# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 21:00:31 2022
#   Inital geometry file: a 43 line input string
#   Ligand name: 2,5-diaminopyrimidine-4,6-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(O)c(N)c(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
 DDP  DDP  2,5-diaminopyrimidine-4,6-diol  ligand  16  10  .  2016-12-19  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DDP
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
 DDP  C5   C  CR6   0  -0.072  -15.2907  36.0603  39.5516
 DDP  N7   N  NH2   0  -0.839  -14.7379  36.2488  38.2624
 DDP  C4   C  CR6   0   0.492  -14.4842  35.8970  40.6781
 DDP  N3   N  N     0  -0.525  -14.9546  35.7164  41.9024
 DDP  C2   C  CR6   0   0.548  -16.2792  35.6910  42.0377
 DDP  N2   N  NH2   0  -0.815  -16.7715  35.4707  43.2732
 DDP  N1   N  N     0  -0.521  -17.1599  35.8351  41.0469
 DDP  C6   C  CR6   0   0.482  -16.6571  36.0145  39.8377
 DDP  O6   O  OH1   0  -0.598  -17.5083  36.1600  38.8288
 DDP  O9   O  OH1   0  -0.594  -13.1659  35.9239  40.5292
 DDP  H71  H  HNH2  0   0.355  -15.0154  37.1375  37.8652
 DDP  H72  H  HNH2  0   0.355  -15.0484  35.5322  37.6191
 DDP  H21  H  HNH2  0   0.394  -17.7474  35.6437  43.4404
 DDP  H22  H  HNH2  0   0.394  -16.1527  35.5556  44.0608
 DDP  H61  H  HOH1  0   0.473  -18.4112  36.1030  39.1707
 DDP  H91  H  HOH1  0   0.470  -12.7574  35.7955  41.3962

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
 DDP  C5  N7   single    1.415  0.020  1.415
 DDP  C5  C4   aromatic  1.395  0.020  1.395
 DDP  C5  C6   aromatic  1.397  0.020  1.397
 DDP  N7  H71  single    0.890  0.020  1.040
 DDP  N7  H72  single    0.890  0.020  1.040
 DDP  C4  N3   aromatic  1.324  0.020  1.324
 DDP  C4  O9   single    1.327  0.020  1.327
 DDP  N3  C2   aromatic  1.332  0.020  1.332
 DDP  C2  N2   single    1.348  0.020  1.348
 DDP  C2  N1   aromatic  1.333  0.020  1.333
 DDP  N2  H21  single    0.890  0.020  1.040
 DDP  N2  H22  single    0.890  0.020  1.040
 DDP  N1  C6   aromatic  1.322  0.020  1.322
 DDP  C6  O6   single    1.328  0.020  1.328
 DDP  O6  H61  single    0.850  0.020  0.980
 DDP  O9  H91  single    0.850  0.020  0.980

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
 DDP  C6   C5  C4   113.35  3.000
 DDP  C6   C5  N7   124.97  3.000
 DDP  C4   C5  N7   121.69  3.000
 DDP  H72  N7  H71  106.74  3.000
 DDP  H72  N7  C5   111.40  3.000
 DDP  H71  N7  C5   111.55  3.000
 DDP  O9   C4  N3   117.35  3.000
 DDP  O9   C4  C5   118.78  3.000
 DDP  N3   C4  C5   123.87  3.000
 DDP  C2   N3  C4   116.74  3.000
 DDP  N1   C2  N2   117.23  3.000
 DDP  N1   C2  N3   125.41  3.000
 DDP  N2   C2  N3   117.35  3.000
 DDP  H22  N2  H21  116.93  3.000
 DDP  H22  N2  C2   118.65  3.000
 DDP  H21  N2  C2   118.61  3.000
 DDP  C6   N1  C2   116.31  3.000
 DDP  O6   C6  N1   117.78  3.000
 DDP  O6   C6  C5   117.89  3.000
 DDP  N1   C6  C5   124.33  3.000
 DDP  H61  O6  C6   108.87  3.000
 DDP  H91  O9  C4   108.45  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
 DDP  CONST_01  C2   N3  C4  C5    0.00  0.0  0
 DDP  CONST_02  C2   N1  C6  C5    0.00  0.0  0
 DDP  CONST_03  N1   C6  C5  C4    0.00  0.0  0
 DDP  CONST_04  N1   C2  N3  C4    0.00  0.0  0
 DDP  CONST_05  C6   C5  C4  N3    0.00  0.0  0
 DDP  CONST_06  C6   N1  C2  N3    0.00  0.0  0
 DDP  CONST_07  N3   C4  C5  N7  180.00  0.0  0
 DDP  CONST_08  N1   C6  C5  N7  180.00  0.0  0
 DDP  CONST_09  O6   C6  C5  C4  180.00  0.0  0
 DDP  CONST_10  N2   C2  N3  C4  180.00  0.0  0
 DDP  CONST_11  O9   C4  N3  C2  180.00  0.0  0
 DDP  CONST_12  O6   C6  N1  C2  180.00  0.0  0
 DDP  CONST_13  C6   N1  C2  N2  180.00  0.0  0
 DDP  CONST_14  O9   C4  C5  C6  180.00  0.0  0
 DDP  CONST_17  H21  N2  C2  N3  180.00  0.0  0
 DDP  CONST_18  H22  N2  C2  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
 DDP  plan-1  C5   0.020
 DDP  plan-1  N7   0.020
 DDP  plan-1  C4   0.020
 DDP  plan-1  N3   0.020
 DDP  plan-1  C2   0.020
 DDP  plan-1  N2   0.020
 DDP  plan-1  N1   0.020
 DDP  plan-1  C6   0.020
 DDP  plan-1  O6   0.020
 DDP  plan-1  O9   0.020
 DDP  plan-2  C5   0.020
 DDP  plan-2  N7   0.020
 DDP  plan-2  H71  0.020
 DDP  plan-2  H72  0.020
 DDP  plan-3  C2   0.020
 DDP  plan-3  N2   0.020
 DDP  plan-3  H21  0.020
 DDP  plan-3  H22  0.020

