# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:47:23 2022
#   Inital geometry file: a 160 line input string
#   Ligand name: N-(3-carboxypropanoyl)-L-valyl-N-[(1R)-2-phenyl-1-phosphonoethyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](NC(=O)CCC(O)=O)C(=O)N1CCC[C@H]1C(=O)N[C@@H](Cc2ccccc2)[P](O)(O)=O
#
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
 1ZG  1ZG  N-(3-carboxypropanoyl)-L-valyl-N-[(1R)-2-phenyl-1-phosphonoethyl]-L-prolinamide  peptide  63  34  .  2019-03-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1ZG
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
 1ZG  C1    C  C      0   0.416  13.8038  47.1115  -0.7945
 1ZG  O1    O  O      0  -0.618  12.9978  47.5364  -1.6464
 1ZG  O2    O  OC    -1  -0.599  15.0390  47.0050  -0.9168
 1ZG  C2    C  CH2    0  -0.582  13.1753  46.6675   0.5439
 1ZG  C3    C  CH2    0  -0.548  14.1723  46.2547   1.6253
 1ZG  C4    C  C      0   0.527  13.4279  45.8310   2.8692
 1ZG  O3    O  O      0  -0.504  12.9624  46.6401   3.6630
 1ZG  N     N  NH1    0  -0.631  13.2723  44.5003   3.0078
 1ZG  CA    C  CH1    0  -0.185  12.4192  43.8918   4.0010
 1ZG  C     C  C      0   0.573  12.9997  42.5140   4.3021
 1ZG  O     O  O      0  -0.498  13.4654  41.8388   3.3895
 1ZG  CB    C  CH1    0  -0.225  10.9520  43.8177   3.5038
 1ZG  CG1   C  CH3    0  -0.664  10.7700  42.9449   2.2661
 1ZG  CG2   C  CH3    0  -0.684   9.9787  43.3959   4.5973
 1ZG  N1    N  NT     0  -0.469  12.9782  42.0610   5.5618
 1ZG  CA1   C  CH1    0  -0.207  13.4472  40.7159   5.8363
 1ZG  C5    C  C      0   0.540  12.5093  39.6681   5.2389
 1ZG  O4    O  O      0  -0.500  11.3079  39.8788   5.1132
 1ZG  CB1   C  CH2    0  -0.476  13.4362  40.6282   7.3711
 1ZG  CG    C  CH2    0  -0.466  12.3917  41.6574   7.7865
 1ZG  CD    C  CH2    0  -0.286  12.5856  42.7759   6.7738
 1ZG  N2    N  NH1    0  -0.604  13.1168  38.5169   4.9545
 1ZG  CA2   C  CH1    0  -0.354  12.4649  37.2426   4.7215
 1ZG  P     P  P      0   1.185  13.0974  36.0634   6.0527
 1ZG  O1P   O  O      0  -0.883  12.5712  34.6832   5.6490
 1ZG  O2P   O  OP    -1  -0.884  12.5115  36.6177   7.3565
 1ZG  CB2   C  CH2    0  -0.511  12.7458  36.7362   3.3037
 1ZG  CG3   C  CR6    0   0.163  12.3217  37.6961   2.2306
 1ZG  CD1   C  CR16   0  -0.310  10.9769  37.8262   1.8820
 1ZG  CD2   C  CR16   0  -0.323  13.2474  38.5101   1.5831
 1ZG  CE1   C  CR16   0  -0.241  10.5701  38.7397   0.9201
 1ZG  CE2   C  CR16   0  -0.239  12.8479  39.4264   0.6172
 1ZG  CZ    C  CR16   0  -0.275  11.5065  39.5455   0.2822
 1ZG  OGG   O  OP    -1  -0.893  14.6222  36.2252   5.9324
 1ZG  H21   H  HCH2   0   0.229  12.5422  47.4782   0.9157
 1ZG  H22   H  HCH2   0   0.230  12.4921  45.8350   0.3389
 1ZG  H31   H  HCH2   0   0.235  14.8096  45.4504   1.2546
 1ZG  H32   H  HCH2   0   0.243  14.8225  47.0940   1.8761
 1ZG  H     H  HNH1   0   0.396  13.6564  43.8893   2.3040
 1ZG  HA    H  HCH1   0   0.277  12.4428  44.5241   4.8898
 1ZG  HB    H  HCH1   0   0.239  10.7091  44.8480   3.2251
 1ZG  HG11  H  HCH3   0   0.226  11.4730  43.1941   1.4705
 1ZG  HG12  H  HCH3   0   0.220  10.8801  41.8841   2.4953
 1ZG  HG13  H  HCH3   0   0.229   9.7652  43.0878   1.8665
 1ZG  HG21  H  HCH3   0   0.230  10.0085  44.0725   5.4528
 1ZG  HG22  H  HCH3   0   0.239   8.9580  43.4060   4.2127
 1ZG  HG23  H  HCH3   0   0.231  10.1840  42.3848   4.9525
 1ZG  HA1   H  HCH1   0   0.277  14.4583  40.5718   5.4465
 1ZG  HB2   H  HCH2   0   0.253  13.2201  39.6182   7.7223
 1ZG  HB3   H  HCH2   0   0.254  14.4178  40.9067   7.7587
 1ZG  HG2   H  HCH2   0   0.244  11.3856  41.2447   7.7009
 1ZG  HG3   H  HCH2   0   0.253  12.5230  42.0079   8.8091
 1ZG  HD2   H  HCH2   0   0.248  13.3813  43.4580   7.0874
 1ZG  HD3   H  HCH2   0   0.263  11.6792  43.3581   6.6326
 1ZG  HN2   H  HNH1   0   0.371  14.0981  38.4308   5.1851
 1ZG  HA2   H  HCH1   0   0.212  11.3893  37.3907   4.8345
 1ZG  HB1   H  HCH2   0   0.217  13.8149  36.5246   3.2109
 1ZG  HB21  H  HCH2   0   0.230  12.2260  35.7839   3.1843
 1ZG  HD1   H  HCR6   0   0.238  10.2386  37.2021   2.3735
 1ZG  HD21  H  HCR6   0   0.236  14.2977  38.4240   1.8373
 1ZG  HE1   H  HCR6   0   0.246   9.5211  38.8219   0.6641
 1ZG  HE2   H  HCR6   0   0.245  13.5868  40.0480   0.1270
 1ZG  HZ    H  HCR6   0   0.245  11.1916  40.2587  -0.4689

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
 1ZG  C1   O1    deloc     1.247  0.020  1.247
 1ZG  C1   O2    deloc     1.246  0.020  1.246
 1ZG  C1   C2    single    1.544  0.020  1.544
 1ZG  C2   C3    single    1.528  0.020  1.528
 1ZG  C2   H21   single    0.970  0.020  1.090
 1ZG  C2   H22   single    0.970  0.020  1.090
 1ZG  C3   C4    single    1.510  0.020  1.510
 1ZG  C3   H31   single    0.970  0.020  1.090
 1ZG  C3   H32   single    0.970  0.020  1.090
 1ZG  C4   O3    double    1.225  0.020  1.225
 1ZG  N    CA    single    1.458  0.019  1.458
 1ZG  N    H     single    0.860  0.020  0.860
 1ZG  CA   C     single    1.525  0.021  1.525
 1ZG  CA   CB    single    1.521  0.033  1.521
 1ZG  CA   HA    single    0.970  0.020  0.970
 1ZG  C    O     double    1.231  0.020  1.231
 1ZG  CB   CG1   single    1.525  0.020  1.525
 1ZG  CB   CG2   single    1.523  0.020  1.523
 1ZG  CB   HB    single    0.970  0.020  1.090
 1ZG  CG1  HG11  single    0.970  0.020  1.090
 1ZG  CG1  HG12  single    0.970  0.020  1.090
 1ZG  CG1  HG13  single    0.970  0.020  1.090
 1ZG  CG2  HG21  single    0.970  0.020  1.090
 1ZG  CG2  HG22  single    0.970  0.020  1.090
 1ZG  CG2  HG23  single    0.970  0.020  1.090
 1ZG  N1   CA1   single    1.451  0.020  1.451
 1ZG  N1   CD    single    1.461  0.020  1.461
 1ZG  CA1  C5    single    1.528  0.020  1.528
 1ZG  CA1  CB1   single    1.537  0.020  1.537
 1ZG  CA1  HA1   single    0.970  0.020  1.090
 1ZG  C5   O4    double    1.226  0.020  1.226
 1ZG  CB1  CG    single    1.524  0.020  1.524
 1ZG  CB1  HB2   single    0.970  0.020  1.090
 1ZG  CB1  HB3   single    0.970  0.020  1.090
 1ZG  CG   CD    single    1.521  0.020  1.521
 1ZG  CG   HG2   single    0.970  0.020  1.090
 1ZG  CG   HG3   single    0.970  0.020  1.090
 1ZG  CD   HD2   single    0.970  0.020  1.090
 1ZG  CD   HD3   single    0.970  0.020  1.090
 1ZG  N2   CA2   single    1.450  0.020  1.450
 1ZG  N2   HN2   single    0.890  0.020  1.040
 1ZG  CA2  P     single    1.888  0.020  1.888
 1ZG  CA2  CB2   single    1.532  0.020  1.532
 1ZG  CA2  HA2   single    0.970  0.020  1.090
 1ZG  P    O1P   deloc     1.531  0.020  1.531
 1ZG  P    O2P   deloc     1.533  0.020  1.533
 1ZG  P    OGG   deloc     1.538  0.020  1.538
 1ZG  CB2  CG3   single    1.501  0.020  1.501
 1ZG  CB2  HB1   single    0.970  0.020  1.090
 1ZG  CB2  HB21  single    0.970  0.020  1.090
 1ZG  CG3  CD1   aromatic  1.395  0.020  1.395
 1ZG  CG3  CD2   aromatic  1.392  0.020  1.392
 1ZG  CD1  CE1   aromatic  1.388  0.020  1.388
 1ZG  CD1  HD1   single    0.930  0.020  1.080
 1ZG  CD2  CE2   aromatic  1.390  0.020  1.390
 1ZG  CD2  HD21  single    0.930  0.020  1.080
 1ZG  CE1  CZ    aromatic  1.390  0.020  1.390
 1ZG  CE1  HE1   single    0.930  0.020  1.080
 1ZG  CE2  CZ    aromatic  1.388  0.020  1.388
 1ZG  CE2  HE2   single    0.930  0.020  1.080
 1ZG  CZ   HZ    single    0.930  0.020  1.080
 1ZG  C4   N     single    1.347  0.020  1.347
 1ZG  C    N1    single    1.339  0.020  1.339
 1ZG  C5   N2    single    1.332  0.020  1.332

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
 1ZG  C2    C1   O2    117.66  3.000
 1ZG  C2    C1   O1    115.28  3.000
 1ZG  O2    C1   O1    127.06  3.000
 1ZG  H22   C2   H21   105.41  3.000
 1ZG  H22   C2   C3    109.51  3.000
 1ZG  H21   C2   C3    109.72  3.000
 1ZG  H22   C2   C1    108.06  3.000
 1ZG  H21   C2   C1    108.49  3.000
 1ZG  C3    C2   C1    115.19  3.000
 1ZG  H32   C3   H31   107.29  3.000
 1ZG  H32   C3   C4    108.68  3.000
 1ZG  H31   C3   C4    111.16  3.000
 1ZG  H32   C3   C2    110.11  3.000
 1ZG  H31   C3   C2    109.87  3.000
 1ZG  C4    C3   C2    109.70  3.000
 1ZG  N     C4   O3    122.81  3.000
 1ZG  N     C4   C3    114.76  3.000
 1ZG  O3    C4   C3    122.38  3.000
 1ZG  H     N    CA    114.00  3.000
 1ZG  H     N    C4    118.88  3.000
 1ZG  CA    N    C4    123.74  3.000
 1ZG  HA    CA   CB    109.00  3.000
 1ZG  HA    CA   C     110.00  3.000
 1ZG  CB    CA   C     110.50  1.500
 1ZG  HA    CA   N     110.00  3.000
 1ZG  CB    CA   N     110.40  1.500
 1ZG  C     CA   N     111.00  2.800
 1ZG  N1    C    O     121.31  3.000
 1ZG  N1    C    CA    119.04  3.000
 1ZG  O     C    CA    120.80  1.700
 1ZG  HB    CB   CG2   107.56  3.000
 1ZG  HB    CB   CG1   107.79  3.000
 1ZG  CG2   CB   CG1   110.35  3.000
 1ZG  HB    CB   CA    104.27  3.000
 1ZG  CG2   CB   CA    112.80  3.000
 1ZG  CG1   CB   CA    113.60  3.000
 1ZG  HG13  CG1  HG12  107.30  3.000
 1ZG  HG13  CG1  HG11  107.26  3.000
 1ZG  HG12  CG1  HG11  108.08  3.000
 1ZG  HG13  CG1  CB    109.40  3.000
 1ZG  HG12  CG1  CB    111.95  3.000
 1ZG  HG11  CG1  CB    112.60  3.000
 1ZG  HG23  CG2  HG22  107.42  3.000
 1ZG  HG23  CG2  HG21  108.32  3.000
 1ZG  HG22  CG2  HG21  107.23  3.000
 1ZG  HG23  CG2  CB    111.72  3.000
 1ZG  HG22  CG2  CB    110.01  3.000
 1ZG  HG21  CG2  CB    111.94  3.000
 1ZG  CD    N1   CA1   112.56  3.000
 1ZG  CD    N1   C     128.27  3.000
 1ZG  CA1   N1   C     119.11  3.000
 1ZG  HA1   CA1  CB1   110.80  3.000
 1ZG  HA1   CA1  C5    109.75  3.000
 1ZG  CB1   CA1  C5    110.29  3.000
 1ZG  HA1   CA1  N1    110.72  3.000
 1ZG  CB1   CA1  N1    103.86  3.000
 1ZG  C5    CA1  N1    111.31  3.000
 1ZG  N2    C5   O4    124.98  3.000
 1ZG  N2    C5   CA1   113.33  3.000
 1ZG  O4    C5   CA1   121.58  3.000
 1ZG  HB3   CB1  HB2   107.46  3.000
 1ZG  HB3   CB1  CG    110.32  3.000
 1ZG  HB2   CB1  CG    113.69  3.000
 1ZG  HB3   CB1  CA1   109.48  3.000
 1ZG  HB2   CB1  CA1   112.06  3.000
 1ZG  CG    CB1  CA1   103.79  3.000
 1ZG  HG3   CG   HG2   107.86  3.000
 1ZG  HG3   CG   CD    111.91  3.000
 1ZG  HG2   CG   CD    110.09  3.000
 1ZG  HG3   CG   CB1   112.99  3.000
 1ZG  HG2   CG   CB1   110.81  3.000
 1ZG  CD    CG   CB1   103.16  3.000
 1ZG  HD3   CD   HD2   108.05  3.000
 1ZG  HD3   CD   CG    111.97  3.000
 1ZG  HD2   CD   CG    111.12  3.000
 1ZG  HD3   CD   N1    112.25  3.000
 1ZG  HD2   CD   N1    110.34  3.000
 1ZG  CG    CD   N1    103.11  3.000
 1ZG  HN2   N2   CA2   113.45  3.000
 1ZG  HN2   N2   C5    117.85  3.000
 1ZG  CA2   N2   C5    126.05  3.000
 1ZG  HA2   CA2  CB2   108.75  3.000
 1ZG  HA2   CA2  P     110.00  3.000
 1ZG  CB2   CA2  P     112.64  3.000
 1ZG  HA2   CA2  N2    107.88  3.000
 1ZG  CB2   CA2  N2    110.90  3.000
 1ZG  P     CA2  N2    106.56  3.000
 1ZG  OGG   P    O2P   114.04  3.000
 1ZG  OGG   P    O1P   114.51  3.000
 1ZG  O2P   P    O1P   114.76  3.000
 1ZG  OGG   P    CA2   102.20  3.000
 1ZG  O2P   P    CA2   104.23  3.000
 1ZG  O1P   P    CA2   105.19  3.000
 1ZG  HB21  CB2  HB1   106.71  3.000
 1ZG  HB21  CB2  CG3   110.19  3.000
 1ZG  HB1   CB2  CG3   109.83  3.000
 1ZG  HB21  CB2  CA2   107.60  3.000
 1ZG  HB1   CB2  CA2   108.77  3.000
 1ZG  CG3   CB2  CA2   113.49  3.000
 1ZG  CD2   CG3  CD1   118.04  3.000
 1ZG  CD2   CG3  CB2   121.23  3.000
 1ZG  CD1   CG3  CB2   120.71  3.000
 1ZG  HD1   CD1  CE1   119.57  3.000
 1ZG  HD1   CD1  CG3   119.29  3.000
 1ZG  CE1   CD1  CG3   121.14  3.000
 1ZG  HD21  CD2  CE2   119.59  3.000
 1ZG  HD21  CD2  CG3   119.25  3.000
 1ZG  CE2   CD2  CG3   121.16  3.000
 1ZG  HE1   CE1  CZ    120.00  3.000
 1ZG  HE1   CE1  CD1   119.86  3.000
 1ZG  CZ    CE1  CD1   120.15  3.000
 1ZG  HE2   CE2  CZ    120.06  3.000
 1ZG  HE2   CE2  CD2   119.79  3.000
 1ZG  CZ    CE2  CD2   120.14  3.000
 1ZG  HZ    CZ   CE2   120.34  3.000
 1ZG  HZ    CZ   CE1   120.29  3.000
 1ZG  CE2   CZ   CE1   119.37  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
 1ZG  CONST_01  CZ    CE1  CD1  CG3     0.00   0.0  0
 1ZG  CONST_02  CZ    CE2  CD2  CG3     0.00   0.0  0
 1ZG  CONST_03  CE2   CD2  CG3  CD1     0.00   0.0  0
 1ZG  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 1ZG  CONST_05  CE1   CD1  CG3  CD2     0.00   0.0  0
 1ZG  CONST_06  CE1   CZ   CE2  CD2     0.00   0.0  0
 1ZG  CONST_07  CE1   CD1  CG3  CB2   180.00   0.0  0
 1ZG  CONST_08  CE2   CD2  CG3  CB2   180.00   0.0  0
 1ZG  CONST_09  HE1   CE1  CD1  CG3   180.00   0.0  0
 1ZG  CONST_10  HE2   CE2  CD2  CG3   180.00   0.0  0
 1ZG  CONST_11  HD21  CD2  CG3  CD1   180.00   0.0  0
 1ZG  CONST_12  HZ    CZ   CE1  CD1   180.00   0.0  0
 1ZG  CONST_13  HD1   CD1  CG3  CD2   180.00   0.0  0
 1ZG  CONST_14  CA1   N1   C    CA    180.00   0.0  0
 1ZG  CONST_15  CD    N1   C    CA      0.00   0.0  0
 1ZG  CONST_16  CA1   N1   C    O       0.00   0.0  0
 1ZG  CONST_17  CD    N1   C    O     180.00   0.0  0
 1ZG  CONST_19  HN2   N2   C5   CA1     0.00   0.0  0
 1ZG  CONST_20  CA    N    C4   C3    180.00   0.0  0
 1ZG  CONST_21  CA    N    C4   O3      0.00   0.0  0
 1ZG  CONST_22  CA2   N2   C5   O4      0.00   0.0  0
 1ZG  CONST_23  H     N    C4   C3      0.00   0.0  0
 1ZG  Var_01    CB1   CG   CD   N1     33.33  30.0  1
 1ZG  Var_02    CG    CD   N1   CA1   -18.40  30.0  1
 1ZG  Var_03    CD    CG   CB1  CA1   -36.34  30.0  1
 1ZG  Var_04    CD1   CG3  CB2  CA2   -76.82  30.0  2
 1ZG  Var_05    C4    C3   C2   C1   -179.36  30.0  3
 1ZG  Var_06    C3    C2   C1   O1   -175.25  30.0  3
 1ZG  Var_07    O3    C4   C3   C2    -79.25  30.0  3
 1ZG  Var_08    HG11  CG1  CB   CA    -50.26  30.0  3
 1ZG  Var_09    HG21  CG2  CB   CA     58.12  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
 1ZG  chir_01  CA   N   C    CB   positiv
 1ZG  chir_02  CA1  N1  CB1  C5   negativ
 1ZG  chir_03  CA2  P   N2   CB2  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
 1ZG  plan-1  CB2   0.020
 1ZG  plan-1  CG3   0.020
 1ZG  plan-1  CD1   0.020
 1ZG  plan-1  CD2   0.020
 1ZG  plan-1  CE1   0.020
 1ZG  plan-1  CE2   0.020
 1ZG  plan-1  CZ    0.020
 1ZG  plan-1  HD1   0.020
 1ZG  plan-1  HD21  0.020
 1ZG  plan-1  HE1   0.020
 1ZG  plan-1  HE2   0.020
 1ZG  plan-1  HZ    0.020
 1ZG  plan-2  CA    0.020
 1ZG  plan-2  C     0.020
 1ZG  plan-2  O     0.020
 1ZG  plan-2  N1    0.020
 1ZG  plan-2  CA1   0.020
 1ZG  plan-2  CD    0.020
 1ZG  plan-3  CA1   0.020
 1ZG  plan-3  C5    0.020
 1ZG  plan-3  O4    0.020
 1ZG  plan-3  N2    0.020
 1ZG  plan-3  CA2   0.020
 1ZG  plan-3  HN2   0.020
 1ZG  plan-4  C3    0.020
 1ZG  plan-4  C4    0.020
 1ZG  plan-4  O3    0.020
 1ZG  plan-4  N     0.020
 1ZG  plan-4  CA    0.020
 1ZG  plan-4  H     0.020
 1ZG  plan-5  C1    0.020
 1ZG  plan-5  O1    0.020
 1ZG  plan-5  O2    0.020
 1ZG  plan-5  C2    0.020

