# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 08:17:12 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: pyridine-3,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccncc1N
#
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
 L89  L89  'pyridine-3,4-diamine     '  ligand  15  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_L89
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
 L89  N2  N  NH2   0  -0.859   1.7619   1.3793  -0.1009
 L89  C4  C  CR6   0   0.152   0.5544   0.6858  -0.0281
 L89  C   C  CR6   0   0.349   0.5693  -0.7245   0.0203
 L89  N   N  NH2   0  -0.846   1.7654  -1.3918   0.0764
 L89  C3  C  CR16  0  -0.159  -0.6790   1.3176  -0.0596
 L89  N1  N  N     0  -0.423  -1.8548   0.6913  -0.0470
 L89  C2  C  CR16  0  -0.098  -1.8308  -0.6322   0.0204
 L89  C1  C  CR16  0  -0.395  -0.6617  -1.3754   0.0566
 L89  H1  H  HNH2  0   0.375   1.6421   2.3814  -0.0606
 L89  H2  H  HNH2  0   0.373   2.4273   1.1026   0.6093
 L89  H3  H  HNH2  0   0.382   2.5355  -0.9496  -0.4026
 L89  H4  H  HNH2  0   0.386   1.7230  -2.3814  -0.1074
 L89  H5  H  HCR6  0   0.251  -0.7080   2.4036  -0.1020
 L89  H6  H  HCR6  0   0.248  -2.7892  -1.1403   0.0415
 L89  H7  H  HCR6  0   0.264  -0.7074  -2.4569   0.0949

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
 L89  N   C   single    1.371  0.020  1.371
 L89  N2  C4  single    1.394  0.020  1.394
 L89  C   C4  aromatic  1.411  0.020  1.411
 L89  C   C1  aromatic  1.393  0.020  1.393
 L89  C4  C3  aromatic  1.386  0.020  1.386
 L89  C1  C2  aromatic  1.386  0.020  1.386
 L89  C3  N1  aromatic  1.332  0.020  1.332
 L89  C2  N1  aromatic  1.325  0.020  1.325
 L89  N2  H1  single    0.890  0.020  1.040
 L89  N2  H2  single    0.890  0.020  1.040
 L89  N   H3  single    0.890  0.020  1.040
 L89  N   H4  single    0.890  0.020  1.040
 L89  C3  H5  single    0.930  0.020  1.080
 L89  C2  H6  single    0.930  0.020  1.080
 L89  C1  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
 L89  H2  N2  H1  108.75  3.000
 L89  H2  N2  C4  113.37  3.000
 L89  H1  N2  C4  112.87  3.000
 L89  C3  C4  C   117.75  3.000
 L89  C3  C4  N2  122.87  3.000
 L89  C   C4  N2  119.32  3.000
 L89  C1  C   N   122.86  3.000
 L89  C1  C   C4  117.29  3.000
 L89  N   C   C4  119.81  3.000
 L89  H4  N   H3  112.09  3.000
 L89  H4  N   C   115.72  3.000
 L89  H3  N   C   115.67  3.000
 L89  H5  C3  N1  116.51  3.000
 L89  H5  C3  C4  118.68  3.000
 L89  N1  C3  C4  124.81  3.000
 L89  C2  N1  C3  117.00  3.000
 L89  H6  C2  C1  119.57  3.000
 L89  H6  C2  N1  116.91  3.000
 L89  C1  C2  N1  123.51  3.000
 L89  H7  C1  C2  120.06  3.000
 L89  H7  C1  C   120.32  3.000
 L89  C2  C1  C   119.62  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
 L89  CONST_01  C2  C1  C   C4    0.00  0.0  0
 L89  CONST_02  C2  N1  C3  C4    0.00  0.0  0
 L89  CONST_03  N1  C3  C4  C     0.00  0.0  0
 L89  CONST_04  N1  C2  C1  C     0.00  0.0  0
 L89  CONST_05  C1  C   C4  C3    0.00  0.0  0
 L89  CONST_06  C1  C2  N1  C3    0.00  0.0  0
 L89  CONST_07  C1  C   C4  N2  180.00  0.0  0
 L89  CONST_08  N1  C3  C4  N2  180.00  0.0  0
 L89  CONST_09  C3  C4  C   N   180.00  0.0  0
 L89  CONST_10  C2  C1  C   N   180.00  0.0  0
 L89  CONST_11  H7  C1  C   C4  180.00  0.0  0
 L89  CONST_12  H5  C3  C4  C   180.00  0.0  0
 L89  CONST_13  H6  C2  C1  C   180.00  0.0  0
 L89  CONST_15  H4  N   C   C4  180.00  0.0  0
 L89  CONST_16  H1  N2  C4  C   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
 L89  plan-1  N2  0.020
 L89  plan-1  C4  0.020
 L89  plan-1  C   0.020
 L89  plan-1  N   0.020
 L89  plan-1  C3  0.020
 L89  plan-1  N1  0.020
 L89  plan-1  C2  0.020
 L89  plan-1  C1  0.020
 L89  plan-1  H5  0.020
 L89  plan-1  H6  0.020
 L89  plan-1  H7  0.020
 L89  plan-2  N2  0.020
 L89  plan-2  C4  0.020
 L89  plan-2  H1  0.020
 L89  plan-2  H2  0.020
 L89  plan-3  C   0.020
 L89  plan-3  N   0.020
 L89  plan-3  H3  0.020
 L89  plan-3  H4  0.020

