# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 19:02:41 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: (6R)-6-hydroxy-4-nitrocyclohexa-2,4-dien-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C]1C=C(C=CC1=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
 XX2  XX2  (6R)-6-hydroxy-4-nitrocyclohexa-2,4-dien-1-one  ligand  15  11  .  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_XX2
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
 XX2  O11  O  O     -1  -0.367   3.4565  -1.9271   2.6931
 XX2  N9   N  N      1   0.330   3.3217  -2.7252   1.7955
 XX2  O10  O  O      0  -0.371   3.9807  -3.7309   1.6751
 XX2  C4   C  CR6    0   0.279   2.2998  -2.4536   0.7993
 XX2  C3   C  CR16   0  -0.393   2.1094  -3.3747  -0.2151
 XX2  C2   C  CR6    0   0.302   1.1378  -3.1237  -1.1694
 XX2  O8   O  OC     0  -0.560   0.8722  -3.9303  -2.1753
 XX2  C5   C  CR16   0  -0.253   1.5477  -1.2631   0.9084
 XX2  C6   C  CR16   0  -0.351   0.5918  -1.0013  -0.0206
 XX2  C1   C  CR6    0   0.328   0.3235  -1.9059  -1.1145
 XX2  O7   O  O      0  -0.380  -0.5389  -1.6866  -1.9690
 XX2  H3   H  HCR6   0   0.327   2.7040  -4.2771  -0.2686
 XX2  HO8  H  H      0   0.498   1.4367  -4.7157  -2.1623
 XX2  H5   H  HCR6   0   0.310   1.7278  -0.5681   1.7145
 XX2  H6   H  HCR6   0   0.299   0.0024  -0.0960   0.0373

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
 XX2  O11  N9   single    1.209  0.020  1.209
 XX2  N9   O10  double    1.208  0.020  1.208
 XX2  N9   C4   single    1.453  0.020  1.453
 XX2  C4   C3   aromatic  1.383  0.020  1.383
 XX2  C4   C5   aromatic  1.412  0.020  1.412
 XX2  C3   C2   aromatic  1.385  0.020  1.385
 XX2  C3   H3   single    0.930  0.020  1.080
 XX2  C2   O8   single    1.316  0.020  1.316
 XX2  C2   C1   aromatic  1.466  0.020  1.466
 XX2  O8   HO8  single    0.850  0.020  0.980
 XX2  C5   C6   aromatic  1.358  0.020  1.358
 XX2  C5   H5   single    0.930  0.020  1.080
 XX2  C6   C1   aromatic  1.445  0.020  1.445
 XX2  C6   H6   single    0.930  0.020  1.080
 XX2  C1   O7   double    1.234  0.020  1.234

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
 XX2  C4   N9  O10  118.09  3.000
 XX2  C4   N9  O11  117.67  3.000
 XX2  O10  N9  O11  124.24  3.000
 XX2  C5   C4  C3   122.99  3.000
 XX2  C5   C4  N9   118.63  3.000
 XX2  C3   C4  N9   118.37  3.000
 XX2  H3   C3  C2   120.17  3.000
 XX2  H3   C3  C4   121.06  3.000
 XX2  C2   C3  C4   118.76  3.000
 XX2  C1   C2  O8   115.19  3.000
 XX2  C1   C2  C3   120.96  3.000
 XX2  O8   C2  C3   123.85  3.000
 XX2  HO8  O8  C2   111.68  3.000
 XX2  H5   C5  C6   120.26  3.000
 XX2  H5   C5  C4   120.76  3.000
 XX2  C6   C5  C4   118.97  3.000
 XX2  H6   C6  C1   117.60  3.000
 XX2  H6   C6  C5   120.54  3.000
 XX2  C1   C6  C5   121.86  3.000
 XX2  O7   C1  C6   122.89  3.000
 XX2  O7   C1  C2   120.66  3.000
 XX2  C6   C1  C2   116.45  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
 XX2  CONST_01  C1  C2  C3  C4     0.00  0.0  0
 XX2  CONST_02  C1  C6  C5  C4     0.00  0.0  0
 XX2  CONST_03  C6  C5  C4  C3     0.00  0.0  0
 XX2  CONST_04  C6  C1  C2  C3     0.00  0.0  0
 XX2  CONST_05  C5  C4  C3  C2     0.00  0.0  0
 XX2  CONST_06  C5  C6  C1  C2     0.00  0.0  0
 XX2  CONST_07  C2  C3  C4  N9   180.00  0.0  0
 XX2  CONST_08  C6  C5  C4  N9   180.00  0.0  0
 XX2  CONST_09  O8  C2  C3  C4   180.00  0.0  0
 XX2  CONST_10  O7  C1  C2  C3   180.00  0.0  0
 XX2  CONST_11  C6  C1  C2  O8   180.00  0.0  0
 XX2  CONST_12  O7  C1  C6  C5   180.00  0.0  0
 XX2  CONST_13  H6  C6  C5  C4   180.00  0.0  0
 XX2  CONST_14  H5  C5  C4  C3   180.00  0.0  0
 XX2  CONST_15  H3  C3  C4  C5   180.00  0.0  0
 XX2  CONST_16  C3  C4  N9  O11  180.00  0.0  0
 XX2  CONST_17  C5  C4  N9  O11    0.00  0.0  0
 XX2  CONST_18  C3  C4  N9  O10    0.00  0.0  0
 XX2  CONST_19  C5  C4  N9  O10  180.00  0.0  0

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
 XX2  plan-1  N9   0.020
 XX2  plan-1  C4   0.020
 XX2  plan-1  C3   0.020
 XX2  plan-1  C2   0.020
 XX2  plan-1  O8   0.020
 XX2  plan-1  C5   0.020
 XX2  plan-1  C6   0.020
 XX2  plan-1  C1   0.020
 XX2  plan-1  O7   0.020
 XX2  plan-1  H3   0.020
 XX2  plan-1  H5   0.020
 XX2  plan-1  H6   0.020
 XX2  plan-2  O11  0.020
 XX2  plan-2  N9   0.020
 XX2  plan-2  O10  0.020
 XX2  plan-2  C4   0.020

