# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 16:44:21 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: 4-nitrophenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)[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
 NPO  NPO  '4-nitrophenol            '  ligand  15  10  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NPO
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
 NPO  C1  C  CR6    0   0.081  -0.0026  -0.0180  -0.6161
 NPO  C2  C  CR16   0  -0.204   1.1924  -0.0033   0.0925
 NPO  C3  C  CR16   0  -0.290   1.1551   0.0010   1.4728
 NPO  C4  C  CR6    0   0.320  -0.0667  -0.0038   2.1453
 NPO  C5  C  CR16   0  -0.301  -1.2551  -0.0165   1.4195
 NPO  C6  C  CR16   0  -0.227  -1.2273  -0.0311   0.0374
 NPO  OH  O  OH1    0  -0.631  -0.1153  -0.0347   3.4981
 NPO  N1  N  N      1   0.375   0.0305  -0.0127  -2.0654
 NPO  O2  O  O     -1  -0.245  -1.0225  -0.0328  -2.6598
 NPO  O3  O  O      0  -0.467   1.1096  -0.0603  -2.6097
 NPO  H2  H  HCR6   0   0.295   2.1478   0.0064  -0.4123
 NPO  H3  H  HCR6   0   0.279   2.0778  -0.0240   2.0380
 NPO  H5  H  HCR6   0   0.278  -2.2030  -0.0422   1.9404
 NPO  H6  H  HCR6   0   0.291  -2.1578  -0.0285  -0.5117
 NPO  HO  H  HOH1   0   0.447   0.2605   0.7717   3.8713

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
 NPO  C1  C2  aromatic  1.389  0.020  1.389
 NPO  C1  C6  aromatic  1.388  0.020  1.388
 NPO  C1  N1  single    1.450  0.020  1.450
 NPO  C2  C3  aromatic  1.381  0.020  1.381
 NPO  C2  H2  single    0.930  0.020  1.080
 NPO  C3  C4  aromatic  1.395  0.020  1.395
 NPO  C3  H3  single    0.930  0.020  1.080
 NPO  C4  C5  aromatic  1.393  0.020  1.393
 NPO  C4  OH  single    1.354  0.020  1.354
 NPO  C5  C6  aromatic  1.382  0.020  1.382
 NPO  C5  H5  single    0.930  0.020  1.080
 NPO  C6  H6  single    0.930  0.020  1.080
 NPO  OH  HO  single    0.850  0.020  0.980
 NPO  N1  O2  single    1.209  0.020  1.209
 NPO  N1  O3  double    1.210  0.020  1.210

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
 NPO  N1  C1  C6  119.39  3.000
 NPO  N1  C1  C2  119.35  3.000
 NPO  C6  C1  C2  121.25  3.000
 NPO  H2  C2  C3  119.40  3.000
 NPO  H2  C2  C1  121.49  3.000
 NPO  C3  C2  C1  119.11  3.000
 NPO  H3  C3  C4  119.66  3.000
 NPO  H3  C3  C2  119.93  3.000
 NPO  C4  C3  C2  120.38  3.000
 NPO  OH  C4  C5  119.33  3.000
 NPO  OH  C4  C3  120.89  3.000
 NPO  C5  C4  C3  119.75  3.000
 NPO  H5  C5  C6  119.91  3.000
 NPO  H5  C5  C4  119.80  3.000
 NPO  C6  C5  C4  120.27  3.000
 NPO  H6  C6  C5  119.39  3.000
 NPO  H6  C6  C1  121.37  3.000
 NPO  C5  C6  C1  119.22  3.000
 NPO  HO  OH  C4  110.69  3.000
 NPO  O3  N1  O2  123.71  3.000
 NPO  O3  N1  C1  118.04  3.000
 NPO  O2  N1  C1  118.13  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
 NPO  CONST_01  C4  C3  C2  C1    0.00  0.0  0
 NPO  CONST_02  C4  C5  C6  C1    0.00  0.0  0
 NPO  CONST_03  C5  C6  C1  C2    0.00  0.0  0
 NPO  CONST_04  C5  C4  C3  C2    0.00  0.0  0
 NPO  CONST_05  C6  C1  C2  C3    0.00  0.0  0
 NPO  CONST_06  C6  C5  C4  C3    0.00  0.0  0
 NPO  CONST_07  OH  C4  C3  C2  180.00  0.0  0
 NPO  CONST_08  N1  C1  C2  C3  180.00  0.0  0
 NPO  CONST_09  N1  C1  C6  C5  180.00  0.0  0
 NPO  CONST_10  OH  C4  C5  C6  180.00  0.0  0
 NPO  CONST_11  H3  C3  C2  C1  180.00  0.0  0
 NPO  CONST_12  H5  C5  C6  C1  180.00  0.0  0
 NPO  CONST_13  H6  C6  C1  C2  180.00  0.0  0
 NPO  CONST_14  H2  C2  C3  C4  180.00  0.0  0
 NPO  CONST_15  O2  N1  C1  C2  180.00  0.0  0
 NPO  CONST_16  O3  N1  C1  C2    0.00  0.0  0
 NPO  CONST_17  O2  N1  C1  C6    0.00  0.0  0
 NPO  CONST_18  O3  N1  C1  C6  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
 NPO  plan-1  C1  0.020
 NPO  plan-1  C2  0.020
 NPO  plan-1  C3  0.020
 NPO  plan-1  C4  0.020
 NPO  plan-1  C5  0.020
 NPO  plan-1  C6  0.020
 NPO  plan-1  OH  0.020
 NPO  plan-1  N1  0.020
 NPO  plan-1  H2  0.020
 NPO  plan-1  H3  0.020
 NPO  plan-1  H5  0.020
 NPO  plan-1  H6  0.020
 NPO  plan-2  C1  0.020
 NPO  plan-2  N1  0.020
 NPO  plan-2  O2  0.020
 NPO  plan-2  O3  0.020

