  HOH1   0   0.508  -0.0798   2.4241   2.5461
 XXP  H4    H  H      0   0.284   3.0176  -0.0308   0.0424
 XXP  H3    H  H      0   0.277   1.1091  -1.3803  -0.2181

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
 XXP  O8   N7    double  1.215  0.020  1.215
 XXP  N7   C5    single  1.429  0.020  1.429
 XXP  N7   O9    single  1.215  0.020  1.215
 XXP  C5   C4    single  1.462  0.020  1.462
 XXP  C5   C6    double  1.351  0.020  1.351
 XXP  C6   O10   single  1.313  0.020  1.313
 XXP  C6   H6    single  0.930  0.020  1.080
 XXP  O10  HO10  single  0.850  0.020  0.980
 XXP  C4   C3    double  1.334  0.020  1.334
 XXP  C4   H4    single  0.930  0.020  1.080
 XXP  C3   C2    single  1.485  0.020  1.485
 XXP  C3   H3    single  0.930  0.020  1.080
 XXP  C2   O11   double  1.209  0.020  1.209
 XXP  C2   C1    single  1.548  0.020  1.548
 XXP  C1   O12   deloc   1.243  0.020  1.243
 XXP  C1   O13   deloc   1.237  0.020  1.237

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
 XXP  C5    N7   O9   116.79  3.000
 XXP  O9    N7   O8   123.03  3.000
 XXP  C5    N7   O8   120.17  3.000
 XXP  C4    C5   C6   125.84  3.000
 XXP  C6    C5   N7   117.29  3.000
 XXP  C4    C5   N7   116.69  3.000
 XXP  H6    C6   O10  117.87  3.000
 XXP  H6    C6   C5   121.19  3.000
 XXP  O10   C6   C5   120.93  3.000
 XXP  HO10  O10  C6   110.80  3.000
 XXP  H4    C4   C3   117.96  3.000
 XXP  H4    C4   C5   116.31  3.000
 XXP  C3    C4   C5   125.55  3.000
 XXP  H3    C3   C2   116.68  3.000
 XXP  H3    C3   C4   118.05  3.000
 XXP  C2    C3   C4   125.26  3.000
 XXP  C1    C2   O11  121.98  3.000
 XXP  C1    C2   C3   116.31  3.000
 XXP  O11   C2   C3   121.71  3.000
 XXP  O13   C1   O12  129.28  3.000
 XXP  O13   C1   C2   116.15  3.000
 XXP  O12   C1   C2   114.57  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
 XXP  Var_01  O10  C6  C5  N7  -178.51   0.0  2
 XXP  Var_02  C2   C3  C4  C5     9.07   0.0  2
 XXP  Var_03  C3   C4  C5  N7  -138.24  30.0  2
 XXP  Var_04  O11  C2  C3  C4    42.24  30.0  2
 XXP  Var_05  O12  C1  C2  C3     9.38  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
 XXP  plan-1  C3   0.020
 XXP  plan-1  C2   0.020
 XXP  plan-1  O11  0.020
 XXP  plan-1  C1   0.020
 XXP  plan-2  C2   0.020
 XXP  plan-2  C1   0.020
 XXP  plan-2  O12  0.020
 XXP  plan-2  O13  0.020
 XXP  plan-3  O8   0.020
 XXP  plan-3  N7   0.020
 XXP  plan-3  O9   0.020
 XXP  plan-3  C5   0.020
 XXP  plan-4  N7   0.020
 XXP  plan-4  C5   0.020
 XXP  plan-4  C6   0.020
 XXP  plan-4  O10  0.020
 XXP  plan-4  C4   0.020
 XXP  plan-4  H6   0.020
 XXP  plan-5  C5   0.020
 XXP  plan-5  C4   0.020
 XXP  plan-5  C3   0.020
 XXP  plan-5  C2   0.020
 XXP  plan-5  H4   0.020
 XXP  plan-5  H3   0.020

