# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 07:55:18 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: pyridine-2,5-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(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
 DA1  DA1  'pyridine-2,5-diamine     '  ligand  15  8  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DA1
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
 DA1  N1    N  N     0  -0.443  -0.7139  -1.1375   0.0928
 DA1  C7    C  CR6   0   0.401  -1.3625   0.0179   0.1112
 DA1  N2    N  NH2   0  -0.839  -2.7352  -0.0209   0.2589
 DA1  C2    C  CR16  0  -0.367  -0.6724   1.2362   0.0417
 DA1  C3    C  CR16  0  -0.209   0.7021   1.2235  -0.0524
 DA1  C5    C  CR6   0   0.189   1.3954   0.0080  -0.0713
 DA1  N3    N  NH2   0  -0.863   2.7773  -0.0497  -0.2251
 DA1  C4    C  CR16  0  -0.144   0.6138  -1.1389   0.0082
 DA1  HN21  H  HNH2  0   0.378  -3.2323   0.7741  -0.1101
 DA1  HN22  H  HNH2  0   0.371  -3.1560  -0.8901  -0.0306
 DA1  H2    H  HCR6  0   0.264  -1.2108   2.1756   0.0622
 DA1  H3    H  HCR6  0   0.268   1.2448   2.1601  -0.1130
 DA1  HN31  H  HNH2  0   0.372   3.2630   0.7536   0.1441
 DA1  HN32  H  HNH2  0   0.371   3.1941  -0.8942   0.1365
 DA1  H4    H  HCR6  0   0.251   1.0902  -2.1158  -0.0007

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
 DA1  N1  C7    aromatic  1.325  0.020  1.325
 DA1  N1  C4    aromatic  1.330  0.020  1.330
 DA1  C7  N2    single    1.381  0.020  1.381
 DA1  C7  C2    aromatic  1.402  0.020  1.402
 DA1  N2  HN21  single    0.890  0.020  1.040
 DA1  N2  HN22  single    0.890  0.020  1.040
 DA1  C2  C3    aromatic  1.378  0.020  1.378
 DA1  C2  H2    single    0.930  0.020  1.080
 DA1  C3  C5    aromatic  1.400  0.020  1.400
 DA1  C3  H3    single    0.930  0.020  1.080
 DA1  C5  N3    single    1.392  0.020  1.392
 DA1  C5  C4    aromatic  1.390  0.020  1.390
 DA1  N3  HN31  single    0.890  0.020  1.040
 DA1  N3  HN32  single    0.890  0.020  1.040
 DA1  C4  H4    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
 DA1  C4    N1  C7    119.36  3.000
 DA1  C2    C7  N2    121.26  3.000
 DA1  C2    C7  N1    121.07  3.000
 DA1  N2    C7  N1    117.61  3.000
 DA1  HN22  N2  HN21  111.67  3.000
 DA1  HN22  N2  C7    114.10  3.000
 DA1  HN21  N2  C7    115.40  3.000
 DA1  H2    C2  C3    120.35  3.000
 DA1  H2    C2  C7    120.54  3.000
 DA1  C3    C2  C7    119.11  3.000
 DA1  H3    C3  C5    120.10  3.000
 DA1  H3    C3  C2    119.69  3.000
 DA1  C5    C3  C2    120.21  3.000
 DA1  C4    C5  N3    122.04  3.000
 DA1  C4    C5  C3    115.93  3.000
 DA1  N3    C5  C3    121.97  3.000
 DA1  HN32  N3  HN31  109.66  3.000
 DA1  HN32  N3  C5    113.91  3.000
 DA1  HN31  N3  C5    113.88  3.000
 DA1  H4    C4  C5    119.64  3.000
 DA1  H4    C4  N1    116.03  3.000
 DA1  C5    C4  N1    124.33  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
 DA1  CONST_01  C3  C2  C7  N1    0.00  0.0  0
 DA1  CONST_02  C3  C5  C4  N1    0.00  0.0  0
 DA1  CONST_03  C5  C4  N1  C7    0.00  0.0  0
 DA1  CONST_04  C5  C3  C2  C7    0.00  0.0  0
 DA1  CONST_05  C4  N1  C7  C2    0.00  0.0  0
 DA1  CONST_06  C4  C5  C3  C2    0.00  0.0  0
 DA1  CONST_07  N3  C5  C4  N1  180.00  0.0  0
 DA1  CONST_08  C4  N1  C7  N2  180.00  0.0  0
 DA1  CONST_09  C3  C2  C7  N2  180.00  0.0  0
 DA1  CONST_10  N3  C5  C3  C2  180.00  0.0  0
 DA1  CONST_11  H2  C2  C7  N1  180.00  0.0  0
 DA1  CONST_12  H4  C4  N1  C7  180.00  0.0  0
 DA1  CONST_13  H3  C3  C2  C7  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
 DA1  plan-1  N1    0.020
 DA1  plan-1  C7    0.020
 DA1  plan-1  N2    0.020
 DA1  plan-1  C2    0.020
 DA1  plan-1  C3    0.020
 DA1  plan-1  C5    0.020
 DA1  plan-1  N3    0.020
 DA1  plan-1  C4    0.020
 DA1  plan-1  H2    0.020
 DA1  plan-1  H3    0.020
 DA1  plan-1  H4    0.020
 DA1  plan-2  C7    0.020
 DA1  plan-2  N2    0.020
 DA1  plan-2  HN21  0.020
 DA1  plan-2  HN22  0.020
 DA1  plan-3  C5    0.020
 DA1  plan-3  N3    0.020
 DA1  plan-3  HN31  0.020
 DA1  plan-3  HN32  0.020

