# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:21:00 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 2-(aminomethyl)-4-chloro-1-methylpyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1ccc(Cl)cc1CN
#
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
 NNX  NNX  2-(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_NNX
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
 NNX  CL2   CL  CL    0  -0.032   3.0423  -0.4322   0.0919
 NNX  N18   N   NH2   0  -0.785  -2.7598  -1.5591  -0.7138
 NNX  C19   C   CH2   0  -0.385  -2.0438  -1.3328   0.5270
 NNX  C20   C   CR6   0   0.448  -0.9154  -0.3681   0.2920
 NNX  N21   N   NR6   1  -0.455  -1.1794   0.9290   0.0205
 NNX  C22   C   CR16  0  -0.333   0.3955  -0.7963   0.3167
 NNX  C23   C   CR6   0   0.127   1.4228   0.0989   0.0647
 NNX  C24   C   CR16  0  -0.311   1.1281   1.4242  -0.2117
 NNX  C25   C   CR16  0   0.076  -0.1905   1.8007  -0.2224
 NNX  HN18  H   HNH2  0   0.365  -2.2358  -2.1888  -1.3072
 NNX  HN1A  H   HNH2  0   0.374  -3.6422  -2.0109  -0.5145
 NNX  H19   H   HCH2  0   0.286  -2.7299  -0.9119   1.2641
 NNX  H19A  H   HCH2  0   0.270  -1.6196  -2.2333   0.9809
 NNX  H22   H   HCR6  0   0.332   0.6020  -1.8345   0.5332
 NNX  H24   H   HCR6  0   0.333   1.8942   2.1575  -0.4138
 NNX  H25   H   HCR6  0   0.356  -0.4809   2.8196  -0.4270
 NNX  H27   H   HCH3  0   0.295  -2.9468   1.4124   1.0405
 NNX  H27A  H   HCH3  0   0.290  -2.5744   2.4373  -0.3550
 NNX  H27B  H   HCH3  0   0.299  -3.1680   0.7807  -0.6108
 NNX  C27   C   CH3   0  -0.548  -2.5636   1.4214   0.0228

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
 NNX  CL2  C23   single    1.705  0.020  1.705
 NNX  N18  C19   single    1.450  0.020  1.450
 NNX  C19  C20   single    1.503  0.020  1.503
 NNX  C20  N21   aromatic  1.351  0.020  1.351
 NNX  C20  C22   aromatic  1.379  0.020  1.379
 NNX  N21  C25   aromatic  1.340  0.020  1.340
 NNX  N21  C27   single    1.469  0.020  1.469
 NNX  C22  C23   aromatic  1.386  0.020  1.386
 NNX  C23  C24   aromatic  1.386  0.020  1.386
 NNX  C24  C25   aromatic  1.371  0.020  1.371
 NNX  N18  HN18  single    0.890  0.020  1.040
 NNX  N18  HN1A  single    0.890  0.020  1.040
 NNX  C19  H19   single    0.970  0.020  1.090
 NNX  C19  H19A  single    0.970  0.020  1.090
 NNX  C22  H22   single    0.930  0.020  1.080
 NNX  C24  H24   single    0.930  0.020  1.080
 NNX  C25  H25   single    0.930  0.020  1.080
 NNX  C27  H27   single    0.970  0.020  1.090
 NNX  C27  H27A  single    0.970  0.020  1.090
 NNX  C27  H27B  single    0.970  0.020  1.090

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
 NNX  HN1A  N18  HN18  106.84  3.000
 NNX  HN1A  N18  C19   109.39  3.000
 NNX  HN18  N18  C19   110.07  3.000
 NNX  H19A  C19  H19   106.32  3.000
 NNX  H19A  C19  C20   107.59  3.000
 NNX  H19   C19  C20   109.27  3.000
 NNX  H19A  C19  N18   114.70  3.000
 NNX  H19   C19  N18   109.12  3.000
 NNX  C20   C19  N18   109.70  3.000
 NNX  C22   C20  N21   119.17  3.000
 NNX  C22   C20  C19   120.76  3.000
 NNX  N21   C20  C19   120.06  3.000
 NNX  C27   N21  C25   118.52  3.000
 NNX  C27   N21  C20   120.36  3.000
 NNX  C25   N21  C20   121.10  3.000
 NNX  H22   C22  C23   121.03  3.000
 NNX  H22   C22  C20   118.92  3.000
 NNX  C23   C22  C20   120.05  3.000
 NNX  C24   C23  C22   119.77  3.000
 NNX  C24   C23  CL2   120.22  3.000
 NNX  C22   C23  CL2   120.02  3.000
 NNX  H24   C24  C25   119.63  3.000
 NNX  H24   C24  C23   122.42  3.000
 NNX  C25   C24  C23   117.95  3.000
 NNX  H25   C25  C24   121.30  3.000
 NNX  H25   C25  N21   116.74  3.000
 NNX  C24   C25  N21   121.97  3.000
 NNX  H27B  C27  H27A  110.14  3.000
 NNX  H27B  C27  H27   110.20  3.000
 NNX  H27A  C27  H27   109.30  3.000
 NNX  H27B  C27  N21   109.03  3.000
 NNX  H27A  C27  N21   108.84  3.000
 NNX  H27   C27  N21   109.31  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
 NNX  CONST_01  C24   C25  N21  C20    0.00   0.0  0
 NNX  CONST_02  C24   C23  C22  C20    0.00   0.0  0
 NNX  CONST_03  C23   C22  C20  N21    0.00   0.0  0
 NNX  CONST_04  C23   C24  C25  N21    0.00   0.0  0
 NNX  CONST_05  C25   N21  C20  C22    0.00   0.0  0
 NNX  CONST_06  C25   C24  C23  C22    0.00   0.0  0
 NNX  CONST_07  C20   C22  C23  CL2  180.00   0.0  0
 NNX  CONST_08  C25   C24  C23  CL2  180.00   0.0  0
 NNX  CONST_09  C25   N21  C20  C19  180.00   0.0  0
 NNX  CONST_10  C23   C22  C20  C19  180.00   0.0  0
 NNX  CONST_11  C27   N21  C20  C22  180.00   0.0  0
 NNX  CONST_12  C27   N21  C25  C24  180.00   0.0  0
 NNX  CONST_13  H25   C25  N21  C20  180.00   0.0  0
 NNX  CONST_14  H22   C22  C20  N21  180.00   0.0  0
 NNX  CONST_15  H24   C24  C25  N21  180.00   0.0  0
 NNX  Var_01    N21   C20  C19  N18   69.36  30.0  2
 NNX  Var_02    H27   C27  N21  C20   68.82  30.0  2
 NNX  Var_03    HN18  N18  C19  C20   77.14  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
 NNX  plan-1  CL2  0.020
 NNX  plan-1  C19  0.020
 NNX  plan-1  C20  0.020
 NNX  plan-1  N21  0.020
 NNX  plan-1  C22  0.020
 NNX  plan-1  C23  0.020
 NNX  plan-1  C24  0.020
 NNX  plan-1  C25  0.020
 NNX  plan-1  H22  0.020
 NNX  plan-1  H24  0.020
 NNX  plan-1  H25  0.020
 NNX  plan-1  C27  0.020

