# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:30:19 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 4-(aminomethyl)-1-methylpyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1ccc(CN)cc1
#
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
 NNK  NNK  4-(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 GRAND
;

data_comp_NNK
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
 NNK  N16   N  NH2   0  -0.798   3.1576   0.7587  -0.3293
 NNK  C17   C  CH2   0  -0.329   2.4448  -0.3314   0.2940
 NNK  C18   C  CR6   0   0.221   0.9571  -0.2090   0.1470
 NNK  C22   C  CR16  0  -0.379   0.1285  -1.2781   0.4889
 NNK  C23   C  CR16  0   0.096  -1.2314  -1.1621   0.3680
 NNK  N24   N  NR6   1  -0.418  -1.7870  -0.0271  -0.0842
 NNK  C25   C  CH3   0  -0.532  -3.2464   0.0763  -0.1689
 NNK  C26   C  CR16  0   0.098  -1.0192   1.0160  -0.4217
 NNK  C27   C  CR16  0  -0.383   0.3496   0.9528  -0.3162
 NNK  HN16  H  HNH2  0   0.369   4.1107   0.7721   0.0066
 NNK  HN1A  H  HNH2  0   0.357   3.2117   0.6113  -1.3289
 NNK  H17   H  HCH2  0   0.248   2.7372  -1.3303  -0.0551
 NNK  H17A  H  HCH2  0   0.279   2.6554  -0.3229   1.3677
 NNK  H22   H  HCR6  0   0.307   0.5381  -2.2118   0.8480
 NNK  H23   H  HCR6  0   0.345  -1.9062  -1.9664   0.6205
 NNK  H25   H  HCH3  0   0.297  -3.6447   0.3546   0.8034
 NNK  H25A  H  HCH3  0   0.286  -3.5105   0.8299  -0.9027
 NNK  H25B  H  HCH3  0   0.288  -3.6562  -0.8808  -0.4741
 NNK  H26   H  HCR6  0   0.345  -1.5281   1.8984  -0.7795
 NNK  H27   H  HCR6  0   0.305   0.9388   1.8112  -0.6016

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
 NNK  N16  C17   single    1.444  0.020  1.444
 NNK  C17  C18   single    1.500  0.020  1.500
 NNK  C18  C22   aromatic  1.395  0.020  1.395
 NNK  C18  C27   aromatic  1.391  0.020  1.391
 NNK  C22  C23   aromatic  1.370  0.020  1.370
 NNK  C23  N24   aromatic  1.342  0.020  1.342
 NNK  N24  C25   single    1.465  0.020  1.465
 NNK  N24  C26   aromatic  1.338  0.020  1.338
 NNK  C26  C27   aromatic  1.374  0.020  1.374
 NNK  N16  HN16  single    0.890  0.020  1.040
 NNK  N16  HN1A  single    0.890  0.020  1.040
 NNK  C17  H17   single    0.970  0.020  1.090
 NNK  C17  H17A  single    0.970  0.020  1.090
 NNK  C22  H22   single    0.930  0.020  1.080
 NNK  C23  H23   single    0.930  0.020  1.080
 NNK  C25  H25   single    0.970  0.020  1.090
 NNK  C25  H25A  single    0.970  0.020  1.090
 NNK  C25  H25B  single    0.970  0.020  1.090
 NNK  C26  H26   single    0.930  0.020  1.080
 NNK  C27  H27   single    0.930  0.020  1.080

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
 NNK  HN1A  N16  HN16  106.25  3.000
 NNK  HN1A  N16  C17   110.05  3.000
 NNK  HN16  N16  C17   109.40  3.000
 NNK  H17A  C17  H17   105.53  3.000
 NNK  H17A  C17  C18   106.65  3.000
 NNK  H17   C17  C18   107.89  3.000
 NNK  H17A  C17  N16   108.82  3.000
 NNK  H17   C17  N16   114.72  3.000
 NNK  C18   C17  N16   112.69  3.000
 NNK  C27   C18  C22   117.54  3.000
 NNK  C27   C18  C17   122.28  3.000
 NNK  C22   C18  C17   120.17  3.000
 NNK  H22   C22  C23   118.59  3.000
 NNK  H22   C22  C18   121.21  3.000
 NNK  C23   C22  C18   120.20  3.000
 NNK  H23   C23  N24   116.74  3.000
 NNK  H23   C23  C22   122.45  3.000
 NNK  N24   C23  C22   120.81  3.000
 NNK  C26   N24  C25   120.11  3.000
 NNK  C26   N24  C23   120.43  3.000
 NNK  C25   N24  C23   119.43  3.000
 NNK  H25B  C25  H25A  109.31  3.000
 NNK  H25B  C25  H25   109.82  3.000
 NNK  H25A  C25  H25   109.76  3.000
 NNK  H25B  C25  N24   109.28  3.000
 NNK  H25A  C25  N24   109.31  3.000
 NNK  H25   C25  N24   109.35  3.000
 NNK  H26   C26  C27   122.17  3.000
 NNK  H26   C26  N24   116.75  3.000
 NNK  C27   C26  N24   121.08  3.000
 NNK  H27   C27  C26   119.13  3.000
 NNK  H27   C27  C18   120.93  3.000
 NNK  C26   C27  C18   119.94  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
 NNK  CONST_01  N24   C23  C22  C18    0.00   0.0  0
 NNK  CONST_02  N24   C26  C27  C18    0.00   0.0  0
 NNK  CONST_03  C26   C27  C18  C22    0.00   0.0  0
 NNK  CONST_04  C26   N24  C23  C22    0.00   0.0  0
 NNK  CONST_05  C27   C18  C22  C23    0.00   0.0  0
 NNK  CONST_06  C27   C26  N24  C23    0.00   0.0  0
 NNK  CONST_07  C23   C22  C18  C17  180.00   0.0  0
 NNK  CONST_08  C26   C27  C18  C17  180.00   0.0  0
 NNK  CONST_09  C25   N24  C23  C22  180.00   0.0  0
 NNK  CONST_10  C27   C26  N24  C25  180.00   0.0  0
 NNK  CONST_11  H23   C23  C22  C18  180.00   0.0  0
 NNK  CONST_12  H26   C26  C27  C18  180.00   0.0  0
 NNK  CONST_13  H27   C27  C18  C22  180.00   0.0  0
 NNK  CONST_14  H22   C22  C23  N24  180.00   0.0  0
 NNK  Var_01    C22   C18  C17  N16  169.25  30.0  2
 NNK  Var_02    H25   C25  N24  C23   83.29  30.0  2
 NNK  Var_03    HN16  N16  C17  C18  164.54  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
 NNK  plan-1  C17  0.020
 NNK  plan-1  C18  0.020
 NNK  plan-1  C22  0.020
 NNK  plan-1  C23  0.020
 NNK  plan-1  N24  0.020
 NNK  plan-1  C25  0.020
 NNK  plan-1  C26  0.020
 NNK  plan-1  C27  0.020
 NNK  plan-1  H22  0.020
 NNK  plan-1  H23  0.020
 NNK  plan-1  H26  0.020
 NNK  plan-1  H27  0.020

