# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 08:16:10 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 2-aminopyrimido[4,5-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2ncncc2C(=O)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
 29H  29H  2-aminopyrimido[4,5-d]pyrimidin-4(3H)-one  ligand  17  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_29H
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
 29H  NAH  N  NR16  0  -0.720   1.8137   0.7287   0.0182
 29H  CAJ  C  CR6   0   0.570   0.6330   1.4420   0.0258
 29H  OAB  O  O     0  -0.440   0.6274   2.6562   0.0309
 29H  C5   C  CR66  0  -0.286  -0.5387   0.5839   0.0270
 29H  C6   C  CR16  0  -0.009  -1.8326   1.0818   0.0368
 29H  N1   N  N     0  -0.418  -2.8914   0.2917   0.0373
 29H  C2   C  CR16  0   0.059  -2.6314  -1.0191   0.0276
 29H  N3   N  N     0  -0.424  -1.4580  -1.6078   0.0177
 29H  C4   C  CR66  0   0.429  -0.3736  -0.8149   0.0179
 29H  NAG  N  N     0  -0.499   0.8293  -1.4138   0.0099
 29H  CAI  C  CR6   0   0.713   1.8850  -0.6359   0.0115
 29H  NAA  N  NH2   0  -0.814   3.0980  -1.1724   0.0081
 29H  H1   H  HNR6  0   0.434   2.6710   1.2680   0.0152
 29H  H2   H  HCR6  0   0.286  -2.0067   2.1525   0.0450
 29H  H3   H  HCR6  0   0.268  -3.4971  -1.6734   0.0277
 29H  H4   H  HNH2  0   0.426   3.9390  -0.6207   0.0053
 29H  H5   H  HNH2  0   0.423   3.1893  -2.1741  -0.0035

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
 29H  NAA  CAI  single    1.326  0.020  1.326
 29H  CAI  NAH  single    1.366  0.020  1.366
 29H  CAI  NAG  double    1.311  0.020  1.311
 29H  NAH  CAJ  single    1.379  0.020  1.379
 29H  NAG  C4   single    1.344  0.020  1.344
 29H  CAJ  OAB  double    1.214  0.020  1.214
 29H  CAJ  C5   single    1.452  0.020  1.452
 29H  C4   C5   aromatic  1.409  0.020  1.409
 29H  C4   N3   aromatic  1.343  0.020  1.343
 29H  C5   C6   aromatic  1.386  0.020  1.386
 29H  N3   C2   aromatic  1.313  0.020  1.313
 29H  C6   N1   aromatic  1.321  0.020  1.321
 29H  C2   N1   aromatic  1.336  0.020  1.336
 29H  NAH  H1   single    0.860  0.020  1.020
 29H  C6   H2   single    0.930  0.020  1.080
 29H  C2   H3   single    0.930  0.020  1.080
 29H  NAA  H4   single    0.860  0.020  1.020
 29H  NAA  H5   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
 29H  H1   NAH  CAI  119.18  3.000
 29H  H1   NAH  CAJ  116.69  3.000
 29H  CAI  NAH  CAJ  124.13  3.000
 29H  C5   CAJ  OAB  125.95  3.000
 29H  C5   CAJ  NAH  112.64  3.000
 29H  OAB  CAJ  NAH  121.40  3.000
 29H  C4   C5   C6   117.78  3.000
 29H  C6   C5   CAJ  122.74  3.000
 29H  C4   C5   CAJ  119.48  3.000
 29H  H2   C6   N1   117.50  3.000
 29H  H2   C6   C5   120.28  3.000
 29H  N1   C6   C5   122.22  3.000
 29H  C2   N1   C6   115.52  3.000
 29H  H3   C2   N3   116.27  3.000
 29H  H3   C2   N1   115.87  3.000
 29H  N3   C2   N1   127.86  3.000
 29H  C4   N3   C2   117.18  3.000
 29H  NAG  C4   N3   117.36  3.000
 29H  N3   C4   C5   119.44  3.000
 29H  NAG  C4   C5   123.20  3.000
 29H  CAI  NAG  C4   117.15  3.000
 29H  NAA  CAI  NAG  119.75  3.000
 29H  NAG  CAI  NAH  123.40  3.000
 29H  NAA  CAI  NAH  116.85  3.000
 29H  H5   NAA  H4   118.06  3.000
 29H  H5   NAA  CAI  119.06  3.000
 29H  H4   NAA  CAI  122.88  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
 29H  CONST_01  C2   N3   C4   C5     0.00  0.0  0
 29H  CONST_02  C2   N1   C6   C5     0.00  0.0  0
 29H  CONST_03  N3   C4   C5   C6     0.00  0.0  0
 29H  CONST_04  N3   C2   N1   C6     0.00  0.0  0
 29H  CONST_05  C4   C5   C6   N1     0.00  0.0  0
 29H  CONST_06  C4   N3   C2   N1     0.00  0.0  0
 29H  CONST_07  C4   NAG  CAI  NAH    0.00  0.0  0
 29H  CONST_08  NAG  CAI  NAH  CAJ    0.00  0.0  0
 29H  CONST_09  CAI  NAH  CAJ  C5     0.00  0.0  0
 29H  CONST_10  NAA  CAI  NAH  CAJ  180.00  0.0  0
 29H  CONST_11  CAI  NAH  CAJ  OAB  180.00  0.0  0
 29H  CONST_12  NAA  CAI  NAG  C4   180.00  0.0  0
 29H  CONST_13  H2   C6   C5   CAJ    0.00  0.0  0
 29H  CONST_14  H3   C2   N1   C6   180.00  0.0  0
 29H  CONST_15  H1   NAH  CAJ  C5   180.00  0.0  0
 29H  CONST_16  H4   NAA  CAI  NAH    0.00  0.0  0
 29H  CONST_17  H5   NAA  CAI  NAH  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
 29H  plan-1  NAH  0.020
 29H  plan-1  CAJ  0.020
 29H  plan-1  OAB  0.020
 29H  plan-1  C5   0.020
 29H  plan-1  C6   0.020
 29H  plan-1  N1   0.020
 29H  plan-1  C2   0.020
 29H  plan-1  N3   0.020
 29H  plan-1  C4   0.020
 29H  plan-1  NAG  0.020
 29H  plan-1  CAI  0.020
 29H  plan-1  NAA  0.020
 29H  plan-1  H1   0.020
 29H  plan-1  H2   0.020
 29H  plan-1  H3   0.020
 29H  plan-1  H4   0.020
 29H  plan-1  H5   0.020

