# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 08:06:31 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: pyrimido[4,5-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(N)c2cncnc2n1
#
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
 29G  29G  pyrimido[4,5-d]pyrimidine-2,4-diamine  ligand  18  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_29G
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
 29G  NAB  N  NH2   0  -0.818   0.6486   2.6763   0.0312
 29G  CAJ  C  CR6   0   0.513   0.6876   1.3480   0.0159
 29G  NAG  N  N     0  -0.508   1.8626   0.7580  -0.0008
 29G  C5   C  CR66  0  -0.206  -0.5205   0.5607   0.0206
 29G  C6   C  CR16  0  -0.025  -1.8235   1.0426   0.0384
 29G  N1   N  N     0  -0.420  -2.8747   0.2464   0.0433
 29G  C2   C  CR16  0   0.053  -2.6058  -1.0661   0.0297
 29G  N3   N  N     0  -0.426  -1.4329  -1.6454   0.0126
 29G  C4   C  CR66  0   0.410  -0.3472  -0.8433   0.0086
 29G  NAH  N  N     0  -0.502   0.8528  -1.4197  -0.0066
 29G  CAI  C  CR6   0   0.564   1.8931  -0.5901  -0.0115
 29G  NAA  N  NH2   0  -0.806   3.1104  -1.1371  -0.0283
 29G  H1   H  HNH2  0   0.420  -0.2079   3.1999   0.0313
 29G  H2   H  HNH2  0   0.411   1.5091   3.1978   0.0187
 29G  H3   H  HCR6  0   0.269  -2.0310   2.1083   0.0497
 29G  H4   H  HCR6  0   0.264  -3.4696  -1.7233   0.0329
 29G  H5   H  HNH2  0   0.404   3.9316  -0.5584  -0.0331
 29G  H6   H  HNH2  0   0.404   3.2194  -2.1358  -0.0364

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
 29G  NAA  CAI  single    1.335  0.020  1.335
 29G  CAI  NAG  aromatic  1.349  0.020  1.349
 29G  CAI  NAH  aromatic  1.331  0.020  1.331
 29G  NAG  CAJ  aromatic  1.315  0.020  1.315
 29G  NAH  C4   aromatic  1.331  0.020  1.331
 29G  CAJ  NAB  single    1.329  0.020  1.329
 29G  CAJ  C5   aromatic  1.442  0.020  1.442
 29G  C4   C5   aromatic  1.415  0.020  1.415
 29G  C4   N3   aromatic  1.350  0.020  1.350
 29G  C5   C6   aromatic  1.389  0.020  1.389
 29G  N3   C2   aromatic  1.308  0.020  1.308
 29G  C6   N1   aromatic  1.319  0.020  1.319
 29G  C2   N1   aromatic  1.340  0.020  1.340
 29G  NAB  H1   single    0.860  0.020  1.020
 29G  NAB  H2   single    0.860  0.020  1.020
 29G  C6   H3   single    0.930  0.020  1.080
 29G  C2   H4   single    0.930  0.020  1.080
 29G  NAA  H5   single    0.860  0.020  1.020
 29G  NAA  H6   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
 29G  H2   NAB  H1   117.33  3.000
 29G  H2   NAB  CAJ  119.53  3.000
 29G  H1   NAB  CAJ  123.12  3.000
 29G  C5   CAJ  NAG  120.25  3.000
 29G  C5   CAJ  NAB  121.41  3.000
 29G  NAG  CAJ  NAB  118.35  3.000
 29G  CAI  NAG  CAJ  117.96  3.000
 29G  C4   C5   C6   117.33  3.000
 29G  C6   C5   CAJ  126.61  3.000
 29G  C4   C5   CAJ  116.05  3.000
 29G  H3   C6   N1   116.12  3.000
 29G  H3   C6   C5   121.32  3.000
 29G  N1   C6   C5   122.57  3.000
 29G  C2   N1   C6   115.56  3.000
 29G  H4   C2   N3   116.45  3.000
 29G  H4   C2   N1   115.68  3.000
 29G  N3   C2   N1   127.87  3.000
 29G  C4   N3   C2   117.26  3.000
 29G  NAH  C4   N3   117.89  3.000
 29G  N3   C4   C5   119.42  3.000
 29G  NAH  C4   C5   122.70  3.000
 29G  CAI  NAH  C4   115.78  3.000
 29G  NAA  CAI  NAH  117.24  3.000
 29G  NAH  CAI  NAG  127.27  3.000
 29G  NAA  CAI  NAG  115.49  3.000
 29G  H6   NAA  H5   118.94  3.000
 29G  H6   NAA  CAI  120.42  3.000
 29G  H5   NAA  CAI  120.64  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
 29G  CONST_01  NAH  CAI  NAG  CAJ    0.00  0.0  0
 29G  CONST_02  NAH  C4   C5   CAJ    0.00  0.0  0
 29G  CONST_03  N3   C4   C5   CAJ  180.00  0.0  0
 29G  CONST_04  N1   C6   C5   CAJ  180.00  0.0  0
 29G  CONST_05  C4   NAH  CAI  NAG    0.00  0.0  0
 29G  CONST_06  C4   C5   CAJ  NAG    0.00  0.0  0
 29G  CONST_07  C6   C5   CAJ  NAG  180.00  0.0  0
 29G  CONST_08  CAI  NAG  CAJ  C5     0.00  0.0  0
 29G  CONST_09  CAI  NAH  C4   C5     0.00  0.0  0
 29G  CONST_10  C2   N3   C4   C5     0.00  0.0  0
 29G  CONST_11  C2   N1   C6   C5     0.00  0.0  0
 29G  CONST_12  NAH  C4   C5   C6   180.00  0.0  0
 29G  CONST_13  N3   C4   C5   C6     0.00  0.0  0
 29G  CONST_14  N3   C2   N1   C6     0.00  0.0  0
 29G  CONST_15  C4   C5   C6   N1     0.00  0.0  0
 29G  CONST_16  C4   N3   C2   N1     0.00  0.0  0
 29G  CONST_17  NAH  C4   N3   C2   180.00  0.0  0
 29G  CONST_18  CAI  NAH  C4   N3   180.00  0.0  0
 29G  CONST_19  CAI  NAG  CAJ  NAB  180.00  0.0  0
 29G  CONST_20  C4   C5   CAJ  NAB  180.00  0.0  0
 29G  CONST_21  C6   C5   CAJ  NAB    0.00  0.0  0
 29G  CONST_22  NAA  CAI  NAG  CAJ  180.00  0.0  0
 29G  CONST_23  NAA  CAI  NAH  C4   180.00  0.0  0
 29G  CONST_24  H3   C6   C5   CAJ    0.00  0.0  0
 29G  CONST_25  H4   C2   N1   C6   180.00  0.0  0
 29G  CONST_26  H5   NAA  CAI  NAG    0.00  0.0  0
 29G  CONST_27  H6   NAA  CAI  NAG  180.00  0.0  0
 29G  CONST_28  H1   NAB  CAJ  NAG  180.00  0.0  0
 29G  CONST_29  H2   NAB  CAJ  NAG    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
 29G  plan-1  NAB  0.020
 29G  plan-1  CAJ  0.020
 29G  plan-1  NAG  0.020
 29G  plan-1  C5   0.020
 29G  plan-1  C6   0.020
 29G  plan-1  N1   0.020
 29G  plan-1  C2   0.020
 29G  plan-1  N3   0.020
 29G  plan-1  C4   0.020
 29G  plan-1  NAH  0.020
 29G  plan-1  CAI  0.020
 29G  plan-1  NAA  0.020
 29G  plan-1  H3   0.020
 29G  plan-1  H4   0.020
 29G  plan-2  NAB  0.020
 29G  plan-2  CAJ  0.020
 29G  plan-2  H1   0.020
 29G  plan-2  H2   0.020
 29G  plan-3  CAI  0.020
 29G  plan-3  NAA  0.020
 29G  plan-3  H5   0.020
 29G  plan-3  H6   0.020

