# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 10:40:08 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 4-amino-8-(4-aminophenyl)pyrido[2,3-d]pyrimidin-5(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(cc1)N2C=CC(=O)c3c(N)ncnc23
#
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
 3WJ  3WJ  4-amino-8-(4-aminophenyl)pyrido[2,3-d]pyrimidin-5(8H)-one  ligand  30  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3WJ
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
 3WJ  C2   C  CR66  0   0.528  -0.7916   0.2547  -0.0403
 3WJ  C3   C  CR6   0   0.235   1.5489  -0.4026   0.0864
 3WJ  N6   N  N     0  -0.466  -0.3479   1.4939  -0.2587
 3WJ  C7   C  CR16  0  -0.246   2.2116   0.0108   1.2319
 3WJ  C8   C  CR16  0  -0.249   2.2462  -0.5308  -1.1048
 3WJ  C9   C  CR16  0  -0.483  -1.5197  -2.3935   0.4189
 3WJ  C10  C  CR6   0   0.464  -2.5914  -1.4459   0.2486
 3WJ  C11  C  CR6   0   0.511  -3.0500   1.0100  -0.1939
 3WJ  C12  C  CR16  0   0.070  -1.2813   2.4076  -0.4308
 3WJ  C13  C  CR16  0  -0.335   3.5647   0.2919   1.1905
 3WJ  C14  C  CR16  0  -0.334   3.6003  -0.2524  -1.1528
 3WJ  N1   N  NR6   0  -0.618   0.1542  -0.7189   0.1380
 3WJ  C4   C  CR16  0   0.043  -0.2283  -2.0055   0.3589
 3WJ  C5   C  CR66  0  -0.310  -2.1496  -0.0805   0.0103
 3WJ  O15  O  O     0  -0.499  -3.7836  -1.7739   0.3007
 3WJ  N16  N  N     0  -0.465  -2.5908   2.2485  -0.4140
 3WJ  N17  N  NH2   0  -0.815  -4.3646   0.8390  -0.1738
 3WJ  C18  C  CR6   0   0.322   4.2872   0.1660  -0.0047
 3WJ  N19  N  NH2   0  -0.857   5.6398   0.3959  -0.0371
 3WJ  H1   H  HCR6  0   0.265   1.6690   0.1155   2.1632
 3WJ  H2   H  HCR6  0   0.266   1.7316  -0.8493  -2.0026
 3WJ  H3   H  HCR6  0   0.278  -1.7515  -3.4340   0.5980
 3WJ  H4   H  HCR6  0   0.261  -0.9288   3.4186  -0.6091
 3WJ  H5   H  HCR6  0   0.264   4.0710   0.6131   2.0924
 3WJ  H6   H  HCR6  0   0.264   4.1346  -0.3570  -2.0893
 3WJ  H7   H  HCR6  0   0.319   0.5822  -2.7089   0.4850
 3WJ  H8   H  HNH2  0   0.420  -4.7461  -0.0812  -0.0134
 3WJ  H9   H  HNH2  0   0.402  -4.9703   1.6256  -0.3354
 3WJ  H10  H  HNH2  0   0.383   6.0094   0.9880   0.6888
 3WJ  H11  H  HNH2  0   0.384   6.0368   0.6035  -0.9390

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
 3WJ  N16  C12  aromatic  1.319  0.020  1.319
 3WJ  N16  C11  aromatic  1.339  0.020  1.339
 3WJ  C12  N6   aromatic  1.317  0.020  1.317
 3WJ  N17  C11  single    1.326  0.020  1.326
 3WJ  C11  C5   aromatic  1.429  0.020  1.429
 3WJ  N6   C2   aromatic  1.334  0.020  1.334
 3WJ  C5   C2   aromatic  1.400  0.020  1.400
 3WJ  C5   C10  single    1.455  0.020  1.455
 3WJ  C2   N1   single    1.369  0.020  1.369
 3WJ  O15  C10  double    1.238  0.020  1.238
 3WJ  C10  C9   single    1.441  0.020  1.441
 3WJ  N1   C3   single    1.431  0.020  1.431
 3WJ  N1   C4   single    1.360  0.020  1.360
 3WJ  C3   C8   aromatic  1.386  0.020  1.386
 3WJ  C3   C7   aromatic  1.386  0.020  1.386
 3WJ  C8   C14  aromatic  1.383  0.020  1.383
 3WJ  C7   C13  aromatic  1.383  0.020  1.383
 3WJ  C14  C18  aromatic  1.402  0.020  1.402
 3WJ  C9   C4   double    1.350  0.020  1.350
 3WJ  C13  C18  aromatic  1.402  0.020  1.402
 3WJ  C18  N19  single    1.372  0.020  1.372
 3WJ  C7   H1   single    0.930  0.020  1.080
 3WJ  C8   H2   single    0.930  0.020  1.080
 3WJ  C9   H3   single    0.930  0.020  1.080
 3WJ  C12  H4   single    0.930  0.020  1.080
 3WJ  C13  H5   single    0.930  0.020  1.080
 3WJ  C14  H6   single    0.930  0.020  1.080
 3WJ  C4   H7   single    0.930  0.020  1.080
 3WJ  N17  H8   single    0.860  0.020  1.020
 3WJ  N17  H9   single    0.860  0.020  1.020
 3WJ  N19  H10  single    0.890  0.020  1.040
 3WJ  N19  H11  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
 3WJ  C5   C2   N1   119.69  3.000
 3WJ  N1   C2   N6   116.88  3.000
 3WJ  C5   C2   N6   123.44  3.000
 3WJ  N1   C3   C8   120.05  3.000
 3WJ  C8   C3   C7   119.81  3.000
 3WJ  N1   C3   C7   120.13  3.000
 3WJ  C12  N6   C2   115.46  3.000
 3WJ  H1   C7   C13  119.77  3.000
 3WJ  H1   C7   C3   119.99  3.000
 3WJ  C13  C7   C3   120.24  3.000
 3WJ  H2   C8   C14  119.72  3.000
 3WJ  H2   C8   C3   120.04  3.000
 3WJ  C14  C8   C3   120.24  3.000
 3WJ  H3   C9   C4   119.29  3.000
 3WJ  H3   C9   C10  119.55  3.000
 3WJ  C4   C9   C10  121.15  3.000
 3WJ  O15  C10  C5   123.25  3.000
 3WJ  O15  C10  C9   122.49  3.000
 3WJ  C5   C10  C9   114.26  3.000
 3WJ  N17  C11  N16  117.50  3.000
 3WJ  N17  C11  C5   121.61  3.000
 3WJ  N16  C11  C5   120.89  3.000
 3WJ  H4   C12  N16  115.90  3.000
 3WJ  H4   C12  N6   115.94  3.000
 3WJ  N16  C12  N6   128.17  3.000
 3WJ  H5   C13  C18  119.71  3.000
 3WJ  H5   C13  C7   119.52  3.000
 3WJ  C18  C13  C7   120.77  3.000
 3WJ  H6   C14  C18  119.68  3.000
 3WJ  H6   C14  C8   119.56  3.000
 3WJ  C18  C14  C8   120.75  3.000
 3WJ  C4   N1   C3   119.27  3.000
 3WJ  C4   N1   C2   119.97  3.000
 3WJ  C3   N1   C2   120.76  3.000
 3WJ  H7   C4   N1   115.08  3.000
 3WJ  H7   C4   C9   121.69  3.000
 3WJ  N1   C4   C9   123.24  3.000
 3WJ  C11  C5   C10  123.26  3.000
 3WJ  C10  C5   C2   121.69  3.000
 3WJ  C11  C5   C2   115.05  3.000
 3WJ  C12  N16  C11  117.00  3.000
 3WJ  H9   N17  H8   120.73  3.000
 3WJ  H9   N17  C11  119.59  3.000
 3WJ  H8   N17  C11  119.67  3.000
 3WJ  N19  C18  C14  120.91  3.000
 3WJ  N19  C18  C13  120.85  3.000
 3WJ  C14  C18  C13  118.19  3.000
 3WJ  H11  N19  H10  112.31  3.000
 3WJ  H11  N19  C18  116.37  3.000
 3WJ  H10  N19  C18  116.31  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
 3WJ  CONST_01  N16  C12  N6   C2     0.00   0.0  0
 3WJ  CONST_02  N16  C11  C5   C2     0.00   0.0  0
 3WJ  CONST_03  C18  C14  C8   C3     0.00   0.0  0
 3WJ  CONST_04  C18  C13  C7   C3     0.00   0.0  0
 3WJ  CONST_05  C11  N16  C12  N6     0.00   0.0  0
 3WJ  CONST_06  C11  C5   C2   N6     0.00   0.0  0
 3WJ  CONST_07  C14  C8   C3   C7     0.00   0.0  0
 3WJ  CONST_08  C14  C18  C13  C7     0.00   0.0  0
 3WJ  CONST_09  C13  C7   C3   C8     0.00   0.0  0
 3WJ  CONST_10  C13  C18  C14  C8     0.00   0.0  0
 3WJ  CONST_11  C5   C11  N16  C12    0.00   0.0  0
 3WJ  CONST_12  C5   C2   N6   C12    0.00   0.0  0
 3WJ  CONST_13  N1   C3   C7   C13  180.00   0.0  0
 3WJ  CONST_14  N1   C3   C8   C14  180.00   0.0  0
 3WJ  CONST_15  N17  C11  C5   C2   180.00   0.0  0
 3WJ  CONST_16  N19  C18  C13  C7   180.00   0.0  0
 3WJ  CONST_17  N19  C18  C14  C8   180.00   0.0  0
 3WJ  CONST_18  N17  C11  C5   C10    0.00   0.0  0
 3WJ  CONST_19  N17  C11  N16  C12  180.00   0.0  0
 3WJ  CONST_20  H4   C12  N6   C2   180.00   0.0  0
 3WJ  CONST_21  H6   C14  C8   C3   180.00   0.0  0
 3WJ  CONST_22  H5   C13  C7   C3   180.00   0.0  0
 3WJ  CONST_23  H2   C8   C3   C7   180.00   0.0  0
 3WJ  CONST_24  H1   C7   C3   C8   180.00   0.0  0
 3WJ  CONST_27  H8   N17  C11  C5     0.00   0.0  0
 3WJ  CONST_28  H9   N17  C11  C5   180.00   0.0  0
 3WJ  Var_01    C8   C3   N1   C2   -93.49  30.0  2

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
 3WJ  plan-1  C3   0.020
 3WJ  plan-1  C7   0.020
 3WJ  plan-1  C8   0.020
 3WJ  plan-1  C13  0.020
 3WJ  plan-1  C14  0.020
 3WJ  plan-1  N1   0.020
 3WJ  plan-1  C18  0.020
 3WJ  plan-1  N19  0.020
 3WJ  plan-1  H1   0.020
 3WJ  plan-1  H2   0.020
 3WJ  plan-1  H5   0.020
 3WJ  plan-1  H6   0.020
 3WJ  plan-2  C2   0.020
 3WJ  plan-2  C3   0.020
 3WJ  plan-2  N6   0.020
 3WJ  plan-2  C9   0.020
 3WJ  plan-2  C10  0.020
 3WJ  plan-2  C11  0.020
 3WJ  plan-2  C12  0.020
 3WJ  plan-2  N1   0.020
 3WJ  plan-2  C4   0.020
 3WJ  plan-2  C5   0.020
 3WJ  plan-2  O15  0.020
 3WJ  plan-2  N16  0.020
 3WJ  plan-2  N17  0.020
 3WJ  plan-2  H3   0.020
 3WJ  plan-2  H4   0.020
 3WJ  plan-2  H7   0.020
 3WJ  plan-3  C11  0.020
 3WJ  plan-3  N17  0.020
 3WJ  plan-3  H8   0.020
 3WJ  plan-3  H9   0.020
 3WJ  plan-4  C18  0.020
 3WJ  plan-4  N19  0.020
 3WJ  plan-4  H10  0.020
 3WJ  plan-4  H11  0.020

