# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 23:58:18 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: 5,6-diaminopyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=C(N)C(=O)NC(=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
 URN  URN  5,6-diaminopyrimidine-2,4(1H,3H)-dione  ligand  16  10  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_URN
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
 URN  O4    O  OC    0  -0.497   0.8134  -2.3750   0.1398
 URN  C4    C  CR6   0   0.528   0.3756  -1.2322   0.0770
 URN  N3    N  NR16  0  -0.723  -1.0092  -1.0361   0.0735
 URN  C5    C  CR6   0  -0.112   1.1586  -0.0445   0.0086
 URN  N5    N  NH2   0  -0.839   2.5747  -0.0660   0.0128
 URN  C6    C  CR6   0   0.635   0.5258   1.1792  -0.0581
 URN  N6    N  NH2   0  -0.822   1.1945   2.3290  -0.1442
 URN  N1    N  NR16  0  -0.733  -0.8408   1.2472  -0.0560
 URN  C2    C  CR6   0   0.665  -1.6662   0.1543   0.0067
 URN  O2    O  OC    0  -0.487  -2.8779   0.2556   0.0027
 URN  HN3   H  HNR6  0   0.417  -1.5890  -1.8634   0.1175
 URN  HN51  H  HNH2  0   0.356   2.9351  -0.5266   0.8387
 URN  HN52  H  HNH2  0   0.356   2.9412  -0.5701  -0.7847
 URN  HN61  H  HNH2  0   0.411   2.1981   2.2862  -0.0812
 URN  HN62  H  HNH2  0   0.413   0.7436   3.2244  -0.0776
 URN  HN1   H  HNR6  0   0.431  -1.2967   2.1474  -0.1102

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
 URN  O4  C4    double    1.225  0.020  1.225
 URN  C4  N3    aromatic  1.399  0.020  1.399
 URN  C4  C5    aromatic  1.424  0.020  1.424
 URN  N3  C2    aromatic  1.361  0.020  1.361
 URN  N3  HN3   single    0.860  0.020  1.020
 URN  C5  N5    single    1.416  0.020  1.416
 URN  C5  C6    aromatic  1.379  0.020  1.379
 URN  N5  HN51  single    0.890  0.020  1.040
 URN  N5  HN52  single    0.890  0.020  1.040
 URN  C6  N6    single    1.333  0.020  1.333
 URN  C6  N1    aromatic  1.368  0.020  1.368
 URN  N6  HN61  single    0.860  0.020  1.020
 URN  N6  HN62  single    0.860  0.020  1.020
 URN  N1  C2    aromatic  1.371  0.020  1.371
 URN  N1  HN1   single    0.860  0.020  1.020
 URN  C2  O2    double    1.216  0.020  1.216

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
 URN  C5    C4  N3    115.30  3.000
 URN  C5    C4  O4    125.71  3.000
 URN  N3    C4  O4    118.99  3.000
 URN  HN3   N3  C2    116.16  3.000
 URN  HN3   N3  C4    116.92  3.000
 URN  C2    N3  C4    126.92  3.000
 URN  C6    C5  N5    118.19  3.000
 URN  C6    C5  C4    119.34  3.000
 URN  N5    C5  C4    122.48  3.000
 URN  HN52  N5  HN51  106.71  3.000
 URN  HN52  N5  C5    111.55  3.000
 URN  HN51  N5  C5    111.43  3.000
 URN  N1    C6  N6    117.28  3.000
 URN  N1    C6  C5    120.15  3.000
 URN  N6    C6  C5    122.57  3.000
 URN  HN62  N6  HN61  118.77  3.000
 URN  HN62  N6  C6    122.63  3.000
 URN  HN61  N6  C6    117.36  3.000
 URN  HN1   N1  C2    116.17  3.000
 URN  HN1   N1  C6    119.65  3.000
 URN  C2    N1  C6    124.18  3.000
 URN  O2    C2  N1    122.24  3.000
 URN  O2    C2  N3    123.64  3.000
 URN  N1    C2  N3    114.12  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
 URN  CONST_01  N1    C2  N3  C4    0.00  0.0  0
 URN  CONST_02  N1    C6  C5  C4    0.00  0.0  0
 URN  CONST_03  C6    C5  C4  N3    0.00  0.0  0
 URN  CONST_04  C6    N1  C2  N3    0.00  0.0  0
 URN  CONST_05  C2    N3  C4  C5    0.00  0.0  0
 URN  CONST_06  C2    N1  C6  C5    0.00  0.0  0
 URN  CONST_07  C2    N3  C4  O4  180.00  0.0  0
 URN  CONST_08  C6    C5  C4  O4  180.00  0.0  0
 URN  CONST_09  O2    C2  N3  C4  180.00  0.0  0
 URN  CONST_10  N6    C6  C5  C4  180.00  0.0  0
 URN  CONST_11  N5    C5  C4  N3  180.00  0.0  0
 URN  CONST_12  N1    C6  C5  N5  180.00  0.0  0
 URN  CONST_13  O2    C2  N1  C6  180.00  0.0  0
 URN  CONST_14  C2    N1  C6  N6  180.00  0.0  0
 URN  CONST_15  HN1   N1  C2  N3  180.00  0.0  0
 URN  CONST_16  HN3   N3  C4  C5  180.00  0.0  0
 URN  CONST_19  HN61  N6  C6  C5    0.00  0.0  0
 URN  CONST_20  HN62  N6  C6  C5  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
 URN  plan-1  O4    0.020
 URN  plan-1  C4    0.020
 URN  plan-1  N3    0.020
 URN  plan-1  C5    0.020
 URN  plan-1  N5    0.020
 URN  plan-1  C6    0.020
 URN  plan-1  N6    0.020
 URN  plan-1  N1    0.020
 URN  plan-1  C2    0.020
 URN  plan-1  O2    0.020
 URN  plan-1  HN3   0.020
 URN  plan-1  HN1   0.020
 URN  plan-2  C5    0.020
 URN  plan-2  N5    0.020
 URN  plan-2  HN51  0.020
 URN  plan-2  HN52  0.020
 URN  plan-3  C6    0.020
 URN  plan-3  N6    0.020
 URN  plan-3  HN61  0.020
 URN  plan-3  HN62  0.020

