# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 16:58:06 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: 3-nitropyridin-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ncccc1[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
 8PJ  8PJ  '3-nitropyridin-2-ol      '  ligand  14  10  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8PJ
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
 8PJ  N1  N  N      0  -0.425   1.9052  -0.9682   0.1025
 8PJ  C4  C  CR6    0   0.505   0.5839  -0.9688   0.1432
 8PJ  C5  C  CR16   0  -0.028   2.5523   0.1785  -0.0081
 8PJ  C1  C  CR16   0  -0.337   1.9279   1.4178  -0.0873
 8PJ  C2  C  CR16   0  -0.168   0.5519   1.4432  -0.0473
 8PJ  C3  C  CR6    0   0.054  -0.1391   0.2427   0.0691
 8PJ  O1  O  OH1    0  -0.579   0.0340  -2.1595   0.2539
 8PJ  N2  N  N      1   0.367  -1.5746   0.2679   0.1082
 8PJ  O2  O  O      0  -0.358  -2.1418   1.3268   0.0369
 8PJ  O3  O  O     -1  -0.422  -2.1663  -0.7969   0.2126
 8PJ  H1  H  HCR6   0   0.293   3.6336   0.1126  -0.0369
 8PJ  H2  H  HCR6   0   0.291   2.5057   2.3252  -0.1771
 8PJ  H4  H  HCR6   0   0.319   0.0164   2.3800  -0.1082
 8PJ  H3  H  HOH1   0   0.487  -0.9370  -2.0616   0.2754

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
 8PJ  C5  C1  aromatic  1.390  0.020  1.390
 8PJ  C5  N1  aromatic  1.321  0.020  1.321
 8PJ  C1  C2  aromatic  1.377  0.020  1.377
 8PJ  N1  C4  aromatic  1.322  0.020  1.322
 8PJ  C2  C3  aromatic  1.390  0.020  1.390
 8PJ  C4  C3  aromatic  1.413  0.020  1.413
 8PJ  C4  O1  single    1.316  0.020  1.316
 8PJ  C3  N2  single    1.436  0.020  1.436
 8PJ  N2  O2  double    1.203  0.020  1.203
 8PJ  N2  O3  single    1.223  0.020  1.223
 8PJ  C5  H1  single    0.930  0.020  1.080
 8PJ  C1  H2  single    0.930  0.020  1.080
 8PJ  C2  H4  single    0.930  0.020  1.080
 8PJ  O1  H3  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
 8PJ  C5  N1  C4  119.51  3.000
 8PJ  O1  C4  C3  124.50  3.000
 8PJ  O1  C4  N1  114.87  3.000
 8PJ  C3  C4  N1  120.63  3.000
 8PJ  H1  C5  C1  120.06  3.000
 8PJ  H1  C5  N1  115.99  3.000
 8PJ  C1  C5  N1  123.95  3.000
 8PJ  H2  C1  C2  121.46  3.000
 8PJ  H2  C1  C5  120.91  3.000
 8PJ  C2  C1  C5  117.63  3.000
 8PJ  H4  C2  C3  120.46  3.000
 8PJ  H4  C2  C1  120.64  3.000
 8PJ  C3  C2  C1  118.90  3.000
 8PJ  N2  C3  C2  118.95  3.000
 8PJ  N2  C3  C4  121.67  3.000
 8PJ  C2  C3  C4  119.38  3.000
 8PJ  H3  O1  C4  109.07  3.000
 8PJ  O3  N2  O2  122.91  3.000
 8PJ  O3  N2  C3  118.09  3.000
 8PJ  O2  N2  C3  119.01  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
 8PJ  CONST_01  C2  C1  C5  N1    0.00  0.0  0
 8PJ  CONST_02  C2  C3  C4  N1    0.00  0.0  0
 8PJ  CONST_03  C1  C5  N1  C4    0.00  0.0  0
 8PJ  CONST_04  C1  C2  C3  C4    0.00  0.0  0
 8PJ  CONST_05  C3  C2  C1  C5    0.00  0.0  0
 8PJ  CONST_06  C3  C4  N1  C5    0.00  0.0  0
 8PJ  CONST_07  N2  C3  C4  N1  180.00  0.0  0
 8PJ  CONST_08  O1  C4  N1  C5  180.00  0.0  0
 8PJ  CONST_09  N2  C3  C2  C1  180.00  0.0  0
 8PJ  CONST_10  O1  C4  C3  C2  180.00  0.0  0
 8PJ  CONST_11  H2  C1  C5  N1  180.00  0.0  0
 8PJ  CONST_12  H1  C5  N1  C4  180.00  0.0  0
 8PJ  CONST_13  H4  C2  C3  C4  180.00  0.0  0
 8PJ  CONST_14  O2  N2  C3  C4  180.00  0.0  0
 8PJ  CONST_15  O3  N2  C3  C4    0.00  0.0  0
 8PJ  CONST_16  O2  N2  C3  C2    0.00  0.0  0
 8PJ  CONST_17  O3  N2  C3  C2  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
 8PJ  plan-1  N1  0.020
 8PJ  plan-1  C4  0.020
 8PJ  plan-1  C5  0.020
 8PJ  plan-1  C1  0.020
 8PJ  plan-1  C2  0.020
 8PJ  plan-1  C3  0.020
 8PJ  plan-1  O1  0.020
 8PJ  plan-1  N2  0.020
 8PJ  plan-1  H1  0.020
 8PJ  plan-1  H2  0.020
 8PJ  plan-1  H4  0.020
 8PJ  plan-2  C3  0.020
 8PJ  plan-2  N2  0.020
 8PJ  plan-2  O2  0.020
 8PJ  plan-2  O3  0.020

