# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 15:44:46 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 1-methyl-3-nitrobenzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(c1)[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
 3NT  3NT  '1-methyl-3-nitrobenzene  '  ligand  17  10  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3NT
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
 3NT  C1    C  CR6    0   0.099   1.8140  -0.4983  -0.0264
 3NT  C2    C  CR16   0  -0.317   0.4711  -0.8563  -0.0257
 3NT  C3    C  CR6    0   0.268  -0.5033   0.1309  -0.0018
 3NT  C4    C  CR16   0  -0.285  -0.1851   1.4805   0.0192
 3NT  C5    C  CR16   0  -0.235   1.1538   1.8335   0.0155
 3NT  C6    C  CR16   0  -0.271   2.1394   0.8571  -0.0086
 3NT  C7    C  CH3    0  -0.718   2.8838  -1.5494  -0.0245
 3NT  N3    N  N      1   0.329  -1.9049  -0.2642  -0.0046
 3NT  O1N   O  O      0  -0.379  -2.7420   0.6075   0.0093
 3NT  O2N   O  O     -1  -0.380  -2.1651  -1.4445  -0.0201
 3NT  H2    H  HCR6   0   0.289   0.1960  -1.9019  -0.0460
 3NT  H4    H  HCR6   0   0.296  -0.9505   2.2420   0.0344
 3NT  H5    H  HCR6   0   0.276   1.4281   2.8795   0.0269
 3NT  H6    H  HCR6   0   0.268   3.1814   1.1531  -0.0171
 3NT  H7C1  H  HCH3   0   0.258   3.1732  -1.8031   0.9969
 3NT  H7C2  H  HCH3   0   0.251   2.5452  -2.4658  -0.5056
 3NT  H7C3  H  HCH3   0   0.252   3.7793  -1.2056  -0.5404

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
 3NT  C1  C2    aromatic  1.390  0.020  1.390
 3NT  C1  C6    aromatic  1.394  0.020  1.394
 3NT  C1  C7    single    1.500  0.020  1.500
 3NT  C2  C3    aromatic  1.387  0.020  1.387
 3NT  C2  H2    single    0.930  0.020  1.080
 3NT  C3  C4    aromatic  1.387  0.020  1.387
 3NT  C3  N3    single    1.456  0.020  1.456
 3NT  C4  C5    aromatic  1.385  0.020  1.385
 3NT  C4  H4    single    0.930  0.020  1.080
 3NT  C5  C6    aromatic  1.388  0.020  1.388
 3NT  C5  H5    single    0.930  0.020  1.080
 3NT  C6  H6    single    0.930  0.020  1.080
 3NT  C7  H7C1  single    0.970  0.020  1.090
 3NT  C7  H7C2  single    0.970  0.020  1.090
 3NT  C7  H7C3  single    0.970  0.020  1.090
 3NT  N3  O1N   double    1.209  0.020  1.209
 3NT  N3  O2N   single    1.209  0.020  1.209

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
 3NT  C7    C1  C6    120.99  3.000
 3NT  C7    C1  C2    120.58  3.000
 3NT  C6    C1  C2    118.42  3.000
 3NT  H2    C2  C3    120.64  3.000
 3NT  H2    C2  C1    119.66  3.000
 3NT  C3    C2  C1    119.69  3.000
 3NT  N3    C3  C4    119.01  3.000
 3NT  N3    C3  C2    118.88  3.000
 3NT  C4    C3  C2    122.12  3.000
 3NT  H4    C4  C5    120.38  3.000
 3NT  H4    C4  C3    121.60  3.000
 3NT  C5    C4  C3    118.03  3.000
 3NT  H5    C5  C6    120.05  3.000
 3NT  H5    C5  C4    119.45  3.000
 3NT  C6    C5  C4    120.50  3.000
 3NT  H6    C6  C5    119.41  3.000
 3NT  H6    C6  C1    119.34  3.000
 3NT  C5    C6  C1    121.24  3.000
 3NT  H7C3  C7  H7C2  108.19  3.000
 3NT  H7C3  C7  H7C1  107.37  3.000
 3NT  H7C2  C7  H7C1  107.47  3.000
 3NT  H7C3  C7  C1    111.39  3.000
 3NT  H7C2  C7  C1    111.55  3.000
 3NT  H7C1  C7  C1    110.68  3.000
 3NT  O2N   N3  O1N   123.73  3.000
 3NT  O2N   N3  C3    118.17  3.000
 3NT  O1N   N3  C3    118.09  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
 3NT  CONST_01  C4    C3  C2  C1    0.00   0.0  0
 3NT  CONST_02  C4    C5  C6  C1    0.00   0.0  0
 3NT  CONST_03  C5    C6  C1  C2    0.00   0.0  0
 3NT  CONST_04  C5    C4  C3  C2    0.00   0.0  0
 3NT  CONST_05  C6    C1  C2  C3    0.00   0.0  0
 3NT  CONST_06  C6    C5  C4  C3    0.00   0.0  0
 3NT  CONST_07  N3    C3  C2  C1  180.00   0.0  0
 3NT  CONST_08  C7    C1  C2  C3  180.00   0.0  0
 3NT  CONST_09  N3    C3  C4  C5  180.00   0.0  0
 3NT  CONST_10  C7    C1  C6  C5  180.00   0.0  0
 3NT  CONST_11  H5    C5  C6  C1  180.00   0.0  0
 3NT  CONST_12  H6    C6  C1  C2  180.00   0.0  0
 3NT  CONST_13  H4    C4  C3  C2  180.00   0.0  0
 3NT  CONST_14  H2    C2  C3  C4  180.00   0.0  0
 3NT  CONST_15  O1N   N3  C3  C2  180.00   0.0  0
 3NT  CONST_16  O2N   N3  C3  C2    0.00   0.0  0
 3NT  CONST_17  O1N   N3  C3  C4    0.00   0.0  0
 3NT  CONST_18  O2N   N3  C3  C4  180.00   0.0  0
 3NT  Var_01    H7C1  C7  C1  C2  -91.15  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
 3NT  plan-1  C1   0.020
 3NT  plan-1  C2   0.020
 3NT  plan-1  C3   0.020
 3NT  plan-1  C4   0.020
 3NT  plan-1  C5   0.020
 3NT  plan-1  C6   0.020
 3NT  plan-1  C7   0.020
 3NT  plan-1  N3   0.020
 3NT  plan-1  H2   0.020
 3NT  plan-1  H4   0.020
 3NT  plan-1  H5   0.020
 3NT  plan-1  H6   0.020
 3NT  plan-2  C3   0.020
 3NT  plan-2  N3   0.020
 3NT  plan-2  O1N  0.020
 3NT  plan-2  O2N  0.020

