# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 11:05:17 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 2-azanyl-3,7-dihydropyrrolo[2,3-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]ccc2C(=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
 QY8  QY8  2-azanyl-3,7-dihydropyrrolo[2,3-d]pyrimidin-4-one  ligand  17  11  .  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_QY8
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
 QY8  C1  C  CR6   0   0.671  -23.4552  22.3226  -26.6114
 QY8  N1  N  NH2   0  -0.832  -24.0067  21.1575  -26.2169
 QY8  O1  O  O     0  -0.474  -20.4820  24.0354  -25.7134
 QY8  C2  C  CR56  0   0.492  -23.4398  24.2457  -27.7262
 QY8  N2  N  N     0  -0.506  -24.0830  23.0920  -27.4575
 QY8  C3  C  CR56  0  -0.198  -22.2201  24.6791  -27.2110
 QY8  N3  N  NR15  0  -0.657  -23.8861  25.1986  -28.5703
 QY8  C4  C  CR15  0  -0.405  -21.9388  25.9535  -27.7860
 QY8  N4  N  NR16  0  -0.721  -22.2556  22.6554  -26.0494
 QY8  C5  C  CR15  0  -0.037  -22.9826  26.2387  -28.6138
 QY8  C6  C  CR6   0   0.500  -21.5442  23.8372  -26.2838
 QY8  H1  H  HNH2  0   0.405  -24.7867  20.8216  -26.7567
 QY8  H2  H  HNH2  0   0.408  -23.4341  20.4449  -25.7951
 QY8  H3  H  HNR5  0   0.408  -24.7484  25.1525  -29.0895
 QY8  H4  H  HCR5  0   0.250  -21.0763  26.5755  -27.6097
 QY8  H5  H  HNR6  0   0.418  -21.8326  22.0100  -25.3949
 QY8  H6  H  HCR5  0   0.278  -23.1656  27.0967  -29.2388

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
 QY8  N3  C5  aromatic  1.378  0.020  1.378
 QY8  N3  C2  aromatic  1.349  0.020  1.349
 QY8  C5  C4  aromatic  1.362  0.020  1.362
 QY8  C4  C3  aromatic  1.426  0.020  1.426
 QY8  C2  N2  single    1.348  0.020  1.348
 QY8  C2  C3  aromatic  1.393  0.020  1.393
 QY8  N2  C1  double    1.305  0.020  1.305
 QY8  C3  C6  single    1.423  0.020  1.423
 QY8  C1  N1  single    1.348  0.020  1.348
 QY8  C1  N4  single    1.366  0.020  1.366
 QY8  C6  N4  single    1.399  0.020  1.399
 QY8  C6  O1  double    1.222  0.020  1.222
 QY8  N1  H1  single    0.890  0.020  1.040
 QY8  N1  H2  single    0.890  0.020  1.040
 QY8  N3  H3  single    0.860  0.020  1.020
 QY8  C4  H4  single    0.930  0.020  1.080
 QY8  N4  H5  single    0.860  0.020  1.020
 QY8  C5  H6  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
 QY8  N4  C1  N2  123.07  3.000
 QY8  N4  C1  N1  116.71  3.000
 QY8  N2  C1  N1  120.18  3.000
 QY8  H2  N1  H1  115.43  3.000
 QY8  H2  N1  C1  120.11  3.000
 QY8  H1  N1  C1  116.66  3.000
 QY8  N3  C2  C3  107.53  3.000
 QY8  C3  C2  N2  127.61  3.000
 QY8  N3  C2  N2  124.85  3.000
 QY8  C2  N2  C1  113.86  3.000
 QY8  C6  C3  C4  134.24  3.000
 QY8  C6  C3  C2  118.21  3.000
 QY8  C4  C3  C2  107.55  3.000
 QY8  H3  N3  C5  125.40  3.000
 QY8  H3  N3  C2  124.98  3.000
 QY8  C5  N3  C2  109.63  3.000
 QY8  H4  C4  C5  126.27  3.000
 QY8  H4  C4  C3  127.41  3.000
 QY8  C5  C4  C3  106.31  3.000
 QY8  H5  N4  C6  115.76  3.000
 QY8  H5  N4  C1  118.55  3.000
 QY8  C6  N4  C1  125.69  3.000
 QY8  H6  C5  C4  130.50  3.000
 QY8  H6  C5  N3  120.53  3.000
 QY8  C4  C5  N3  108.97  3.000
 QY8  N4  C6  C3  111.55  3.000
 QY8  N4  C6  O1  120.06  3.000
 QY8  C3  C6  O1  128.39  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
 QY8  CONST_01  C4  C5  N3  C2    0.00  0.0  0
 QY8  CONST_02  C5  C4  C3  C2    0.00  0.0  0
 QY8  CONST_03  N3  C5  C4  C3    0.00  0.0  0
 QY8  CONST_04  C5  N3  C2  C3    0.00  0.0  0
 QY8  CONST_05  C4  C3  C2  N3    0.00  0.0  0
 QY8  CONST_06  C3  C6  N4  C1    0.00  0.0  0
 QY8  CONST_07  N4  C1  N2  C2    0.00  0.0  0
 QY8  CONST_08  C6  N4  C1  N2    0.00  0.0  0
 QY8  CONST_09  O1  C6  N4  C1  180.00  0.0  0
 QY8  CONST_10  C2  N2  C1  N1  180.00  0.0  0
 QY8  CONST_11  C6  N4  C1  N1  180.00  0.0  0
 QY8  CONST_12  H6  C5  N3  C2  180.00  0.0  0
 QY8  CONST_13  H4  C4  C3  C2  180.00  0.0  0
 QY8  CONST_14  H3  N3  C2  N2    0.00  0.0  0
 QY8  CONST_15  H5  N4  C1  N2  180.00  0.0  0
 QY8  CONST_16  H1  N1  C1  N2    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
 QY8  plan-1  C1  0.020
 QY8  plan-1  N1  0.020
 QY8  plan-1  O1  0.020
 QY8  plan-1  C2  0.020
 QY8  plan-1  N2  0.020
 QY8  plan-1  C3  0.020
 QY8  plan-1  N3  0.020
 QY8  plan-1  C4  0.020
 QY8  plan-1  N4  0.020
 QY8  plan-1  C5  0.020
 QY8  plan-1  C6  0.020
 QY8  plan-1  H1  0.020
 QY8  plan-1  H2  0.020
 QY8  plan-1  H3  0.020
 QY8  plan-1  H4  0.020
 QY8  plan-1  H5  0.020
 QY8  plan-1  H6  0.020

