# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:32:24 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  50  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  -0.721  -0.8550  -0.3793   7.9479
 DZF  C2    C  CR6    0   0.694   0.0367   0.3714   8.6443
 DZF  NA2   N  NH2    0  -0.816   0.0327   0.2356   9.9680
 DZF  N3    N  N      0  -0.530   0.8740   1.2123   8.0855
 DZF  C4    C  CR6    0   0.444   0.8949   1.3778   6.7382
 DZF  O4    O  OC     0  -0.476   1.6664   2.1616   6.2006
 DZF  C4A   C  CR66   0  -0.222  -0.0468   0.5726   5.9341
 DZF  C5    C  CR16   0  -0.188  -0.1172   0.6330   4.5514
 DZF  C6    C  CR6    0  -0.014  -1.0342  -0.1575   3.8750
 DZF  C7    C  CR16   0  -0.079  -1.8469  -0.9892   4.6411
 DZF  N8    N  N      0  -0.432  -1.8016  -1.0679   5.9628
 DZF  C8A   C  CR66   0   0.529  -0.9181  -0.3032   6.5817
 DZF  C9    C  CH2    0  -0.345  -1.1269  -0.1451   2.3780
 DZF  N10   N  NH1    0  -0.682   0.0692  -0.7266   1.8094
 DZF  C11   C  CR6    0  -0.077   0.7612  -0.9953  -2.3194
 DZF  C12   C  CR16   0  -0.260   1.5384  -1.7015  -1.3972
 DZF  C13   C  CR16   0  -0.332   1.3074  -1.6078  -0.0431
 DZF  C14   C  CR6    0   0.376   0.2623  -0.8117   0.4576
 DZF  C15   C  CR16   0  -0.339  -0.5336  -0.1186  -0.4645
 DZF  C16   C  CR16   0  -0.284  -0.2766  -0.2103  -1.8226
 DZF  O     O  O      0  -0.511   1.6502  -2.1516  -4.1823
 DZF  N     N  NH1    0  -0.640   0.5619  -0.2223  -4.5943
 DZF  CA    C  CH1    0  -0.179   0.8380  -0.2390  -6.0127
 DZF  CB    C  CH2    0  -0.448  -0.0988   0.7307  -6.7345
 DZF  CG    C  CH2    0  -0.576  -1.5719   0.3931  -6.5693
 DZF  CD    C  C      0   0.412  -2.5520   1.2725  -7.3669
 DZF  OE1   O  O      0  -0.608  -2.0807   2.1965  -8.0583
 DZF  OE2   O  OC    -1  -0.634  -3.7616   0.9803  -7.2512
 DZF  CT    C  C      0   0.410   2.3142   0.0972  -6.3424
 DZF  O1    O  O      0  -0.621   2.6818  -0.2158  -7.4934
 DZF  O2    O  OC    -1  -0.603   2.9863   0.6716  -5.4689
 DZF  HN1   H  HNR6   0   0.427  -1.4836  -1.0151   8.4202
 DZF  HN21  H  HNH2   0   0.417   0.7235   0.7286  10.5067
 DZF  HN22  H  HNH2   0   0.420  -0.5342  -0.4472  10.4402
 DZF  H5    H  HCR6   0   0.274   0.5429   1.3002   4.0103
 DZF  H7    H  HCR6   0   0.275  -2.5768  -1.6269   4.1527
 DZF  H91   H  HCH2   0   0.247  -2.0354  -0.6711   2.0579
 DZF  H92   H  HCH2   0   0.259  -1.2246   0.8868   2.0312
 DZF  HN0   H  HNH1   0   0.387   0.4687  -1.4813   2.3459
 DZF  H12   H  HCR6   0   0.251   2.3440  -2.3323  -1.7497
 DZF  H13   H  HCR6   0   0.260   1.9339  -2.1592   0.6483
 DZF  H15   H  HCR6   0   0.271  -1.3703   0.4816  -0.1337
 DZF  H16   H  HCR6   0   0.248  -0.9373   0.3252  -2.4937
 DZF  HN    H  HNH1   0   0.387   0.2918   0.6615  -4.1940
 DZF  HA    H  HCH1   0   0.222   0.6307  -1.2474  -6.3824
 DZF  HB1   H  HCH2   0   0.210   0.0977   1.7507  -6.3868
 DZF  HB2   H  HCH2   0   0.226   0.1655   0.7167  -7.7923
 DZF  HG1   H  HCH2   0   0.218  -1.7403  -0.6517  -6.8558
 DZF  HG2   H  HCH2   0   0.220  -1.8608   0.4425  -5.5138
 DZF  C     C  C      0   0.536   1.0409  -1.1681  -3.7702

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  1.370  0.020  1.370
 DZF  N1   HN1   single    0.860  0.020  1.020
 DZF  C2   NA2   single    1.331  0.020  1.331
 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  1.477  0.020  1.477
 DZF  C4A  C5    aromatic  1.386  0.020  1.386
 DZF  C4A  C8A   aromatic  1.395  0.020  1.395
 DZF  C5   C6    aromatic  1.387  0.020  1.387
 DZF  C5   H5    single    0.930  0.020  1.080
 DZF  C6   C7    aromatic  1.393  0.020  1.393
 DZF  C6   C9    single    1.500  0.020  1.500
 DZF  C7   N8    aromatic  1.325  0.020  1.325
 DZF  C7   H7    single    0.930  0.020  1.080
 DZF  N8   C8A   aromatic  1.322  0.020  1.322
 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    1.368  0.020  1.368
 DZF  N10  HN0   single    0.890  0.020  1.040
 DZF  C11  C12   aromatic  1.398  0.020  1.398
 DZF  C11  C16   aromatic  1.393  0.020  1.393
 DZF  C11  C     single    1.488  0.020  1.488
 DZF  C12  C13   aromatic  1.377  0.020  1.377
 DZF  C12  H12   single    0.930  0.020  1.080
 DZF  C13  C14   aromatic  1.406  0.020  1.406
 DZF  C13  H13   single    0.930  0.020  1.080
 DZF  C14  C15   aromatic  1.401  0.020  1.401
 DZF  C15  C16   aromatic  1.385  0.020  1.385
 DZF  C15  H15   single    0.930  0.020  1.080
 DZF  C16  H16   single    0.930  0.020  1.080
 DZF  C    O     double    1.228  0.020  1.228
 DZF  C    N     single    1.343  0.020  1.343
 DZF  N    CA    single    1.445  0.020  1.445
 DZF  N    HN    single    0.890  0.020  1.040
 DZF  CA   CB    single    1.529  0.020  1.529
 DZF  CA   CT    single    1.550  0.020  1.550
 DZF  CA   HA    single    0.970  0.020  1.090
 DZF  CB   CG    single    1.520  0.020  1.520
 DZF  CB   HB1   single    0.970  0.020  1.090
 DZF  CB   HB2   single    0.970  0.020  1.090
 DZF  CG   CD    single    1.539  0.020  1.539
 DZF  CG   HG1   single    0.970  0.020  1.090
 DZF  CG   HG2   single    0.970  0.020  1.090
 DZF  CD   OE1   deloc     1.247  0.020  1.247
 DZF  CD   OE2   deloc     1.250  0.020  1.250
 DZF  CT   O1    deloc     1.248  0.020  1.248
 DZF  CT   O2    deloc     1.243  0.020  1.243

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   118.18  3.000
 DZF  HN1   N1   C2    121.09  3.000
 DZF  C8A   N1   C2    120.73  3.000
 DZF  N3    C2   NA2   119.41  3.000
 DZF  N3    C2   N1    123.72  3.000
 DZF  NA2   C2   N1    116.86  3.000
 DZF  HN22  NA2  HN21  117.96  3.000
 DZF  HN22  NA2  C2    122.56  3.000
 DZF  HN21  NA2  C2    118.75  3.000
 DZF  C4    N3   C2    120.72  3.000
 DZF  C4A   C4   O4    120.78  3.000
 DZF  C4A   C4   N3    117.64  3.000
 DZF  O4    C4   N3    121.58  3.000
 DZF  C8A   C4A  C5    117.31  3.000
 DZF  C8A   C4A  C4    119.19  3.000
 DZF  C5    C4A  C4    123.49  3.000
 DZF  H5    C5   C6    120.68  3.000
 DZF  H5    C5   C4A   119.62  3.000
 DZF  C6    C5   C4A   119.70  3.000
 DZF  C9    C6   C7    121.20  3.000
 DZF  C9    C6   C5    121.53  3.000
 DZF  C7    C6   C5    117.25  3.000
 DZF  H7    C7   N8    115.92  3.000
 DZF  H7    C7   C6    119.72  3.000
 DZF  N8    C7   C6    124.36  3.000
 DZF  C8A   N8   C7    117.09  3.000
 DZF  N8    C8A  C4A   124.28  3.000
 DZF  N8    C8A  N1    117.74  3.000
 DZF  C4A   C8A  N1    117.98  3.000
 DZF  H92   C9   H91   106.61  3.000
 DZF  H92   C9   N10   109.20  3.000
 DZF  H91   C9   N10   112.16  3.000
 DZF  H92   C9   C6    109.27  3.000
 DZF  H91   C9   C6    109.77  3.000
 DZF  N10   C9   C6    109.75  3.000
 DZF  HN0   N10  C14   115.03  3.000
 DZF  HN0   N10  C9    114.80  3.000
 DZF  C14   N10  C9    122.01  3.000
 DZF  C     C11  C16   123.61  3.000
 DZF  C     C11  C12   118.70  3.000
 DZF  C16   C11  C12   117.63  3.000
 DZF  H12   C12  C13   119.01  3.000
 DZF  H12   C12  C11   119.57  3.000
 DZF  C13   C12  C11   121.42  3.000
 DZF  H13   C13  C14   119.38  3.000
 DZF  H13   C13  C12   119.73  3.000
 DZF  C14   C13  C12   120.90  3.000
 DZF  C15   C14  C13   117.89  3.000
 DZF  C15   C14  N10   122.63  3.000
 DZF  C13   C14  N10   119.47  3.000
 DZF  H15   C15  C16   118.70  3.000
 DZF  H15   C15  C14   120.83  3.000
 DZF  C16   C15  C14   120.46  3.000
 DZF  H16   C16  C15   117.48  3.000
 DZF  H16   C16  C11   120.80  3.000
 DZF  C15   C16  C11   121.69  3.000
 DZF  HN    N    CA    116.84  3.000
 DZF  HN    N    C     118.03  3.000
 DZF  CA    N    C     121.74  3.000
 DZF  HA    CA   CT    107.98  3.000
 DZF  HA    CA   CB    107.99  3.000
 DZF  CT    CA   CB    110.21  3.000
 DZF  HA    CA   N     107.83  3.000
 DZF  CT    CA   N     112.85  3.000
 DZF  CB    CA   N     109.82  3.000
 DZF  HB2   CB   HB1   106.05  3.000
 DZF  HB2   CB   CG    109.72  3.000
 DZF  HB1   CB   CG    110.25  3.000
 DZF  HB2   CB   CA    107.54  3.000
 DZF  HB1   CB   CA    109.31  3.000
 DZF  CG    CB   CA    113.67  3.000
 DZF  HG2   CG   HG1   104.73  3.000
 DZF  HG2   CG   CD    107.80  3.000
 DZF  HG1   CG   CD    108.13  3.000
 DZF  HG2   CG   CB    110.50  3.000
 DZF  HG1   CG   CB    109.39  3.000
 DZF  CD    CG   CB    115.71  3.000
 DZF  OE2   CD   OE1   126.19  3.000
 DZF  OE2   CD   CG    115.77  3.000
 DZF  OE1   CD   CG    118.04  3.000
 DZF  O2    CT   O1    127.21  3.000
 DZF  O2    CT   CA    117.77  3.000
 DZF  O1    CT   CA    114.99  3.000
 DZF  N     C    O     122.35  3.000
 DZF  N     C    C11   116.72  3.000
 DZF  O     C    C11   120.90  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  Var_01    N10   C9   C6   C5     67.84  30.0  2
 DZF  Var_02    C14   N10  C9   C6   -178.42  30.0  3
 DZF  Var_03    O     C    C11  C12    20.31  30.0  2
 DZF  Var_04    CD    CG   CB   CA   -175.37  30.0  3
 DZF  Var_05    OE1   CD   CG   CB     -1.29  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-3  CA    0.020
 DZF  plan-3  CT    0.020
 DZF  plan-3  O1    0.020
 DZF  plan-3  O2    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

