# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 06:28:15 2022
#   Inital geometry file: a 156 line input string
#   Ligand name: N-(3-carboxypropanoyl)-L-valyl-N-[(1R)-5-amino-1-phosphonopentyl]-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](CCCCN)[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
 0H8  0H8  N-(3-carboxypropanoyl)-L-valyl-N-[(1R)-5-amino-1-phosphonopentyl]-L-prolinamide  peptide  64  32  .  2019-03-22  2022-03-08
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0H8
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
 0H8  C1    C  C      0   0.417  14.2575  48.0277   0.2925
 0H8  O1    O  O      0  -0.618  13.6207  49.0741   0.0565
 0H8  O2    O  OC    -1  -0.599  15.2742  47.6188  -0.3004
 0H8  C2    C  CH2    0  -0.585  13.7107  47.1707   1.4565
 0H8  C3    C  CH2    0  -0.551  14.3936  45.8162   1.6354
 0H8  C4    C  C      0   0.525  13.8162  45.0467   2.7999
 0H8  O4    O  O      0  -0.497  14.3883  44.9274   3.8769
 0H8  N     N  NH1    0  -0.634  12.5963  44.5178   2.5894
 0H8  CA    C  CH1    0  -0.151  11.8957  43.7823   3.6126
 0H8  C     C  C      0   0.569  12.6842  42.5139   3.9523
 0H8  O     O  O      0  -0.498  13.2062  41.8553   3.0618
 0H8  CB    C  CH1    0  -0.272  10.4615  43.4674   3.1330
 0H8  CG1   C  CH3    0  -0.658  10.3868  42.4945   1.9579
 0H8  CG2   C  CH3    0  -0.679   9.5722  42.9783   4.2703
 0H8  N1    N  NR5    0  -0.467  12.7600  42.1328   5.2377
 0H8  CA1   C  CR15   0  -0.207  13.4199  40.8856   5.5650
 0H8  C5    C  C      0   0.540  12.6177  39.6859   5.0663
 0H8  O3    O  O      0  -0.504  11.3988  39.7314   4.9367
 0H8  CB1   C  CH2    0  -0.478  13.4773  40.8869   7.1016
 0H8  CG    C  CH2    0  -0.466  12.3114  41.7809   7.5042
 0H8  CD    C  CH2    0  -0.284  12.3064  42.8531   6.4242
 0H8  N2    N  NH1    0  -0.604  13.3657  38.6021   4.8651
 0H8  CA2   C  CH1    0  -0.368  12.8790  37.2369   4.7616
 0H8  P     P  P      0   1.182  13.5507  36.3187   6.2659
 0H8  O1P   O  O      0  -0.887  12.8663  37.0046   7.4584
 0H8  O2P   O  OP    -1  -0.886  13.1520  34.8531   6.0630
 0H8  CB2   C  CH2    0  -0.405  13.2662  36.6306   3.4172
 0H8  CG3   C  CH2    0  -0.410  12.7623  37.4202   2.2137
 0H8  CD1   C  CH2    0  -0.419  13.0979  36.7684   0.8786
 0H8  CE    C  CH2    0  -0.269  12.6345  37.5969  -0.3099
 0H8  NZ    N  NH2    0  -0.798  12.9544  36.9404  -1.5704
 0H8  H21   H  HCH2   0   0.233  13.8024  47.7528   2.3803
 0H8  H22   H  HCH2   0   0.226  12.6355  47.0357   1.3067
 0H8  H31   H  HCH2   0   0.240  14.2900  45.2271   0.7206
 0H8  H32   H  HCH2   0   0.244  15.4596  45.9532   1.8120
 0H8  H     H  HNH1   0   0.401  12.1794  44.6000   1.6762
 0H8  HA    H  HCH1   0   0.270  11.8117  44.4231   4.4944
 0H8  HB    H  HCH1   0   0.246  10.0613  44.4314   2.7992
 0H8  HG11  H  HCH3   0   0.231   9.3648  42.4675   1.5785
 0H8  HG12  H  HCH3   0   0.227  11.0332  42.7724   1.1247
 0H8  HG13  H  HCH3   0   0.225  10.6517  41.4813   2.2596
 0H8  HG21  H  HCH3   0   0.240   8.5571  42.8195   3.9044
 0H8  HG22  H  HCH3   0   0.233   9.9225  42.0295   4.6800
 0H8  HG23  H  HCH3   0   0.232   9.5141  43.7042   5.0824
 0H8  HA1   H  HCR5   0   0.273  14.4273  40.8542   5.1414
 0H8  HB2   H  HCH2   0   0.252  13.4173  39.8782   7.5124
 0H8  HB3   H  HCH2   0   0.251  14.4223  41.3238   7.4289
 0H8  HG2   H  HCH2   0   0.242  11.3736  41.2236   7.4833
 0H8  HG3   H  HCH2   0   0.251  12.4250  42.2062   8.5004
 0H8  HD2   H  HCH2   0   0.242  13.0011  43.6628   6.6679
 0H8  HD3   H  HCH2   0   0.259  11.3180  43.2857   6.2924
 0H8  HN2   H  HNH1   0   0.368  14.3470  38.6639   5.1011
 0H8  HA2   H  HCH1   0   0.201  11.7885  37.2725   4.8221
 0H8  HB1   H  HCH2   0   0.191  14.3568  36.5357   3.3619
 0H8  HB21  H  HCH2   0   0.202  12.8724  35.6115   3.3772
 0H8  HG1   H  HCH2   0   0.198  11.6763  37.5464   2.2933
 0H8  HG24  H  HCH2   0   0.204  13.1838  38.4301   2.2381
 0H8  HD1   H  HCH2   0   0.204  14.1816  36.6161   0.8101
 0H8  HD21  H  HCH2   0   0.206  12.6437  35.7742   0.8219
 0H8  HE1   H  HCH2   0   0.207  11.5489  37.7201  -0.2554
 0H8  HE2   H  HCH2   0   0.183  13.0605  38.6075  -0.2222
 0H8  HNZ1  H  HNH2   0   0.342  12.6131  37.5030  -2.3396
 0H8  HNZ2  H  HNH2   0   0.334  13.9608  36.9127  -1.6832
 0H8  O8    O  OP    -1  -0.896  15.0643  36.5846   6.1785

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
 0H8  C1   O1    deloc   1.247  0.020  1.247
 0H8  C1   O2    deloc   1.246  0.020  1.246
 0H8  C1   C2    single  1.545  0.020  1.545
 0H8  C2   C3    single  1.527  0.020  1.527
 0H8  C2   H21   single  0.970  0.020  1.090
 0H8  C2   H22   single  0.970  0.020  1.090
 0H8  C3   C4    single  1.510  0.020  1.510
 0H8  C3   H31   single  0.970  0.020  1.090
 0H8  C3   H32   single  0.970  0.020  1.090
 0H8  C4   O4    double  1.225  0.020  1.225
 0H8  C4   N     single  1.346  0.020  1.346
 0H8  N    CA    single  1.458  0.019  1.458
 0H8  N    H     single  0.860  0.020  0.860
 0H8  CA   C     single  1.525  0.021  1.525
 0H8  CA   CB    single  1.521  0.033  1.521
 0H8  CA   HA    single  0.970  0.020  0.970
 0H8  C    O     double  1.231  0.020  1.231
 0H8  C    N1    single  1.343  0.020  1.343
 0H8  CB   CG1   single  1.527  0.020  1.527
 0H8  CB   CG2   single  1.524  0.020  1.524
 0H8  CB   HB    single  0.970  0.020  1.090
 0H8  CG1  HG11  single  0.970  0.020  1.090
 0H8  CG1  HG12  single  0.970  0.020  1.090
 0H8  CG1  HG13  single  0.970  0.020  1.090
 0H8  CG2  HG21  single  0.970  0.020  1.090
 0H8  CG2  HG22  single  0.970  0.020  1.090
 0H8  CG2  HG23  single  0.970  0.020  1.090
 0H8  N1   CA1   single  1.448  0.020  1.448
 0H8  N1   CD    single  1.460  0.020  1.460
 0H8  CA1  C5    single  1.527  0.020  1.527
 0H8  CA1  CB1   single  1.538  0.020  1.538
 0H8  CA1  HA1   single  0.970  0.020  1.090
 0H8  C5   O3    double  1.227  0.020  1.227
 0H8  C5   N2    single  1.332  0.020  1.332
 0H8  CB1  CG    single  1.523  0.020  1.523
 0H8  CB1  HB2   single  0.970  0.020  1.090
 0H8  CB1  HB3   single  0.970  0.020  1.090
 0H8  CG   CD    single  1.522  0.020  1.522
 0H8  CG   HG2   single  0.970  0.020  1.090
 0H8  CG   HG3   single  0.970  0.020  1.090
 0H8  CD   HD2   single  0.970  0.020  1.090
 0H8  CD   HD3   single  0.970  0.020  1.090
 0H8  N2   CA2   single  1.453  0.020  1.453
 0H8  N2   HN2   single  0.890  0.020  1.040
 0H8  CA2  P     single  1.886  0.020  1.886
 0H8  CA2  CB2   single  1.525  0.020  1.525
 0H8  CA2  HA2   single  0.970  0.020  1.090
 0H8  P    O1P   deloc   1.537  0.020  1.537
 0H8  P    O2P   deloc   1.532  0.020  1.532
 0H8  CB2  CG3   single  1.525  0.020  1.525
 0H8  CB2  HB1   single  0.970  0.020  1.090
 0H8  CB2  HB21  single  0.970  0.020  1.090
 0H8  CG3  CD1   single  1.523  0.020  1.523
 0H8  CG3  HG1   single  0.970  0.020  1.090
 0H8  CG3  HG24  single  0.970  0.020  1.090
 0H8  CD1  CE    single  1.521  0.020  1.521
 0H8  CD1  HD1   single  0.970  0.020  1.090
 0H8  CD1  HD21  single  0.970  0.020  1.090
 0H8  CE   NZ    single  1.457  0.020  1.457
 0H8  CE   HE1   single  0.970  0.020  1.090
 0H8  CE   HE2   single  0.970  0.020  1.090
 0H8  NZ   HNZ1  single  0.890  0.020  1.040
 0H8  NZ   HNZ2  single  0.890  0.020  1.040
 0H8  O8   P     deloc   1.539  0.020  1.539

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
 0H8  C2    C1   O2    117.72  3.000
 0H8  C2    C1   O1    115.29  3.000
 0H8  O2    C1   O1    127.00  3.000
 0H8  H22   C2   H21   105.27  3.000
 0H8  H22   C2   C3    110.24  3.000
 0H8  H21   C2   C3    109.57  3.000
 0H8  H22   C2   C1    108.24  3.000
 0H8  H21   C2   C1    108.11  3.000
 0H8  C3    C2   C1    114.95  3.000
 0H8  H32   C3   H31   107.23  3.000
 0H8  H32   C3   C4    108.26  3.000
 0H8  H31   C3   C4    109.54  3.000
 0H8  H32   C3   C2    110.18  3.000
 0H8  H31   C3   C2    109.73  3.000
 0H8  C4    C3   C2    111.79  3.000
 0H8  N     C4   O4    121.48  3.000
 0H8  N     C4   C3    115.21  3.000
 0H8  O4    C4   C3    123.28  3.000
 0H8  H     N    CA    114.00  3.000
 0H8  H     N    C4    119.00  3.000
 0H8  CA    N    C4    121.99  3.000
 0H8  HA    CA   CB    109.00  3.000
 0H8  HA    CA   C     110.00  3.000
 0H8  CB    CA   C     110.50  1.500
 0H8  HA    CA   N     110.00  3.000
 0H8  CB    CA   N     110.40  1.500
 0H8  C     CA   N     111.00  2.800
 0H8  N1    C    O     121.30  3.000
 0H8  N1    C    CA    118.45  3.000
 0H8  O     C    CA    120.80  1.700
 0H8  HB    CB   CG2   107.25  3.000
 0H8  HB    CB   CG1   107.95  3.000
 0H8  CG2   CB   CG1   109.94  3.000
 0H8  HB    CB   CA    104.73  3.000
 0H8  CG2   CB   CA    112.05  3.000
 0H8  CG1   CB   CA    114.46  3.000
 0H8  HG13  CG1  HG12  107.73  3.000
 0H8  HG13  CG1  HG11  107.53  3.000
 0H8  HG12  CG1  HG11  107.22  3.000
 0H8  HG13  CG1  CB    111.55  3.000
 0H8  HG12  CG1  CB    113.36  3.000
 0H8  HG11  CG1  CB    109.22  3.000
 0H8  HG23  CG2  HG22  108.43  3.000
 0H8  HG23  CG2  HG21  107.28  3.000
 0H8  HG22  CG2  HG21  107.34  3.000
 0H8  HG23  CG2  CB    111.90  3.000
 0H8  HG22  CG2  CB    111.83  3.000
 0H8  HG21  CG2  CB    109.84  3.000
 0H8  CD    N1   CA1   112.50  3.000
 0H8  CD    N1   C     128.34  3.000
 0H8  CA1   N1   C     119.10  3.000
 0H8  HA1   CA1  CB1   110.66  3.000
 0H8  HA1   CA1  C5    109.57  3.000
 0H8  CB1   CA1  C5    110.28  3.000
 0H8  HA1   CA1  N1    110.92  3.000
 0H8  CB1   CA1  N1    104.01  3.000
 0H8  C5    CA1  N1    111.31  3.000
 0H8  N2    C5   O3    124.91  3.000
 0H8  N2    C5   CA1   113.17  3.000
 0H8  O3    C5   CA1   121.83  3.000
 0H8  HB3   CB1  HB2   107.75  3.000
 0H8  HB3   CB1  CG    110.39  3.000
 0H8  HB2   CB1  CG    113.64  3.000
 0H8  HB3   CB1  CA1   109.41  3.000
 0H8  HB2   CB1  CA1   111.94  3.000
 0H8  CG    CB1  CA1   103.66  3.000
 0H8  HG3   CG   HG2   107.86  3.000
 0H8  HG3   CG   CD    111.98  3.000
 0H8  HG2   CG   CD    110.08  3.000
 0H8  HG3   CG   CB1   113.03  3.000
 0H8  HG2   CG   CB1   110.67  3.000
 0H8  CD    CG   CB1   103.20  3.000
 0H8  HD3   CD   HD2   108.05  3.000
 0H8  HD3   CD   CG    111.68  3.000
 0H8  HD2   CD   CG    111.17  3.000
 0H8  HD3   CD   N1    112.35  3.000
 0H8  HD2   CD   N1    110.40  3.000
 0H8  CG    CD   N1    103.18  3.000
 0H8  HN2   N2   CA2   113.52  3.000
 0H8  HN2   N2   C5    117.39  3.000
 0H8  CA2   N2   C5    125.95  3.000
 0H8  HA2   CA2  CB2   108.37  3.000
 0H8  HA2   CA2  P     109.10  3.000
 0H8  CB2   CA2  P     114.78  3.000
 0H8  HA2   CA2  N2    107.44  3.000
 0H8  CB2   CA2  N2    110.57  3.000
 0H8  P     CA2  N2    106.34  3.000
 0H8  O8    P    O2P   114.43  3.000
 0H8  O8    P    O1P   113.89  3.000
 0H8  O2P   P    O1P   114.44  3.000
 0H8  O8    P    CA2   102.76  3.000
 0H8  O2P   P    CA2   105.51  3.000
 0H8  O1P   P    CA2   104.07  3.000
 0H8  HB21  CB2  HB1   106.01  3.000
 0H8  HB21  CB2  CG3   109.56  3.000
 0H8  HB1   CB2  CG3   109.50  3.000
 0H8  HB21  CB2  CA2   108.15  3.000
 0H8  HB1   CB2  CA2   109.36  3.000
 0H8  CG3   CB2  CA2   113.95  3.000
 0H8  HG24  CG3  HG1   105.88  3.000
 0H8  HG24  CG3  CD1   109.24  3.000
 0H8  HG1   CG3  CD1   109.34  3.000
 0H8  HG24  CG3  CB2   109.45  3.000
 0H8  HG1   CG3  CB2   109.24  3.000
 0H8  CD1   CG3  CB2   113.41  3.000
 0H8  HD21  CD1  HD1   106.30  3.000
 0H8  HD21  CD1  CE    109.13  3.000
 0H8  HD1   CD1  CE    109.15  3.000
 0H8  HD21  CD1  CG3   110.04  3.000
 0H8  HD1   CD1  CG3   109.39  3.000
 0H8  CE    CD1  CG3   112.62  3.000
 0H8  HE2   CE   HE1   106.07  3.000
 0H8  HE2   CE   NZ    113.44  3.000
 0H8  HE1   CE   NZ    108.17  3.000
 0H8  HE2   CE   CD1   108.67  3.000
 0H8  HE1   CE   CD1   108.96  3.000
 0H8  NZ    CE   CD1   111.33  3.000
 0H8  HNZ2  NZ   HNZ1  105.40  3.000
 0H8  HNZ2  NZ   CE    109.07  3.000
 0H8  HNZ1  NZ   CE    109.45  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
 0H8  CONST_01  CA1   N1   C    CA    180.00   0.0  0
 0H8  CONST_02  CD    N1   C    CA      0.00   0.0  0
 0H8  CONST_03  CA1   N1   C    O       0.00   0.0  0
 0H8  CONST_04  CD    N1   C    O     180.00   0.0  0
 0H8  CONST_06  HN2   N2   C5   CA1     0.00   0.0  0
 0H8  CONST_07  CA    N    C4   C3    180.00   0.0  0
 0H8  CONST_08  CA    N    C4   O4      0.00   0.0  0
 0H8  CONST_09  CA2   N2   C5   O3      0.00   0.0  0
 0H8  CONST_10  H     N    C4   C3      0.00   0.0  0
 0H8  Var_01    CB1   CG   CD   N1     33.10  30.0  1
 0H8  Var_02    CG    CD   N1   CA1   -17.95  30.0  1
 0H8  Var_03    C4    C3   C2   C1    179.33  30.0  3
 0H8  Var_04    C3    C2   C1   O1    173.21  30.0  3
 0H8  Var_05    O4    C4   C3   C2   -104.50  30.0  3
 0H8  Var_06    CD1   CG3  CB2  CA2  -177.22  30.0  3
 0H8  Var_07    CE    CD1  CG3  CB2  -177.80  30.0  3
 0H8  Var_08    NZ    CE   CD1  CG3  -179.29  30.0  3
 0H8  Var_09    HG11  CG1  CB   CA   -170.18  30.0  3
 0H8  Var_10    HG21  CG2  CB   CA    176.91  30.0  3
 0H8  Var_11    HNZ1  NZ   CE   CD1   178.54  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
 0H8  chir_01  CA   N   C   CB   positiv
 0H8  chir_02  CA1  N1  C5  CB1  positiv
 0H8  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
 0H8  plan-1  C3   0.020
 0H8  plan-1  C4   0.020
 0H8  plan-1  O4   0.020
 0H8  plan-1  N    0.020
 0H8  plan-1  CA   0.020
 0H8  plan-1  H    0.020
 0H8  plan-2  CA   0.020
 0H8  plan-2  C    0.020
 0H8  plan-2  O    0.020
 0H8  plan-2  N1   0.020
 0H8  plan-2  CA1  0.020
 0H8  plan-2  CD   0.020
 0H8  plan-3  CA1  0.020
 0H8  plan-3  C5   0.020
 0H8  plan-3  O3   0.020
 0H8  plan-3  N2   0.020
 0H8  plan-3  CA2  0.020
 0H8  plan-3  HN2  0.020
 0H8  plan-4  C1   0.020
 0H8  plan-4  O1   0.020
 0H8  plan-4  O2   0.020
 0H8  plan-4  C2   0.020

