# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 22:07:50 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: 2-azanyl-5-nitro-benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(cc1C(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
 6R6  6R6  '2-azanyl-5-nitro-benzoic acid'  ligand  18  13  .  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_6R6
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
 6R6  C01  C  CR16   0  -0.271   1.2483   1.5777  -0.0021
 6R6  C02  C  CR16   0  -0.340  -0.0039   2.1260   0.0152
 6R6  C03  C  CR6    0   0.357  -1.1685   1.3180   0.0181
 6R6  C04  C  CR6    0  -0.198  -1.0162  -0.1001   0.0065
 6R6  C05  C  CR16   0  -0.321   0.2586  -0.6269  -0.0103
 6R6  C06  C  CR6    0   0.232   1.3882   0.1859  -0.0160
 6R6  N07  N  N      1   0.316   2.6889  -0.3968  -0.0366
 6R6  O08  O  O      0  -0.418   2.7901  -1.6091  -0.0538
 6R6  O09  O  O     -1  -0.418   3.6569   0.3412  -0.0367
 6R6  C10  C  C      0   0.455  -2.1979  -1.0592   0.0090
 6R6  O11  O  OC    -1  -0.575  -1.9388  -2.2734   0.0162
 6R6  O12  O  O      0  -0.600  -3.3468  -0.5550   0.0005
 6R6  N13  N  NH2    0  -0.849  -2.3723   1.8929   0.0332
 6R6  H1   H  HCR6   0   0.285   2.1119   2.2270  -0.0050
 6R6  H2   H  HCR6   0   0.268  -0.1151   3.2032   0.0255
 6R6  H3   H  HCR6   0   0.276   0.3573  -1.7029  -0.0191
 6R6  H5   H  HNH2   0   0.395  -2.4723   2.8926   0.0360
 6R6  H6   H  HNH2   0   0.407  -3.1766   1.2744   0.0249

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
 6R6  O09  N07  single    1.217  0.020  1.217
 6R6  O08  N07  double    1.217  0.020  1.217
 6R6  N07  C06  single    1.425  0.020  1.425
 6R6  C06  C05  aromatic  1.392  0.020  1.392
 6R6  C06  C01  aromatic  1.399  0.020  1.399
 6R6  C05  C04  aromatic  1.379  0.020  1.379
 6R6  C01  C02  aromatic  1.367  0.020  1.367
 6R6  O12  C10  deloc     1.255  0.020  1.255
 6R6  C04  C10  single    1.522  0.020  1.522
 6R6  C04  C03  aromatic  1.426  0.020  1.426
 6R6  C02  C03  aromatic  1.417  0.020  1.417
 6R6  C10  O11  deloc     1.242  0.020  1.242
 6R6  C03  N13  single    1.334  0.020  1.334
 6R6  C01  H1   single    0.930  0.020  1.080
 6R6  C02  H2   single    0.930  0.020  1.080
 6R6  C05  H3   single    0.930  0.020  1.080
 6R6  N13  H5   single    0.860  0.020  1.020
 6R6  N13  H6   single    0.860  0.020  1.020

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
 6R6  H1   C01  C06  121.20  3.000
 6R6  H1   C01  C02  119.41  3.000
 6R6  C06  C01  C02  119.39  3.000
 6R6  H2   C02  C03  118.86  3.000
 6R6  H2   C02  C01  119.54  3.000
 6R6  C03  C02  C01  121.59  3.000
 6R6  N13  C03  C04  121.66  3.000
 6R6  N13  C03  C02  119.71  3.000
 6R6  C04  C03  C02  118.63  3.000
 6R6  C10  C04  C05  118.48  3.000
 6R6  C10  C04  C03  122.93  3.000
 6R6  C05  C04  C03  118.59  3.000
 6R6  H3   C05  C06  120.49  3.000
 6R6  H3   C05  C04  117.70  3.000
 6R6  C06  C05  C04  121.81  3.000
 6R6  N07  C06  C05  120.14  3.000
 6R6  C05  C06  C01  119.99  3.000
 6R6  N07  C06  C01  119.87  3.000
 6R6  O09  N07  O08  122.55  3.000
 6R6  O08  N07  C06  118.91  3.000
 6R6  O09  N07  C06  118.54  3.000
 6R6  O12  C10  O11  125.74  3.000
 6R6  O11  C10  C04  117.02  3.000
 6R6  O12  C10  C04  117.24  3.000
 6R6  H6   N13  H5   121.85  3.000
 6R6  H6   N13  C03  116.90  3.000
 6R6  H5   N13  C03  121.24  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
 6R6  CONST_01  C04  C05  C06  C01    0.00   0.0  0
 6R6  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 6R6  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 6R6  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 6R6  CONST_05  C06  C05  C04  C03    0.00   0.0  0
 6R6  CONST_06  C06  C01  C02  C03    0.00   0.0  0
 6R6  CONST_07  N13  C03  C02  C01  180.00   0.0  0
 6R6  CONST_08  N07  C06  C01  C02  180.00   0.0  0
 6R6  CONST_09  C10  C04  C03  C02  180.00   0.0  0
 6R6  CONST_10  N07  C06  C05  C04  180.00   0.0  0
 6R6  CONST_11  N13  C03  C04  C05  180.00   0.0  0
 6R6  CONST_12  C10  C04  C05  C06  180.00   0.0  0
 6R6  CONST_13  H3   C05  C06  C01  180.00   0.0  0
 6R6  CONST_14  H1   C01  C02  C03  180.00   0.0  0
 6R6  CONST_15  H2   C02  C03  C04  180.00   0.0  0
 6R6  CONST_16  O09  N07  C06  C01    0.00   0.0  0
 6R6  CONST_17  O08  N07  C06  C01  180.00   0.0  0
 6R6  CONST_18  O09  N07  C06  C05  180.00   0.0  0
 6R6  CONST_19  O08  N07  C06  C05    0.00   0.0  0
 6R6  CONST_20  H5   N13  C03  C02    0.00   0.0  0
 6R6  CONST_21  H6   N13  C03  C02  180.00   0.0  0
 6R6  Var_01    O12  C10  C04  C03    1.10  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
 6R6  plan-1  C01  0.020
 6R6  plan-1  C02  0.020
 6R6  plan-1  C03  0.020
 6R6  plan-1  C04  0.020
 6R6  plan-1  C05  0.020
 6R6  plan-1  C06  0.020
 6R6  plan-1  N07  0.020
 6R6  plan-1  C10  0.020
 6R6  plan-1  N13  0.020
 6R6  plan-1  H1   0.020
 6R6  plan-1  H2   0.020
 6R6  plan-1  H3   0.020
 6R6  plan-2  C06  0.020
 6R6  plan-2  N07  0.020
 6R6  plan-2  O08  0.020
 6R6  plan-2  O09  0.020
 6R6  plan-3  C03  0.020
 6R6  plan-3  N13  0.020
 6R6  plan-3  H5   0.020
 6R6  plan-3  H6   0.020
 6R6  plan-4  C04  0.020
 6R6  plan-4  C10  0.020
 6R6  plan-4  O11  0.020
 6R6  plan-4  O12  0.020

