# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:02:33 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 3-(aminomethyl)-4-chloro-1-methylpyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1ccc(Cl)c(CN)c1
#
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
 NNT  NNT  3-(aminomethyl)-4-chloro-1-methylpyridinium  ligand  20  10  .  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_NNT
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
 NNT  C12   C   CH2   0  -0.372   1.1172   1.7673  -0.4739
 NNT  C13   C   CR6   0   0.070   0.1229   0.6622  -0.2559
 NNT  C17   C   CR16  0   0.054  -1.2240   0.9480  -0.2184
 NNT  C19   C   CR16  0   0.092  -1.7942  -1.2664   0.2131
 NNT  C20   C   CR16  0  -0.311  -0.4732  -1.6365   0.1896
 NNT  C21   C   CR6   0   0.083   0.4913  -0.6663  -0.0400
 NNT  N24   N   NH2   0  -0.782   1.8513   2.0056   0.7534
 NNT  N25   N   NR6   1  -0.422  -2.1495   0.0072   0.0117
 NNT  CL28  CL  CL    0  -0.029   2.1312  -1.1273  -0.0872
 NNT  H12   H   HCH2  0   0.265   1.8204   1.4597  -1.2497
 NNT  H12A  H   HCH2  0   0.245   0.5859   2.6412  -0.8674
 NNT  H17   H   HCR6  0   0.349  -1.5881   1.9532  -0.3766
 NNT  H18   H   HCH3  0   0.301  -3.9860   0.1491  -0.9815
 NNT  H18A  H   HCH3  0   0.292  -4.0907  -0.2157   0.7567
 NNT  H18B  H   HCH3  0   0.290  -3.6789   1.4203   0.2214
 NNT  H19   H   HCR6  0   0.357  -2.5869  -1.9778   0.3883
 NNT  H20   H   HCR6  0   0.335  -0.2108  -2.6714   0.3514
 NNT  HN24  H   HNH2  0   0.364   2.6653   2.5714   0.5535
 NNT  HN2A  H   HNH2  0   0.353   1.2814   2.5391   1.3968
 NNT  C18   C   CH3   0  -0.532  -3.5725   0.3642   0.0004

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
 NNT  C12  C13   single    1.502  0.020  1.502
 NNT  C12  N24   single    1.450  0.020  1.450
 NNT  C13  C17   aromatic  1.377  0.020  1.377
 NNT  C13  C21   aromatic  1.395  0.020  1.395
 NNT  C17  N25   aromatic  1.340  0.020  1.340
 NNT  C18  N25   single    1.467  0.020  1.467
 NNT  C19  C20   aromatic  1.372  0.020  1.372
 NNT  C19  N25   aromatic  1.338  0.020  1.338
 NNT  C20  C21   aromatic  1.387  0.020  1.387
 NNT  C21  CL28  single    1.704  0.020  1.704
 NNT  C12  H12   single    0.970  0.020  1.090
 NNT  C12  H12A  single    0.970  0.020  1.090
 NNT  C17  H17   single    0.930  0.020  1.080
 NNT  C18  H18   single    0.970  0.020  1.090
 NNT  C18  H18A  single    0.970  0.020  1.090
 NNT  C18  H18B  single    0.970  0.020  1.090
 NNT  C19  H19   single    0.930  0.020  1.080
 NNT  C20  H20   single    0.930  0.020  1.080
 NNT  N24  HN24  single    0.890  0.020  1.040
 NNT  N24  HN2A  single    0.890  0.020  1.040

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
 NNT  H12A  C12  H12   106.37  3.000
 NNT  H12A  C12  N24   114.73  3.000
 NNT  H12   C12  N24   108.77  3.000
 NNT  H12A  C12  C13   108.53  3.000
 NNT  H12   C12  C13   108.80  3.000
 NNT  N24   C12  C13   109.46  3.000
 NNT  C21   C13  C17   116.84  3.000
 NNT  C21   C13  C12   123.23  3.000
 NNT  C17   C13  C12   119.90  3.000
 NNT  H17   C17  N25   116.47  3.000
 NNT  H17   C17  C13   121.23  3.000
 NNT  N25   C17  C13   122.31  3.000
 NNT  H19   C19  N25   117.19  3.000
 NNT  H19   C19  C20   122.15  3.000
 NNT  N25   C19  C20   120.66  3.000
 NNT  H20   C20  C21   121.75  3.000
 NNT  H20   C20  C19   119.33  3.000
 NNT  C21   C20  C19   118.92  3.000
 NNT  CL28  C21  C20   118.97  3.000
 NNT  CL28  C21  C13   120.49  3.000
 NNT  C20   C21  C13   120.53  3.000
 NNT  HN2A  N24  HN24  106.51  3.000
 NNT  HN2A  N24  C12   109.87  3.000
 NNT  HN24  N24  C12   109.40  3.000
 NNT  C19   N25  C18   119.37  3.000
 NNT  C19   N25  C17   120.74  3.000
 NNT  C18   N25  C17   119.86  3.000
 NNT  H18B  C18  H18A  109.37  3.000
 NNT  H18B  C18  H18   109.85  3.000
 NNT  H18A  C18  H18   110.01  3.000
 NNT  H18B  C18  N25   109.31  3.000
 NNT  H18A  C18  N25   109.14  3.000
 NNT  H18   C18  N25   109.14  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
 NNT  CONST_01  C19   N25  C17  C13    0.00   0.0  0
 NNT  CONST_02  C19   C20  C21  C13    0.00   0.0  0
 NNT  CONST_03  C20   C21  C13  C17    0.00   0.0  0
 NNT  CONST_04  C20   C19  N25  C17    0.00   0.0  0
 NNT  CONST_05  N25   C17  C13  C21    0.00   0.0  0
 NNT  CONST_06  N25   C19  C20  C21    0.00   0.0  0
 NNT  CONST_07  N25   C17  C13  C12  180.00   0.0  0
 NNT  CONST_08  C20   C21  C13  C12  180.00   0.0  0
 NNT  CONST_09  C18   N25  C17  C13  180.00   0.0  0
 NNT  CONST_10  CL28  C21  C13  C17  180.00   0.0  0
 NNT  CONST_11  C20   C19  N25  C18  180.00   0.0  0
 NNT  CONST_12  CL28  C21  C20  C19  180.00   0.0  0
 NNT  CONST_13  H20   C20  C21  C13  180.00   0.0  0
 NNT  CONST_14  H19   C19  N25  C17  180.00   0.0  0
 NNT  CONST_15  H17   C17  N25  C19  180.00   0.0  0
 NNT  Var_01    N24   C12  C13  C17  109.43  30.0  2
 NNT  Var_02    H18   C18  N25  C17   95.85  30.0  2
 NNT  Var_03    HN24  N24  C12  C13  165.81  30.0  3

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
 NNT  plan-1  C12   0.020
 NNT  plan-1  C13   0.020
 NNT  plan-1  C17   0.020
 NNT  plan-1  C19   0.020
 NNT  plan-1  C20   0.020
 NNT  plan-1  C21   0.020
 NNT  plan-1  N25   0.020
 NNT  plan-1  CL28  0.020
 NNT  plan-1  H17   0.020
 NNT  plan-1  H19   0.020
 NNT  plan-1  H20   0.020
 NNT  plan-1  C18   0.020

