# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 19:45:19 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 3-carbamoyl-1-methylpyridin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1cccc(c1)C(N)=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
 8GC  8GC  3-carbamoyl-1-methylpyridin-1-ium  ligand  19  10  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_8GC
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
 8GC  C2   C  C     0   0.536  -1.9711   0.3409  -0.0226
 8GC  C4   C  CR6   0  -0.157  -0.5637  -0.1930  -0.0013
 8GC  C5   C  CR16  0  -0.108  -0.2074  -1.5359  -0.0049
 8GC  C6   C  CR16  0  -0.325   1.1319  -1.8920   0.0175
 8GC  C7   C  CR16  0   0.091   2.0888  -0.9078   0.0445
 8GC  C10  C  CR16  0   0.119   0.4468   0.7481   0.0259
 8GC  N8   N  NR6   1  -0.419   1.7312   0.3843   0.0496
 8GC  N3   N  NH2   0  -0.820  -2.9545  -0.5587  -0.0312
 8GC  O1   O  O     0  -0.460  -2.1537   1.5473  -0.0346
 8GC  H1   H  HCR6  0   0.305  -0.9455  -2.3251  -0.0233
 8GC  H2   H  HCR6  0   0.327   1.4361  -2.9274   0.0153
 8GC  H3   H  HCR6  0   0.357   3.1468  -1.1210   0.0631
 8GC  H4   H  HCH3  0   0.304   3.0303   1.6449  -0.9987
 8GC  H5   H  HCH3  0   0.293   2.4003   2.3101   0.5263
 8GC  H6   H  HCH3  0   0.292   3.6470   1.0544   0.5606
 8GC  H7   H  HCR6  0   0.351   0.2416   1.8082   0.0323
 8GC  H8   H  HNH2  0   0.421  -3.9115  -0.2428  -0.0372
 8GC  H9   H  HNH2  0   0.425  -2.8136  -1.5527  -0.0008
 8GC  C9   C  CH3   0  -0.531   2.7729   1.4195   0.0326

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
 8GC  C7   C6   aromatic  1.373  0.020  1.373
 8GC  C7   N8   aromatic  1.341  0.020  1.341
 8GC  C6   C5   aromatic  1.386  0.020  1.386
 8GC  C9   N8   single    1.469  0.020  1.469
 8GC  N8   C10  aromatic  1.335  0.020  1.335
 8GC  C5   C4   aromatic  1.389  0.020  1.389
 8GC  C10  C4   aromatic  1.381  0.020  1.381
 8GC  C4   C2   single    1.505  0.020  1.505
 8GC  C2   N3   single    1.333  0.020  1.333
 8GC  C2   O1   double    1.220  0.020  1.220
 8GC  C5   H1   single    0.930  0.020  1.080
 8GC  C6   H2   single    0.930  0.020  1.080
 8GC  C7   H3   single    0.930  0.020  1.080
 8GC  C9   H4   single    0.970  0.020  1.090
 8GC  C9   H5   single    0.970  0.020  1.090
 8GC  C9   H6   single    0.970  0.020  1.090
 8GC  C10  H7   single    0.930  0.020  1.080
 8GC  N3   H8   single    0.860  0.020  1.020
 8GC  N3   H9   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
 8GC  O1   C2   N3  123.84  3.000
 8GC  O1   C2   C4  119.39  3.000
 8GC  N3   C2   C4  116.77  3.000
 8GC  C10  C4   C5  118.10  3.000
 8GC  C10  C4   C2  116.27  3.000
 8GC  C5   C4   C2  125.63  3.000
 8GC  H1   C5   C6  118.21  3.000
 8GC  H1   C5   C4  122.05  3.000
 8GC  C6   C5   C4  119.74  3.000
 8GC  H2   C6   C7  119.43  3.000
 8GC  H2   C6   C5  121.25  3.000
 8GC  C7   C6   C5  119.32  3.000
 8GC  H3   C7   N8  116.85  3.000
 8GC  H3   C7   C6  122.81  3.000
 8GC  N8   C7   C6  120.33  3.000
 8GC  H7   C10  N8  116.75  3.000
 8GC  H7   C10  C4  122.01  3.000
 8GC  N8   C10  C4  121.24  3.000
 8GC  C10  N8   C9  119.35  3.000
 8GC  C10  N8   C7  121.27  3.000
 8GC  C9   N8   C7  119.35  3.000
 8GC  H9   N3   H8  116.33  3.000
 8GC  H9   N3   C2  124.35  3.000
 8GC  H8   N3   C2  119.28  3.000
 8GC  H6   C9   H5  109.37  3.000
 8GC  H6   C9   H4  109.94  3.000
 8GC  H5   C9   H4  110.07  3.000
 8GC  H6   C9   N8  109.19  3.000
 8GC  H5   C9   N8  109.27  3.000
 8GC  H4   C9   N8  108.98  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
 8GC  CONST_01  C7   C6   C5   C4    0.00   0.0  0
 8GC  CONST_02  C7   N8   C10  C4    0.00   0.0  0
 8GC  CONST_03  N8   C7   C6   C5    0.00   0.0  0
 8GC  CONST_04  N8   C10  C4   C5    0.00   0.0  0
 8GC  CONST_05  C10  N8   C7   C6    0.00   0.0  0
 8GC  CONST_06  C10  C4   C5   C6    0.00   0.0  0
 8GC  CONST_07  C6   C5   C4   C2  180.00   0.0  0
 8GC  CONST_08  N8   C10  C4   C2  180.00   0.0  0
 8GC  CONST_09  C9   N8   C10  C4  180.00   0.0  0
 8GC  CONST_10  C9   N8   C7   C6  180.00   0.0  0
 8GC  CONST_11  H2   C6   C5   C4  180.00   0.0  0
 8GC  CONST_12  H3   C7   C6   C5  180.00   0.0  0
 8GC  CONST_13  H7   C10  C4   C5  180.00   0.0  0
 8GC  CONST_14  H1   C5   C6   C7  180.00   0.0  0
 8GC  CONST_15  H8   N3   C2   C4  180.00   0.0  0
 8GC  CONST_16  H9   N3   C2   C4    0.00   0.0  0
 8GC  Var_01    N3   C2   C4   C5    0.75  30.0  2
 8GC  Var_02    H4   C9   N8   C7   88.18  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
 8GC  plan-1  C2   0.020
 8GC  plan-1  C4   0.020
 8GC  plan-1  C5   0.020
 8GC  plan-1  C6   0.020
 8GC  plan-1  C7   0.020
 8GC  plan-1  C10  0.020
 8GC  plan-1  N8   0.020
 8GC  plan-1  H1   0.020
 8GC  plan-1  H2   0.020
 8GC  plan-1  H3   0.020
 8GC  plan-1  H7   0.020
 8GC  plan-1  C9   0.020
 8GC  plan-2  C2   0.020
 8GC  plan-2  C4   0.020
 8GC  plan-2  N3   0.020
 8GC  plan-2  O1   0.020
 8GC  plan-2  H8   0.020
 8GC  plan-2  H9   0.020

