# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:51:54 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 3,4-dinitrophenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(c(c1)[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
 DNX  DNX  '3,4-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_DNX
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
 DNX  C1   C  CR6    0   0.404   2.4290   0.1032  -0.1246
 DNX  C2   C  CR16   0  -0.386   1.4410  -0.8853  -0.1599
 DNX  C3   C  CR6    0   0.252   0.1182  -0.5187  -0.0895
 DNX  N3   N  N      1   0.347  -0.8566  -1.5980  -0.2374
 DNX  C4   C  CR6    0   0.246  -0.2582   0.8149   0.0285
 DNX  N4   N  N      1   0.338  -1.6360   1.2029   0.2074
 DNX  C5   C  CR16   0  -0.267   0.7289   1.7909   0.0626
 DNX  C6   C  CR16   0  -0.324   2.0598   1.4443  -0.0158
 DNX  O1   O  OH1    0  -0.597   3.7234  -0.1833  -0.1944
 DNX  O31  O  O      0  -0.348  -0.8582  -2.4530   0.6090
 DNX  O32  O  O     -1  -0.354  -1.5464  -1.5758  -1.2228
 DNX  O41  O  O      0  -0.365  -1.9406   2.3425  -0.0470
 DNX  O42  O  O     -1  -0.386  -2.4040   0.3648   0.6220
 DNX  H2   H  HCR6   0   0.327   1.7112  -1.9279  -0.2724
 DNX  H5   H  HCR6   0   0.316   0.4585   2.8308   0.1758
 DNX  H6   H  HCR6   0   0.304   2.8216   2.2108   0.0194
 DNX  HO1  H  HOH1   0   0.493   3.8760  -1.1346  -0.2567

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
 DNX  C1  C2   aromatic  1.398  0.020  1.398
 DNX  C1  C6   aromatic  1.395  0.020  1.395
 DNX  C1  O1   single    1.328  0.020  1.328
 DNX  C2  C3   aromatic  1.375  0.020  1.375
 DNX  C3  N3   single    1.462  0.020  1.462
 DNX  C3  C4   aromatic  1.391  0.020  1.391
 DNX  N3  O31  double    1.203  0.020  1.203
 DNX  N3  O32  single    1.203  0.020  1.203
 DNX  C4  N4   single    1.443  0.020  1.443
 DNX  C4  C5   aromatic  1.389  0.020  1.389
 DNX  N4  O41  double    1.207  0.020  1.207
 DNX  N4  O42  single    1.210  0.020  1.210
 DNX  C5  C6   aromatic  1.377  0.020  1.377
 DNX  C2  H2   single    0.930  0.020  1.080
 DNX  C5  H5   single    0.930  0.020  1.080
 DNX  C6  H6   single    0.930  0.020  1.080
 DNX  O1  HO1  single    0.850  0.020  0.980

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
 DNX  O1   C1  C6   118.01  3.000
 DNX  O1   C1  C2   122.35  3.000
 DNX  C6   C1  C2   119.64  3.000
 DNX  H2   C2  C3   120.14  3.000
 DNX  H2   C2  C1   120.47  3.000
 DNX  C3   C2  C1   119.36  3.000
 DNX  C4   C3  N3   122.42  3.000
 DNX  C4   C3  C2   121.37  3.000
 DNX  N3   C3  C2   116.08  3.000
 DNX  O32  N3  O31  126.06  3.000
 DNX  O32  N3  C3   116.85  3.000
 DNX  O31  N3  C3   117.03  3.000
 DNX  C5   C4  N4   119.14  3.000
 DNX  C5   C4  C3   118.92  3.000
 DNX  N4   C4  C3   121.80  3.000
 DNX  O42  N4  O41  124.49  3.000
 DNX  O42  N4  C4   117.54  3.000
 DNX  O41  N4  C4   117.96  3.000
 DNX  H5   C5  C6   119.34  3.000
 DNX  H5   C5  C4   120.07  3.000
 DNX  C6   C5  C4   120.57  3.000
 DNX  H6   C6  C5   120.03  3.000
 DNX  H6   C6  C1   119.84  3.000
 DNX  C5   C6  C1   120.13  3.000
 DNX  HO1  O1  C1   111.72  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
 DNX  CONST_01  C4  C3  C2  C1    0.00  0.0  0
 DNX  CONST_02  C4  C5  C6  C1    0.00  0.0  0
 DNX  CONST_03  C5  C6  C1  C2    0.00  0.0  0
 DNX  CONST_04  C5  C4  C3  C2    0.00  0.0  0
 DNX  CONST_05  C6  C1  C2  C3    0.00  0.0  0
 DNX  CONST_06  C6  C5  C4  C3    0.00  0.0  0
 DNX  CONST_07  N3  C3  C2  C1  180.00  0.0  0
 DNX  CONST_08  N4  C4  C3  C2  180.00  0.0  0
 DNX  CONST_09  O1  C1  C2  C3  180.00  0.0  0
 DNX  CONST_10  C5  C4  C3  N3  180.00  0.0  0
 DNX  CONST_11  C6  C5  C4  N4  180.00  0.0  0
 DNX  CONST_12  O1  C1  C6  C5  180.00  0.0  0
 DNX  CONST_13  H5  C5  C6  C1  180.00  0.0  0
 DNX  CONST_14  H6  C6  C1  C2  180.00  0.0  0
 DNX  CONST_15  H2  C2  C3  C4  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
 DNX  plan-1  C1   0.020
 DNX  plan-1  C2   0.020
 DNX  plan-1  C3   0.020
 DNX  plan-1  N3   0.020
 DNX  plan-1  C4   0.020
 DNX  plan-1  N4   0.020
 DNX  plan-1  C5   0.020
 DNX  plan-1  C6   0.020
 DNX  plan-1  O1   0.020
 DNX  plan-1  H2   0.020
 DNX  plan-1  H5   0.020
 DNX  plan-1  H6   0.020
 DNX  plan-2  C3   0.020
 DNX  plan-2  N3   0.020
 DNX  plan-2  O31  0.020
 DNX  plan-2  O32  0.020
 DNX  plan-3  C4   0.020
 DNX  plan-3  N4   0.020
 DNX  plan-3  O41  0.020
 DNX  plan-3  O42  0.020

