# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 18:02:44 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: pyrido[3,2-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2cccnc12
#
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
 P4Q  P4Q  pyrido[3,2-d]pyrimidin-4-amine  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_P4Q
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
 P4Q  C4  C  CR16  0  -0.309  11.9194  3.2632  18.8674
 P4Q  C3  C  CR16  0  -0.200  12.6521  2.1646  19.2285
 P4Q  C2  C  CR66  0   0.227  13.9949  2.3424  19.6186
 P4Q  C1  C  CR16  0   0.035  15.9875  1.5716  20.3305
 P4Q  C   C  CR6   0   0.478  15.8632  3.8209  20.0123
 P4Q  C5  C  CR16  0  -0.080  12.5237  4.5344  18.8946
 P4Q  C6  C  CR66  0   0.088  14.4900  3.6536  19.6091
 P4Q  N1  N  N     0  -0.460  16.5841  2.7704  20.3667
 P4Q  N2  N  N     0  -0.460  14.7623  1.2830  19.9859
 P4Q  N3  N  N     0  -0.420  13.7686  4.7270  19.2543
 P4Q  H1  H  HCR6  0   0.280  10.8860  3.1704  18.5624
 P4Q  H2  H  HCR6  0   0.278  12.2270  1.1692  19.2222
 P4Q  H3  H  HCR6  0   0.251  16.6157  0.7380  20.6295
 P4Q  H4  H  HNH2  0   0.406  17.3621  5.1629  20.2991
 P4Q  H5  H  HNH2  0   0.413  15.8621  5.8347  19.7469
 P4Q  H6  H  HCR6  0   0.272  11.9529  5.4105  18.6088
 P4Q  N   N  NH2   0  -0.799  16.4020  5.0338  20.0280

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
 P4Q  C4  C5  aromatic  1.408  0.020  1.408
 P4Q  C4  C3  aromatic  1.369  0.020  1.369
 P4Q  C5  N3  aromatic  1.310  0.020  1.310
 P4Q  C3  C2  aromatic  1.410  0.020  1.410
 P4Q  N3  C6  aromatic  1.341  0.020  1.341
 P4Q  C2  C6  aromatic  1.402  0.020  1.402
 P4Q  C2  N2  aromatic  1.359  0.020  1.359
 P4Q  C6  C   aromatic  1.441  0.020  1.441
 P4Q  N2  C1  aromatic  1.305  0.020  1.305
 P4Q  C   N   single    1.327  0.020  1.327
 P4Q  C   N1  aromatic  1.322  0.020  1.322
 P4Q  C1  N1  aromatic  1.339  0.020  1.339
 P4Q  C4  H1  single    0.930  0.020  1.080
 P4Q  C3  H2  single    0.930  0.020  1.080
 P4Q  C1  H3  single    0.930  0.020  1.080
 P4Q  N   H4  single    0.860  0.020  1.020
 P4Q  N   H5  single    0.860  0.020  1.020
 P4Q  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
 P4Q  H1  C4  C5  119.55  3.000
 P4Q  H1  C4  C3  121.13  3.000
 P4Q  C5  C4  C3  119.32  3.000
 P4Q  H2  C3  C2  119.46  3.000
 P4Q  H2  C3  C4  121.75  3.000
 P4Q  C2  C3  C4  118.79  3.000
 P4Q  N2  C2  C6  122.12  3.000
 P4Q  N2  C2  C3  120.96  3.000
 P4Q  C6  C2  C3  116.91  3.000
 P4Q  H3  C1  N2  116.49  3.000
 P4Q  H3  C1  N1  114.96  3.000
 P4Q  N2  C1  N1  128.55  3.000
 P4Q  N1  C   C6  120.15  3.000
 P4Q  N1  C   N   120.09  3.000
 P4Q  C6  C   N   119.76  3.000
 P4Q  H6  C5  N3  117.00  3.000
 P4Q  H6  C5  C4  119.91  3.000
 P4Q  N3  C5  C4  123.09  3.000
 P4Q  N3  C6  C   119.59  3.000
 P4Q  C   C6  C2  116.32  3.000
 P4Q  N3  C6  C2  124.09  3.000
 P4Q  C   N1  C1  117.45  3.000
 P4Q  C1  N2  C2  115.41  3.000
 P4Q  C6  N3  C5  117.79  3.000
 P4Q  H5  N   H4  119.04  3.000
 P4Q  H5  N   C   120.42  3.000
 P4Q  H4  N   C   120.52  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
 P4Q  CONST_01  C6  N3  C5  C4    0.00  0.0  0
 P4Q  CONST_02  C6  C2  C3  C4    0.00  0.0  0
 P4Q  CONST_03  N2  C2  C3  C4  180.00  0.0  0
 P4Q  CONST_04  N3  C5  C4  C3    0.00  0.0  0
 P4Q  CONST_05  N3  C6  C2  C3    0.00  0.0  0
 P4Q  CONST_06  C   C6  C2  C3  180.00  0.0  0
 P4Q  CONST_07  C1  N2  C2  C3  180.00  0.0  0
 P4Q  CONST_08  C5  C4  C3  C2    0.00  0.0  0
 P4Q  CONST_09  C5  N3  C6  C2    0.00  0.0  0
 P4Q  CONST_10  N1  C   C6  C2    0.00  0.0  0
 P4Q  CONST_11  N1  C1  N2  C2    0.00  0.0  0
 P4Q  CONST_12  C6  C2  N2  C1    0.00  0.0  0
 P4Q  CONST_13  C6  C   N1  C1    0.00  0.0  0
 P4Q  CONST_14  C5  N3  C6  C   180.00  0.0  0
 P4Q  CONST_15  N2  C2  C6  C     0.00  0.0  0
 P4Q  CONST_16  N2  C1  N1  C     0.00  0.0  0
 P4Q  CONST_17  N3  C6  C   N1  180.00  0.0  0
 P4Q  CONST_18  N3  C6  C2  N2  180.00  0.0  0
 P4Q  CONST_19  N   C   C6  C2  180.00  0.0  0
 P4Q  CONST_20  N   C   N1  C1  180.00  0.0  0
 P4Q  CONST_21  N3  C6  C   N     0.00  0.0  0
 P4Q  CONST_22  H6  C5  C4  C3  180.00  0.0  0
 P4Q  CONST_23  H1  C4  C3  C2  180.00  0.0  0
 P4Q  CONST_24  H3  C1  N2  C2  180.00  0.0  0
 P4Q  CONST_25  H2  C3  C4  C5  180.00  0.0  0
 P4Q  CONST_26  H4  N   C   C6  180.00  0.0  0
 P4Q  CONST_27  H5  N   C   C6    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
 P4Q  plan-1  C4  0.020
 P4Q  plan-1  C3  0.020
 P4Q  plan-1  C2  0.020
 P4Q  plan-1  C1  0.020
 P4Q  plan-1  C   0.020
 P4Q  plan-1  C5  0.020
 P4Q  plan-1  C6  0.020
 P4Q  plan-1  N1  0.020
 P4Q  plan-1  N2  0.020
 P4Q  plan-1  N3  0.020
 P4Q  plan-1  H1  0.020
 P4Q  plan-1  H2  0.020
 P4Q  plan-1  H3  0.020
 P4Q  plan-1  H6  0.020
 P4Q  plan-1  N   0.020
 P4Q  plan-2  C   0.020
 P4Q  plan-2  H4  0.020
 P4Q  plan-2  H5  0.020
 P4Q  plan-2  N   0.020

