# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 16:50:03 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: 2,4,6-trinitrophenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1c(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
 TNF  TNF  '2,4,6-trinitrophenol     '  ligand  19  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 PERFECT
;

data_comp_TNF
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
 TNF  C1   C  CR6    0   0.404   1.2622   0.0809   0.0739
 TNF  C2   C  CR6    0   0.209   0.4875   1.2656   0.0327
 TNF  C3   C  CR16   0  -0.323  -0.8891   1.2294  -0.0088
 TNF  C4   C  CR6    0   0.298  -1.5456   0.0132  -0.0106
 TNF  N4   N  N      1   0.329  -2.9964  -0.0139  -0.0568
 TNF  N2   N  N      1   0.345   1.1076   2.5859   0.0306
 TNF  O1   O  OH1    0  -0.536   2.5597   0.1328   0.1157
 TNF  O21  O  O     -1  -0.370   0.3672   3.5409   0.0255
 TNF  O22  O  O      0  -0.351   2.3083   2.6613   0.0321
 TNF  O41  O  O     -1  -0.361  -3.5750   1.0435  -0.1031
 TNF  C6   C  CR6    0   0.198   0.5305  -1.1358   0.0692
 TNF  C5   C  CR16   0  -0.324  -0.8479  -1.1737   0.0282
 TNF  O42  O  O      0  -0.362  -3.5360  -1.0929  -0.0461
 TNF  N6   N  N      1   0.374   1.2221  -2.4067   0.1069
 TNF  O61  O  O     -1  -0.331   0.5774  -3.4168   0.0938
 TNF  O62  O  O      0  -0.408   2.4427  -2.3927   0.1498
 TNF  H3   H  HCR6   0   0.353  -1.4504   2.1519  -0.0398
 TNF  H1   H  HOH1   0   0.502   2.9113  -0.7859   0.1431
 TNF  H5   H  HCR6   0   0.354  -1.3665  -2.1217   0.0261

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
 TNF  C1  C2   aromatic  1.416  0.020  1.416
 TNF  C1  O1   single    1.299  0.020  1.299
 TNF  C1  C6   aromatic  1.420  0.020  1.420
 TNF  C2  C3   aromatic  1.378  0.020  1.378
 TNF  C2  N2   single    1.459  0.020  1.459
 TNF  C3  C4   aromatic  1.382  0.020  1.382
 TNF  C3  H3   single    0.930  0.020  1.080
 TNF  C4  N4   single    1.452  0.020  1.452
 TNF  C4  C5   aromatic  1.377  0.020  1.377
 TNF  N4  O41  single    1.206  0.020  1.206
 TNF  N4  O42  double    1.206  0.020  1.206
 TNF  N2  O21  single    1.208  0.020  1.208
 TNF  N2  O22  double    1.203  0.020  1.203
 TNF  O1  H1   single    0.850  0.020  0.980
 TNF  C6  C5   aromatic  1.380  0.020  1.380
 TNF  C6  N6   single    1.447  0.020  1.447
 TNF  C5  H5   single    0.930  0.020  1.080
 TNF  N6  O61  single    1.198  0.020  1.198
 TNF  N6  O62  double    1.221  0.020  1.221

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
 TNF  C6   C1  O1   123.30  3.000
 TNF  C6   C1  C2   115.78  3.000
 TNF  O1   C1  C2   120.92  3.000
 TNF  N2   C2  C3   116.64  3.000
 TNF  N2   C2  C1   121.65  3.000
 TNF  C3   C2  C1   121.71  3.000
 TNF  H3   C3  C4   120.31  3.000
 TNF  H3   C3  C2   119.84  3.000
 TNF  C4   C3  C2   119.85  3.000
 TNF  C5   C4  N4   119.40  3.000
 TNF  C5   C4  C3   121.18  3.000
 TNF  N4   C4  C3   119.42  3.000
 TNF  O42  N4  O41  124.74  3.000
 TNF  O42  N4  C4   117.61  3.000
 TNF  O41  N4  C4   117.65  3.000
 TNF  O22  N2  O21  124.20  3.000
 TNF  O22  N2  C2   118.74  3.000
 TNF  O21  N2  C2   117.06  3.000
 TNF  H1   O1  C1   108.69  3.000
 TNF  N6   C6  C5   117.01  3.000
 TNF  N6   C6  C1   120.40  3.000
 TNF  C5   C6  C1   122.59  3.000
 TNF  H5   C5  C6   120.24  3.000
 TNF  H5   C5  C4   120.86  3.000
 TNF  C6   C5  C4   118.90  3.000
 TNF  O62  N6  O61  123.21  3.000
 TNF  O62  N6  C6   117.93  3.000
 TNF  O61  N6  C6   118.86  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
 TNF  CONST_01  C4   C3  C2  C1     0.00  0.0  0
 TNF  CONST_02  C4   C5  C6  C1     0.00  0.0  0
 TNF  CONST_03  C5   C6  C1  C2     0.00  0.0  0
 TNF  CONST_04  C5   C4  C3  C2     0.00  0.0  0
 TNF  CONST_05  C6   C1  C2  C3     0.00  0.0  0
 TNF  CONST_06  C6   C5  C4  C3     0.00  0.0  0
 TNF  CONST_07  N6   C6  C1  C2   180.00  0.0  0
 TNF  CONST_08  N4   C4  C3  C2   180.00  0.0  0
 TNF  CONST_09  O1   C1  C2  C3   180.00  0.0  0
 TNF  CONST_10  N2   C2  C3  C4   180.00  0.0  0
 TNF  CONST_11  N6   C6  C5  C4   180.00  0.0  0
 TNF  CONST_12  C6   C5  C4  N4   180.00  0.0  0
 TNF  CONST_13  C6   C1  C2  N2   180.00  0.0  0
 TNF  CONST_14  C5   C6  C1  O1   180.00  0.0  0
 TNF  CONST_15  H3   C3  C2  C1   180.00  0.0  0
 TNF  CONST_16  H5   C5  C6  C1   180.00  0.0  0
 TNF  CONST_17  O21  N2  C2  C1   180.00  0.0  0
 TNF  CONST_18  O22  N2  C2  C1     0.00  0.0  0
 TNF  CONST_19  O61  N6  C6  C1   180.00  0.0  0
 TNF  CONST_20  O62  N6  C6  C1     0.00  0.0  0
 TNF  CONST_21  O21  N2  C2  C3     0.00  0.0  0
 TNF  CONST_22  O22  N2  C2  C3   180.00  0.0  0
 TNF  CONST_23  O41  N4  C4  C3     0.00  0.0  0
 TNF  CONST_24  O42  N4  C4  C3   180.00  0.0  0
 TNF  CONST_25  C5   C4  N4  O41  180.00  0.0  0
 TNF  CONST_26  O42  N4  C4  C5     0.00  0.0  0
 TNF  CONST_27  O61  N6  C6  C5     0.00  0.0  0
 TNF  CONST_28  O62  N6  C6  C5   180.00  0.0  0

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
 TNF  plan-1  C1   0.020
 TNF  plan-1  C2   0.020
 TNF  plan-1  C3   0.020
 TNF  plan-1  C4   0.020
 TNF  plan-1  N4   0.020
 TNF  plan-1  N2   0.020
 TNF  plan-1  O1   0.020
 TNF  plan-1  C6   0.020
 TNF  plan-1  C5   0.020
 TNF  plan-1  N6   0.020
 TNF  plan-1  H3   0.020
 TNF  plan-1  H5   0.020
 TNF  plan-2  C4   0.020
 TNF  plan-2  N4   0.020
 TNF  plan-2  O41  0.020
 TNF  plan-2  O42  0.020
 TNF  plan-3  C2   0.020
 TNF  plan-3  N2   0.020
 TNF  plan-3  O21  0.020
 TNF  plan-3  O22  0.020
 TNF  plan-4  C6   0.020
 TNF  plan-4  N6   0.020
 TNF  plan-4  O61  0.020
 TNF  plan-4  O62  0.020

