# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 01:18:09 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: N-[(4-{[(2-amino-4-oxo-1,4-dihydropyrido[2,3-d]pyrimidin-6-yl)methyl]amino}phenyl)carbonyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2cc(CNc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)cnc2N1
#
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
 DZF  DZF  'N-[(4-{[(2-amino-4-oxo-1,4-dihydropyrido[2,3-d]pyrimidin-6-yl)methyl]amino}phenyl)carbonyl]-L-glutamic acid'  ligand  52  32  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DZF
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
 DZF  N1    N  NR16  0  -0.720  -0.7478  -0.6984   7.9002
 DZF  C2    C  CR6   0   0.695  -0.2391   0.2096   8.7723
 DZF  NA2   N  NH2   0  -0.816  -0.2879  -0.1045  10.0641
 DZF  N3    N  N     0  -0.531   0.2901   1.3526   8.4061
 DZF  C4    C  CR6   0   0.444   0.3586   1.6965   7.0945
 DZF  O4    O  OC    0  -0.477   0.8503   2.7586   6.7344
 DZF  C4A   C  CR66  0  -0.224  -0.1854   0.7430   6.1076
 DZF  C5    C  CR16  0  -0.204  -0.1818   0.9721   4.7376
 DZF  C6    C  CR6   0  -0.016  -0.7205   0.0276   3.8828
 DZF  C7    C  CR16  0  -0.058  -1.2428  -1.1324   4.4589
 DZF  N8    N  N     0  -0.431  -1.2561  -1.3791   5.7571
 DZF  C8A   C  CR66  0   0.528  -0.7362  -0.4553   6.5528
 DZF  C9    C  CH2   0  -0.344  -0.7329   0.2105   2.3938
 DZF  N10   N  NH1   0  -0.683   0.2381  -0.6681   1.7805
 DZF  C11   C  CR6   0  -0.076   0.7926  -0.9971  -2.3568
 DZF  C12   C  CR16  0  -0.256   1.6890  -1.5721  -1.4504
 DZF  C13   C  CR16  0  -0.333   1.5122  -1.4457  -0.0921
 DZF  C14   C  CR6   0   0.388   0.4077  -0.7470   0.4307
 DZF  C15   C  CR16  0  -0.341  -0.4989  -0.1775  -0.4766
 DZF  C16   C  CR16  0  -0.274  -0.3021  -0.3071  -1.8395
 DZF  O     O  O     0  -0.490   1.7462  -2.0654  -4.2472
 DZF  N     N  NH1   0  -0.669   0.4169  -0.3008  -4.6384
 DZF  CA    C  CH1   0  -0.168   0.6162  -0.3958  -6.0600
 DZF  CB    C  CH2   0  -0.479  -0.2686   0.6159  -6.7926
 DZF  CG    C  CH2   0  -0.577  -1.7462   0.3242  -6.5836
 DZF  CD    C  C     0   0.556  -2.6392   1.2723  -7.3358
 DZF  OE1   O  O     0  -0.442  -2.2584   2.1591  -8.0580
 DZF  OE2   O  OH1   0  -0.595  -3.9234   1.0155  -7.1128
 DZF  CT    C  C     0   0.539   2.0643  -0.1829  -6.4767
 DZF  O1    O  O     0  -0.441   2.5425  -0.6815  -7.4643
 DZF  O2    O  OH1   0  -0.584   2.7120   0.6527  -5.6820
 DZF  HN1   H  HNR6  0   0.428  -1.1445  -1.5695   8.2251
 DZF  HN21  H  HNH2  0   0.418   0.0424   0.5629  10.7394
 DZF  HN22  H  HNH2  0   0.421  -0.7157  -0.9486  10.4027
 DZF  H5    H  HCR6  0   0.275   0.2392   1.8918   4.3506
 DZF  H7    H  HCR6  0   0.277  -1.6799  -1.8979   3.8257
 DZF  H91   H  HCH2  0   0.260  -1.7278  -0.0289   2.0095
 DZF  H92   H  HCH2  0   0.251  -0.5451   1.2631   2.1495
 DZF  HN0   H  HNH1  0   0.390   1.0506  -0.8789   2.3383
 DZF  H12   H  HCR6  0   0.256   2.5478  -2.1179  -1.8190
 DZF  H13   H  HCR6  0   0.263   2.2293  -1.8930   0.5861
 DZF  H15   H  HCR6  0   0.274  -1.3689   0.3616  -0.1273
 DZF  H16   H  HCR6  0   0.247  -1.0439   0.1313  -2.4961
 DZF  HN    H  HNH1  0   0.406   0.0769   0.5726  -4.2683
 DZF  HA    H  HCH1  0   0.290   0.3462  -1.3998  -6.3974
 DZF  HB1   H  HCH2  0   0.261  -0.0247   1.6275  -6.4586
 DZF  HB2   H  HCH2  0   0.273  -0.0337   0.5677  -7.8566
 DZF  HG1   H  HCH2  0   0.290  -1.9825  -0.6943  -6.9067
 DZF  HG2   H  HCH2  0   0.283  -2.0215   0.3677  -5.5263
 DZF  HOE2  H  HOH1  0   0.481  -4.4777   1.6365  -7.6089
 DZF  HO2   H  HOH1  0   0.485   3.6153   0.7870  -6.0069
 DZF  C     C  C     0   0.553   1.0329  -1.1725  -3.8056

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
 DZF  N1   C2    aromatic  1.358  0.020  1.358
 DZF  N1   C8A   aromatic  1.369  0.020  1.369
 DZF  N1   HN1   single    0.860  0.020  1.020
 DZF  C2   NA2   single    1.330  0.020  1.330
 DZF  C2   N3    aromatic  1.312  0.020  1.312
 DZF  NA2  HN21  single    0.860  0.020  1.020
 DZF  NA2  HN22  single    0.860  0.020  1.020
 DZF  N3   C4    aromatic  1.358  0.020  1.358
 DZF  C4   O4    double    1.224  0.020  1.224
 DZF  C4   C4A   aromatic  1.476  0.020  1.476
 DZF  C4A  C5    aromatic  1.389  0.020  1.389
 DZF  C4A  C8A   aromatic  1.392  0.020  1.392
 DZF  C5   C6    aromatic  1.383  0.020  1.383
 DZF  C5   H5    single    0.930  0.020  1.080
 DZF  C6   C7    aromatic  1.397  0.020  1.397
 DZF  C6   C9    single    1.500  0.020  1.500
 DZF  C7   N8    aromatic  1.322  0.020  1.322
 DZF  C7   H7    single    0.930  0.020  1.080
 DZF  N8   C8A   aromatic  1.325  0.020  1.325
 DZF  C9   N10   single    1.446  0.020  1.446
 DZF  C9   H91   single    0.970  0.020  1.090
 DZF  C9   H92   single    0.970  0.020  1.090
 DZF  N10  C14   single    1.363  0.020  1.363
 DZF  N10  HN0   single    0.890  0.020  1.040
 DZF  C11  C12   aromatic  1.398  0.020  1.398
 DZF  C11  C16   aromatic  1.394  0.020  1.394
 DZF  C11  C     single    1.479  0.020  1.479
 DZF  C12  C13   aromatic  1.376  0.020  1.376
 DZF  C12  H12   single    0.930  0.020  1.080
 DZF  C13  C14   aromatic  1.408  0.020  1.408
 DZF  C13  H13   single    0.930  0.020  1.080
 DZF  C14  C15   aromatic  1.403  0.020  1.403
 DZF  C15  C16   aromatic  1.383  0.020  1.383
 DZF  C15  H15   single    0.930  0.020  1.080
 DZF  C16  H16   single    0.930  0.020  1.080
 DZF  C    O     double    1.225  0.020  1.225
 DZF  C    N     single    1.354  0.020  1.354
 DZF  N    CA    single    1.439  0.020  1.439
 DZF  N    HN    single    0.860  0.020  1.020
 DZF  CA   CB    single    1.531  0.020  1.531
 DZF  CA   CT    single    1.522  0.020  1.522
 DZF  CA   HA    single    0.970  0.020  1.090
 DZF  CB   CG    single    1.521  0.020  1.521
 DZF  CB   HB1   single    0.970  0.020  1.090
 DZF  CB   HB2   single    0.970  0.020  1.090
 DZF  CG   CD    single    1.504  0.020  1.504
 DZF  CG   HG1   single    0.970  0.020  1.090
 DZF  CG   HG2   single    0.970  0.020  1.090
 DZF  CD   OE1   double    1.205  0.020  1.205
 DZF  CD   OE2   single    1.328  0.020  1.328
 DZF  OE2  HOE2  single    0.850  0.020  0.980
 DZF  CT   O1    double    1.205  0.020  1.205
 DZF  CT   O2    single    1.323  0.020  1.323
 DZF  O2   HO2   single    0.850  0.020  0.980

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
 DZF  HN1   N1   C8A   118.21  3.000
 DZF  HN1   N1   C2    121.12  3.000
 DZF  C8A   N1   C2    120.68  3.000
 DZF  N3    C2   NA2   119.45  3.000
 DZF  N3    C2   N1    123.67  3.000
 DZF  NA2   C2   N1    116.88  3.000
 DZF  HN22  NA2  HN21  118.10  3.000
 DZF  HN22  NA2  C2    122.75  3.000
 DZF  HN21  NA2  C2    118.92  3.000
 DZF  C4    N3   C2    120.72  3.000
 DZF  C4A   C4   O4    120.78  3.000
 DZF  C4A   C4   N3    117.62  3.000
 DZF  O4    C4   N3    121.60  3.000
 DZF  C8A   C4A  C5    117.28  3.000
 DZF  C8A   C4A  C4    119.22  3.000
 DZF  C5    C4A  C4    123.50  3.000
 DZF  H5    C5   C6    120.69  3.000
 DZF  H5    C5   C4A   119.57  3.000
 DZF  C6    C5   C4A   119.74  3.000
 DZF  C9    C6   C7    120.50  3.000
 DZF  C9    C6   C5    122.24  3.000
 DZF  C7    C6   C5    117.25  3.000
 DZF  H7    C7   N8    115.94  3.000
 DZF  H7    C7   C6    119.72  3.000
 DZF  N8    C7   C6    124.34  3.000
 DZF  C8A   N8   C7    117.11  3.000
 DZF  N8    C8A  C4A   124.28  3.000
 DZF  N8    C8A  N1    117.62  3.000
 DZF  C4A   C8A  N1    118.09  3.000
 DZF  H92   C9   H91   106.71  3.000
 DZF  H92   C9   N10   111.94  3.000
 DZF  H91   C9   N10   109.21  3.000
 DZF  H92   C9   C6    109.67  3.000
 DZF  H91   C9   C6    109.26  3.000
 DZF  N10   C9   C6    109.96  3.000
 DZF  HN0   N10  C14   115.84  3.000
 DZF  HN0   N10  C9    115.70  3.000
 DZF  C14   N10  C9    122.61  3.000
 DZF  C     C11  C16   123.36  3.000
 DZF  C     C11  C12   118.82  3.000
 DZF  C16   C11  C12   117.81  3.000
 DZF  H12   C12  C13   118.98  3.000
 DZF  H12   C12  C11   119.69  3.000
 DZF  C13   C12  C11   121.32  3.000
 DZF  H13   C13  C14   119.45  3.000
 DZF  H13   C13  C12   119.67  3.000
 DZF  C14   C13  C12   120.88  3.000
 DZF  C15   C14  C13   117.92  3.000
 DZF  C15   C14  N10   122.45  3.000
 DZF  C13   C14  N10   119.62  3.000
 DZF  H15   C15  C16   118.65  3.000
 DZF  H15   C15  C14   120.87  3.000
 DZF  C16   C15  C14   120.47  3.000
 DZF  H16   C16  C15   117.50  3.000
 DZF  H16   C16  C11   120.89  3.000
 DZF  C15   C16  C11   121.60  3.000
 DZF  HN    N    CA    117.83  3.000
 DZF  HN    N    C     119.06  3.000
 DZF  CA    N    C     120.15  3.000
 DZF  HA    CA   CT    106.20  3.000
 DZF  HA    CA   CB    108.46  3.000
 DZF  CT    CA   CB    109.06  3.000
 DZF  HA    CA   N     109.36  3.000
 DZF  CT    CA   N     113.15  3.000
 DZF  CB    CA   N     110.44  3.000
 DZF  HB2   CB   HB1   106.92  3.000
 DZF  HB2   CB   CG    109.57  3.000
 DZF  HB1   CB   CG    110.63  3.000
 DZF  HB2   CB   CA    108.25  3.000
 DZF  HB1   CB   CA    109.66  3.000
 DZF  CG    CB   CA    111.66  3.000
 DZF  HG2   CG   HG1   105.55  3.000
 DZF  HG2   CG   CD    108.00  3.000
 DZF  HG1   CG   CD    108.11  3.000
 DZF  HG2   CG   CB    111.71  3.000
 DZF  HG1   CG   CB    110.35  3.000
 DZF  CD    CG   CB    112.78  3.000
 DZF  OE2   CD   OE1   123.24  3.000
 DZF  OE2   CD   CG    111.60  3.000
 DZF  OE1   CD   CG    125.16  3.000
 DZF  HOE2  OE2  CD    110.07  3.000
 DZF  O2    CT   O1    124.02  3.000
 DZF  O2    CT   CA    112.95  3.000
 DZF  O1    CT   CA    122.95  3.000
 DZF  HO2   O2   CT    110.03  3.000
 DZF  N     C    O     120.83  3.000
 DZF  N     C    C11   116.89  3.000
 DZF  O     C    C11   122.28  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
 DZF  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 DZF  CONST_02  C4    C4A  C8A  N1      0.00   0.0  0
 DZF  CONST_03  C5    C4A  C8A  N1    180.00   0.0  0
 DZF  CONST_04  C7    N8   C8A  N1    180.00   0.0  0
 DZF  CONST_05  C4A   C8A  N1   C2      0.00   0.0  0
 DZF  CONST_06  N8    C8A  N1   C2    180.00   0.0  0
 DZF  CONST_07  C4A   C4   N3   C2      0.00   0.0  0
 DZF  CONST_08  C8A   N1   C2   N3      0.00   0.0  0
 DZF  CONST_09  C5    C4A  C4   N3    180.00   0.0  0
 DZF  CONST_10  C8A   C4A  C4   N3      0.00   0.0  0
 DZF  CONST_11  C6    C5   C4A  C4    180.00   0.0  0
 DZF  CONST_12  N8    C8A  C4A  C4    180.00   0.0  0
 DZF  CONST_13  C7    C6   C5   C4A     0.00   0.0  0
 DZF  CONST_14  C7    N8   C8A  C4A     0.00   0.0  0
 DZF  CONST_15  N8    C8A  C4A  C5      0.00   0.0  0
 DZF  CONST_16  N8    C7   C6   C5      0.00   0.0  0
 DZF  CONST_17  C8A   C4A  C5   C6      0.00   0.0  0
 DZF  CONST_18  C8A   N8   C7   C6      0.00   0.0  0
 DZF  CONST_19  C14   C13  C12  C11     0.00   0.0  0
 DZF  CONST_20  C14   C15  C16  C11     0.00   0.0  0
 DZF  CONST_21  C15   C16  C11  C12     0.00   0.0  0
 DZF  CONST_22  C15   C14  C13  C12     0.00   0.0  0
 DZF  CONST_23  C16   C11  C12  C13     0.00   0.0  0
 DZF  CONST_24  C16   C15  C14  C13     0.00   0.0  0
 DZF  CONST_25  O4    C4   N3   C2    180.00   0.0  0
 DZF  CONST_26  C8A   N1   C2   NA2   180.00   0.0  0
 DZF  CONST_27  C4    N3   C2   NA2   180.00   0.0  0
 DZF  CONST_28  C5    C4A  C4   O4      0.00   0.0  0
 DZF  CONST_29  C8A   C4A  C4   O4    180.00   0.0  0
 DZF  CONST_30  C9    C6   C5   C4A   180.00   0.0  0
 DZF  CONST_31  C9    C6   C7   N8    180.00   0.0  0
 DZF  CONST_32  C12   C13  C14  N10   180.00   0.0  0
 DZF  CONST_33  C16   C15  C14  N10   180.00   0.0  0
 DZF  CONST_34  C     C11  C12  C13   180.00   0.0  0
 DZF  CONST_35  C     C11  C16  C15   180.00   0.0  0
 DZF  CONST_36  HN1   N1   C2   N3    180.00   0.0  0
 DZF  CONST_37  H5    C5   C4A  C4      0.00   0.0  0
 DZF  CONST_38  H7    C7   C6   C5    180.00   0.0  0
 DZF  CONST_39  H13   C13  C12  C11   180.00   0.0  0
 DZF  CONST_40  H15   C15  C16  C11   180.00   0.0  0
 DZF  CONST_41  H16   C16  C11  C12   180.00   0.0  0
 DZF  CONST_42  H12   C12  C13  C14   180.00   0.0  0
 DZF  CONST_43  C13   C14  N10  C9    180.00   0.0  0
 DZF  CONST_44  C15   C14  N10  C9      0.00   0.0  0
 DZF  CONST_45  HN21  NA2  C2   N1    180.00   0.0  0
 DZF  CONST_46  HN22  NA2  C2   N1      0.00   0.0  0
 DZF  CONST_48  CA    N    C    C11   180.00   0.0  0
 DZF  CONST_50  CA    N    C    O       0.00   0.0  0
 DZF  CONST_51  HO2   O2   CT   CA    180.00   0.0  0
 DZF  CONST_52  HOE2  OE2  CD   CG    180.00   0.0  0
 DZF  Var_01    N10   C9   C6   C5    107.07  30.0  2
 DZF  Var_02    C14   N10  C9   C6    177.58  30.0  3
 DZF  Var_03    O     C    C11  C12    19.87  30.0  2
 DZF  Var_04    CD    CG   CB   CA   -177.80  30.0  3
 DZF  Var_05    OE1   CD   CG   CB      1.56  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 DZF  chir_01  CA  N  CB  CT  negativ

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
 DZF  plan-1  N10   0.020
 DZF  plan-1  C11   0.020
 DZF  plan-1  C12   0.020
 DZF  plan-1  C13   0.020
 DZF  plan-1  C14   0.020
 DZF  plan-1  C15   0.020
 DZF  plan-1  C16   0.020
 DZF  plan-1  H12   0.020
 DZF  plan-1  H13   0.020
 DZF  plan-1  H15   0.020
 DZF  plan-1  H16   0.020
 DZF  plan-1  C     0.020
 DZF  plan-2  CG    0.020
 DZF  plan-2  CD    0.020
 DZF  plan-2  OE1   0.020
 DZF  plan-2  OE2   0.020
 DZF  plan-2  HOE2  0.020
 DZF  plan-3  CA    0.020
 DZF  plan-3  CT    0.020
 DZF  plan-3  O1    0.020
 DZF  plan-3  O2    0.020
 DZF  plan-3  HO2   0.020
 DZF  plan-4  N1    0.020
 DZF  plan-4  C2    0.020
 DZF  plan-4  NA2   0.020
 DZF  plan-4  N3    0.020
 DZF  plan-4  C4    0.020
 DZF  plan-4  O4    0.020
 DZF  plan-4  C4A   0.020
 DZF  plan-4  C5    0.020
 DZF  plan-4  C6    0.020
 DZF  plan-4  C7    0.020
 DZF  plan-4  N8    0.020
 DZF  plan-4  C8A   0.020
 DZF  plan-4  C9    0.020
 DZF  plan-4  HN1   0.020
 DZF  plan-4  H5    0.020
 DZF  plan-4  H7    0.020
 DZF  plan-5  C11   0.020
 DZF  plan-5  O     0.020
 DZF  plan-5  N     0.020
 DZF  plan-5  CA    0.020
 DZF  plan-5  HN    0.020
 DZF  plan-5  C     0.020
 DZF  plan-6  C2    0.020
 DZF  plan-6  NA2   0.020
 DZF  plan-6  HN21  0.020
 DZF  plan-6  HN22  0.020
 DZF  plan-7  C9    0.020
 DZF  plan-7  N10   0.020
 DZF  plan-7  C14   0.020
 DZF  plan-7  HN0   0.020

