# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 13:23:16 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 3H-pyrido[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC=Nc2cnccc12
#
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
 N5J  N5J  3H-pyrido[3,4-d]pyrimidin-4-one  ligand  16  11  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N5J
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
 N5J  O    O  O     0  -0.436   1.7811  -2.0239  -0.0134
 N5J  C1   C  CR6   0   0.573   1.3722  -0.8805  -0.0072
 N5J  N1   N  NR16  0  -0.660   2.2195   0.2037   0.0036
 N5J  C2   C  CR16  0   0.150   1.8042   1.4973   0.0109
 N5J  N2   N  N     0  -0.448   0.5792   1.8727   0.0090
 N5J  C3   C  CR66  0   0.169  -0.3631   0.8730  -0.0029
 N5J  N3   N  N     0  -0.383  -2.6907   0.3204  -0.0206
 N5J  C4   C  CR16  0  -0.106  -1.7266   1.2120  -0.0081
 N5J  C5   C  CR16  0  -0.070  -2.3653  -0.9786  -0.0277
 N5J  C6   C  CR16  0  -0.340  -1.0639  -1.4293  -0.0232
 N5J  C7   C  CR66  0  -0.031  -0.0379  -0.4863  -0.0108
 N5J  HN1  H  HNR6  0   0.439   3.2157   0.0229   0.0046
 N5J  H2   H  HCR6  0   0.306   2.5989   2.2321   0.0204
 N5J  H4   H  HCR6  0   0.277  -2.0055   2.2609  -0.0012
 N5J  H5   H  HCR6  0   0.275  -3.1883  -1.6823  -0.0379
 N5J  H6   H  HCR6  0   0.284  -0.8481  -2.4888  -0.0293

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
 N5J  O   C1   double    1.214  0.020  1.214
 N5J  C1  N1   single    1.376  0.020  1.376
 N5J  C1  C7   single    1.464  0.020  1.464
 N5J  N1  C2   single    1.359  0.020  1.359
 N5J  C2  N2   double    1.281  0.020  1.281
 N5J  N2  C3   single    1.374  0.020  1.374
 N5J  C3  C4   aromatic  1.405  0.020  1.405
 N5J  C3  C7   aromatic  1.398  0.020  1.398
 N5J  N3  C4   aromatic  1.313  0.020  1.313
 N5J  N3  C5   aromatic  1.339  0.020  1.339
 N5J  C5  C6   aromatic  1.377  0.020  1.377
 N5J  C6  C7   aromatic  1.394  0.020  1.394
 N5J  N1  HN1  single    0.860  0.020  1.020
 N5J  C2  H2   single    0.930  0.020  1.080
 N5J  C4  H4   single    0.930  0.020  1.080
 N5J  C5  H5   single    0.930  0.020  1.080
 N5J  C6  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
 N5J  C7   C1  N1  112.39  3.000
 N5J  C7   C1  O   125.30  3.000
 N5J  N1   C1  O   122.31  3.000
 N5J  HN1  N1  C2  118.08  3.000
 N5J  HN1  N1  C1  117.73  3.000
 N5J  C2   N1  C1  124.19  3.000
 N5J  H2   C2  N2  120.21  3.000
 N5J  H2   C2  N1  114.96  3.000
 N5J  N2   C2  N1  124.83  3.000
 N5J  C3   N2  C2  116.27  3.000
 N5J  C7   C3  C4  117.42  3.000
 N5J  C7   C3  N2  123.24  3.000
 N5J  C4   C3  N2  119.34  3.000
 N5J  C5   N3  C4  118.70  3.000
 N5J  H4   C4  N3  117.87  3.000
 N5J  H4   C4  C3  118.86  3.000
 N5J  N3   C4  C3  123.27  3.000
 N5J  H5   C5  C6  120.36  3.000
 N5J  H5   C5  N3  116.47  3.000
 N5J  C6   C5  N3  123.17  3.000
 N5J  H6   C6  C7  121.08  3.000
 N5J  H6   C6  C5  120.62  3.000
 N5J  C7   C6  C5  118.31  3.000
 N5J  C6   C7  C3  119.14  3.000
 N5J  C6   C7  C1  121.79  3.000
 N5J  C3   C7  C1  119.07  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
 N5J  CONST_01  C5   N3  C4  C3    0.00  0.0  0
 N5J  CONST_02  C5   C6  C7  C3    0.00  0.0  0
 N5J  CONST_03  C7   C3  C4  N3    0.00  0.0  0
 N5J  CONST_04  C7   C6  C5  N3    0.00  0.0  0
 N5J  CONST_05  C6   C7  C3  C4    0.00  0.0  0
 N5J  CONST_06  C6   C5  N3  C4    0.00  0.0  0
 N5J  CONST_07  N2   C2  N1  C1    0.00  0.0  0
 N5J  CONST_08  C3   N2  C2  N1    0.00  0.0  0
 N5J  CONST_09  C7   C1  N1  C2    0.00  0.0  0
 N5J  CONST_10  C2   N1  C1  O   180.00  0.0  0
 N5J  CONST_11  H6   C6  C7  C1    0.00  0.0  0
 N5J  CONST_12  H4   C4  C3  N2    0.00  0.0  0
 N5J  CONST_13  H5   C5  N3  C4  180.00  0.0  0
 N5J  CONST_14  H2   C2  N1  C1  180.00  0.0  0
 N5J  CONST_15  HN1  N1  C2  N2  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
 N5J  plan-1  O    0.020
 N5J  plan-1  C1   0.020
 N5J  plan-1  N1   0.020
 N5J  plan-1  C2   0.020
 N5J  plan-1  N2   0.020
 N5J  plan-1  C3   0.020
 N5J  plan-1  N3   0.020
 N5J  plan-1  C4   0.020
 N5J  plan-1  C5   0.020
 N5J  plan-1  C6   0.020
 N5J  plan-1  C7   0.020
 N5J  plan-1  HN1  0.020
 N5J  plan-1  H2   0.020
 N5J  plan-1  H4   0.020
 N5J  plan-1  H5   0.020
 N5J  plan-1  H6   0.020

