# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 18:50:31 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: 3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC=Nc2cc[nH]c12
#
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
 9HX  9HX  3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one  ligand  15  10  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9HX
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
 9HX  C9   C  CR15  0  -0.428   0.9479   0.0026  -2.0503
 9HX  C8   C  CR15  0   0.017  -0.3534   0.0109  -2.4960
 9HX  N7   N  NR15  0  -0.661  -1.1963   0.0221  -1.4359
 9HX  C5   C  CR56  0  -0.022  -0.4654   0.0214  -0.2907
 9HX  C6   C  CR6   0   0.475  -0.9098   0.0309   1.0652
 9HX  O6   O  OC    0  -0.430  -2.0533   0.0417   1.4846
 9HX  N1   N  NR16  0  -0.555   0.1958   0.0263   1.9124
 9HX  C2   C  CR16  0   0.117   1.4978   0.0143   1.5076
 9HX  N3   N  N     0  -0.482   1.8909   0.0056   0.2866
 9HX  C4   C  CR56  0   0.291   0.8825   0.0093  -0.6375
 9HX  H9   H  HCR5  0   0.246   1.8323  -0.0073  -2.6655
 9HX  H8   H  HCR5  0   0.280  -0.7359   0.0093  -3.5030
 9HX  HN7  H  HNR5  0   0.413  -2.2008   0.0291  -1.4911
 9HX  HN1  H  HNR6  0   0.437   0.0044   0.0333   2.9042
 9HX  H2   H  HCR6  0   0.305   2.2256   0.0125   2.3096

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
 9HX  C9  C8   aromatic  1.376  0.020  1.376
 9HX  C9  C4   aromatic  1.414  0.020  1.414
 9HX  C9  H9   single    0.930  0.020  1.080
 9HX  C8  N7   aromatic  1.354  0.020  1.354
 9HX  C8  H8   single    0.930  0.020  1.080
 9HX  N7  C5   aromatic  1.359  0.020  1.359
 9HX  N7  HN7  single    0.860  0.020  1.020
 9HX  C5  C6   aromatic  1.427  0.020  1.427
 9HX  C5  C4   aromatic  1.392  0.020  1.392
 9HX  C6  O6   double    1.218  0.020  1.218
 9HX  C6  N1   aromatic  1.393  0.020  1.393
 9HX  N1  C2   aromatic  1.363  0.020  1.363
 9HX  N1  HN1  single    0.860  0.020  1.020
 9HX  C2  N3   aromatic  1.283  0.020  1.283
 9HX  C2  H2   single    0.930  0.020  1.080
 9HX  N3  C4   aromatic  1.368  0.020  1.368

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
 9HX  H9   C9  C4  127.47  3.000
 9HX  H9   C9  C8  126.27  3.000
 9HX  C4   C9  C8  106.26  3.000
 9HX  H8   C8  N7  120.72  3.000
 9HX  H8   C8  C9  129.70  3.000
 9HX  N7   C8  C9  109.58  3.000
 9HX  HN7  N7  C5  125.69  3.000
 9HX  HN7  N7  C8  125.34  3.000
 9HX  C5   N7  C8  108.96  3.000
 9HX  C4   C5  C6  122.58  3.000
 9HX  C4   C5  N7  108.12  3.000
 9HX  C6   C5  N7  129.30  3.000
 9HX  N1   C6  O6  122.39  3.000
 9HX  N1   C6  C5  109.31  3.000
 9HX  O6   C6  C5  128.29  3.000
 9HX  HN1  N1  C2  118.19  3.000
 9HX  HN1  N1  C6  116.54  3.000
 9HX  C2   N1  C6  125.27  3.000
 9HX  H2   C2  N3  119.93  3.000
 9HX  H2   C2  N1  114.95  3.000
 9HX  N3   C2  N1  125.12  3.000
 9HX  C4   N3  C2  114.65  3.000
 9HX  N3   C4  C5  123.07  3.000
 9HX  N3   C4  C9  129.85  3.000
 9HX  C5   C4  C9  107.08  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
 9HX  CONST_01  C5   N7  C8  C9    0.00  0.0  0
 9HX  CONST_02  N7   C5  C4  C9    0.00  0.0  0
 9HX  CONST_03  C6   C5  C4  C9  180.00  0.0  0
 9HX  CONST_04  C2   N3  C4  C9  180.00  0.0  0
 9HX  CONST_05  C5   C4  C9  C8    0.00  0.0  0
 9HX  CONST_06  N3   C4  C9  C8  180.00  0.0  0
 9HX  CONST_07  C6   C5  N7  C8  180.00  0.0  0
 9HX  CONST_08  C4   C5  N7  C8    0.00  0.0  0
 9HX  CONST_09  C4   C9  C8  N7    0.00  0.0  0
 9HX  CONST_10  N1   C6  C5  N7  180.00  0.0  0
 9HX  CONST_11  N3   C4  C5  N7  180.00  0.0  0
 9HX  CONST_12  C2   N1  C6  C5    0.00  0.0  0
 9HX  CONST_13  C2   N3  C4  C5    0.00  0.0  0
 9HX  CONST_14  N3   C4  C5  C6    0.00  0.0  0
 9HX  CONST_15  N3   C2  N1  C6    0.00  0.0  0
 9HX  CONST_16  C4   C5  C6  N1    0.00  0.0  0
 9HX  CONST_17  C4   N3  C2  N1    0.00  0.0  0
 9HX  CONST_18  O6   C6  C5  N7    0.00  0.0  0
 9HX  CONST_19  C4   C5  C6  O6  180.00  0.0  0
 9HX  CONST_20  C2   N1  C6  O6  180.00  0.0  0
 9HX  CONST_21  HN7  N7  C8  C9  180.00  0.0  0
 9HX  CONST_22  H9   C9  C8  N7  180.00  0.0  0
 9HX  CONST_23  H8   C8  N7  C5  180.00  0.0  0
 9HX  CONST_24  HN1  N1  C6  C5  180.00  0.0  0
 9HX  CONST_25  H2   C2  N1  C6  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
 9HX  plan-1  C9   0.020
 9HX  plan-1  C8   0.020
 9HX  plan-1  N7   0.020
 9HX  plan-1  C5   0.020
 9HX  plan-1  C6   0.020
 9HX  plan-1  O6   0.020
 9HX  plan-1  N1   0.020
 9HX  plan-1  C2   0.020
 9HX  plan-1  N3   0.020
 9HX  plan-1  C4   0.020
 9HX  plan-1  H9   0.020
 9HX  plan-1  H8   0.020
 9HX  plan-1  HN7  0.020
 9HX  plan-1  HN1  0.020
 9HX  plan-1  H2   0.020

