# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 07:59:14 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccccn1
#
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
 WM1  WM1  'pyridine-2-carboxamide   '  ligand  15  9  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WM1
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
 WM1  CAD  C  CR16  0  -0.300  -0.5193  -1.2664  -0.0073
 WM1  CAG  C  CR16  0  -0.147  -1.9042  -1.1920  -0.0019
 WM1  CAH  C  CR16  0  -0.317  -2.5078   0.0548   0.0187
 WM1  CAI  C  CR16  0  -0.064  -1.6961   1.1819   0.0350
 WM1  NAF  N  N     0  -0.432  -0.3738   1.1163   0.0318
 WM1  CAE  C  CR6   0   0.122   0.2022  -0.0813   0.0103
 WM1  CAB  C  C     0   0.494   1.7062  -0.1263   0.0044
 WM1  OAC  O  O     0  -0.478   2.3021  -1.1941  -0.0317
 WM1  NAA  N  NH2   0  -0.805   2.2996   1.0681   0.0433
 WM1  H1   H  HCR6  0   0.277  -0.0111  -2.2200  -0.0231
 WM1  H2   H  HCR6  0   0.281  -2.5018  -2.0936  -0.0143
 WM1  H3   H  HCR6  0   0.280  -3.5838   0.1592   0.0230
 WM1  H4   H  HCR6  0   0.272  -2.1334   2.1734   0.0526
 WM1  H5   H  HNH2  0   0.410   1.7498   1.9112   0.0647
 WM1  H6   H  HNH2  0   0.405   3.3031   1.1421   0.0348

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
 WM1  CAD  CAG  aromatic  1.387  0.020  1.387
 WM1  CAD  CAE  aromatic  1.388  0.020  1.388
 WM1  CAG  CAH  aromatic  1.385  0.020  1.385
 WM1  OAC  CAB  double    1.223  0.020  1.223
 WM1  CAB  CAE  single    1.505  0.020  1.505
 WM1  CAB  NAA  single    1.334  0.020  1.334
 WM1  CAE  NAF  aromatic  1.329  0.020  1.329
 WM1  CAH  CAI  aromatic  1.389  0.020  1.389
 WM1  NAF  CAI  aromatic  1.324  0.020  1.324
 WM1  CAD  H1   single    0.930  0.020  1.080
 WM1  CAG  H2   single    0.930  0.020  1.080
 WM1  CAH  H3   single    0.930  0.020  1.080
 WM1  CAI  H4   single    0.930  0.020  1.080
 WM1  NAA  H5   single    0.860  0.020  1.020
 WM1  NAA  H6   single    0.860  0.020  1.020

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
 WM1  H1   CAD  CAE  120.61  3.000
 WM1  H1   CAD  CAG  121.13  3.000
 WM1  CAE  CAD  CAG  118.25  3.000
 WM1  H2   CAG  CAH  120.64  3.000
 WM1  H2   CAG  CAD  120.45  3.000
 WM1  CAH  CAG  CAD  118.91  3.000
 WM1  H3   CAH  CAI  120.21  3.000
 WM1  H3   CAH  CAG  121.37  3.000
 WM1  CAI  CAH  CAG  118.41  3.000
 WM1  H4   CAI  NAF  116.63  3.000
 WM1  H4   CAI  CAH  120.45  3.000
 WM1  NAF  CAI  CAH  122.92  3.000
 WM1  CAE  NAF  CAI  118.52  3.000
 WM1  CAB  CAE  NAF  117.40  3.000
 WM1  NAF  CAE  CAD  122.98  3.000
 WM1  CAB  CAE  CAD  119.62  3.000
 WM1  NAA  CAB  OAC  124.45  3.000
 WM1  NAA  CAB  CAE  114.68  3.000
 WM1  OAC  CAB  CAE  120.87  3.000
 WM1  H6   NAA  H5   118.90  3.000
 WM1  H6   NAA  CAB  120.60  3.000
 WM1  H5   NAA  CAB  120.49  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
 WM1  CONST_01  CAI  CAH  CAG  CAD    0.00   0.0  0
 WM1  CONST_02  CAI  NAF  CAE  CAD    0.00   0.0  0
 WM1  CONST_03  NAF  CAE  CAD  CAG    0.00   0.0  0
 WM1  CONST_04  NAF  CAI  CAH  CAG    0.00   0.0  0
 WM1  CONST_05  CAE  CAD  CAG  CAH    0.00   0.0  0
 WM1  CONST_06  CAE  NAF  CAI  CAH    0.00   0.0  0
 WM1  CONST_07  CAB  CAE  CAD  CAG  180.00   0.0  0
 WM1  CONST_08  CAB  CAE  NAF  CAI  180.00   0.0  0
 WM1  CONST_09  H3   CAH  CAG  CAD  180.00   0.0  0
 WM1  CONST_10  H4   CAI  CAH  CAG  180.00   0.0  0
 WM1  CONST_11  H1   CAD  CAG  CAH  180.00   0.0  0
 WM1  CONST_12  H2   CAG  CAH  CAI  180.00   0.0  0
 WM1  CONST_13  H5   NAA  CAB  CAE    0.00   0.0  0
 WM1  CONST_14  H6   NAA  CAB  CAE  180.00   0.0  0
 WM1  Var_01    OAC  CAB  CAE  CAD    0.87  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
 WM1  plan-1  CAD  0.020
 WM1  plan-1  CAG  0.020
 WM1  plan-1  CAH  0.020
 WM1  plan-1  CAI  0.020
 WM1  plan-1  NAF  0.020
 WM1  plan-1  CAE  0.020
 WM1  plan-1  CAB  0.020
 WM1  plan-1  H1   0.020
 WM1  plan-1  H2   0.020
 WM1  plan-1  H3   0.020
 WM1  plan-1  H4   0.020
 WM1  plan-2  CAE  0.020
 WM1  plan-2  CAB  0.020
 WM1  plan-2  OAC  0.020
 WM1  plan-2  NAA  0.020
 WM1  plan-2  H5   0.020
 WM1  plan-2  H6   0.020

