# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 08:31:27 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 2-amino-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2cc[nH]c2C(=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
 9DG  9DG  2-amino-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one  ligand  17  11  .  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_9DG
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
 9DG  C9    C  CR15  0  -0.426   1.6811   0.0361  -1.7276
 9DG  C8    C  CR15  0  -0.016   0.7217   0.0114  -2.7172
 9DG  N7    N  NR15  0  -0.644  -0.5080  -0.0087  -2.1596
 9DG  C5    C  CR56  0   0.116  -0.3731   0.0029  -0.8006
 9DG  C6    C  CR6   0   0.511  -1.3671  -0.0105   0.2123
 9DG  O6    O  O     0  -0.487  -2.5834  -0.0341   0.0810
 9DG  N1    N  NR16  0  -0.717  -0.7744   0.0109   1.4704
 9DG  C2    C  CR6   0   0.634   0.5749   0.0332   1.7144
 9DG  N2    N  NH2   0  -0.838   0.9393   0.1017   3.0184
 9DG  N3    N  N     0  -0.511   1.4728   0.0401   0.7772
 9DG  C4    C  CR56  0   0.200   0.9846   0.0304  -0.4952
 9DG  H9    H  HCR5  0   0.252   2.7488   0.0541  -1.8752
 9DG  H8    H  HCR5  0   0.286   0.8408   0.0073  -3.7883
 9DG  HN7   H  HNR5  0   0.416  -1.3777  -0.0286  -2.6659
 9DG  HN1   H  HNR6  0   0.421  -1.4098   0.0242   2.2574
 9DG  HN21  H  HNH2  0   0.400   1.9119  -0.0803   3.2042
 9DG  HN22  H  HNH2  0   0.402   0.3110  -0.2583   3.7179

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
 9DG  C9  C8    aromatic  1.379  0.020  1.379
 9DG  C9  C4    aromatic  1.416  0.020  1.416
 9DG  C9  H9    single    0.930  0.020  1.080
 9DG  C8  N7    aromatic  1.350  0.020  1.350
 9DG  C8  H8    single    0.930  0.020  1.080
 9DG  N7  C5    aromatic  1.366  0.020  1.366
 9DG  N7  HN7   single    0.860  0.020  1.020
 9DG  C5  C6    single    1.419  0.020  1.419
 9DG  C5  C4    aromatic  1.392  0.020  1.392
 9DG  C6  O6    double    1.224  0.020  1.224
 9DG  C6  N1    single    1.391  0.020  1.391
 9DG  N1  C2    single    1.371  0.020  1.371
 9DG  N1  HN1   single    0.860  0.020  1.020
 9DG  C2  N2    single    1.356  0.020  1.356
 9DG  C2  N3    double    1.298  0.020  1.298
 9DG  N2  HN21  single    0.890  0.020  1.040
 9DG  N2  HN22  single    0.890  0.020  1.040
 9DG  N3  C4    single    1.363  0.020  1.363

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
 9DG  H9    C9  C4    127.34  3.000
 9DG  H9    C9  C8    126.25  3.000
 9DG  C4    C9  C8    106.41  3.000
 9DG  H8    C8  N7    120.73  3.000
 9DG  H8    C8  C9    129.54  3.000
 9DG  N7    C8  C9    109.74  3.000
 9DG  HN7   N7  C5    125.87  3.000
 9DG  HN7   N7  C8    125.41  3.000
 9DG  C5    N7  C8    108.71  3.000
 9DG  C4    C5  C6    121.79  3.000
 9DG  C4    C5  N7    108.35  3.000
 9DG  C6    C5  N7    129.86  3.000
 9DG  N1    C6  O6    121.39  3.000
 9DG  N1    C6  C5    110.30  3.000
 9DG  O6    C6  C5    128.30  3.000
 9DG  HN1   N1  C2    118.64  3.000
 9DG  HN1   N1  C6    115.87  3.000
 9DG  C2    N1  C6    125.48  3.000
 9DG  N3    C2  N2    120.55  3.000
 9DG  N3    C2  N1    123.52  3.000
 9DG  N2    C2  N1    115.88  3.000
 9DG  HN22  N2  HN21  114.21  3.000
 9DG  HN22  N2  C2    118.84  3.000
 9DG  HN21  N2  C2    115.35  3.000
 9DG  C4    N3  C2    115.23  3.000
 9DG  N3    C4  C5    123.67  3.000
 9DG  N3    C4  C9    129.54  3.000
 9DG  C5    C4  C9    106.80  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
 9DG  CONST_01  C5    N7  C8  C9    0.00  0.0  0
 9DG  CONST_02  N7    C5  C4  C9    0.00  0.0  0
 9DG  CONST_03  C5    C4  C9  C8    0.00  0.0  0
 9DG  CONST_04  C4    C5  N7  C8    0.00  0.0  0
 9DG  CONST_05  C4    C9  C8  N7    0.00  0.0  0
 9DG  CONST_06  C2    N1  C6  C5    0.00  0.0  0
 9DG  CONST_07  N3    C2  N1  C6    0.00  0.0  0
 9DG  CONST_08  C4    N3  C2  N1    0.00  0.0  0
 9DG  CONST_09  N2    C2  N1  C6  180.00  0.0  0
 9DG  CONST_10  C2    N1  C6  O6  180.00  0.0  0
 9DG  CONST_11  C4    N3  C2  N2  180.00  0.0  0
 9DG  CONST_12  HN7   N7  C8  C9  180.00  0.0  0
 9DG  CONST_13  H9    C9  C8  N7  180.00  0.0  0
 9DG  CONST_14  H8    C8  N7  C5  180.00  0.0  0
 9DG  CONST_15  HN1   N1  C6  C5  180.00  0.0  0
 9DG  CONST_16  HN21  N2  C2  N1  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
 9DG  plan-1  C9    0.020
 9DG  plan-1  C8    0.020
 9DG  plan-1  N7    0.020
 9DG  plan-1  C5    0.020
 9DG  plan-1  C6    0.020
 9DG  plan-1  O6    0.020
 9DG  plan-1  N1    0.020
 9DG  plan-1  C2    0.020
 9DG  plan-1  N2    0.020
 9DG  plan-1  N3    0.020
 9DG  plan-1  C4    0.020
 9DG  plan-1  H9    0.020
 9DG  plan-1  H8    0.020
 9DG  plan-1  HN7   0.020
 9DG  plan-1  HN1   0.020
 9DG  plan-1  HN21  0.020
 9DG  plan-1  HN22  0.020

