# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:22:36 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccnc1
#
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
 NIO  NIO  'pyridine-3-carboxylic acid'  ligand  13  9  .  2020-10-20  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NIO
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
 NIO  N   N  N      0  -0.407   1.2120  -0.0266  -1.8419
 NIO  C1  C  CR16   0  -0.087   1.1431  -0.0248  -0.5147
 NIO  C2  C  CR6    0  -0.190  -0.0472  -0.0152   0.2072
 NIO  C3  C  CR16   0  -0.176  -1.2298  -0.0068  -0.5232
 NIO  C4  C  CR16   0  -0.321  -1.1754  -0.0085  -1.9082
 NIO  C5  C  CR16   0  -0.072   0.0692  -0.0185  -2.5197
 NIO  C6  C  C      0   0.400  -0.0502  -0.0140   1.7298
 NIO  O1  O  O      0  -0.590  -1.1672  -0.0073   2.2788
 NIO  O2  O  OC    -1  -0.591   1.0636  -0.0200   2.2861
 NIO  H1  H  HCR6   0   0.252   2.0889  -0.0318   0.0158
 NIO  H3  H  HCR6   0   0.259  -2.1819   0.0011  -0.0088
 NIO  H4  H  HCR6   0   0.264  -2.0756  -0.0021  -2.5079
 NIO  H5  H  HCR6   0   0.259   0.1467  -0.0198  -3.6018

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
 NIO  N   C1  aromatic  1.329  0.020  1.329
 NIO  N   C5  aromatic  1.329  0.020  1.329
 NIO  C1  C2  aromatic  1.392  0.020  1.392
 NIO  C1  H1  single    0.930  0.020  1.080
 NIO  C2  C3  aromatic  1.390  0.020  1.390
 NIO  C2  C6  single    1.523  0.020  1.523
 NIO  C3  C4  aromatic  1.386  0.020  1.386
 NIO  C3  H3  single    0.930  0.020  1.080
 NIO  C4  C5  aromatic  1.387  0.020  1.387
 NIO  C4  H4  single    0.930  0.020  1.080
 NIO  C5  H5  single    0.930  0.020  1.080
 NIO  C6  O1  deloc     1.245  0.020  1.245
 NIO  C6  O2  deloc     1.245  0.020  1.245

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
 NIO  C5  N   C1  117.70  3.000
 NIO  H1  C1  C2  119.47  3.000
 NIO  H1  C1  N   116.32  3.000
 NIO  C2  C1  N   124.21  3.000
 NIO  C6  C2  C3  121.59  3.000
 NIO  C6  C2  C1  121.35  3.000
 NIO  C3  C2  C1  117.06  3.000
 NIO  H3  C3  C4  120.63  3.000
 NIO  H3  C3  C2  119.92  3.000
 NIO  C4  C3  C2  119.45  3.000
 NIO  H4  C4  C5  120.17  3.000
 NIO  H4  C4  C3  121.42  3.000
 NIO  C5  C4  C3  118.41  3.000
 NIO  H5  C5  C4  120.26  3.000
 NIO  H5  C5  N   116.58  3.000
 NIO  C4  C5  N   123.16  3.000
 NIO  O2  C6  O1  127.29  3.000
 NIO  O2  C6  C2  116.43  3.000
 NIO  O1  C6  C2  116.28  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
 NIO  CONST_01  C3  C2  C1  N      0.00   0.0  0
 NIO  CONST_02  C3  C4  C5  N      0.00   0.0  0
 NIO  CONST_03  C4  C5  N   C1     0.00   0.0  0
 NIO  CONST_04  C4  C3  C2  C1     0.00   0.0  0
 NIO  CONST_05  C5  N   C1  C2     0.00   0.0  0
 NIO  CONST_06  C5  C4  C3  C2     0.00   0.0  0
 NIO  CONST_07  C6  C2  C1  N    180.00   0.0  0
 NIO  CONST_08  C6  C2  C3  C4   180.00   0.0  0
 NIO  CONST_09  H4  C4  C5  N    180.00   0.0  0
 NIO  CONST_10  H5  C5  N   C1   180.00   0.0  0
 NIO  CONST_11  H3  C3  C2  C1   180.00   0.0  0
 NIO  CONST_12  H1  C1  C2  C3   180.00   0.0  0
 NIO  Var_01    O1  C6  C2  C1  -179.89  30.0  2

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
 NIO  plan-1  N   0.020
 NIO  plan-1  C1  0.020
 NIO  plan-1  C2  0.020
 NIO  plan-1  C3  0.020
 NIO  plan-1  C4  0.020
 NIO  plan-1  C5  0.020
 NIO  plan-1  C6  0.020
 NIO  plan-1  H1  0.020
 NIO  plan-1  H3  0.020
 NIO  plan-1  H4  0.020
 NIO  plan-1  H5  0.020
 NIO  plan-2  C2  0.020
 NIO  plan-2  C6  0.020
 NIO  plan-2  O1  0.020
 NIO  plan-2  O2  0.020

