# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 23:29:16 2022
#   Inital geometry file: a 143 line input string
#   Ligand name: N-[(4-{2-[(6R)-2-amino-4-oxo-1,4,5,6,7,8-hexahydropyrido[2,3-d]pyrimidin-6-yl]ethyl}phenyl)carbonyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)C2=C(NC[C@H](CCc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)C2)N1
#
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
 DDF  DDF  'N-[(4-{2-[(6R)-2-amino-4-oxo-1,4,5,6,7,8-hexahydropyrido[2,3-d]pyrimidin-6-yl]ethyl}phenyl)carbonyl]-L-glutamic acid'  ligand  55  32  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DDF
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
 DDF  N1    N  NC1    0  -0.737  23.0388  56.9180  22.8712
 DDF  C2    C  C      0   0.649  23.5172  56.3413  24.0069
 DDF  NA2   N  NH2    0  -0.827  24.8582  56.2305  24.1027
 DDF  N3    N  N      0  -0.527  22.7508  55.8761  24.9436
 DDF  C4    C  C      0   0.403  21.3786  55.9513  24.8098
 DDF  O4    O  OC     0  -0.515  20.6595  55.4940  25.7025
 DDF  C4A   C  C      0  -0.265  20.8293  56.5642  23.6274
 DDF  C5    C  CH2    0  -0.455  19.3463  56.7007  23.4379
 DDF  C6    C  CH1    0  -0.303  19.0161  57.7917  22.4143
 DDF  C7    C  CH2    0  -0.280  19.8821  57.5811  21.1769
 DDF  N8    N  NH1    0  -0.674  21.2838  57.6397  21.5370
 DDF  C8A   C  C      0   0.649  21.6877  57.0306  22.6714
 DDF  C9    C  CH2    0  -0.398  19.1828  59.2037  22.9804
 DDF  C10   C  CH2    0  -0.514  18.0905  59.5772  23.9853
 DDF  C11   C  C      0  -0.047  18.4872  63.6623  25.3185
 DDF  C12   C  C1     0  -0.258  19.0596  62.6201  26.0435
 DDF  C13   C  C1     0  -0.302  18.9377  61.3091  25.6120
 DDF  C14   C  C      0   0.142  18.2211  60.9960  24.4587
 DDF  C15   C  C1     0  -0.294  17.6442  62.0409  23.7415
 DDF  C16   C  C1     0  -0.279  17.7753  63.3557  24.1598
 DDF  O     O  O      0  -0.503  18.7342  65.2650  27.0509
 DDF  N     N  NH1    0  -0.647  18.5413  66.0285  24.9316
 DDF  CA    C  CH1    0  -0.173  18.4783  67.4490  25.2113
 DDF  CB    C  CH2    0  -0.413  19.8797  68.0242  25.4653
 DDF  CG    C  CH2    0  -0.577  19.8912  69.4794  25.9082
 DDF  CD    C  C      0   0.405  21.2623  70.0232  26.3590
 DDF  OE1   O  O      0  -0.623  21.3923  71.2654  26.3295
 DDF  OE2   O  OC    -1  -0.608  22.1169  69.1994  26.7443
 DDF  CT    C  C      0   0.412  17.7899  68.1305  24.0019
 DDF  O1    O  O      0  -0.601  17.9603  67.5739  22.8960
 DDF  O2    O  OC    -1  -0.590  17.1549  69.1733  24.2304
 DDF  HN1   H  HNC1   0   0.425  23.6795  57.2523  22.1648
 DDF  HN21  H  HNH2   0   0.402  25.2217  55.9736  25.0048
 DDF  HN22  H  HNH2   0   0.405  25.4610  56.8066  23.5387
 DDF  H51   H  HCH2   0   0.238  18.9051  55.7526  23.1127
 DDF  H52   H  HCH2   0   0.240  18.8724  56.9253  24.3958
 DDF  H6    H  HCH1   0   0.245  17.9756  57.6725  22.0968
 DDF  H71   H  HCH2   0   0.241  19.6361  56.6172  20.7166
 DDF  H72   H  HCH2   0   0.254  19.6907  58.3565  20.4349
 DDF  HN8   H  HNH1   0   0.398  21.9487  57.7654  20.7907
 DDF  H91   H  HCH2   0   0.232  20.1617  59.3136  23.4558
 DDF  H92   H  HCH2   0   0.231  19.1597  59.9232  22.1559
 DDF  H101  H  HCH2   0   0.240  17.1123  59.4375  23.5169
 DDF  H102  H  HCH2   0   0.246  18.1247  58.9043  24.8455
 DDF  H12   H  H      0   0.251  19.6051  62.8356  26.9530
 DDF  H13   H  H      0   0.247  19.3943  60.5128  26.1884
 DDF  H15   H  H      0   0.248  17.0696  61.8219  22.8490
 DDF  H16   H  H      0   0.251  17.2831  64.1328  23.5874
 DDF  HN    H  HNH1   0   0.387  18.5051  65.8104  23.9460
 DDF  HA    H  HCH1   0   0.216  17.8694  67.6046  26.1064
 DDF  HB1   H  HCH2   0   0.217  20.3593  67.4156  26.2333
 DDF  HB2   H  HCH2   0   0.199  20.4787  67.9002  24.5567
 DDF  HG1   H  HCH2   0   0.211  19.4978  70.1257  25.1221
 DDF  HG2   H  HCH2   0   0.212  19.1970  69.5996  26.7504
 DDF  C     C  C      0   0.511  18.6027  65.0591  25.8472

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
 DDF  N1   C2    aromatic  1.361  0.020  1.361
 DDF  N1   C8A   aromatic  1.370  0.020  1.370
 DDF  N1   HN1   single    0.860  0.020  1.020
 DDF  C2   NA2   single    1.349  0.020  1.349
 DDF  C2   N3    aromatic  1.297  0.020  1.297
 DDF  NA2  HN21  single    0.890  0.020  1.040
 DDF  NA2  HN22  single    0.890  0.020  1.040
 DDF  N3   C4    aromatic  1.381  0.020  1.381
 DDF  C4   O4    double    1.234  0.020  1.234
 DDF  C4   C4A   aromatic  1.441  0.020  1.441
 DDF  C4A  C5    single    1.501  0.020  1.501
 DDF  C4A  C8A   aromatic  1.367  0.020  1.367
 DDF  C5   C6    single    1.532  0.020  1.532
 DDF  C5   H51   single    0.970  0.020  1.090
 DDF  C5   H52   single    0.970  0.020  1.090
 DDF  C6   C7    single    1.525  0.020  1.525
 DDF  C6   C9    single    1.530  0.020  1.530
 DDF  C6   H6    single    0.970  0.020  1.090
 DDF  C7   N8    single    1.448  0.020  1.448
 DDF  C7   H71   single    0.970  0.020  1.090
 DDF  C7   H72   single    0.970  0.020  1.090
 DDF  N8   C8A   single    1.349  0.020  1.349
 DDF  N8   HN8   single    0.890  0.020  1.040
 DDF  C9   C10   single    1.530  0.020  1.530
 DDF  C9   H91   single    0.970  0.020  1.090
 DDF  C9   H92   single    0.970  0.020  1.090
 DDF  C10  C14   single    1.501  0.020  1.501
 DDF  C10  H101  single    0.970  0.020  1.090
 DDF  C10  H102  single    0.970  0.020  1.090
 DDF  C11  C12   aromatic  1.393  0.020  1.393
 DDF  C11  C16   aromatic  1.394  0.020  1.394
 DDF  C11  C     single    1.498  0.020  1.498
 DDF  C12  C13   aromatic  1.386  0.020  1.386
 DDF  C12  H12   single    0.930  0.020  1.080
 DDF  C13  C14   aromatic  1.393  0.020  1.393
 DDF  C13  H13   single    0.930  0.020  1.080
 DDF  C14  C15   aromatic  1.393  0.020  1.393
 DDF  C15  C16   aromatic  1.386  0.020  1.386
 DDF  C15  H15   single    0.930  0.020  1.080
 DDF  C16  H16   single    0.930  0.020  1.080
 DDF  C    O     double    1.228  0.020  1.228
 DDF  C    N     single    1.335  0.020  1.335
 DDF  N    CA    single    1.449  0.020  1.449
 DDF  N    HN    single    0.860  0.020  1.020
 DDF  CA   CB    single    1.536  0.020  1.536
 DDF  CA   CT    single    1.550  0.020  1.550
 DDF  CA   HA    single    0.970  0.020  1.090
 DDF  CB   CG    single    1.521  0.020  1.521
 DDF  CB   HB1   single    0.970  0.020  1.090
 DDF  CB   HB2   single    0.970  0.020  1.090
 DDF  CG   CD    single    1.542  0.020  1.542
 DDF  CG   HG1   single    0.970  0.020  1.090
 DDF  CG   HG2   single    0.970  0.020  1.090
 DDF  CD   OE1   deloc     1.249  0.020  1.249
 DDF  CD   OE2   deloc     1.248  0.020  1.248
 DDF  CT   O1    deloc     1.250  0.020  1.250
 DDF  CT   O2    deloc     1.242  0.020  1.242

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
 DDF  HN1   N1   C8A   119.74  3.000
 DDF  HN1   N1   C2    120.05  3.000
 DDF  C8A   N1   C2    120.21  3.000
 DDF  N3    C2   NA2   120.45  3.000
 DDF  N3    C2   N1    123.18  3.000
 DDF  NA2   C2   N1    116.34  3.000
 DDF  HN22  NA2  HN21  115.61  3.000
 DDF  HN22  NA2  C2    120.56  3.000
 DDF  HN21  NA2  C2    116.35  3.000
 DDF  C4    N3   C2    119.86  3.000
 DDF  C4A   C4   O4    121.95  3.000
 DDF  C4A   C4   N3    118.79  3.000
 DDF  O4    C4   N3    119.26  3.000
 DDF  C8A   C4A  C5    120.07  3.000
 DDF  C8A   C4A  C4    118.67  3.000
 DDF  C5    C4A  C4    121.26  3.000
 DDF  H52   C5   H51   105.29  3.000
 DDF  H52   C5   C6    110.25  3.000
 DDF  H51   C5   C6    109.34  3.000
 DDF  H52   C5   C4A   109.67  3.000
 DDF  H51   C5   C4A   110.90  3.000
 DDF  C6    C5   C4A   111.23  3.000
 DDF  H6    C6   C9    108.14  3.000
 DDF  H6    C6   C7    106.83  3.000
 DDF  C9    C6   C7    111.45  3.000
 DDF  H6    C6   C5    108.73  3.000
 DDF  C9    C6   C5    112.73  3.000
 DDF  C7    C6   C5    108.75  3.000
 DDF  H72   C7   H71   107.47  3.000
 DDF  H72   C7   N8    108.08  3.000
 DDF  H71   C7   N8    110.93  3.000
 DDF  H72   C7   C6    110.75  3.000
 DDF  H71   C7   C6    109.56  3.000
 DDF  N8    C7   C6    110.02  3.000
 DDF  HN8   N8   C8A   118.78  3.000
 DDF  HN8   N8   C7    117.37  3.000
 DDF  C8A   N8   C7    118.71  3.000
 DDF  N8    C8A  C4A   123.64  3.000
 DDF  N8    C8A  N1    117.05  3.000
 DDF  C4A   C8A  N1    119.29  3.000
 DDF  H92   C9   H91   106.27  3.000
 DDF  H92   C9   C10   108.61  3.000
 DDF  H91   C9   C10   109.20  3.000
 DDF  H92   C9   C6    109.00  3.000
 DDF  H91   C9   C6    110.54  3.000
 DDF  C10   C9   C6    112.98  3.000
 DDF  H102  C10  H101  106.65  3.000
 DDF  H102  C10  C14   109.33  3.000
 DDF  H101  C10  C14   109.49  3.000
 DDF  H102  C10  C9    110.13  3.000
 DDF  H101  C10  C9    109.02  3.000
 DDF  C14   C10  C9    112.06  3.000
 DDF  C     C11  C16   122.54  3.000
 DDF  C     C11  C12   118.84  3.000
 DDF  C16   C11  C12   118.55  3.000
 DDF  H12   C12  C13   119.64  3.000
 DDF  H12   C12  C11   119.71  3.000
 DDF  C13   C12  C11   120.65  3.000
 DDF  H13   C13  C14   119.45  3.000
 DDF  H13   C13  C12   119.50  3.000
 DDF  C14   C13  C12   121.04  3.000
 DDF  C15   C14  C13   118.09  3.000
 DDF  C15   C14  C10   120.70  3.000
 DDF  C13   C14  C10   121.20  3.000
 DDF  H15   C15  C16   119.37  3.000
 DDF  H15   C15  C14   119.49  3.000
 DDF  C16   C15  C14   121.14  3.000
 DDF  H16   C16  C15   118.55  3.000
 DDF  H16   C16  C11   120.89  3.000
 DDF  C15   C16  C11   120.52  3.000
 DDF  HN    N    CA    113.48  3.000
 DDF  HN    N    C     120.94  3.000
 DDF  CA    N    C     125.56  3.000
 DDF  HA    CA   CT    109.20  3.000
 DDF  HA    CA   CB    108.62  3.000
 DDF  CT    CA   CB    111.70  3.000
 DDF  HA    CA   N     108.75  3.000
 DDF  CT    CA   N     107.44  3.000
 DDF  CB    CA   N     111.06  3.000
 DDF  HB2   CB   HB1   106.29  3.000
 DDF  HB2   CB   CG    110.22  3.000
 DDF  HB1   CB   CG    108.98  3.000
 DDF  HB2   CB   CA    108.63  3.000
 DDF  HB1   CB   CA    107.98  3.000
 DDF  CG    CB   CA    114.41  3.000
 DDF  HG2   CG   HG1   105.06  3.000
 DDF  HG2   CG   CD    107.41  3.000
 DDF  HG1   CG   CD    108.79  3.000
 DDF  HG2   CG   CB    108.87  3.000
 DDF  HG1   CG   CB    110.75  3.000
 DDF  CD    CG   CB    115.41  3.000
 DDF  OE2   CD   OE1   126.32  3.000
 DDF  OE2   CD   CG    117.79  3.000
 DDF  OE1   CD   CG    115.86  3.000
 DDF  O2    CT   O1    127.33  3.000
 DDF  O2    CT   CA    116.92  3.000
 DDF  O1    CT   CA    115.73  3.000
 DDF  N     C    O     123.73  3.000
 DDF  N     C    C11   115.57  3.000
 DDF  O     C    C11   120.70  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
 DDF  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 DDF  CONST_02  C4    C4A  C8A  N1      0.00   0.0  0
 DDF  CONST_03  C4A   C8A  N1   C2      0.00   0.0  0
 DDF  CONST_04  C4A   C4   N3   C2      0.00   0.0  0
 DDF  CONST_05  C8A   N1   C2   N3      0.00   0.0  0
 DDF  CONST_06  C8A   C4A  C4   N3      0.00   0.0  0
 DDF  CONST_07  C14   C13  C12  C11     0.00   0.0  0
 DDF  CONST_08  C14   C15  C16  C11     0.00   0.0  0
 DDF  CONST_09  C15   C16  C11  C12     0.00   0.0  0
 DDF  CONST_10  C15   C14  C13  C12     0.00   0.0  0
 DDF  CONST_11  C16   C11  C12  C13     0.00   0.0  0
 DDF  CONST_12  C16   C15  C14  C13     0.00   0.0  0
 DDF  CONST_13  O4    C4   N3   C2    180.00   0.0  0
 DDF  CONST_14  C8A   N1   C2   NA2   180.00   0.0  0
 DDF  CONST_15  C4    N3   C2   NA2   180.00   0.0  0
 DDF  CONST_16  C5    C4A  C4   O4      0.00   0.0  0
 DDF  CONST_17  C8A   C4A  C4   O4    180.00   0.0  0
 DDF  CONST_18  C12   C13  C14  C10   180.00   0.0  0
 DDF  CONST_19  C16   C15  C14  C10   180.00   0.0  0
 DDF  CONST_20  C     C11  C12  C13   180.00   0.0  0
 DDF  CONST_21  C     C11  C16  C15   180.00   0.0  0
 DDF  CONST_22  HN1   N1   C2   N3    180.00   0.0  0
 DDF  CONST_23  H13   C13  C12  C11   180.00   0.0  0
 DDF  CONST_24  H15   C15  C16  C11   180.00   0.0  0
 DDF  CONST_25  H16   C16  C11  C12   180.00   0.0  0
 DDF  CONST_26  H12   C12  C13  C14   180.00   0.0  0
 DDF  CONST_27  HN21  NA2  C2   N1    180.00   0.0  0
 DDF  CONST_29  CA    N    C    C11   180.00   0.0  0
 DDF  CONST_30  HN    N    C    C11     0.00   0.0  0
 DDF  CONST_31  CA    N    C    O       0.00   0.0  0
 DDF  Var_01    C7    N8   C8A  N1    169.72  30.0  1
 DDF  Var_02    C6    C5   C4A  C4    159.35  30.0  1
 DDF  Var_03    C8A   N8   C7   C6     41.81  30.0  1
 DDF  Var_04    C14   C10  C9   C6   -176.22  30.0  3
 DDF  Var_05    C13   C14  C10  C9    -92.65  30.0  2
 DDF  Var_06    O     C    C11  C12   -26.35  30.0  2
 DDF  Var_07    CD    CG   CB   CA    171.80  30.0  3
 DDF  Var_08    OE1   CD   CG   CB    158.82  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
 DDF  chir_01  C6  C5  C7  C9  positiv
 DDF  chir_02  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
 DDF  plan-1  C10   0.020
 DDF  plan-1  C11   0.020
 DDF  plan-1  C12   0.020
 DDF  plan-1  C13   0.020
 DDF  plan-1  C14   0.020
 DDF  plan-1  C15   0.020
 DDF  plan-1  C16   0.020
 DDF  plan-1  H12   0.020
 DDF  plan-1  H13   0.020
 DDF  plan-1  H15   0.020
 DDF  plan-1  H16   0.020
 DDF  plan-1  C     0.020
 DDF  plan-2  CA    0.020
 DDF  plan-2  CT    0.020
 DDF  plan-2  O1    0.020
 DDF  plan-2  O2    0.020
 DDF  plan-3  C11   0.020
 DDF  plan-3  O     0.020
 DDF  plan-3  N     0.020
 DDF  plan-3  CA    0.020
 DDF  plan-3  HN    0.020
 DDF  plan-3  C     0.020
 DDF  plan-4  C2    0.020
 DDF  plan-4  NA2   0.020
 DDF  plan-4  HN21  0.020
 DDF  plan-4  HN22  0.020
 DDF  plan-5  N1    0.020
 DDF  plan-5  C2    0.020
 DDF  plan-5  NA2   0.020
 DDF  plan-5  N3    0.020
 DDF  plan-5  C4    0.020
 DDF  plan-5  O4    0.020
 DDF  plan-5  C4A   0.020
 DDF  plan-5  C5    0.020
 DDF  plan-5  N8    0.020
 DDF  plan-5  C8A   0.020
 DDF  plan-5  HN1   0.020
 DDF  plan-6  CG    0.020
 DDF  plan-6  CD    0.020
 DDF  plan-6  OE1   0.020
 DDF  plan-6  OE2   0.020

