# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 21:10:17 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: pyridine-2,3-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccnc1C(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
 NTM  NTM  'pyridine-2,3-dicarboxylic acid'  ligand  15  12  .  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_NTM
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
 NTM  N1  N  N      0  -0.436  -0.8774  -0.1261  -1.7422
 NTM  C2  C  CR6    0   0.076  -0.5223  -0.0420  -0.4613
 NTM  C3  C  CR6    0  -0.121   0.8113   0.0853  -0.0559
 NTM  C4  C  CR16   0  -0.182   1.7863   0.1048  -1.0431
 NTM  C5  C  CR16   0  -0.331   1.4175   0.0287  -2.3787
 NTM  C6  C  CR16   0  -0.091   0.0703  -0.0893  -2.6730
 NTM  C7  C  C      0   0.379  -1.6555  -0.1799   0.5428
 NTM  O1  O  O      0  -0.609  -1.5435  -1.1241   1.3458
 NTM  O2  O  OC    -1  -0.607  -2.5993   0.6221   0.4337
 NTM  C8  C  C      0   0.365   1.2040   0.2483   1.3998
 NTM  O3  O  O      0  -0.598   0.5413   1.0704   2.0576
 NTM  O4  O  OC    -1  -0.605   2.1811  -0.4205   1.7880
 NTM  H4  H  HCR6   0   0.255   2.8314   0.1963  -0.7725
 NTM  H5  H  HCR6   0   0.257   2.1529   0.0564  -3.1713
 NTM  H6  H  HCR6   0   0.249  -0.2610  -0.1594  -3.7042

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
 NTM  N1  C2  aromatic  1.332  0.020  1.332
 NTM  N1  C6  aromatic  1.329  0.020  1.329
 NTM  C2  C3  aromatic  1.400  0.020  1.400
 NTM  C2  C7  single    1.520  0.020  1.520
 NTM  C3  C4  aromatic  1.388  0.020  1.388
 NTM  C3  C8  single    1.517  0.020  1.517
 NTM  C4  C5  aromatic  1.388  0.020  1.388
 NTM  C4  H4  single    0.930  0.020  1.080
 NTM  C5  C6  aromatic  1.384  0.020  1.384
 NTM  C5  H5  single    0.930  0.020  1.080
 NTM  C6  H6  single    0.930  0.020  1.080
 NTM  C7  O1  deloc     1.245  0.020  1.245
 NTM  C7  O2  deloc     1.243  0.020  1.243
 NTM  C8  O3  deloc     1.244  0.020  1.244
 NTM  C8  O4  deloc     1.246  0.020  1.246

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
 NTM  C6  N1  C2  118.80  3.000
 NTM  C7  C2  C3  121.82  3.000
 NTM  C7  C2  N1  115.51  3.000
 NTM  C3  C2  N1  122.57  3.000
 NTM  C8  C3  C4  119.96  3.000
 NTM  C8  C3  C2  122.31  3.000
 NTM  C4  C3  C2  117.69  3.000
 NTM  H4  C4  C5  120.09  3.000
 NTM  H4  C4  C3  120.09  3.000
 NTM  C5  C4  C3  119.81  3.000
 NTM  H5  C5  C6  120.54  3.000
 NTM  H5  C5  C4  121.55  3.000
 NTM  C6  C5  C4  117.91  3.000
 NTM  H6  C6  C5  120.31  3.000
 NTM  H6  C6  N1  116.49  3.000
 NTM  C5  C6  N1  123.20  3.000
 NTM  O2  C7  O1  127.90  3.000
 NTM  O2  C7  C2  116.70  3.000
 NTM  O1  C7  C2  115.33  3.000
 NTM  O4  C8  O3  127.42  3.000
 NTM  O4  C8  C3  116.38  3.000
 NTM  O3  C8  C3  116.15  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
 NTM  CONST_01  C4  C3  C2  N1    0.00   0.0  0
 NTM  CONST_02  C4  C5  C6  N1    0.00   0.0  0
 NTM  CONST_03  C5  C6  N1  C2    0.00   0.0  0
 NTM  CONST_04  C5  C4  C3  C2    0.00   0.0  0
 NTM  CONST_05  C6  N1  C2  C3    0.00   0.0  0
 NTM  CONST_06  C6  C5  C4  C3    0.00   0.0  0
 NTM  CONST_07  C8  C3  C2  N1  180.00   0.0  0
 NTM  CONST_08  C7  C2  C3  C4  180.00   0.0  0
 NTM  CONST_09  C8  C3  C4  C5  180.00   0.0  0
 NTM  CONST_10  C7  C2  N1  C6  180.00   0.0  0
 NTM  CONST_11  H5  C5  C6  N1  180.00   0.0  0
 NTM  CONST_12  H6  C6  N1  C2  180.00   0.0  0
 NTM  CONST_13  H4  C4  C3  C2  180.00   0.0  0
 NTM  Var_01    O1  C7  C2  N1  120.37  30.0  2
 NTM  Var_02    O3  C8  C3  C2  -45.71  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
 NTM  plan-1  N1  0.020
 NTM  plan-1  C2  0.020
 NTM  plan-1  C3  0.020
 NTM  plan-1  C4  0.020
 NTM  plan-1  C5  0.020
 NTM  plan-1  C6  0.020
 NTM  plan-1  C7  0.020
 NTM  plan-1  C8  0.020
 NTM  plan-1  H4  0.020
 NTM  plan-1  H5  0.020
 NTM  plan-1  H6  0.020
 NTM  plan-2  C2  0.020
 NTM  plan-2  C7  0.020
 NTM  plan-2  O1  0.020
 NTM  plan-2  O2  0.020
 NTM  plan-3  C3  0.020
 NTM  plan-3  C8  0.020
 NTM  plan-3  O3  0.020
 NTM  plan-3  O4  0.020

