# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 04:36:57 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 4-nitrobenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)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
 4NB  4NB  '4-nitrobenzoic acid      '  ligand  17  12  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4NB
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
 4NB  C    C  C      0   0.552   2.8722  -0.0995   0.0135
 4NB  O1   O  OH1    0  -0.576   3.4428   1.0954   0.0315
 4NB  O2   O  O      0  -0.417   3.4890  -1.1338   0.0158
 4NB  C1   C  CR6    0  -0.064   1.3855  -0.0266  -0.0066
 4NB  C2   C  CR16   0  -0.233   0.7044   1.1874  -0.0124
 4NB  C3   C  CR16   0  -0.235  -0.6789   1.2112  -0.0253
 4NB  C4   C  CR6    0   0.268  -1.3677   0.0095  -0.0324
 4NB  C5   C  CR16   0  -0.238  -0.7109  -1.2109  -0.0281
 4NB  C6   C  CR16   0  -0.231   0.6711  -1.2207  -0.0155
 4NB  N    N  N      1   0.332  -2.8278   0.0291  -0.0411
 4NB  O1'  O  O     -1  -0.368  -3.4042  -1.0311  -0.0508
 4NB  O2'  O  O      0  -0.366  -3.3773   1.1030  -0.0364
 4NB  HO1  H  HOH1   0   0.466   4.4034   0.9946   0.0521
 4NB  H2   H  HCR6   0   0.268   1.2377   2.1264  -0.0062
 4NB  H3   H  HCR6   0   0.287  -1.1989   2.1570  -0.0284
 4NB  H5   H  HCR6   0   0.286  -1.2564  -2.1423  -0.0325
 4NB  H6   H  HCR6   0   0.267   1.1928  -2.1668  -0.0114

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
 4NB  C   O1   single    1.324  0.020  1.324
 4NB  C   O2   double    1.204  0.020  1.204
 4NB  C   C1   single    1.489  0.020  1.489
 4NB  O1  HO1  single    0.850  0.020  0.980
 4NB  C1  C2   aromatic  1.392  0.020  1.392
 4NB  C1  C6   aromatic  1.391  0.020  1.391
 4NB  C2  C3   aromatic  1.384  0.020  1.384
 4NB  C2  H2   single    0.930  0.020  1.080
 4NB  C3  C4   aromatic  1.385  0.020  1.385
 4NB  C3  H3   single    0.930  0.020  1.080
 4NB  C4  C5   aromatic  1.386  0.020  1.386
 4NB  C4  N    single    1.460  0.020  1.460
 4NB  C5  C6   aromatic  1.382  0.020  1.382
 4NB  C5  H5   single    0.930  0.020  1.080
 4NB  C6  H6   single    0.930  0.020  1.080
 4NB  N   O1'  single    1.207  0.020  1.207
 4NB  N   O2'  double    1.206  0.020  1.206

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
 4NB  C1   C   O2   123.61  3.000
 4NB  C1   C   O1   112.73  3.000
 4NB  O2   C   O1   123.66  3.000
 4NB  HO1  O1  C    109.55  3.000
 4NB  C6   C1  C2   119.81  3.000
 4NB  C6   C1  C    118.09  3.000
 4NB  C2   C1  C    122.10  3.000
 4NB  H2   C2  C3   118.61  3.000
 4NB  H2   C2  C1   121.11  3.000
 4NB  C3   C2  C1   120.28  3.000
 4NB  H3   C3  C4   121.38  3.000
 4NB  H3   C3  C2   119.78  3.000
 4NB  C4   C3  C2   118.84  3.000
 4NB  N    C4  C5   119.06  3.000
 4NB  N    C4  C3   119.05  3.000
 4NB  C5   C4  C3   121.89  3.000
 4NB  H5   C5  C6   119.95  3.000
 4NB  H5   C5  C4   121.35  3.000
 4NB  C6   C5  C4   118.70  3.000
 4NB  H6   C6  C5   119.28  3.000
 4NB  H6   C6  C1   120.24  3.000
 4NB  C5   C6  C1   120.48  3.000
 4NB  O2'  N   O1'  124.37  3.000
 4NB  O2'  N   C4   117.86  3.000
 4NB  O1'  N   C4   117.77  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
 4NB  CONST_01  C4   C3  C2  C1    0.00   0.0  0
 4NB  CONST_02  C4   C5  C6  C1    0.00   0.0  0
 4NB  CONST_03  C5   C6  C1  C2    0.00   0.0  0
 4NB  CONST_04  C5   C4  C3  C2    0.00   0.0  0
 4NB  CONST_05  C6   C1  C2  C3    0.00   0.0  0
 4NB  CONST_06  C6   C5  C4  C3    0.00   0.0  0
 4NB  CONST_07  C3   C2  C1  C   180.00   0.0  0
 4NB  CONST_08  C5   C6  C1  C   180.00   0.0  0
 4NB  CONST_09  N    C4  C3  C2  180.00   0.0  0
 4NB  CONST_10  N    C4  C5  C6  180.00   0.0  0
 4NB  CONST_11  H3   C3  C2  C1  180.00   0.0  0
 4NB  CONST_12  H5   C5  C6  C1  180.00   0.0  0
 4NB  CONST_13  H6   C6  C1  C2  180.00   0.0  0
 4NB  CONST_14  H2   C2  C3  C4  180.00   0.0  0
 4NB  CONST_15  O1'  N   C4  C3  180.00   0.0  0
 4NB  CONST_16  O2'  N   C4  C3    0.00   0.0  0
 4NB  CONST_17  O1'  N   C4  C5    0.00   0.0  0
 4NB  CONST_18  O2'  N   C4  C5  180.00   0.0  0
 4NB  CONST_19  HO1  O1  C   C1  180.00   0.0  0
 4NB  Var_01    C2   C1  C   O1    0.32  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
 4NB  plan-1  C    0.020
 4NB  plan-1  C1   0.020
 4NB  plan-1  C2   0.020
 4NB  plan-1  C3   0.020
 4NB  plan-1  C4   0.020
 4NB  plan-1  C5   0.020
 4NB  plan-1  C6   0.020
 4NB  plan-1  N    0.020
 4NB  plan-1  H2   0.020
 4NB  plan-1  H3   0.020
 4NB  plan-1  H5   0.020
 4NB  plan-1  H6   0.020
 4NB  plan-2  C4   0.020
 4NB  plan-2  N    0.020
 4NB  plan-2  O1'  0.020
 4NB  plan-2  O2'  0.020
 4NB  plan-3  C    0.020
 4NB  plan-3  O1   0.020
 4NB  plan-3  O2   0.020
 4NB  plan-3  C1   0.020
 4NB  plan-3  HO1  0.020

