# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 23:07:05 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 2-nitro-N-phenyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccccc1C(=O)Nc2ccccc2
#
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
 NBI  NBI  2-nitro-N-phenyl-benzamide  ligand  28  18  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NBI
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
 NBI  C1   C  CR6    0   0.240  -2.4986   0.3703  -0.0116
 NBI  N1   N  NH1    0  -0.724   0.8760  -0.4670   0.2448
 NBI  O1   O  O      0  -0.440   0.0688   0.2947  -1.7546
 NBI  C2   C  CR6    0  -0.064  -1.4701  -0.5535  -0.1721
 NBI  N2   N  N      1   0.329  -2.2082   1.7928  -0.0921
 NBI  O2   O  O     -1  -0.365  -3.0940   2.5330  -0.4436
 NBI  C3   C  CR16   0  -0.253  -1.7757  -1.8994  -0.0260
 NBI  O3   O  O      0  -0.372  -1.0974   2.1533   0.2185
 NBI  C4   C  CR16   0  -0.218  -3.0696  -2.3041   0.2765
 NBI  C5   C  CR16   0  -0.254  -4.0775  -1.3651   0.4286
 NBI  C6   C  CR16   0  -0.262  -3.7953  -0.0160   0.2805
 NBI  C7   C  C      0   0.501  -0.0943  -0.1712  -0.6445
 NBI  C8   C  CR6    0   0.375   2.2630  -0.3083   0.1284
 NBI  C9   C  CR16   0  -0.345   3.0249  -0.6534   1.2472
 NBI  C10  C  CR16   0  -0.244   4.4036  -0.5366   1.2240
 NBI  C11  C  CR16   0  -0.270   5.0498  -0.0737   0.0846
 NBI  C12  C  CR16   0  -0.244   4.2924   0.2694  -1.0250
 NBI  C13  C  CR16   0  -0.314   2.9075   0.1582  -1.0175
 NBI  HN1  H  HNH1   0   0.427   0.5631  -0.8121   1.1407
 NBI  H3   H  HCR6   0   0.290  -1.0005  -2.6419  -0.1634
 NBI  H4   H  HCR6   0   0.285  -3.2870  -3.3574   0.3894
 NBI  H5   H  HCR6   0   0.286  -5.0842  -1.6763   0.6694
 NBI  H6   H  HCR6   0   0.304  -4.5742   0.7206   0.4158
 NBI  H9   H  HCR6   0   0.272   2.5331  -1.0182   2.1413
 NBI  H10  H  HCR6   0   0.262   4.9730  -0.8119   2.1022
 NBI  H11  H  HCR6   0   0.257   6.1275   0.0176   0.0636
 NBI  H12  H  HCR6   0   0.260   4.7794   0.6324  -1.9207
 NBI  H13  H  HCR6   0   0.282   2.3511   0.4352  -1.8974

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
 NBI  C1   C2   aromatic  1.392  0.020  1.392
 NBI  C1   N2   single    1.454  0.020  1.454
 NBI  C1   C6   aromatic  1.384  0.020  1.384
 NBI  N1   C7   single    1.349  0.020  1.349
 NBI  N1   C8   single    1.401  0.020  1.401
 NBI  O1   C7   double    1.215  0.020  1.215
 NBI  C2   C3   aromatic  1.388  0.020  1.388
 NBI  C2   C7   single    1.504  0.020  1.504
 NBI  N2   O2   single    1.207  0.020  1.207
 NBI  N2   O3   double    1.208  0.020  1.208
 NBI  C3   C4   aromatic  1.389  0.020  1.389
 NBI  C4   C5   aromatic  1.386  0.020  1.386
 NBI  C5   C6   aromatic  1.386  0.020  1.386
 NBI  C8   C9   aromatic  1.397  0.020  1.397
 NBI  C8   C13  aromatic  1.395  0.020  1.395
 NBI  C9   C10  aromatic  1.384  0.020  1.384
 NBI  C10  C11  aromatic  1.389  0.020  1.389
 NBI  C11  C12  aromatic  1.387  0.020  1.387
 NBI  C12  C13  aromatic  1.389  0.020  1.389
 NBI  N1   HN1  single    0.860  0.020  1.020
 NBI  C3   H3   single    0.930  0.020  1.080
 NBI  C4   H4   single    0.930  0.020  1.080
 NBI  C5   H5   single    0.930  0.020  1.080
 NBI  C6   H6   single    0.930  0.020  1.080
 NBI  C9   H9   single    0.930  0.020  1.080
 NBI  C10  H10  single    0.930  0.020  1.080
 NBI  C11  H11  single    0.930  0.020  1.080
 NBI  C12  H12  single    0.930  0.020  1.080
 NBI  C13  H13  single    0.930  0.020  1.080

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
 NBI  C6   C1   N2   118.15  3.000
 NBI  C6   C1   C2   122.10  3.000
 NBI  N2   C1   C2   119.69  3.000
 NBI  HN1  N1   C8   114.79  3.000
 NBI  HN1  N1   C7   115.91  3.000
 NBI  C8   N1   C7   129.23  3.000
 NBI  C7   C2   C3   118.75  3.000
 NBI  C7   C2   C1   122.92  3.000
 NBI  C3   C2   C1   117.95  3.000
 NBI  O3   N2   O2   124.51  3.000
 NBI  O3   N2   C1   117.47  3.000
 NBI  O2   N2   C1   118.01  3.000
 NBI  H3   C3   C4   119.67  3.000
 NBI  H3   C3   C2   119.62  3.000
 NBI  C4   C3   C2   120.70  3.000
 NBI  H4   C4   C5   120.15  3.000
 NBI  H4   C4   C3   119.59  3.000
 NBI  C5   C4   C3   120.26  3.000
 NBI  H5   C5   C6   119.58  3.000
 NBI  H5   C5   C4   120.44  3.000
 NBI  C6   C5   C4   119.98  3.000
 NBI  H6   C6   C5   120.22  3.000
 NBI  H6   C6   C1   120.76  3.000
 NBI  C5   C6   C1   119.00  3.000
 NBI  C2   C7   O1   120.48  3.000
 NBI  C2   C7   N1   113.27  3.000
 NBI  O1   C7   N1   126.15  3.000
 NBI  C13  C8   C9   119.24  3.000
 NBI  C13  C8   N1   124.30  3.000
 NBI  C9   C8   N1   116.45  3.000
 NBI  H9   C9   C10  119.63  3.000
 NBI  H9   C9   C8   119.77  3.000
 NBI  C10  C9   C8   120.61  3.000
 NBI  H10  C10  C11  120.37  3.000
 NBI  H10  C10  C9   119.28  3.000
 NBI  C11  C10  C9   120.35  3.000
 NBI  H11  C11  C12  120.51  3.000
 NBI  H11  C11  C10  120.50  3.000
 NBI  C12  C11  C10  118.99  3.000
 NBI  H12  C12  C13  118.67  3.000
 NBI  H12  C12  C11  119.97  3.000
 NBI  C13  C12  C11  121.36  3.000
 NBI  H13  C13  C12  119.34  3.000
 NBI  H13  C13  C8   121.21  3.000
 NBI  C12  C13  C8   119.45  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
 NBI  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 NBI  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 NBI  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 NBI  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 NBI  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 NBI  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 NBI  CONST_07  C11  C10  C9   C8     0.00   0.0  0
 NBI  CONST_08  C11  C12  C13  C8     0.00   0.0  0
 NBI  CONST_09  C12  C13  C8   C9     0.00   0.0  0
 NBI  CONST_10  C12  C11  C10  C9     0.00   0.0  0
 NBI  CONST_11  C13  C8   C9   C10    0.00   0.0  0
 NBI  CONST_12  C13  C12  C11  C10    0.00   0.0  0
 NBI  CONST_13  C10  C9   C8   N1   180.00   0.0  0
 NBI  CONST_14  C12  C13  C8   N1   180.00   0.0  0
 NBI  CONST_15  C3   C2   C1   N2   180.00   0.0  0
 NBI  CONST_16  C5   C6   C1   N2   180.00   0.0  0
 NBI  CONST_17  C7   C2   C3   C4   180.00   0.0  0
 NBI  CONST_18  C7   C2   C1   C6   180.00   0.0  0
 NBI  CONST_19  H3   C3   C2   C1   180.00   0.0  0
 NBI  CONST_20  H5   C5   C6   C1   180.00   0.0  0
 NBI  CONST_21  H6   C6   C1   C2   180.00   0.0  0
 NBI  CONST_22  H4   C4   C3   C2   180.00   0.0  0
 NBI  CONST_23  H10  C10  C9   C8   180.00   0.0  0
 NBI  CONST_24  H12  C12  C13  C8   180.00   0.0  0
 NBI  CONST_25  H13  C13  C8   C9   180.00   0.0  0
 NBI  CONST_26  H11  C11  C10  C9   180.00   0.0  0
 NBI  CONST_27  H9   C9   C10  C11  180.00   0.0  0
 NBI  CONST_28  C8   N1   C7   C2   180.00   0.0  0
 NBI  CONST_33  C9   C8   N1   C7   180.00   0.0  0
 NBI  CONST_34  C13  C8   N1   C7     0.00   0.0  0
 NBI  CONST_35  HN1  N1   C8   C9     0.00   0.0  0
 NBI  CONST_36  C8   N1   C7   O1     0.00   0.0  0
 NBI  Var_01    N1   C7   C2   C1   120.06  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
 NBI  plan-1  C1   0.020
 NBI  plan-1  C2   0.020
 NBI  plan-1  N2   0.020
 NBI  plan-1  C3   0.020
 NBI  plan-1  C4   0.020
 NBI  plan-1  C5   0.020
 NBI  plan-1  C6   0.020
 NBI  plan-1  C7   0.020
 NBI  plan-1  H3   0.020
 NBI  plan-1  H4   0.020
 NBI  plan-1  H5   0.020
 NBI  plan-1  H6   0.020
 NBI  plan-2  N1   0.020
 NBI  plan-2  C8   0.020
 NBI  plan-2  C9   0.020
 NBI  plan-2  C10  0.020
 NBI  plan-2  C11  0.020
 NBI  plan-2  C12  0.020
 NBI  plan-2  C13  0.020
 NBI  plan-2  H9   0.020
 NBI  plan-2  H10  0.020
 NBI  plan-2  H11  0.020
 NBI  plan-2  H12  0.020
 NBI  plan-2  H13  0.020
 NBI  plan-3  N1   0.020
 NBI  plan-3  O1   0.020
 NBI  plan-3  C2   0.020
 NBI  plan-3  C7   0.020
 NBI  plan-3  C8   0.020
 NBI  plan-3  HN1  0.020
 NBI  plan-4  C1   0.020
 NBI  plan-4  N2   0.020
 NBI  plan-4  O2   0.020
 NBI  plan-4  O3   0.020

