# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:50:10 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 2,4-dinitrophenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1[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
 DNF  DNF  '2,4-dinitrophenol        '  ligand  17  13  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DNF
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
 DNF  C1   C  CR6    0   0.403   1.1504   1.3279   0.1026
 DNF  O1   O  OH1    0  -0.578   2.3078   1.9476   0.1591
 DNF  C2   C  CR6    0   0.187   0.9756  -0.0725   0.0776
 DNF  N2   N  N      1   0.369   2.1097  -0.9616   0.1132
 DNF  O21  O  O      0  -0.414   3.2231  -0.4625   0.1587
 DNF  O22  O  O     -1  -0.350   1.9230  -2.1488   0.0967
 DNF  C3   C  CR16   0  -0.330  -0.2886  -0.6418   0.0175
 DNF  C4   C  CR6    0   0.260  -1.3897   0.1802  -0.0181
 DNF  N4   N  N      1   0.329  -2.7107  -0.4100  -0.0812
 DNF  O41  O  O      0  -0.376  -2.7961  -1.6151  -0.1108
 DNF  O42  O  O     -1  -0.373  -3.6592   0.3381  -0.1012
 DNF  C5   C  CR16   0  -0.236  -1.2529   1.5700   0.0055
 DNF  C6   C  CR16   0  -0.346  -0.0024   2.1263   0.0647
 DNF  HO1  H  HOH1   0   0.492   3.0306   1.2915   0.1785
 DNF  H3   H  HCR6   0   0.338  -0.3958  -1.7165  -0.0004
 DNF  H5   H  HCR6   0   0.318  -2.1177   2.2165  -0.0233
 DNF  H6   H  HCR6   0   0.309   0.1147   3.2012   0.0823

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
 DNF  C1  O1   single    1.314  0.020  1.314
 DNF  C1  C2   aromatic  1.411  0.020  1.411
 DNF  C1  C6   aromatic  1.403  0.020  1.403
 DNF  O1  HO1  single    0.850  0.020  0.980
 DNF  C2  N2   single    1.442  0.020  1.442
 DNF  C2  C3   aromatic  1.388  0.020  1.388
 DNF  N2  O21  double    1.221  0.020  1.221
 DNF  N2  O22  single    1.202  0.020  1.202
 DNF  C3  C4   aromatic  1.375  0.020  1.375
 DNF  C3  H3   single    0.930  0.020  1.080
 DNF  C4  N4   single    1.448  0.020  1.448
 DNF  C4  C5   aromatic  1.397  0.020  1.397
 DNF  N4  O41  double    1.208  0.020  1.208
 DNF  N4  O42  single    1.208  0.020  1.208
 DNF  C5  C6   aromatic  1.370  0.020  1.370
 DNF  C5  H5   single    0.930  0.020  1.080
 DNF  C6  H6   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
 DNF  C6   C1  C2   117.54  3.000
 DNF  C6   C1  O1   117.17  3.000
 DNF  C2   C1  O1   125.29  3.000
 DNF  HO1  O1  C1   109.64  3.000
 DNF  C3   C2  N2   117.69  3.000
 DNF  C3   C2  C1   121.38  3.000
 DNF  N2   C2  C1   120.94  3.000
 DNF  O22  N2  O21  123.08  3.000
 DNF  O22  N2  C2   119.13  3.000
 DNF  O21  N2  C2   117.79  3.000
 DNF  H3   C3  C4   121.01  3.000
 DNF  H3   C3  C2   119.95  3.000
 DNF  C4   C3  C2   119.04  3.000
 DNF  C5   C4  N4   119.71  3.000
 DNF  C5   C4  C3   121.08  3.000
 DNF  N4   C4  C3   119.21  3.000
 DNF  O42  N4  O41  124.16  3.000
 DNF  O42  N4  C4   117.67  3.000
 DNF  O41  N4  C4   118.17  3.000
 DNF  H5   C5  C6   119.27  3.000
 DNF  H5   C5  C4   121.12  3.000
 DNF  C6   C5  C4   119.61  3.000
 DNF  H6   C6  C5   120.21  3.000
 DNF  H6   C6  C1   118.44  3.000
 DNF  C5   C6  C1   121.35  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
 DNF  CONST_01  C4   C3  C2  C1     0.00  0.0  0
 DNF  CONST_02  C4   C5  C6  C1     0.00  0.0  0
 DNF  CONST_03  C5   C6  C1  C2     0.00  0.0  0
 DNF  CONST_04  C5   C4  C3  C2     0.00  0.0  0
 DNF  CONST_05  C6   C1  C2  C3     0.00  0.0  0
 DNF  CONST_06  C6   C5  C4  C3     0.00  0.0  0
 DNF  CONST_07  C3   C2  C1  O1   180.00  0.0  0
 DNF  CONST_08  C5   C6  C1  O1   180.00  0.0  0
 DNF  CONST_09  N4   C4  C3  C2   180.00  0.0  0
 DNF  CONST_10  C6   C1  C2  N2   180.00  0.0  0
 DNF  CONST_11  C4   C3  C2  N2   180.00  0.0  0
 DNF  CONST_12  C6   C5  C4  N4   180.00  0.0  0
 DNF  CONST_13  H3   C3  C2  C1   180.00  0.0  0
 DNF  CONST_14  H5   C5  C6  C1   180.00  0.0  0
 DNF  CONST_15  H6   C6  C1  C2   180.00  0.0  0
 DNF  CONST_16  O21  N2  C2  C1     0.00  0.0  0
 DNF  CONST_17  O22  N2  C2  C1   180.00  0.0  0
 DNF  CONST_18  C3   C2  N2  O21  180.00  0.0  0
 DNF  CONST_19  C3   C2  N2  O22    0.00  0.0  0
 DNF  CONST_20  O41  N4  C4  C3     0.00  0.0  0
 DNF  CONST_21  O42  N4  C4  C3   180.00  0.0  0
 DNF  CONST_22  C5   C4  N4  O41  180.00  0.0  0
 DNF  CONST_23  C5   C4  N4  O42    0.00  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
 DNF  plan-1  C1   0.020
 DNF  plan-1  O1   0.020
 DNF  plan-1  C2   0.020
 DNF  plan-1  N2   0.020
 DNF  plan-1  C3   0.020
 DNF  plan-1  C4   0.020
 DNF  plan-1  N4   0.020
 DNF  plan-1  C5   0.020
 DNF  plan-1  C6   0.020
 DNF  plan-1  H3   0.020
 DNF  plan-1  H5   0.020
 DNF  plan-1  H6   0.020
 DNF  plan-2  C2   0.020
 DNF  plan-2  N2   0.020
 DNF  plan-2  O21  0.020
 DNF  plan-2  O22  0.020
 DNF  plan-3  C4   0.020
 DNF  plan-3  N4   0.020
 DNF  plan-3  O41  0.020
 DNF  plan-3  O42  0.020

