# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 06:33:40 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: pyrimidine-2,4,6-triamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(N)nc(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
 3AY  3AY  pyrimidine-2,4,6-triamine  ligand  16  9  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3AY
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
 3AY  NAA   N  NH2   0  -0.834   2.3784   1.3034  -0.1475
 3AY  C6    C  CR6   0   0.486   1.1761   0.6836  -0.0971
 3AY  C5    C  CR16  0  -0.519  -0.0150   1.4090  -0.0754
 3AY  N1    N  N     0  -0.532   1.1955  -0.6536  -0.1035
 3AY  C2    C  CR6   0   0.525   0.0099  -1.2583  -0.0931
 3AY  NAH   N  NH2   0  -0.821   0.0224  -2.6148  -0.1447
 3AY  N3    N  N     0  -0.532  -1.1866  -0.6762  -0.0701
 3AY  C4    C  CR6   0   0.486  -1.1921   0.6612  -0.0641
 3AY  NAI   N  NH2   0  -0.834  -2.4073   1.2579  -0.0813
 3AY  HAA1  H  HNH2  0   0.392   2.4323   2.2809   0.0807
 3AY  HAA2  H  HNH2  0   0.384   3.1938   0.7579   0.0747
 3AY  H5    H  HCR6  0   0.256  -0.0252   2.4906  -0.0635
 3AY  HAH1  H  HNH2  0   0.384  -0.8209  -3.0950   0.1190
 3AY  HAH2  H  HNH2  0   0.384   0.8810  -3.0784   0.0985
 3AY  HAI1  H  HNH2  0   0.392  -2.4733   2.2337   0.1513
 3AY  HAI2  H  HNH2  0   0.384  -3.2048   0.6967   0.1659

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
 3AY  NAA  C6    single    1.354  0.020  1.354
 3AY  NAA  HAA1  single    0.890  0.020  1.040
 3AY  NAA  HAA2  single    0.890  0.020  1.040
 3AY  C6   C5    aromatic  1.395  0.020  1.395
 3AY  C6   N1    aromatic  1.337  0.020  1.337
 3AY  C5   C4    aromatic  1.395  0.020  1.395
 3AY  C5   H5    single    0.930  0.020  1.080
 3AY  N1   C2    aromatic  1.331  0.020  1.331
 3AY  C2   NAH   single    1.358  0.020  1.358
 3AY  C2   N3    aromatic  1.331  0.020  1.331
 3AY  NAH  HAH1  single    0.890  0.020  1.040
 3AY  NAH  HAH2  single    0.890  0.020  1.040
 3AY  N3   C4    aromatic  1.337  0.020  1.337
 3AY  C4   NAI   single    1.354  0.020  1.354
 3AY  NAI  HAI1  single    0.890  0.020  1.040
 3AY  NAI  HAI2  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
 3AY  HAA2  NAA  HAA1  115.71  3.000
 3AY  HAA2  NAA  C6    117.61  3.000
 3AY  HAA1  NAA  C6    118.98  3.000
 3AY  N1    C6   C5    122.17  3.000
 3AY  N1    C6   NAA   116.41  3.000
 3AY  C5    C6   NAA   121.40  3.000
 3AY  H5    C5   C4    121.88  3.000
 3AY  H5    C5   C6    121.89  3.000
 3AY  C4    C5   C6    116.23  3.000
 3AY  C2    N1   C6    116.19  3.000
 3AY  N3    C2   NAH   116.49  3.000
 3AY  N3    C2   N1    127.04  3.000
 3AY  NAH   C2   N1    116.45  3.000
 3AY  HAH2  NAH  HAH1  115.62  3.000
 3AY  HAH2  NAH  C2    117.35  3.000
 3AY  HAH1  NAH  C2    117.35  3.000
 3AY  C4    N3   C2    116.18  3.000
 3AY  NAI   C4   N3    116.38  3.000
 3AY  NAI   C4   C5    121.41  3.000
 3AY  N3    C4   C5    122.19  3.000
 3AY  HAI2  NAI  HAI1  115.64  3.000
 3AY  HAI2  NAI  C4    117.55  3.000
 3AY  HAI1  NAI  C4    118.93  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
 3AY  CONST_01  N3   C4  C5  C6     0.00  0.0  0
 3AY  CONST_02  N3   C2  N1  C6     0.00  0.0  0
 3AY  CONST_03  C2   N1  C6  C5     0.00  0.0  0
 3AY  CONST_04  C2   N3  C4  C5     0.00  0.0  0
 3AY  CONST_05  C4   C5  C6  N1     0.00  0.0  0
 3AY  CONST_06  C4   N3  C2  N1     0.00  0.0  0
 3AY  CONST_07  C4   C5  C6  NAA  180.00  0.0  0
 3AY  CONST_08  C2   N1  C6  NAA  180.00  0.0  0
 3AY  CONST_09  NAI  C4  C5  C6   180.00  0.0  0
 3AY  CONST_10  NAH  C2  N1  C6   180.00  0.0  0
 3AY  CONST_11  NAI  C4  N3  C2   180.00  0.0  0
 3AY  CONST_12  C4   N3  C2  NAH  180.00  0.0  0
 3AY  CONST_13  H5   C5  C6  N1   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
 3AY  plan-1  NAA   0.020
 3AY  plan-1  C6    0.020
 3AY  plan-1  C5    0.020
 3AY  plan-1  N1    0.020
 3AY  plan-1  C2    0.020
 3AY  plan-1  NAH   0.020
 3AY  plan-1  N3    0.020
 3AY  plan-1  C4    0.020
 3AY  plan-1  NAI   0.020
 3AY  plan-1  H5    0.020
 3AY  plan-2  NAA   0.020
 3AY  plan-2  C6    0.020
 3AY  plan-2  HAA1  0.020
 3AY  plan-2  HAA2  0.020
 3AY  plan-3  C2    0.020
 3AY  plan-3  NAH   0.020
 3AY  plan-3  HAH1  0.020
 3AY  plan-3  HAH2  0.020
 3AY  plan-4  C4    0.020
 3AY  plan-4  NAI   0.020
 3AY  plan-4  HAI1  0.020
 3AY  plan-4  HAI2  0.020

