# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 01:41:30 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 3,9-dihydro-1H-purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=O)c2nc[nH]c2N1
#
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
 XAN  XAN  3,9-dihydro-1H-purine-2,6-dione  ligand  15  11  .  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_XAN
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
 XAN  N9   N  NR15  0  -0.635  -1.4137  -0.0434   1.8075
 XAN  C4   C  CR56  0   0.621  -0.8415  -0.0333   0.5914
 XAN  N3   N  NR16  0  -0.727  -1.4270  -0.0127  -0.6318
 XAN  C2   C  CR6   0   0.671  -0.6463  -0.0051  -1.7601
 XAN  O2   O  OC    0  -0.474  -1.1150   0.0138  -2.8791
 XAN  N1   N  NR16  0  -0.733   0.7120  -0.0200  -1.5262
 XAN  C6   C  CR6   0   0.521   1.4082  -0.0403  -0.3151
 XAN  O6   O  OC    0  -0.453   2.6230  -0.0494  -0.2945
 XAN  C5   C  CR56  0  -0.066   0.5143  -0.0477   0.8050
 XAN  N7   N  N     0  -0.428   0.7772  -0.0659   2.1497
 XAN  C8   C  CR15  0   0.099  -0.3881  -0.0627   2.7179
 XAN  HN9  H  HNR5  0   0.439  -2.4003  -0.0364   2.0206
 XAN  HN3  H  HNR6  0   0.441  -2.4307  -0.0041  -0.7462
 XAN  HN1  H  HNR6  0   0.428   1.2825  -0.0109  -2.3624
 XAN  H8   H  HCR5  0   0.296  -0.5825  -0.0732   3.7785

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
 XAN  N9  C4   aromatic  1.344  0.020  1.344
 XAN  N9  C8   aromatic  1.372  0.020  1.372
 XAN  N9  HN9  single    0.860  0.020  1.020
 XAN  C4  N3   aromatic  1.356  0.020  1.356
 XAN  C4  C5   aromatic  1.373  0.020  1.373
 XAN  N3  C2   aromatic  1.372  0.020  1.372
 XAN  N3  HN3  single    0.860  0.020  1.020
 XAN  C2  O2   double    1.213  0.020  1.213
 XAN  C2  N1   aromatic  1.378  0.020  1.378
 XAN  N1  C6   aromatic  1.397  0.020  1.397
 XAN  N1  HN1  single    0.860  0.020  1.020
 XAN  C6  O6   double    1.215  0.020  1.215
 XAN  C6  C5   aromatic  1.433  0.020  1.433
 XAN  C5  N7   aromatic  1.370  0.020  1.370
 XAN  N7  C8   aromatic  1.296  0.020  1.296
 XAN  C8  H8   single    0.930  0.020  1.080

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
 XAN  HN9  N9  C8  126.22  3.000
 XAN  HN9  N9  C4  127.38  3.000
 XAN  C8   N9  C4  106.40  3.000
 XAN  C5   C4  N3  124.53  3.000
 XAN  C5   C4  N9  106.24  3.000
 XAN  N3   C4  N9  129.23  3.000
 XAN  HN3  N3  C2  118.17  3.000
 XAN  HN3  N3  C4  122.08  3.000
 XAN  C2   N3  C4  119.74  3.000
 XAN  N1   C2  O2  122.50  3.000
 XAN  N1   C2  N3  114.91  3.000
 XAN  O2   C2  N3  122.59  3.000
 XAN  HN1  N1  C6  115.81  3.000
 XAN  HN1  N1  C2  114.52  3.000
 XAN  C6   N1  C2  129.66  3.000
 XAN  C5   C6  O6  127.61  3.000
 XAN  C5   C6  N1  111.52  3.000
 XAN  O6   C6  N1  120.87  3.000
 XAN  N7   C5  C6  130.35  3.000
 XAN  N7   C5  C4  110.02  3.000
 XAN  C6   C5  C4  119.63  3.000
 XAN  C8   N7  C5  104.93  3.000
 XAN  H8   C8  N7  126.38  3.000
 XAN  H8   C8  N9  121.21  3.000
 XAN  N7   C8  N9  112.41  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
 XAN  CONST_01  C2   N3  C4  N9  180.00  0.0  0
 XAN  CONST_02  C6   C5  C4  N9  180.00  0.0  0
 XAN  CONST_03  N7   C5  C4  N9    0.00  0.0  0
 XAN  CONST_04  C5   N7  C8  N9    0.00  0.0  0
 XAN  CONST_05  N7   C8  N9  C4    0.00  0.0  0
 XAN  CONST_06  N1   C2  N3  C4    0.00  0.0  0
 XAN  CONST_07  N1   C6  C5  C4    0.00  0.0  0
 XAN  CONST_08  C8   N7  C5  C4    0.00  0.0  0
 XAN  CONST_09  C8   N9  C4  N3  180.00  0.0  0
 XAN  CONST_10  C6   C5  C4  N3    0.00  0.0  0
 XAN  CONST_11  N7   C5  C4  N3  180.00  0.0  0
 XAN  CONST_12  C6   N1  C2  N3    0.00  0.0  0
 XAN  CONST_13  C5   C4  N3  C2    0.00  0.0  0
 XAN  CONST_14  C5   C6  N1  C2    0.00  0.0  0
 XAN  CONST_15  N7   C5  C6  N1  180.00  0.0  0
 XAN  CONST_16  C8   N7  C5  C6  180.00  0.0  0
 XAN  CONST_17  C8   N9  C4  C5    0.00  0.0  0
 XAN  CONST_18  O2   C2  N3  C4  180.00  0.0  0
 XAN  CONST_19  O6   C6  C5  C4  180.00  0.0  0
 XAN  CONST_20  O6   C6  N1  C2  180.00  0.0  0
 XAN  CONST_21  C6   N1  C2  O2  180.00  0.0  0
 XAN  CONST_22  N7   C5  C6  O6    0.00  0.0  0
 XAN  CONST_23  HN3  N3  C4  N9    0.00  0.0  0
 XAN  CONST_24  H8   C8  N9  C4  180.00  0.0  0
 XAN  CONST_25  HN9  N9  C4  N3    0.00  0.0  0
 XAN  CONST_26  HN1  N1  C2  N3  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
 XAN  plan-1  N9   0.020
 XAN  plan-1  C4   0.020
 XAN  plan-1  N3   0.020
 XAN  plan-1  C2   0.020
 XAN  plan-1  O2   0.020
 XAN  plan-1  N1   0.020
 XAN  plan-1  C6   0.020
 XAN  plan-1  O6   0.020
 XAN  plan-1  C5   0.020
 XAN  plan-1  N7   0.020
 XAN  plan-1  C8   0.020
 XAN  plan-1  HN9  0.020
 XAN  plan-1  HN3  0.020
 XAN  plan-1  HN1  0.020
 XAN  plan-1  H8   0.020

