# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 09:47:42 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: 5-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(N)nc1
#
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
 LG4  LG4  '5-methylpyridin-2-amine  '  ligand  16  8  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LG4
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
 LG4  N1    N  N     0  -0.456  -0.7070  -1.1484  -0.0839
 LG4  C2    C  CR16  0  -0.110   0.6243  -1.1257  -0.0644
 LG4  C3    C  CR6   0  -0.012   1.3968   0.0208   0.0002
 LG4  C4    C  CR16  0  -0.178   0.6907   1.2279   0.0465
 LG4  C5    C  CR16  0  -0.376  -0.6847   1.2352   0.0232
 LG4  C6    C  CR6   0   0.433  -1.3630   0.0052  -0.0433
 LG4  N7    N  NH2   0  -0.834  -2.7288  -0.0427  -0.1166
 LG4  C8    C  CH3   0  -0.723   2.8949  -0.0270   0.0268
 LG4  H2    H  HCR6  0   0.244   1.1095  -2.0975  -0.1025
 LG4  H4    H  HCR6  0   0.258   1.2285   2.1677   0.1017
 LG4  H5    H  HCR6  0   0.264  -1.2381   2.1653   0.0578
 LG4  HN71  H  HNH2  0   0.386  -3.2338   0.7547   0.2330
 LG4  HN72  H  HNH2  0   0.378  -3.1488  -0.9239   0.1312
 LG4  H81   H  HCH3  0   0.242   3.2938   0.3483   0.9710
 LG4  H82   H  HCH3  0   0.240   3.2591  -1.0462  -0.1018
 LG4  H83   H  HCH3  0   0.241   3.3285   0.5807  -0.7690

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
 LG4  N1  C2    aromatic  1.332  0.020  1.332
 LG4  N1  C6    aromatic  1.328  0.020  1.328
 LG4  C2  C3    aromatic  1.384  0.020  1.384
 LG4  C2  H2    single    0.930  0.020  1.080
 LG4  C3  C4    aromatic  1.399  0.020  1.399
 LG4  C3  C8    single    1.499  0.020  1.499
 LG4  C4  C5    aromatic  1.376  0.020  1.376
 LG4  C4  H4    single    0.930  0.020  1.080
 LG4  C5  C6    aromatic  1.406  0.020  1.406
 LG4  C5  H5    single    0.930  0.020  1.080
 LG4  C6  N7    single    1.369  0.020  1.369
 LG4  N7  HN71  single    0.890  0.020  1.040
 LG4  N7  HN72  single    0.890  0.020  1.040
 LG4  C8  H81   single    0.970  0.020  1.090
 LG4  C8  H82   single    0.970  0.020  1.090
 LG4  C8  H83   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
 LG4  C6    N1  C2    118.59  3.000
 LG4  H2    C2  C3    119.55  3.000
 LG4  H2    C2  N1    115.49  3.000
 LG4  C3    C2  N1    124.95  3.000
 LG4  C8    C3  C4    122.09  3.000
 LG4  C8    C3  C2    122.16  3.000
 LG4  C4    C3  C2    115.76  3.000
 LG4  H4    C4  C5    119.49  3.000
 LG4  H4    C4  C3    119.94  3.000
 LG4  C5    C4  C3    120.57  3.000
 LG4  H5    C5  C6    120.42  3.000
 LG4  H5    C5  C4    121.00  3.000
 LG4  C6    C5  C4    118.58  3.000
 LG4  N7    C6  C5    120.96  3.000
 LG4  N7    C6  N1    117.45  3.000
 LG4  C5    C6  N1    121.55  3.000
 LG4  HN72  N7  HN71  113.48  3.000
 LG4  HN72  N7  C6    115.70  3.000
 LG4  HN71  N7  C6    117.02  3.000
 LG4  H83   C8  H82   107.58  3.000
 LG4  H83   C8  H81   107.11  3.000
 LG4  H82   C8  H81   107.55  3.000
 LG4  H83   C8  C3    111.49  3.000
 LG4  H82   C8  C3    111.20  3.000
 LG4  H81   C8  C3    111.69  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
 LG4  CONST_01  C4   C3  C2  N1     0.00   0.0  0
 LG4  CONST_02  C4   C5  C6  N1     0.00   0.0  0
 LG4  CONST_03  C5   C6  N1  C2     0.00   0.0  0
 LG4  CONST_04  C5   C4  C3  C2     0.00   0.0  0
 LG4  CONST_05  C6   N1  C2  C3     0.00   0.0  0
 LG4  CONST_06  C6   C5  C4  C3     0.00   0.0  0
 LG4  CONST_07  C8   C3  C2  N1   180.00   0.0  0
 LG4  CONST_08  N7   C6  N1  C2   180.00   0.0  0
 LG4  CONST_09  N7   C6  C5  C4   180.00   0.0  0
 LG4  CONST_10  C8   C3  C4  C5   180.00   0.0  0
 LG4  CONST_11  H5   C5  C6  N1   180.00   0.0  0
 LG4  CONST_12  H4   C4  C3  C2   180.00   0.0  0
 LG4  CONST_13  H2   C2  C3  C4   180.00   0.0  0
 LG4  Var_01    H81  C8  C3  C2  -115.01  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
 LG4  plan-1  N1    0.020
 LG4  plan-1  C2    0.020
 LG4  plan-1  C3    0.020
 LG4  plan-1  C4    0.020
 LG4  plan-1  C5    0.020
 LG4  plan-1  C6    0.020
 LG4  plan-1  N7    0.020
 LG4  plan-1  C8    0.020
 LG4  plan-1  H2    0.020
 LG4  plan-1  H4    0.020
 LG4  plan-1  H5    0.020
 LG4  plan-2  C6    0.020
 LG4  plan-2  N7    0.020
 LG4  plan-2  HN71  0.020
 LG4  plan-2  HN72  0.020

