# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 23:02:11 2022
#   Inital geometry file: a 160 line input string
#   Ligand name: N-(3-carboxypropanoyl)-L-valyl-N-[(1S)-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
 VPF  VPF  N-(3-carboxypropanoyl)-L-valyl-N-[(1S)-2-phenyl-1-phosphonoethyl]-L-prolinamide  peptide  63  34  .  2019-03-22  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VPF
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
 VPF  C1    C  C      0   0.413  13.7034  48.4663  -0.0110
 VPF  O1    O  O      0  -0.616  12.9996  49.2015  -0.7318
 VPF  O2    O  OC    -1  -0.604  14.9319  48.2769  -0.1097
 VPF  C2    C  CH2    0  -0.575  12.9648  47.7543   1.1425
 VPF  C3    C  CH2    0  -0.560  13.6927  46.5445   1.7128
 VPF  C4    C  C      0   0.548  12.9858  45.9655   2.9163
 VPF  O3    O  O      0  -0.503  12.7324  46.6402   3.9069
 VPF  N     N  NH1    0  -0.641  12.6665  44.6602   2.8230
 VPF  CA    C  CH1    0  -0.178  12.0173  43.9170   3.8779
 VPF  C     C  C      0   0.569  12.7272  42.5712   3.9746
 VPF  O     O  O      0  -0.506  12.9345  41.9234   2.9515
 VPF  CB    C  CH1    0  -0.223  10.4944  43.7847   3.6511
 VPF  CG1   C  CH3    0  -0.682  10.1040  43.1437   2.3243
 VPF  CG2   C  CH3    0  -0.677   9.8179  43.0735   4.8179
 VPF  N1    N  NT     0  -0.463  13.1132  42.1363   5.1838
 VPF  CA1   C  CH1    0  -0.243  13.9553  40.9451   5.3306
 VPF  C5    C  C      0   0.563  13.1441  39.6540   5.5475
 VPF  O4    O  O      0  -0.501  13.4033  38.9017   6.4806
 VPF  CB1   C  CH2    0  -0.450  14.8157  41.2978   6.5352
 VPF  CG    C  CH2    0  -0.487  13.8471  42.0658   7.4236
 VPF  CD    C  CH2    0  -0.287  13.0624  42.9138   6.4292
 VPF  P     P  P      0   1.212   9.7109  38.6358   3.8364
 VPF  O1P   O  O      0  -0.872  10.0469  39.5921   2.6785
 VPF  CA2   C  CH1    0  -0.361  11.3848  38.2087   4.6015
 VPF  CB2   C  CH2    0  -0.499  12.1612  37.0519   3.9500
 VPF  CG3   C  CR6    0   0.137  12.7115  37.3416   2.5836
 VPF  CD2   C  CR16   0  -0.322  14.0015  37.8461   2.4299
 VPF  CE2   C  CR16   0  -0.243  14.5207  38.1221   1.1704
 VPF  CZ    C  CR16   0  -0.275  13.7548  37.8879   0.0367
 VPF  CE1   C  CR16   0  -0.248  12.4666  37.3834   0.1759
 VPF  CD1   C  CR16   0  -0.285  11.9496  37.1229   1.4368
 VPF  N2    N  NH1    0  -0.632  12.1879  39.4157   4.6483
 VPF  H21   H  HCH2   0   0.230  12.8061  48.4901   1.9380
 VPF  H22   H  HCH2   0   0.220  11.9661  47.4643   0.8049
 VPF  H31   H  HCH2   0   0.235  13.8271  45.7872   0.9374
 VPF  H32   H  HCH2   0   0.251  14.6941  46.8402   2.0334
 VPF  H     H  HNH1   0   0.397  12.8946  44.1633   1.9765
 VPF  HA    H  HCH1   0   0.280  12.1475  44.4936   4.7928
 VPF  HB    H  HCH1   0   0.235  10.1383  44.8203   3.6398
 VPF  HG11  H  HCH3   0   0.223   9.0351  43.2884   2.1584
 VPF  HG12  H  HCH3   0   0.218  10.6235  43.5955   1.4784
 VPF  HG13  H  HCH3   0   0.235  10.2899  42.0700   2.3178
 VPF  HG21  H  HCH3   0   0.238   8.7351  43.0864   4.6888
 VPF  HG22  H  HCH3   0   0.220  10.1189  42.0265   4.8936
 VPF  HG23  H  HCH3   0   0.229  10.0383  43.5604   5.7690
 VPF  HA1   H  HCH1   0   0.291  14.5554  40.8103   4.4268
 VPF  HB2   H  HCH2   0   0.256  15.2470  40.4239   7.0161
 VPF  HB3   H  HCH2   0   0.246  15.6347  41.9452   6.2142
 VPF  HG2   H  HCH2   0   0.245  13.1842  41.3741   7.9456
 VPF  HG3   H  HCH2   0   0.256  14.3403  42.6830   8.1730
 VPF  HD2   H  HCH2   0   0.253  13.5438  43.8842   6.2900
 VPF  HD3   H  HCH2   0   0.263  12.0366  43.0873   6.7525
 VPF  HA2   H  HCH1   0   0.209  11.1827  37.8996   5.6303
 VPF  HB1   H  HCH2   0   0.219  12.9916  36.7720   4.6057
 VPF  HB21  H  HCH2   0   0.227  11.4965  36.1883   3.9072
 VPF  HD21  H  HCR6   0   0.236  14.6146  38.0125   3.3086
 VPF  HE2   H  HCR6   0   0.243  15.5262  38.5132   1.0762
 VPF  HZ    H  HCR6   0   0.243  14.1580  38.0931  -0.9470
 VPF  HE1   H  HCR6   0   0.241  11.8616  37.1981  -0.7032
 VPF  HD1   H  HCR6   0   0.230  10.9364  36.7577   1.5488
 VPF  HN2   H  HNH1   0   0.386  12.0781  40.0348   3.8569
 VPF  O2P   O  OP    -1  -0.888   8.9560  39.3130   4.9876
 VPF  OGG   O  OP    -1  -0.875   9.1210  37.2889   3.4007

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
 VPF  C1   O1    deloc     1.247  0.020  1.247
 VPF  C1   O2    deloc     1.247  0.020  1.247
 VPF  C1   C2    single    1.544  0.020  1.544
 VPF  C2   C3    single    1.523  0.020  1.523
 VPF  C3   C4    single    1.511  0.020  1.511
 VPF  C4   O3    double    1.225  0.020  1.225
 VPF  C4   N     single    1.347  0.020  1.347
 VPF  N    CA    single    1.458  0.019  1.458
 VPF  CA   C     single    1.525  0.021  1.525
 VPF  CA   CB    single    1.521  0.033  1.521
 VPF  C    O     double    1.231  0.020  1.231
 VPF  C    N1    single    1.342  0.020  1.342
 VPF  CB   CG1   single    1.524  0.020  1.524
 VPF  CB   CG2   single    1.525  0.020  1.525
 VPF  N1   CA1   single    1.466  0.020  1.466
 VPF  N1   CD    single    1.469  0.020  1.469
 VPF  CA1  C5    single    1.540  0.020  1.540
 VPF  CA1  CB1   single    1.522  0.020  1.522
 VPF  C5   O4    double    1.226  0.020  1.226
 VPF  C5   N2    single    1.334  0.020  1.334
 VPF  CB1  CG    single    1.522  0.020  1.522
 VPF  CG   CD    single    1.524  0.020  1.524
 VPF  N2   CA2   single    1.451  0.020  1.451
 VPF  CA2  HA2   single    0.970  0.020  1.090
 VPF  CA2  CB2   single    1.538  0.020  1.538
 VPF  CA2  P     single    1.889  0.020  1.889
 VPF  CB2  CG3   single    1.501  0.020  1.501
 VPF  CG3  CD1   aromatic  1.394  0.020  1.394
 VPF  CG3  CD2   aromatic  1.394  0.020  1.394
 VPF  CD1  CE1   aromatic  1.387  0.020  1.387
 VPF  CD2  CE2   aromatic  1.390  0.020  1.390
 VPF  CE1  CZ    aromatic  1.390  0.020  1.390
 VPF  CE2  CZ    aromatic  1.388  0.020  1.388
 VPF  O1P  P     deloc     1.539  0.020  1.539
 VPF  P    O2P   deloc     1.534  0.020  1.534
 VPF  P    OGG   deloc     1.534  0.020  1.534
 VPF  C2   H21   single    0.970  0.020  1.090
 VPF  C2   H22   single    0.970  0.020  1.090
 VPF  C3   H31   single    0.970  0.020  1.090
 VPF  C3   H32   single    0.970  0.020  1.090
 VPF  N    H     single    0.860  0.020  0.860
 VPF  CA   HA    single    0.970  0.020  0.970
 VPF  CB   HB    single    0.970  0.020  1.090
 VPF  CG1  HG11  single    0.970  0.020  1.090
 VPF  CG1  HG12  single    0.970  0.020  1.090
 VPF  CG1  HG13  single    0.970  0.020  1.090
 VPF  CG2  HG21  single    0.970  0.020  1.090
 VPF  CG2  HG22  single    0.970  0.020  1.090
 VPF  CG2  HG23  single    0.970  0.020  1.090
 VPF  CA1  HA1   single    0.970  0.020  1.090
 VPF  CB1  HB2   single    0.970  0.020  1.090
 VPF  CB1  HB3   single    0.970  0.020  1.090
 VPF  CG   HG2   single    0.970  0.020  1.090
 VPF  CG   HG3   single    0.970  0.020  1.090
 VPF  CD   HD2   single    0.970  0.020  1.090
 VPF  CD   HD3   single    0.970  0.020  1.090
 VPF  N2   HN2   single    0.860  0.020  1.020
 VPF  CB2  HB1   single    0.970  0.020  1.090
 VPF  CB2  HB21  single    0.970  0.020  1.090
 VPF  CD1  HD1   single    0.930  0.020  1.080
 VPF  CD2  HD21  single    0.930  0.020  1.080
 VPF  CE1  HE1   single    0.930  0.020  1.080
 VPF  CE2  HE2   single    0.930  0.020  1.080
 VPF  CZ   HZ    single    0.930  0.020  1.080

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
 VPF  C2    C1   O2    117.41  3.000
 VPF  C2    C1   O1    115.71  3.000
 VPF  O2    C1   O1    126.85  3.000
 VPF  H22   C2   H21   105.67  3.000
 VPF  H22   C2   C3    109.97  3.000
 VPF  H21   C2   C3    109.33  3.000
 VPF  H22   C2   C1    109.18  3.000
 VPF  H21   C2   C1    107.59  3.000
 VPF  C3    C2   C1    114.68  3.000
 VPF  H32   C3   H31   106.46  3.000
 VPF  H32   C3   C4    107.39  3.000
 VPF  H31   C3   C4    110.94  3.000
 VPF  H32   C3   C2    109.46  3.000
 VPF  H31   C3   C2    110.11  3.000
 VPF  C4    C3   C2    112.27  3.000
 VPF  N     C4   O3    122.73  3.000
 VPF  N     C4   C3    115.27  3.000
 VPF  O3    C4   C3    121.99  3.000
 VPF  H     N    CA    114.00  3.000
 VPF  H     N    C4    118.84  3.000
 VPF  CA    N    C4    123.68  3.000
 VPF  HA    CA   CB    109.00  3.000
 VPF  HA    CA   C     110.00  3.000
 VPF  CB    CA   C     110.50  1.500
 VPF  HA    CA   N     110.00  3.000
 VPF  CB    CA   N     110.40  1.500
 VPF  C     CA   N     111.00  2.800
 VPF  N1    C    O     122.07  3.000
 VPF  N1    C    CA    118.50  3.000
 VPF  O     C    CA    120.80  1.700
 VPF  HB    CB   CG2   107.74  3.000
 VPF  HB    CB   CG1   107.78  3.000
 VPF  CG2   CB   CG1   110.87  3.000
 VPF  HB    CB   CA    103.95  3.000
 VPF  CG2   CB   CA    111.39  3.000
 VPF  CG1   CB   CA    114.59  3.000
 VPF  HG13  CG1  HG12  108.81  3.000
 VPF  HG13  CG1  HG11  107.27  3.000
 VPF  HG12  CG1  HG11  107.08  3.000
 VPF  HG13  CG1  CB    112.08  3.000
 VPF  HG12  CG1  CB    112.26  3.000
 VPF  HG11  CG1  CB    109.11  3.000
 VPF  HG23  CG2  HG22  108.17  3.000
 VPF  HG23  CG2  HG21  107.36  3.000
 VPF  HG22  CG2  HG21  107.05  3.000
 VPF  HG23  CG2  CB    111.68  3.000
 VPF  HG22  CG2  CB    112.21  3.000
 VPF  HG21  CG2  CB    110.14  3.000
 VPF  CD    N1   CA1   111.41  3.000
 VPF  CD    N1   C     125.62  3.000
 VPF  CA1   N1   C     121.25  3.000
 VPF  HA1   CA1  CB1   111.88  3.000
 VPF  HA1   CA1  C5    107.59  3.000
 VPF  CB1   CA1  C5    112.37  3.000
 VPF  HA1   CA1  N1    109.43  3.000
 VPF  CB1   CA1  N1    102.46  3.000
 VPF  C5    CA1  N1    113.12  3.000
 VPF  N2    C5   O4    123.70  3.000
 VPF  N2    C5   CA1   115.61  3.000
 VPF  O4    C5   CA1   120.67  3.000
 VPF  HB3   CB1  HB2   108.01  3.000
 VPF  HB3   CB1  CG    110.47  3.000
 VPF  HB2   CB1  CG    113.57  3.000
 VPF  HB3   CB1  CA1   109.19  3.000
 VPF  HB2   CB1  CA1   112.85  3.000
 VPF  CG    CB1  CA1   102.66  3.000
 VPF  HG3   CG   HG2   107.77  3.000
 VPF  HG3   CG   CD    111.52  3.000
 VPF  HG2   CG   CD    110.61  3.000
 VPF  HG3   CG   CB1   113.54  3.000
 VPF  HG2   CG   CB1   110.24  3.000
 VPF  CD    CG   CB1   103.15  3.000
 VPF  HD3   CD   HD2   108.14  3.000
 VPF  HD3   CD   CG    112.32  3.000
 VPF  HD2   CD   CG    110.52  3.000
 VPF  HD3   CD   N1    111.62  3.000
 VPF  HD2   CD   N1    110.30  3.000
 VPF  CG    CD   N1    103.93  3.000
 VPF  OGG   P    CA2   104.91  3.000
 VPF  OGG   P    O1P   114.58  3.000
 VPF  CA2   P    O1P   104.58  3.000
 VPF  OGG   P    O2P   114.30  3.000
 VPF  O1P   P    O2P   113.43  3.000
 VPF  CA2   P    O2P   103.40  3.000
 VPF  HA2   CA2  N2    107.90  3.000
 VPF  HA2   CA2  CB2   106.22  3.000
 VPF  N2    CA2  CB2   111.10  3.000
 VPF  CB2   CA2  P     116.47  3.000
 VPF  HA2   CA2  P     106.34  3.000
 VPF  N2    CA2  P     108.39  3.000
 VPF  HB21  CB2  HB1   106.47  3.000
 VPF  HB21  CB2  CG3   109.91  3.000
 VPF  HB1   CB2  CG3   108.46  3.000
 VPF  HB21  CB2  CA2   107.73  3.000
 VPF  HB1   CB2  CA2   108.76  3.000
 VPF  CG3   CB2  CA2   115.18  3.000
 VPF  CD1   CG3  CD2   118.16  3.000
 VPF  CD2   CG3  CB2   120.63  3.000
 VPF  CD1   CG3  CB2   121.21  3.000
 VPF  HD21  CD2  CE2   119.51  3.000
 VPF  HD21  CD2  CG3   119.31  3.000
 VPF  CE2   CD2  CG3   121.17  3.000
 VPF  HE2   CE2  CZ    120.14  3.000
 VPF  HE2   CE2  CD2   119.83  3.000
 VPF  CZ    CE2  CD2   120.03  3.000
 VPF  HZ    CZ   CE1   120.31  3.000
 VPF  HZ    CZ   CE2   120.31  3.000
 VPF  CE1   CZ   CE2   119.38  3.000
 VPF  HE1   CE1  CD1   119.82  3.000
 VPF  HE1   CE1  CZ    119.89  3.000
 VPF  CD1   CE1  CZ    120.29  3.000
 VPF  HD1   CD1  CE1   120.39  3.000
 VPF  HD1   CD1  CG3   118.63  3.000
 VPF  CE1   CD1  CG3   120.97  3.000
 VPF  HN2   N2   CA2   115.10  3.000
 VPF  HN2   N2   C5    119.76  3.000
 VPF  CA2   N2   C5    124.56  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
 VPF  CONST_01  CZ    CE1  CD1  CG3     0.00   0.0  0
 VPF  CONST_02  CZ    CE2  CD2  CG3     0.00   0.0  0
 VPF  CONST_03  CE1   CD1  CG3  CD2     0.00   0.0  0
 VPF  CONST_04  CE1   CZ   CE2  CD2     0.00   0.0  0
 VPF  CONST_05  CD1   CG3  CD2  CE2     0.00   0.0  0
 VPF  CONST_06  CD1   CE1  CZ   CE2     0.00   0.0  0
 VPF  CONST_07  CE1   CD1  CG3  CB2   180.00   0.0  0
 VPF  CONST_08  CE2   CD2  CG3  CB2   180.00   0.0  0
 VPF  CONST_09  HE1   CE1  CD1  CG3   180.00   0.0  0
 VPF  CONST_10  HE2   CE2  CD2  CG3   180.00   0.0  0
 VPF  CONST_11  HD1   CD1  CG3  CD2   180.00   0.0  0
 VPF  CONST_12  HZ    CZ   CE2  CD2   180.00   0.0  0
 VPF  CONST_13  HD21  CD2  CE2  CZ    180.00   0.0  0
 VPF  CONST_14  CA1   N1   C    CA    180.00   0.0  0
 VPF  CONST_15  CD    N1   C    CA      0.00   0.0  0
 VPF  CONST_16  CA1   N1   C    O       0.00   0.0  0
 VPF  CONST_17  CD    N1   C    O     180.00   0.0  0
 VPF  CONST_18  CA2   N2   C5   CA1   180.00   0.0  0
 VPF  CONST_19  HN2   N2   C5   CA1     0.00   0.0  0
 VPF  CONST_20  CA    N    C4   C3    180.00   0.0  0
 VPF  CONST_21  CA    N    C4   O3      0.00   0.0  0
 VPF  CONST_22  CA2   N2   C5   O4      0.00   0.0  0
 VPF  CONST_23  H     N    C4   C3      0.00   0.0  0
 VPF  Var_01    CB1   CG   CD   N1     27.47  30.0  1
 VPF  Var_02    CG    CD   N1   CA1    -4.50  30.0  1
 VPF  Var_03    CD    CG   CB1  CA1   -39.95  30.0  1
 VPF  Var_04    CD1   CG3  CB2  CA2   -87.79  30.0  2
 VPF  Var_05    C4    C3   C2   C1    174.82  30.0  3
 VPF  Var_06    C3    C2   C1   O1    160.86  30.0  3
 VPF  Var_07    O3    C4   C3   C2    -56.39  30.0  3
 VPF  Var_08    HG11  CG1  CB   CA   -167.85  30.0  3
 VPF  Var_09    HG21  CG2  CB   CA    173.91  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
 VPF  chir_01  CA   N   C   CB   positiv
 VPF  chir_02  CA1  N1  C5  CB1  positiv
 VPF  chir_03  CA2  P   N2  CB2  positiv

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
 VPF  plan-1  CB2   0.020
 VPF  plan-1  CG3   0.020
 VPF  plan-1  CD2   0.020
 VPF  plan-1  CE2   0.020
 VPF  plan-1  CZ    0.020
 VPF  plan-1  CE1   0.020
 VPF  plan-1  CD1   0.020
 VPF  plan-1  HD21  0.020
 VPF  plan-1  HE2   0.020
 VPF  plan-1  HZ    0.020
 VPF  plan-1  HE1   0.020
 VPF  plan-1  HD1   0.020
 VPF  plan-2  CA    0.020
 VPF  plan-2  C     0.020
 VPF  plan-2  O     0.020
 VPF  plan-2  N1    0.020
 VPF  plan-2  CA1   0.020
 VPF  plan-2  CD    0.020
 VPF  plan-3  CA1   0.020
 VPF  plan-3  C5    0.020
 VPF  plan-3  O4    0.020
 VPF  plan-3  CA2   0.020
 VPF  plan-3  N2    0.020
 VPF  plan-3  HN2   0.020
 VPF  plan-4  C3    0.020
 VPF  plan-4  C4    0.020
 VPF  plan-4  O3    0.020
 VPF  plan-4  N     0.020
 VPF  plan-4  CA    0.020
 VPF  plan-4  H     0.020
 VPF  plan-5  C1    0.020
 VPF  plan-5  O1    0.020
 VPF  plan-5  O2    0.020
 VPF  plan-5  C2    0.020

