# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 01:54:01 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: pyridine-2,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(N)n1
#
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
 26D  26D  'pyridine-2,6-diamine     '  ligand  15  8  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_26D
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
 26D  N1    N  NH2   0  -0.834   2.3140  -1.0095  -0.1185
 26D  C3    C  CR6   0   0.444   1.1782  -0.2555  -0.0361
 26D  N3    N  N     0  -0.508   0.0267  -0.9231   0.0153
 26D  C5    C  CR16  0  -0.425   1.2386   1.1449  -0.0566
 26D  C6    C  CR16  0  -0.150   0.0385   1.8332  -0.0312
 26D  C4    C  CR16  0  -0.425  -1.1675   1.1564   0.0167
 26D  C2    C  CR6   0   0.444  -1.1191  -0.2443   0.0436
 26D  N2    N  NH2   0  -0.834  -2.2613  -0.9854   0.1510
 26D  HN11  H  HNH2  0   0.386   3.1817  -0.5712   0.1407
 26D  HN12  H  HNH2  0   0.378   2.2338  -1.9689   0.1755
 26D  H5    H  HCR6  0   0.252   2.1877   1.6622  -0.0967
 26D  H6    H  HCR6  0   0.257   0.0430   2.9160  -0.0490
 26D  H4    H  HCR6  0   0.252  -2.1121   1.6829   0.0385
 26D  HN21  H  HNH2  0   0.386  -3.1249  -0.5490  -0.1243
 26D  HN22  H  HNH2  0   0.378  -2.1891  -1.9548  -0.1103

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
 26D  N1  C3    single    1.366  0.020  1.366
 26D  N1  HN11  single    0.890  0.020  1.040
 26D  N1  HN12  single    0.890  0.020  1.040
 26D  C3  N3    aromatic  1.332  0.020  1.332
 26D  C3  C5    aromatic  1.402  0.020  1.402
 26D  N3  C2    aromatic  1.332  0.020  1.332
 26D  C5  C6    aromatic  1.384  0.020  1.384
 26D  C5  H5    single    0.930  0.020  1.080
 26D  C6  C4    aromatic  1.384  0.020  1.384
 26D  C6  H6    single    0.930  0.020  1.080
 26D  C4  C2    aromatic  1.402  0.020  1.402
 26D  C4  H4    single    0.930  0.020  1.080
 26D  C2  N2    single    1.366  0.020  1.366
 26D  N2  HN21  single    0.890  0.020  1.040
 26D  N2  HN22  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
 26D  HN12  N1  HN11  114.12  3.000
 26D  HN12  N1  C3    116.25  3.000
 26D  HN11  N1  C3    117.47  3.000
 26D  C5    C3  N3    122.58  3.000
 26D  C5    C3  N1    120.98  3.000
 26D  N3    C3  N1    116.39  3.000
 26D  C2    N3  C3    119.27  3.000
 26D  H5    C5  C6    121.59  3.000
 26D  H5    C5  C3    121.07  3.000
 26D  C6    C5  C3    117.34  3.000
 26D  H6    C6  C4    119.56  3.000
 26D  H6    C6  C5    119.57  3.000
 26D  C4    C6  C5    120.88  3.000
 26D  H4    C4  C2    121.07  3.000
 26D  H4    C4  C6    121.58  3.000
 26D  C2    C4  C6    117.34  3.000
 26D  N2    C2  C4    120.98  3.000
 26D  N2    C2  N3    116.40  3.000
 26D  C4    C2  N3    122.58  3.000
 26D  HN22  N2  HN21  114.11  3.000
 26D  HN22  N2  C2    116.24  3.000
 26D  HN21  N2  C2    117.45  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
 26D  CONST_01  C4  C2  N3  C3    0.00  0.0  0
 26D  CONST_02  C4  C6  C5  C3    0.00  0.0  0
 26D  CONST_03  C6  C5  C3  N3    0.00  0.0  0
 26D  CONST_04  C6  C4  C2  N3    0.00  0.0  0
 26D  CONST_05  C2  N3  C3  C5    0.00  0.0  0
 26D  CONST_06  C2  C4  C6  C5    0.00  0.0  0
 26D  CONST_07  C2  N3  C3  N1  180.00  0.0  0
 26D  CONST_08  C6  C5  C3  N1  180.00  0.0  0
 26D  CONST_09  N2  C2  N3  C3  180.00  0.0  0
 26D  CONST_10  N2  C2  C4  C6  180.00  0.0  0
 26D  CONST_11  H6  C6  C5  C3  180.00  0.0  0
 26D  CONST_12  H5  C5  C3  N3  180.00  0.0  0
 26D  CONST_13  H4  C4  C2  N3  180.00  0.0  0

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
 26D  plan-1  N1    0.020
 26D  plan-1  C3    0.020
 26D  plan-1  N3    0.020
 26D  plan-1  C5    0.020
 26D  plan-1  C6    0.020
 26D  plan-1  C4    0.020
 26D  plan-1  C2    0.020
 26D  plan-1  N2    0.020
 26D  plan-1  H5    0.020
 26D  plan-1  H6    0.020
 26D  plan-1  H4    0.020
 26D  plan-2  N1    0.020
 26D  plan-2  C3    0.020
 26D  plan-2  HN11  0.020
 26D  plan-2  HN12  0.020
 26D  plan-3  C2    0.020
 26D  plan-3  N2    0.020
 26D  plan-3  HN21  0.020
 26D  plan-3  HN22  0.020

