# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 12:45:40 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  17  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 GRAND
;

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  -0.398  -0.9206  -0.0588  -1.7481
 NTM  C2   C  CR6   0   0.087  -0.5434  -0.0336  -0.4777
 NTM  C3   C  CR6   0  -0.041   0.7881   0.0577  -0.0819
 NTM  C4   C  CR16  0  -0.137   1.7584   0.1100  -1.0757
 NTM  C5   C  CR16  0  -0.302   1.3644   0.0844  -2.4003
 NTM  C6   C  CR16  0  -0.067   0.0080   0.0011  -2.6871
 NTM  C7   C  C     0   0.536  -1.6088  -0.1521   0.5615
 NTM  O1   O  O     0  -0.429  -1.3512  -0.3150   1.7293
 NTM  O2   O  OH1   0  -0.573  -2.8258  -0.0701   0.0687
 NTM  C8   C  C     0   0.463   1.2253   0.1834   1.3438
 NTM  O3   O  O     0  -0.419   1.2530   1.2334   1.9281
 NTM  O4   O  OH1   0  -0.576   1.6631  -0.9661   1.8217
 NTM  H4   H  HCR6  0   0.297   2.8073   0.1773  -0.8183
 NTM  H5   H  HCR6  0   0.291   2.0915   0.1185  -3.1990
 NTM  H6   H  HCR6  0   0.281  -0.3361  -0.0199  -3.7142
 NTM  HO2  H  HOH1  0   0.493  -3.4772  -0.1710   0.7796
 NTM  HO4  H  HOH1  0   0.493   1.9903  -0.8531   2.7283

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  1.325  0.020  1.325
 NTM  N1  C6   aromatic  1.322  0.020  1.322
 NTM  C2  C3   aromatic  1.392  0.020  1.392
 NTM  C2  C7   single    1.493  0.020  1.493
 NTM  C3  C4   aromatic  1.390  0.020  1.390
 NTM  C3  C8   single    1.496  0.020  1.496
 NTM  C4  C5   aromatic  1.382  0.020  1.382
 NTM  C4  H4   single    0.930  0.020  1.080
 NTM  C5  C6   aromatic  1.389  0.020  1.389
 NTM  C5  H5   single    0.930  0.020  1.080
 NTM  C6  H6   single    0.930  0.020  1.080
 NTM  C7  O1   double    1.207  0.020  1.207
 NTM  C7  O2   single    1.315  0.020  1.315
 NTM  O2  HO2  single    0.850  0.020  0.980
 NTM  C8  O3   double    1.202  0.020  1.202
 NTM  C8  O4   single    1.320  0.020  1.320
 NTM  O4  HO4  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
 NTM  C6   N1  C2  118.68  3.000
 NTM  C7   C2  C3  119.33  3.000
 NTM  C7   C2  N1  117.55  3.000
 NTM  C3   C2  N1  123.09  3.000
 NTM  C8   C3  C4  118.30  3.000
 NTM  C8   C3  C2  123.77  3.000
 NTM  C4   C3  C2  117.83  3.000
 NTM  H4   C4  C5  120.36  3.000
 NTM  H4   C4  C3  120.59  3.000
 NTM  C5   C4  C3  119.05  3.000
 NTM  H5   C5  C6  120.42  3.000
 NTM  H5   C5  C4  121.06  3.000
 NTM  C6   C5  C4  118.52  3.000
 NTM  H6   C6  C5  120.47  3.000
 NTM  H6   C6  N1  116.70  3.000
 NTM  C5   C6  N1  122.83  3.000
 NTM  O2   C7  O1  124.63  3.000
 NTM  O2   C7  C2  113.23  3.000
 NTM  O1   C7  C2  122.13  3.000
 NTM  HO2  O2  C7  109.90  3.000
 NTM  O4   C8  O3  125.26  3.000
 NTM  O4   C8  C3  111.64  3.000
 NTM  O3   C8  C3  122.91  3.000
 NTM  HO4  O4  C8  110.41  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  CONST_14  HO2  O2  C7  C2  180.00   0.0  0
 NTM  CONST_15  HO4  O4  C8  C3  180.00   0.0  0
 NTM  Var_01    O1   C7  C2  N1  170.08  30.0  2
 NTM  Var_02    O3   C8  C3  C2  -83.05  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-2  HO2  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
 NTM  plan-3  HO4  0.020

