# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 19:00:51 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: pyridine-2,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccnc1N
#
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
 76X  76X  'pyridine-2,3-diamine     '  ligand  15  8  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_76X
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
 76X  N8  N  NH2   0  -0.859   1.8047  -1.3423  -0.1023
 76X  C3  C  CR6   0   0.167   0.5606  -0.7264  -0.0239
 76X  C2  C  CR6   0   0.371   0.4910   0.6891   0.0329
 76X  N7  N  NH2   0  -0.833   1.6622   1.4136   0.0805
 76X  C4  C  CR16  0  -0.229  -0.6367  -1.4149  -0.0518
 76X  C5  C  CR16  0  -0.345  -1.8449  -0.7177  -0.0082
 76X  C6  C  CR16  0  -0.101  -1.7989   0.6558   0.0790
 76X  N1  N  N     0  -0.444  -0.6541   1.3431   0.0933
 76X  H1  H  HNH2  0   0.374   2.4847  -0.9731   0.5486
 76X  H2  H  HNH2  0   0.378   1.7604  -2.3461  -0.0071
 76X  H3  H  HNH2  0   0.380   2.4191   1.0490  -0.4795
 76X  H4  H  HNH2  0   0.377   1.5315   2.4023  -0.0697
 76X  H5  H  HCR6  0   0.264  -0.6311  -2.4979  -0.0973
 76X  H6  H  HCR6  0   0.254  -2.7901  -1.2424  -0.0300
 76X  H7  H  HCR6  0   0.246  -2.7100   1.2413   0.1314

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
 76X  N8  C3  single    1.390  0.020  1.390
 76X  N7  C2  single    1.378  0.020  1.378
 76X  C3  C2  aromatic  1.418  0.020  1.418
 76X  C3  C4  aromatic  1.381  0.020  1.381
 76X  C2  N1  aromatic  1.320  0.020  1.320
 76X  C4  C5  aromatic  1.396  0.020  1.396
 76X  N1  C6  aromatic  1.335  0.020  1.335
 76X  C6  C5  aromatic  1.377  0.020  1.377
 76X  N8  H1  single    0.890  0.020  1.040
 76X  N8  H2  single    0.890  0.020  1.040
 76X  N7  H3  single    0.890  0.020  1.040
 76X  N7  H4  single    0.890  0.020  1.040
 76X  C4  H5  single    0.930  0.020  1.080
 76X  C5  H6  single    0.930  0.020  1.080
 76X  C6  H7  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
 76X  H2  N8  H1  109.38  3.000
 76X  H2  N8  C3  113.33  3.000
 76X  H1  N8  C3  113.81  3.000
 76X  C4  C3  C2  117.11  3.000
 76X  C4  C3  N8  123.61  3.000
 76X  C2  C3  N8  119.22  3.000
 76X  N1  C2  N7  118.38  3.000
 76X  N1  C2  C3  122.60  3.000
 76X  N7  C2  C3  118.97  3.000
 76X  H4  N7  H3  111.63  3.000
 76X  H4  N7  C2  113.58  3.000
 76X  H3  N7  C2  115.35  3.000
 76X  H5  C4  C5  120.32  3.000
 76X  H5  C4  C3  119.63  3.000
 76X  C5  C4  C3  120.05  3.000
 76X  H6  C5  C6  120.96  3.000
 76X  H6  C5  C4  120.91  3.000
 76X  C6  C5  C4  118.12  3.000
 76X  H7  C6  N1  116.22  3.000
 76X  H7  C6  C5  120.90  3.000
 76X  N1  C6  C5  122.87  3.000
 76X  C6  N1  C2  119.22  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
 76X  CONST_01  C6  N1  C2  C3    0.00  0.0  0
 76X  CONST_02  C6  C5  C4  C3    0.00  0.0  0
 76X  CONST_03  C5  C4  C3  C2    0.00  0.0  0
 76X  CONST_04  C5  C6  N1  C2    0.00  0.0  0
 76X  CONST_05  N1  C2  C3  C4    0.00  0.0  0
 76X  CONST_06  N1  C6  C5  C4    0.00  0.0  0
 76X  CONST_07  N1  C2  C3  N8  180.00  0.0  0
 76X  CONST_08  C5  C4  C3  N8  180.00  0.0  0
 76X  CONST_09  C4  C3  C2  N7  180.00  0.0  0
 76X  CONST_10  C6  N1  C2  N7  180.00  0.0  0
 76X  CONST_11  H6  C5  C4  C3  180.00  0.0  0
 76X  CONST_12  H5  C4  C3  C2  180.00  0.0  0
 76X  CONST_13  H7  C6  N1  C2  180.00  0.0  0
 76X  CONST_15  H4  N7  C2  C3  180.00  0.0  0
 76X  CONST_17  H2  N8  C3  C2  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
 76X  plan-1  N8  0.020
 76X  plan-1  C3  0.020
 76X  plan-1  C2  0.020
 76X  plan-1  N7  0.020
 76X  plan-1  C4  0.020
 76X  plan-1  C5  0.020
 76X  plan-1  C6  0.020
 76X  plan-1  N1  0.020
 76X  plan-1  H5  0.020
 76X  plan-1  H6  0.020
 76X  plan-1  H7  0.020
 76X  plan-2  N8  0.020
 76X  plan-2  C3  0.020
 76X  plan-2  H1  0.020
 76X  plan-2  H2  0.020
 76X  plan-3  C2  0.020
 76X  plan-3  N7  0.020
 76X  plan-3  H3  0.020
 76X  plan-3  H4  0.020

