# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 09:42:54 2020
#   Inital geometry file: a 39 line input string
#   Ligand name: pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccnc(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
 LG3  LG3  'pyrimidine-2,4-diamine   '  ligand  14  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 PERFECT
;

data_comp_LG3
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
 LG3  C2    C  CR6   0   0.534  -1.0943  -0.2654  -0.0724
 LG3  N3    N  N     0  -0.513   0.0391  -0.9670  -0.0340
 LG3  C4    C  CR6   0   0.503   1.1801  -0.2828   0.0160
 LG3  C5    C  CR16  0  -0.444   1.1830   1.1278   0.0256
 LG3  C6    C  CR16  0  -0.032  -0.0502   1.7279  -0.0114
 LG3  N1    N  N     0  -0.493  -1.2051   1.0653  -0.0597
 LG3  N7    N  NH2   0  -0.821  -2.2422  -0.9751  -0.1673
 LG3  N8    N  NH2   0  -0.829   2.3209  -0.9859   0.0748
 LG3  H5    H  HCR6  0   0.263   2.0975   1.7017   0.0661
 LG3  H6    H  HCR6  0   0.258  -0.1217   2.8109  -0.0017
 LG3  HN71  H  HNH2  0   0.389  -3.1091  -0.5028   0.0220
 LG3  HN72  H  HNH2  0   0.388  -2.2120  -1.9589   0.0359
 LG3  HN81  H  HNH2  0   0.404   3.2144  -0.5302   0.0238
 LG3  HN82  H  HNH2  0   0.393   2.2979  -1.9863  -0.0172

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
 LG3  C2  N3    aromatic  1.334  0.020  1.334
 LG3  C2  N1    aromatic  1.335  0.020  1.335
 LG3  C2  N7    single    1.353  0.020  1.353
 LG3  N3  C4    aromatic  1.331  0.020  1.331
 LG3  C4  C5    aromatic  1.411  0.020  1.411
 LG3  C4  N8    single    1.341  0.020  1.341
 LG3  C5  C6    aromatic  1.372  0.020  1.372
 LG3  C5  H5    single    0.930  0.020  1.080
 LG3  C6  N1    aromatic  1.332  0.020  1.332
 LG3  C6  H6    single    0.930  0.020  1.080
 LG3  N7  HN71  single    0.890  0.020  1.040
 LG3  N7  HN72  single    0.890  0.020  1.040
 LG3  N8  HN81  single    0.860  0.020  1.020
 LG3  N8  HN82  single    0.860  0.020  1.020

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
 LG3  N7    C2  N1    116.94  3.000
 LG3  N7    C2  N3    116.56  3.000
 LG3  N1    C2  N3    126.48  3.000
 LG3  C4    N3  C2    117.33  3.000
 LG3  N8    C4  C5    121.47  3.000
 LG3  N8    C4  N3    117.46  3.000
 LG3  C5    C4  N3    121.06  3.000
 LG3  H5    C5  C6    121.97  3.000
 LG3  H5    C5  C4    122.22  3.000
 LG3  C6    C5  C4    115.81  3.000
 LG3  H6    C6  N1    116.07  3.000
 LG3  H6    C6  C5    119.70  3.000
 LG3  N1    C6  C5    124.23  3.000
 LG3  C6    N1  C2    115.09  3.000
 LG3  HN72  N7  HN71  116.60  3.000
 LG3  HN72  N7  C2    118.28  3.000
 LG3  HN71  N7  C2    118.17  3.000
 LG3  HN82  N8  HN81  117.87  3.000
 LG3  HN82  N8  C4    119.89  3.000
 LG3  HN81  N8  C4    121.11  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
 LG3  CONST_01  C5    C4  N3  C2    0.00  0.0  0
 LG3  CONST_02  C5    C6  N1  C2    0.00  0.0  0
 LG3  CONST_03  C6    N1  C2  N3    0.00  0.0  0
 LG3  CONST_04  C6    C5  C4  N3    0.00  0.0  0
 LG3  CONST_05  N1    C2  N3  C4    0.00  0.0  0
 LG3  CONST_06  N1    C6  C5  C4    0.00  0.0  0
 LG3  CONST_07  N8    C4  N3  C2  180.00  0.0  0
 LG3  CONST_08  N7    C2  N3  C4  180.00  0.0  0
 LG3  CONST_09  N8    C4  C5  C6  180.00  0.0  0
 LG3  CONST_10  N7    C2  N1  C6  180.00  0.0  0
 LG3  CONST_11  H6    C6  N1  C2  180.00  0.0  0
 LG3  CONST_12  H5    C5  C4  N3  180.00  0.0  0
 LG3  CONST_13  HN71  N7  C2  N3  180.00  0.0  0
 LG3  CONST_15  HN81  N8  C4  N3  180.00  0.0  0
 LG3  CONST_16  HN82  N8  C4  N3    0.00  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
 LG3  plan-1  C2    0.020
 LG3  plan-1  N3    0.020
 LG3  plan-1  C4    0.020
 LG3  plan-1  C5    0.020
 LG3  plan-1  C6    0.020
 LG3  plan-1  N1    0.020
 LG3  plan-1  N7    0.020
 LG3  plan-1  N8    0.020
 LG3  plan-1  H5    0.020
 LG3  plan-1  H6    0.020
 LG3  plan-2  C2    0.020
 LG3  plan-2  N7    0.020
 LG3  plan-2  HN71  0.020
 LG3  plan-2  HN72  0.020
 LG3  plan-3  C4    0.020
 LG3  plan-3  N8    0.020
 LG3  plan-3  HN81  0.020
 LG3  plan-3  HN82  0.020

