# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 02:47:51 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 2-amino-5-(aminomethyl)-1,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1c[nH]c2NC(=NC(=O)c12)N
#
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
 HNG  HNG  2-amino-5-(aminomethyl)-1,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one  ligand  22  13  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HNG
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
 HNG  N1   N  N     0  -0.536  -1.6704   1.2544   0.0235
 HNG  C2   C  CR6   0   0.662  -2.3569   0.1456   0.0873
 HNG  N3   N  NR16  0  -0.731  -1.7963  -1.0954   0.0664
 HNG  C4   C  CR56  0   0.647  -0.4404  -1.1598  -0.0336
 HNG  C5   C  CR56  0  -0.239   0.3464  -0.0311  -0.1097
 HNG  C6   C  CR6   0   0.420  -0.2993   1.2588  -0.0777
 HNG  O6   O  O     0  -0.508   0.3131   2.3265  -0.1314
 HNG  C7   C  CR5   0  -0.002   1.7028  -0.4856  -0.2108
 HNG  C10  C  CH2   0  -0.398   2.9313   0.3569  -0.3263
 HNG  N11  N  NH2   0  -0.806   3.1596   1.1407   0.8845
 HNG  C8   C  CR15  0  -0.090   1.6498  -1.8479  -0.1865
 HNG  N9   N  NR15  0  -0.664   0.3321  -2.2538  -0.0791
 HNG  N2   N  NH2   0  -0.826  -3.6993   0.1934   0.1439
 HNG  H1   H  HNR6  0   0.432  -2.3640  -1.9284   0.1172
 HNG  H2   H  HCH2  0   0.229   3.7905  -0.3008  -0.4765
 HNG  H3   H  HCH2  0   0.203   2.8549   0.9746  -1.2312
 HNG  H4   H  HNH2  0   0.344   4.0202   1.6632   0.7727
 HNG  H5   H  HNH2  0   0.341   2.4263   1.8372   0.9487
 HNG  H7   H  HCR5  0   0.282   2.4398  -2.5785  -0.2401
 HNG  H8   H  HNR5  0   0.421   0.0194  -3.2107  -0.0457
 HNG  H9   H  HNH2  0   0.407  -4.1157   1.0881   0.3368
 HNG  H10  H  HNH2  0   0.409  -4.2332  -0.6130   0.4218

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
 HNG  N2   C2   single    1.344  0.020  1.344
 HNG  N1   C2   double    1.306  0.020  1.306
 HNG  N1   C6   single    1.375  0.020  1.375
 HNG  O6   C6   double    1.232  0.020  1.232
 HNG  C2   N3   single    1.362  0.020  1.362
 HNG  C6   C5   single    1.443  0.020  1.443
 HNG  N3   C4   single    1.361  0.020  1.361
 HNG  C5   C4   aromatic  1.378  0.020  1.378
 HNG  C5   C7   aromatic  1.434  0.020  1.434
 HNG  C4   N9   aromatic  1.340  0.020  1.340
 HNG  N11  C10  single    1.460  0.020  1.460
 HNG  C7   C10  single    1.494  0.020  1.494
 HNG  C7   C8   aromatic  1.364  0.020  1.364
 HNG  N9   C8   aromatic  1.383  0.020  1.383
 HNG  N3   H1   single    0.860  0.020  1.020
 HNG  C10  H2   single    0.970  0.020  1.090
 HNG  C10  H3   single    0.970  0.020  1.090
 HNG  N11  H4   single    0.890  0.020  1.040
 HNG  N11  H5   single    0.890  0.020  1.040
 HNG  C8   H7   single    0.930  0.020  1.080
 HNG  N9   H8   single    0.860  0.020  1.020
 HNG  N2   H9   single    0.890  0.020  1.040
 HNG  N2   H10  single    0.890  0.020  1.040

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
 HNG  C6   N1   C2   122.05  3.000
 HNG  N2   C2   N3   116.36  3.000
 HNG  N3   C2   N1   123.82  3.000
 HNG  N2   C2   N1   119.79  3.000
 HNG  H1   N3   C4   121.67  3.000
 HNG  H1   N3   C2   121.31  3.000
 HNG  C4   N3   C2   117.02  3.000
 HNG  N9   C4   C5   109.74  3.000
 HNG  N9   C4   N3   127.98  3.000
 HNG  C5   C4   N3   122.28  3.000
 HNG  C7   C5   C6   135.08  3.000
 HNG  C7   C5   C4   106.52  3.000
 HNG  C6   C5   C4   118.40  3.000
 HNG  O6   C6   C5   123.46  3.000
 HNG  C5   C6   N1   116.42  3.000
 HNG  O6   C6   N1   120.11  3.000
 HNG  C8   C7   C10  126.63  3.000
 HNG  C8   C7   C5   106.18  3.000
 HNG  C10  C7   C5   127.19  3.000
 HNG  H3   C10  H2   106.26  3.000
 HNG  H3   C10  N11  113.09  3.000
 HNG  H2   C10  N11  108.31  3.000
 HNG  H3   C10  C7   108.88  3.000
 HNG  H2   C10  C7   108.54  3.000
 HNG  N11  C10  C7   111.54  3.000
 HNG  H5   N11  H4   105.50  3.000
 HNG  H5   N11  C10  107.96  3.000
 HNG  H4   N11  C10  108.55  3.000
 HNG  H7   C8   N9   120.23  3.000
 HNG  H7   C8   C7   130.40  3.000
 HNG  N9   C8   C7   109.37  3.000
 HNG  H8   N9   C8   125.25  3.000
 HNG  H8   N9   C4   126.55  3.000
 HNG  C8   N9   C4   108.19  3.000
 HNG  H10  N2   H9   116.13  3.000
 HNG  H10  N2   C2   120.86  3.000
 HNG  H9   N2   C2   116.95  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
 HNG  CONST_01  C8   C7   C5   C4     0.00   0.0  0
 HNG  CONST_02  C7   C8   N9   C4     0.00   0.0  0
 HNG  CONST_03  C8   N9   C4   C5     0.00   0.0  0
 HNG  CONST_04  N9   C8   C7   C5     0.00   0.0  0
 HNG  CONST_05  N9   C4   C5   C7     0.00   0.0  0
 HNG  CONST_06  C4   N3   C2   N1     0.00   0.0  0
 HNG  CONST_07  C6   N1   C2   N3     0.00   0.0  0
 HNG  CONST_08  C10  C7   C5   C4   180.00   0.0  0
 HNG  CONST_09  C10  C7   C5   C6     0.00   0.0  0
 HNG  CONST_10  N9   C8   C7   C10  180.00   0.0  0
 HNG  CONST_11  N2   C2   N3   C4   180.00   0.0  0
 HNG  CONST_12  N2   C2   N1   C6   180.00   0.0  0
 HNG  CONST_13  H8   N9   C4   N3     0.00   0.0  0
 HNG  CONST_14  H7   C8   N9   C4   180.00   0.0  0
 HNG  CONST_15  H1   N3   C2   N1   180.00   0.0  0
 HNG  CONST_16  H9   N2   C2   N1     0.00   0.0  0
 HNG  Var_01    N11  C10  C7   C5    65.90  30.0  2
 HNG  Var_02    H4   N11  C10  C7   177.69  30.0  3

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
 HNG  plan-1  N1   0.020
 HNG  plan-1  C2   0.020
 HNG  plan-1  N3   0.020
 HNG  plan-1  C4   0.020
 HNG  plan-1  C5   0.020
 HNG  plan-1  C6   0.020
 HNG  plan-1  O6   0.020
 HNG  plan-1  C7   0.020
 HNG  plan-1  C10  0.020
 HNG  plan-1  C8   0.020
 HNG  plan-1  N9   0.020
 HNG  plan-1  N2   0.020
 HNG  plan-1  H1   0.020
 HNG  plan-1  H7   0.020
 HNG  plan-1  H8   0.020
 HNG  plan-1  H9   0.020
 HNG  plan-1  H10  0.020

