# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:23:52 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 3-(aminomethyl)-1-methylpyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1cccc(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
 NNJ  NNJ  3-(aminomethyl)-1-methylpyridinium  ligand  20  9  .  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_NNJ
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
 NNJ  C12   C  CH2   0  -0.337   2.1778   0.6042  -0.4163
 NNJ  C13   C  CR6   0  -0.021   0.7980   0.0742  -0.1270
 NNJ  C17   C  CR16  0   0.061  -0.2976   0.9038  -0.2420
 NNJ  C19   C  CR16  0   0.074  -1.7727  -0.8158   0.3154
 NNJ  C20   C  CR16  0  -0.334  -0.7224  -1.6930   0.4593
 NNJ  C21   C  CR16  0  -0.112   0.5706  -1.2489   0.2401
 NNJ  N26   N  NH2   0  -0.795   3.1847  -0.1053   0.3421
 NNJ  N27   N  NR6   1  -0.407  -1.5424   0.4563  -0.0281
 NNJ  H12   H  HCH2  0   0.270   2.3729   0.4457  -1.4801
 NNJ  H12A  H  HCH2  0   0.237   2.1756   1.6913  -0.2688
 NNJ  H17   H  HCR6  0   0.338  -0.2034   1.9484  -0.5042
 NNJ  H18   H  HCH3  0   0.299  -2.8916   1.4648  -1.2699
 NNJ  H18A  H  HCH3  0   0.287  -3.5344   0.9979   0.3184
 NNJ  H18B  H  HCH3  0   0.291  -2.4013   2.3519   0.1915
 NNJ  H19   H  HCR6  0   0.347  -2.8009  -1.1019   0.4749
 NNJ  H20   H  HCR6  0   0.314  -0.9274  -2.7141   0.7440
 NNJ  H21   H  HCR6  0   0.301   1.4097  -1.9204   0.3582
 NNJ  HN26  H  HNH2  0   0.366   4.1004   0.1107  -0.0274
 NNJ  HN2A  H  HNH2  0   0.354   3.1815   0.2112   1.3032
 NNJ  C18   C  CH3   0  -0.533  -2.6679   1.3797  -0.2099

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
 NNJ  C12  C13   single    1.506  0.020  1.506
 NNJ  C12  N26   single    1.447  0.020  1.447
 NNJ  C13  C17   aromatic  1.379  0.020  1.379
 NNJ  C13  C21   aromatic  1.392  0.020  1.392
 NNJ  C17  N27   aromatic  1.340  0.020  1.340
 NNJ  C18  N27   single    1.467  0.020  1.467
 NNJ  C19  C20   aromatic  1.376  0.020  1.376
 NNJ  C19  N27   aromatic  1.338  0.020  1.338
 NNJ  C20  C21   aromatic  1.385  0.020  1.385
 NNJ  C12  H12   single    0.970  0.020  1.090
 NNJ  C12  H12A  single    0.970  0.020  1.090
 NNJ  C17  H17   single    0.930  0.020  1.080
 NNJ  C18  H18   single    0.970  0.020  1.090
 NNJ  C18  H18A  single    0.970  0.020  1.090
 NNJ  C18  H18B  single    0.970  0.020  1.090
 NNJ  C19  H19   single    0.930  0.020  1.080
 NNJ  C20  H20   single    0.930  0.020  1.080
 NNJ  C21  H21   single    0.930  0.020  1.080
 NNJ  N26  HN26  single    0.890  0.020  1.040
 NNJ  N26  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
 NNJ  H12A  C12  H12   105.96  3.000
 NNJ  H12A  C12  N26   114.64  3.000
 NNJ  H12   C12  N26   108.36  3.000
 NNJ  H12A  C12  C13   108.72  3.000
 NNJ  H12   C12  C13   107.42  3.000
 NNJ  N26   C12  C13   111.37  3.000
 NNJ  C21   C13  C17   117.65  3.000
 NNJ  C21   C13  C12   122.33  3.000
 NNJ  C17   C13  C12   120.01  3.000
 NNJ  H17   C17  N27   116.25  3.000
 NNJ  H17   C17  C13   122.16  3.000
 NNJ  N27   C17  C13   121.59  3.000
 NNJ  H19   C19  N27   117.01  3.000
 NNJ  H19   C19  C20   122.88  3.000
 NNJ  N27   C19  C20   120.11  3.000
 NNJ  H20   C20  C21   121.50  3.000
 NNJ  H20   C20  C19   119.05  3.000
 NNJ  C21   C20  C19   119.46  3.000
 NNJ  H21   C21  C20   120.54  3.000
 NNJ  H21   C21  C13   119.51  3.000
 NNJ  C20   C21  C13   119.95  3.000
 NNJ  HN2A  N26  HN26  106.45  3.000
 NNJ  HN2A  N26  C12   110.02  3.000
 NNJ  HN26  N26  C12   109.51  3.000
 NNJ  C19   N27  C18   119.89  3.000
 NNJ  C19   N27  C17   121.24  3.000
 NNJ  C18   N27  C17   118.86  3.000
 NNJ  H18B  C18  H18A  109.36  3.000
 NNJ  H18B  C18  H18   109.95  3.000
 NNJ  H18A  C18  H18   109.77  3.000
 NNJ  H18B  C18  N27   109.25  3.000
 NNJ  H18A  C18  N27   109.34  3.000
 NNJ  H18   C18  N27   109.15  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
 NNJ  CONST_01  C19   N27  C17  C13    0.00   0.0  0
 NNJ  CONST_02  C19   C20  C21  C13    0.00   0.0  0
 NNJ  CONST_03  C20   C21  C13  C17    0.00   0.0  0
 NNJ  CONST_04  C20   C19  N27  C17    0.00   0.0  0
 NNJ  CONST_05  N27   C17  C13  C21    0.00   0.0  0
 NNJ  CONST_06  N27   C19  C20  C21    0.00   0.0  0
 NNJ  CONST_07  N27   C17  C13  C12  180.00   0.0  0
 NNJ  CONST_08  C20   C21  C13  C12  180.00   0.0  0
 NNJ  CONST_09  C18   N27  C17  C13  180.00   0.0  0
 NNJ  CONST_10  C20   C19  N27  C18  180.00   0.0  0
 NNJ  CONST_11  H20   C20  C21  C13  180.00   0.0  0
 NNJ  CONST_12  H21   C21  C13  C17  180.00   0.0  0
 NNJ  CONST_13  H19   C19  N27  C17  180.00   0.0  0
 NNJ  CONST_14  H17   C17  N27  C19  180.00   0.0  0
 NNJ  Var_01    N26   C12  C13  C17  151.63  30.0  2
 NNJ  Var_02    H18   C18  N27  C17   79.62  30.0  2
 NNJ  Var_03    HN26  N26  C12  C13  166.54  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
 NNJ  plan-1  C12  0.020
 NNJ  plan-1  C13  0.020
 NNJ  plan-1  C17  0.020
 NNJ  plan-1  C19  0.020
 NNJ  plan-1  C20  0.020
 NNJ  plan-1  C21  0.020
 NNJ  plan-1  N27  0.020
 NNJ  plan-1  H17  0.020
 NNJ  plan-1  H19  0.020
 NNJ  plan-1  H20  0.020
 NNJ  plan-1  H21  0.020
 NNJ  plan-1  C18  0.020

