# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 16:52:37 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 2-methyl-1,3,5-trinitrobenzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(cc(cc1[N+]([O-])=O)[N+]([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
 TNL  TNL  2-methyl-1,3,5-trinitrobenzene  ligand  21  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TNL
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
 TNL  C1    C  CR6    0   0.138  -0.0504   0.0573  -1.2750
 TNL  C7    C  CH3    0  -0.716  -0.1211   0.1990  -2.7650
 TNL  C2    C  CR6    0   0.220   1.1583   0.0176  -0.5755
 TNL  N2    N  N      1   0.325   2.4266  -0.0034  -1.3003
 TNL  O21   O  O      0  -0.349   3.3000   0.7262  -0.9044
 TNL  O22   O  O     -1  -0.347   2.5244  -0.7704  -2.2246
 TNL  C3    C  CR16   0  -0.263   1.2584  -0.0122   0.8009
 TNL  C4    C  CR6    0   0.267   0.0907  -0.0348   1.5352
 TNL  N4    N  N      1   0.330   0.1636  -0.0842   2.9900
 TNL  O41   O  O      0  -0.356  -0.8759  -0.0959   3.5998
 TNL  O42   O  O     -1  -0.356   1.2589  -0.1097   3.4923
 TNL  C5    C  CR16   0  -0.265  -1.1442  -0.0022   0.9209
 TNL  C6    C  CR6    0   0.221  -1.1837   0.0269  -0.4587
 TNL  N6    N  N      1   0.326  -2.5192   0.0121  -1.0509
 TNL  O61   O  O      0  -0.350  -3.3515   0.7272  -0.5526
 TNL  O62   O  O     -1  -0.348  -2.7077  -0.7352  -1.9773
 TNL  H7C1  H  HCH3   0   0.292  -0.1501  -0.7775  -3.2470
 TNL  H7C2  H  HCH3   0   0.271  -1.0056   0.7505  -3.0697
 TNL  H7C3  H  HCH3   0   0.271   0.7365   0.7412  -3.1524
 TNL  H3    H  HCR6   0   0.345   2.2246  -0.0325   1.2849
 TNL  H5    H  HCR6   0   0.345  -2.0566  -0.0147   1.5003

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
 TNL  C1  C7    single    1.498  0.020  1.498
 TNL  C1  C2    aromatic  1.397  0.020  1.397
 TNL  C1  C6    aromatic  1.397  0.020  1.397
 TNL  C7  H7C1  single    0.970  0.020  1.090
 TNL  C7  H7C2  single    0.970  0.020  1.090
 TNL  C7  H7C3  single    0.970  0.020  1.090
 TNL  C2  N2    single    1.461  0.020  1.461
 TNL  C2  C3    aromatic  1.380  0.020  1.380
 TNL  N2  O21   double    1.205  0.020  1.205
 TNL  N2  O22   single    1.205  0.020  1.205
 TNL  C3  C4    aromatic  1.380  0.020  1.380
 TNL  C3  H3    single    0.930  0.020  1.080
 TNL  C4  N4    single    1.458  0.020  1.458
 TNL  C4  C5    aromatic  1.380  0.020  1.380
 TNL  N4  O41   double    1.205  0.020  1.205
 TNL  N4  O42   single    1.205  0.020  1.205
 TNL  C5  C6    aromatic  1.381  0.020  1.381
 TNL  C5  H5    single    0.930  0.020  1.080
 TNL  C6  N6    single    1.461  0.020  1.461
 TNL  N6  O61   double    1.205  0.020  1.205
 TNL  N6  O62   single    1.205  0.020  1.205

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
 TNL  C6    C1  C2    114.12  3.000
 TNL  C6    C1  C7    123.01  3.000
 TNL  C2    C1  C7    122.78  3.000
 TNL  H7C3  C7  H7C2  106.83  3.000
 TNL  H7C3  C7  H7C1  108.11  3.000
 TNL  H7C2  C7  H7C1  108.03  3.000
 TNL  H7C3  C7  C1    111.38  3.000
 TNL  H7C2  C7  C1    111.44  3.000
 TNL  H7C1  C7  C1    110.88  3.000
 TNL  C3    C2  N2    115.56  3.000
 TNL  C3    C2  C1    124.24  3.000
 TNL  N2    C2  C1    120.20  3.000
 TNL  O22   N2  O21   125.35  3.000
 TNL  O22   N2  C2    117.40  3.000
 TNL  O21   N2  C2    117.23  3.000
 TNL  H3    C3  C4    121.20  3.000
 TNL  H3    C3  C2    120.78  3.000
 TNL  C4    C3  C2    118.01  3.000
 TNL  C5    C4  N4    119.34  3.000
 TNL  C5    C4  C3    121.35  3.000
 TNL  N4    C4  C3    119.30  3.000
 TNL  O42   N4  O41   124.95  3.000
 TNL  O42   N4  C4    117.53  3.000
 TNL  O41   N4  C4    117.53  3.000
 TNL  H5    C5  C6    120.78  3.000
 TNL  H5    C5  C4    121.11  3.000
 TNL  C6    C5  C4    118.10  3.000
 TNL  N6    C6  C5    115.53  3.000
 TNL  N6    C6  C1    120.33  3.000
 TNL  C5    C6  C1    124.14  3.000
 TNL  O62   N6  O61   125.30  3.000
 TNL  O62   N6  C6    117.44  3.000
 TNL  O61   N6  C6    117.24  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
 TNL  CONST_01  C4    C3  C2  C1     0.00   0.0  0
 TNL  CONST_02  C4    C5  C6  C1     0.00   0.0  0
 TNL  CONST_03  C5    C6  C1  C2     0.00   0.0  0
 TNL  CONST_04  C5    C4  C3  C2     0.00   0.0  0
 TNL  CONST_05  C6    C1  C2  C3     0.00   0.0  0
 TNL  CONST_06  C6    C5  C4  C3     0.00   0.0  0
 TNL  CONST_07  C3    C2  C1  C7   180.00   0.0  0
 TNL  CONST_08  C5    C6  C1  C7   180.00   0.0  0
 TNL  CONST_09  N6    C6  C1  C2   180.00   0.0  0
 TNL  CONST_10  N4    C4  C3  C2   180.00   0.0  0
 TNL  CONST_11  C6    C1  C2  N2   180.00   0.0  0
 TNL  CONST_12  C4    C3  C2  N2   180.00   0.0  0
 TNL  CONST_13  N6    C6  C5  C4   180.00   0.0  0
 TNL  CONST_14  C6    C5  C4  N4   180.00   0.0  0
 TNL  CONST_15  H3    C3  C2  C1   180.00   0.0  0
 TNL  CONST_16  H5    C5  C6  C1   180.00   0.0  0
 TNL  CONST_23  O41   N4  C4  C3   180.00   0.0  0
 TNL  CONST_24  O42   N4  C4  C3     0.00   0.0  0
 TNL  CONST_25  C5    C4  N4  O41    0.00   0.0  0
 TNL  CONST_26  C5    C4  N4  O42  180.00   0.0  0
 TNL  Var_01    H7C1  C7  C1  C2    91.91  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
 TNL  plan-1  C1   0.020
 TNL  plan-1  C7   0.020
 TNL  plan-1  C2   0.020
 TNL  plan-1  N2   0.020
 TNL  plan-1  C3   0.020
 TNL  plan-1  C4   0.020
 TNL  plan-1  N4   0.020
 TNL  plan-1  C5   0.020
 TNL  plan-1  C6   0.020
 TNL  plan-1  N6   0.020
 TNL  plan-1  H3   0.020
 TNL  plan-1  H5   0.020
 TNL  plan-2  C2   0.020
 TNL  plan-2  N2   0.020
 TNL  plan-2  O21  0.020
 TNL  plan-2  O22  0.020
 TNL  plan-3  C4   0.020
 TNL  plan-3  N4   0.020
 TNL  plan-3  O41  0.020
 TNL  plan-3  O42  0.020
 TNL  plan-4  C6   0.020
 TNL  plan-4  N6   0.020
 TNL  plan-4  O61  0.020
 TNL  plan-4  O62  0.020

