# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 03:09:27 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 5-amino-1,2-dimethylpyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(N)c[n+]1C
#
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
 275  275  5-amino-1,2-dimethylpyridinium  ligand  20  9  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_275
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
 275  C1   C  CH3   0  -0.734   2.5781   0.8678   0.0293
 275  C2   C  CR6   0   0.375   1.1185   0.5725   0.0361
 275  C3   C  CR16  0  -0.351   0.1537   1.5699   0.0084
 275  C4   C  CR16  0  -0.164  -1.1888   1.2730   0.0149
 275  C5   C  CR6   0   0.259  -1.6123  -0.0627   0.0511
 275  N6   N  NH2   0  -0.854  -2.9257  -0.4049   0.1082
 275  C7   C  CR16  0  -0.032  -0.6136  -1.0276   0.0725
 275  N8   N  NR6   1  -0.430   0.6881  -0.7013   0.0666
 275  C9   C  CH3   0  -0.539   1.6696  -1.7904   0.0911
 275  H11  H  HCH3  0   0.279   3.0763   0.4796   0.9190
 275  H12  H  HCH3  0   0.279   3.0755   0.4383  -0.8417
 275  H13  H  HCH3  0   0.284   2.7293   1.9435   0.0033
 275  H3   H  HCR6  0   0.304   0.4775   2.6001  -0.0206
 275  H4   H  HCR6  0   0.308  -1.9189   2.0716  -0.0067
 275  H61  H  HNH2  0   0.403  -3.5931   0.2815  -0.2029
 275  H62  H  HNH2  0   0.400  -3.1786  -1.3499  -0.1293
 275  H7   H  HCR6  0   0.336  -0.8440  -2.0821   0.0967
 275  H91  H  HCH3  0   0.292   2.2825  -1.7109   0.9850
 275  H92  H  HCH3  0   0.291   1.1490  -2.7408   0.0984
 275  H93  H  HCH3  0   0.292   2.3014  -1.7348  -0.7910

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
 275  C1  C2   single    1.489  0.020  1.489
 275  C2  C3   aromatic  1.388  0.020  1.388
 275  C2  N8   aromatic  1.345  0.020  1.345
 275  C3  C4   aromatic  1.375  0.020  1.375
 275  C4  C5   aromatic  1.402  0.020  1.402
 275  C5  N6   single    1.358  0.020  1.358
 275  C5  C7   aromatic  1.389  0.020  1.389
 275  C7  N8   aromatic  1.342  0.020  1.342
 275  N8  C9   single    1.466  0.020  1.466
 275  C1  H11  single    0.970  0.020  1.090
 275  C1  H12  single    0.970  0.020  1.090
 275  C1  H13  single    0.970  0.020  1.090
 275  C3  H3   single    0.930  0.020  1.080
 275  C4  H4   single    0.930  0.020  1.080
 275  N6  H61  single    0.890  0.020  1.040
 275  N6  H62  single    0.890  0.020  1.040
 275  C7  H7   single    0.930  0.020  1.080
 275  C9  H91  single    0.970  0.020  1.090
 275  C9  H92  single    0.970  0.020  1.090
 275  C9  H93  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
 275  H13  C1  H12  107.89  3.000
 275  H13  C1  H11  107.95  3.000
 275  H12  C1  H11  107.61  3.000
 275  H13  C1  C2   109.44  3.000
 275  H12  C1  C2   111.87  3.000
 275  H11  C1  C2   111.91  3.000
 275  N8   C2  C3   117.30  3.000
 275  N8   C2  C1   120.11  3.000
 275  C3   C2  C1   122.60  3.000
 275  H3   C3  C4   119.92  3.000
 275  H3   C3  C2   118.52  3.000
 275  C4   C3  C2   121.57  3.000
 275  H4   C4  C5   119.99  3.000
 275  H4   C4  C3   119.95  3.000
 275  C5   C4  C3   120.06  3.000
 275  C7   C5  N6   121.31  3.000
 275  C7   C5  C4   116.43  3.000
 275  N6   C5  C4   122.23  3.000
 275  H62  N6  H61  113.62  3.000
 275  H62  N6  C5   118.00  3.000
 275  H61  N6  C5   117.14  3.000
 275  H7   C7  N8   116.40  3.000
 275  H7   C7  C5   121.69  3.000
 275  N8   C7  C5   121.90  3.000
 275  C9   N8  C7   117.94  3.000
 275  C9   N8  C2   119.32  3.000
 275  C7   N8  C2   122.74  3.000
 275  H93  C9  H92  109.25  3.000
 275  H93  C9  H91  109.64  3.000
 275  H92  C9  H91  109.24  3.000
 275  H93  C9  N8   109.73  3.000
 275  H92  C9  N8   109.26  3.000
 275  H91  C9  N8   109.69  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
 275  CONST_01  C5   C4  C3  C2    0.00   0.0  0
 275  CONST_02  C5   C7  N8  C2    0.00   0.0  0
 275  CONST_03  C7   N8  C2  C3    0.00   0.0  0
 275  CONST_04  C7   C5  C4  C3    0.00   0.0  0
 275  CONST_05  N8   C2  C3  C4    0.00   0.0  0
 275  CONST_06  N8   C7  C5  C4    0.00   0.0  0
 275  CONST_07  C4   C3  C2  C1  180.00   0.0  0
 275  CONST_08  C7   N8  C2  C1  180.00   0.0  0
 275  CONST_09  C9   N8  C2  C3  180.00   0.0  0
 275  CONST_10  N6   C5  C4  C3  180.00   0.0  0
 275  CONST_11  C9   N8  C7  C5  180.00   0.0  0
 275  CONST_12  N8   C7  C5  N6  180.00   0.0  0
 275  CONST_13  H4   C4  C3  C2  180.00   0.0  0
 275  CONST_14  H7   C7  N8  C2  180.00   0.0  0
 275  CONST_15  H3   C3  C4  C5  180.00   0.0  0
 275  Var_01    H91  C9  N8  C2   61.15  30.0  2
 275  Var_02    H11  C1  C2  C3  119.79  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
 275  plan-1  C1   0.020
 275  plan-1  C2   0.020
 275  plan-1  C3   0.020
 275  plan-1  C4   0.020
 275  plan-1  C5   0.020
 275  plan-1  N6   0.020
 275  plan-1  C7   0.020
 275  plan-1  N8   0.020
 275  plan-1  C9   0.020
 275  plan-1  H3   0.020
 275  plan-1  H4   0.020
 275  plan-1  H7   0.020
 275  plan-2  C5   0.020
 275  plan-2  N6   0.020
 275  plan-2  H61  0.020
 275  plan-2  H62  0.020

