# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 10:57:40 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: 7,9-dihydro-1H-purine-2,6,8(3H)-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=O)C2=C(N1)NC(=O)N2
#
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
 URC  URC  7,9-dihydro-1H-purine-2,6,8(3H)-trione  ligand  16  12  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_URC
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
 URC  N1   N  NR16  0  -0.733   0.6175  -0.0133  -1.9605
 URC  C2   C  CR6   0   0.674  -0.7507  -0.0437  -2.0913
 URC  C6   C  CR6   0   0.540   1.3961   0.0125  -0.7993
 URC  N3   N  NR16  0  -0.728  -1.4406  -0.0433  -0.9008
 URC  O11  O  OC    0  -0.471  -1.3096  -0.0688  -3.1672
 URC  C4   C  CR56  0   0.632  -0.7721  -0.0206   0.2745
 URC  C5   C  CR56  0   0.101   0.5831   0.0048   0.3636
 URC  N9   N  NR15  0  -0.712  -1.2829  -0.0182   1.5262
 URC  O13  O  OC    0  -0.464   2.6125   0.0379  -0.8539
 URC  N7   N  NR15  0  -0.724   0.8910   0.0247   1.7171
 URC  C8   C  CR5   0   0.631  -0.2466   0.0091   2.4616
 URC  O24  O  OC    0  -0.490  -0.3713   0.0173   3.6704
 URC  HN1  H  HNR6  0   0.431   1.1283  -0.0098  -2.8345
 URC  HN3  H  HNR6  0   0.445  -2.4503  -0.0591  -0.9354
 URC  HN9  H  HNR5  0   0.439  -2.2601  -0.0328   1.7776
 URC  HN7  H  HNR5  0   0.427   1.8176   0.0375   2.1117

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
 URC  N1  C2   aromatic  1.375  0.020  1.375
 URC  N1  C6   aromatic  1.398  0.020  1.398
 URC  N1  HN1  single    0.860  0.020  1.020
 URC  C2  N3   aromatic  1.376  0.020  1.376
 URC  C2  O11  double    1.213  0.020  1.213
 URC  C6  C5   aromatic  1.419  0.020  1.419
 URC  C6  O13  double    1.218  0.020  1.218
 URC  N3  C4   aromatic  1.352  0.020  1.352
 URC  N3  HN3  single    0.860  0.020  1.020
 URC  C4  C5   aromatic  1.358  0.020  1.358
 URC  C4  N9   aromatic  1.352  0.020  1.352
 URC  C5  N7   aromatic  1.388  0.020  1.388
 URC  N9  C8   aromatic  1.396  0.020  1.396
 URC  N9  HN9  single    0.860  0.020  1.020
 URC  N7  C8   aromatic  1.360  0.020  1.360
 URC  N7  HN7  single    0.860  0.020  1.020
 URC  C8  O24  double    1.215  0.020  1.215

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
 URC  HN1  N1  C6  115.84  3.000
 URC  HN1  N1  C2  114.84  3.000
 URC  C6   N1  C2  129.31  3.000
 URC  O11  C2  N3  122.46  3.000
 URC  O11  C2  N1  122.92  3.000
 URC  N3   C2  N1  114.62  3.000
 URC  O13  C6  C5  127.53  3.000
 URC  O13  C6  N1  121.28  3.000
 URC  C5   C6  N1  111.19  3.000
 URC  HN3  N3  C4  121.61  3.000
 URC  HN3  N3  C2  118.12  3.000
 URC  C4   N3  C2  120.28  3.000
 URC  N9   C4  C5  108.43  3.000
 URC  N9   C4  N3  128.17  3.000
 URC  C5   C4  N3  123.40  3.000
 URC  N7   C5  C4  106.59  3.000
 URC  N7   C5  C6  132.22  3.000
 URC  C4   C5  C6  121.19  3.000
 URC  HN9  N9  C8  123.50  3.000
 URC  HN9  N9  C4  126.62  3.000
 URC  C8   N9  C4  109.87  3.000
 URC  HN7  N7  C8  123.74  3.000
 URC  HN7  N7  C5  125.88  3.000
 URC  C8   N7  C5  110.37  3.000
 URC  O24  C8  N7  129.09  3.000
 URC  O24  C8  N9  126.18  3.000
 URC  N7   C8  N9  104.73  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
 URC  CONST_01  C4   N3  C2  N1     0.00  0.0  0
 URC  CONST_02  C4   C5  C6  N1     0.00  0.0  0
 URC  CONST_03  N7   C5  C6  N1   180.00  0.0  0
 URC  CONST_04  C5   C6  N1  C2     0.00  0.0  0
 URC  CONST_05  C5   C4  N3  C2     0.00  0.0  0
 URC  CONST_06  N9   C4  N3  C2   180.00  0.0  0
 URC  CONST_07  N3   C2  N1  C6     0.00  0.0  0
 URC  CONST_08  N3   C4  C5  C6     0.00  0.0  0
 URC  CONST_09  N9   C4  C5  C6   180.00  0.0  0
 URC  CONST_10  C8   N7  C5  C6   180.00  0.0  0
 URC  CONST_11  N7   C5  C4  N3   180.00  0.0  0
 URC  CONST_12  C8   N9  C4  N3   180.00  0.0  0
 URC  CONST_13  C8   N7  C5  C4     0.00  0.0  0
 URC  CONST_14  N7   C8  N9  C4     0.00  0.0  0
 URC  CONST_15  C8   N9  C4  C5     0.00  0.0  0
 URC  CONST_16  N9   C8  N7  C5     0.00  0.0  0
 URC  CONST_17  N7   C5  C4  N9     0.00  0.0  0
 URC  CONST_18  O13  C6  N1  C2   180.00  0.0  0
 URC  CONST_19  O11  C2  N1  C6   180.00  0.0  0
 URC  CONST_20  C4   N3  C2  O11  180.00  0.0  0
 URC  CONST_21  O13  C6  C5  C4   180.00  0.0  0
 URC  CONST_22  O24  C8  N9  C4   180.00  0.0  0
 URC  CONST_23  O24  C8  N7  C5   180.00  0.0  0
 URC  CONST_24  N7   C5  C6  O13    0.00  0.0  0
 URC  CONST_25  HN3  N3  C2  N1   180.00  0.0  0
 URC  CONST_26  HN7  N7  C5  C6     0.00  0.0  0
 URC  CONST_27  HN1  N1  C2  N3   180.00  0.0  0
 URC  CONST_28  HN9  N9  C4  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
 URC  plan-1  N1   0.020
 URC  plan-1  C2   0.020
 URC  plan-1  C6   0.020
 URC  plan-1  N3   0.020
 URC  plan-1  O11  0.020
 URC  plan-1  C4   0.020
 URC  plan-1  C5   0.020
 URC  plan-1  N9   0.020
 URC  plan-1  O13  0.020
 URC  plan-1  N7   0.020
 URC  plan-1  C8   0.020
 URC  plan-1  O24  0.020
 URC  plan-1  HN1  0.020
 URC  plan-1  HN3  0.020
 URC  plan-1  HN9  0.020
 URC  plan-1  HN7  0.020

