# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 22:12:53 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  14  9  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.401   1.2647   0.0030  -1.8426
 NIO  C1   C  CR16  0  -0.045   1.1876   0.0191  -0.5194
 NIO  C2   C  CR6   0  -0.172  -0.0210   0.0342   0.1743
 NIO  C3   C  CR16  0  -0.140  -1.2012   0.0316  -0.5626
 NIO  C4   C  CR16  0  -0.316  -1.1248   0.0150  -1.9427
 NIO  C5   C  CR16  0  -0.048   0.1306   0.0013  -2.5337
 NIO  C6   C  C     0   0.535  -0.0952   0.0534   1.6554
 NIO  O1   O  O     0  -0.433  -1.1344   0.0686   2.2685
 NIO  O2   O  OH1   0  -0.592   1.0968   0.0524   2.2306
 NIO  H1   H  HCR6  0   0.278   2.1324   0.0200   0.0110
 NIO  H3   H  HCR6  0   0.284  -2.1613   0.0417  -0.0639
 NIO  H4   H  HCR6  0   0.282  -2.0155   0.0124  -2.5548
 NIO  H5   H  HCR6  0   0.277   0.2235  -0.0117  -3.6136
 NIO  HO2  H  HOH1  0   0.491   1.0007   0.0642   3.1946

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  1.326  0.020  1.326
 NIO  N   C5   aromatic  1.328  0.020  1.328
 NIO  C1  C2   aromatic  1.394  0.020  1.394
 NIO  C1  H1   single    0.930  0.020  1.080
 NIO  C2  C3   aromatic  1.391  0.020  1.391
 NIO  C2  C6   single    1.483  0.020  1.483
 NIO  C3  C4   aromatic  1.382  0.020  1.382
 NIO  C3  H3   single    0.930  0.020  1.080
 NIO  C4  C5   aromatic  1.388  0.020  1.388
 NIO  C4  H4   single    0.930  0.020  1.080
 NIO  C5  H5   single    0.930  0.020  1.080
 NIO  C6  O1   double    1.207  0.020  1.207
 NIO  C6  O2   single    1.324  0.020  1.324
 NIO  O2  HO2  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
 NIO  C5   N   C1  118.02  3.000
 NIO  H1   C1  C2  120.83  3.000
 NIO  H1   C1  N   115.97  3.000
 NIO  C2   C1  N   123.20  3.000
 NIO  C6   C2  C3  119.11  3.000
 NIO  C6   C2  C1  122.73  3.000
 NIO  C3   C2  C1  118.16  3.000
 NIO  H3   C3  C4  120.62  3.000
 NIO  H3   C3  C2  120.57  3.000
 NIO  C4   C3  C2  118.81  3.000
 NIO  H4   C4  C5  120.29  3.000
 NIO  H4   C4  C3  121.33  3.000
 NIO  C5   C4  C3  118.38  3.000
 NIO  H5   C5  C4  120.13  3.000
 NIO  H5   C5  N   116.44  3.000
 NIO  C4   C5  N   123.43  3.000
 NIO  O2   C6  O1  123.69  3.000
 NIO  O2   C6  C2  112.89  3.000
 NIO  O1   C6  C2  123.42  3.000
 NIO  HO2  O2  C6  110.07  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  CONST_13  HO2  O2  C6  C2  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
 NIO  plan-2  HO2  0.020

