# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 17:46:21 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@H](CC(C)C)N[P@](O)(=O)CNC(=O)OCc1ccccc1)C(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
 0PJ  0PJ  N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-L-leucine  peptide  64  32  .  2022-03-09  2022-03-09
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0PJ
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
 0PJ  C1    C  C      0   0.749   3.6121   1.5057  -0.9415
 0PJ  O1    O  O      0  -0.524   3.5011   1.6080  -2.1462
 0PJ  O2    O  O2     0  -0.486   4.6655   0.9285  -0.3418
 0PJ  C2    C  CH2    0  -0.231   5.6915   0.4090  -1.1893
 0PJ  C3    C  CR6    0   0.076   6.6094  -0.4053  -0.3273
 0PJ  C4    C  CR16   0  -0.284   6.1651  -1.6050   0.2266
 0PJ  C5    C  CR16   0  -0.242   7.0037  -2.3633   1.0287
 0PJ  C6    C  CR16   0  -0.264   8.3006  -1.9317   1.2854
 0PJ  C7    C  CR16   0  -0.241   8.7517  -0.7407   0.7356
 0PJ  C8    C  CR16   0  -0.303   7.9063   0.0198  -0.0642
 0PJ  N     N  NH1    0  -0.649   2.7502   1.9897  -0.0281
 0PJ  C     C  CH2    0  -0.562   1.3769   2.2984  -0.3768
 0PJ  P     P  P      0   1.233   0.3210   0.7967  -0.1736
 0PJ  O11   O  O      0  -0.813   0.1368   0.5510   1.3070
 0PJ  O21   O  OP    -1  -0.800   0.9289  -0.2810  -1.0394
 0PJ  N1    N  NH1    0  -0.773  -1.1600   1.3575  -0.8090
 0PJ  CA    C  CH1    0  -0.230  -2.4099   1.1013  -0.1377
 0PJ  C9    C  C      0   0.570  -3.0857  -0.1658  -0.6526
 0PJ  O     O  O      0  -0.519  -3.0288  -0.4920  -1.8332
 0PJ  CB    C  CH2    0  -0.388  -3.3908   2.2701  -0.2903
 0PJ  CG    C  CH1    0  -0.220  -2.8714   3.5988   0.2572
 0PJ  CD1   C  CH3    0  -0.652  -3.9205   4.6872   0.0499
 0PJ  CD2   C  CH3    0  -0.674  -2.4834   3.5038   1.7301
 0PJ  N2    N  NH1    0  -0.617  -3.7436  -0.8725   0.2746
 0PJ  CA1   C  CH1    0  -0.199  -4.6642  -1.9335  -0.0540
 0PJ  CC    C  C      0   0.413  -5.9823  -1.4085  -0.6809
 0PJ  O3    O  O      0  -0.589  -6.1881  -0.1833  -0.6609
 0PJ  CB1   C  CH2    0  -0.442  -4.9602  -2.7645   1.1939
 0PJ  CG1   C  CH1    0  -0.223  -3.7340  -3.3434   1.9042
 0PJ  CD11  C  CH3    0  -0.651  -4.1736  -4.1302   3.1352
 0PJ  CD21  C  CH3    0  -0.659  -2.8885  -4.2136   0.9813
 0PJ  OXT   O  OC    -1  -0.620  -6.7328  -2.2930  -1.1420
 0PJ  H21   H  HCH2   0   0.245   5.2537  -0.2116  -1.9739
 0PJ  H22   H  HCH2   0   0.244   6.2360   1.2250  -1.6707
 0PJ  H41   H  HCR6   0   0.254   5.1584  -1.9521   0.0244
 0PJ  H51   H  HCR6   0   0.258   6.6488  -3.2941   1.4517
 0PJ  H61   H  HCR6   0   0.258   8.9554  -2.5238   1.9113
 0PJ  H71   H  HCR6   0   0.257   9.7605  -0.4004   0.9297
 0PJ  H81   H  HCR6   0   0.255   8.2614   0.9516  -0.4879
 0PJ  HN2   H  HNH1   0   0.388   2.9142   1.7302   0.9327
 0PJ  H1    H  HCH2   0   0.247   1.0201   3.1084   0.2622
 0PJ  H2    H  HCH2   0   0.246   1.3453   2.6660  -1.4018
 0PJ  H     H  HNH1   0   0.351  -1.2432   1.2600  -1.8129
 0PJ  HA    H  HCH1   0   0.252  -2.1879   0.9641   0.9216
 0PJ  HB2   H  HCH2   0   0.217  -3.6366   2.3910  -1.3511
 0PJ  HB3   H  HCH2   0   0.216  -4.3305   2.0093   0.2094
 0PJ  HG    H  HCH1   0   0.215  -1.9757   3.8682  -0.3113
 0PJ  HD11  H  HCH3   0   0.210  -4.8417   4.4460   0.5869
 0PJ  HD12  H  HCH3   0   0.221  -3.5686   5.6537   0.4149
 0PJ  HD13  H  HCH3   0   0.221  -4.1755   4.8047  -1.0051
 0PJ  HD21  H  HCH3   0   0.233  -1.6543   2.8134   1.8906
 0PJ  HD22  H  HCH3   0   0.222  -2.1770   4.4780   2.1159
 0PJ  HD23  H  HCH3   0   0.208  -3.3264   3.1595   2.3359
 0PJ  H3    H  HNH1   0   0.383  -3.8173  -0.4673   1.1944
 0PJ  HA1   H  HCH1   0   0.233  -4.1808  -2.5781  -0.7928
 0PJ  HB21  H  HCH2   0   0.221  -5.5240  -2.1519   1.9083
 0PJ  HB31  H  HCH2   0   0.226  -5.6252  -3.5810   0.9021
 0PJ  HG1   H  HCH1   0   0.212  -3.1091  -2.5118   2.2484
 0PJ  HD14  H  HCH3   0   0.222  -4.7524  -3.5081   3.8209
 0PJ  HD15  H  HCH3   0   0.211  -4.7986  -4.9813   2.8533
 0PJ  HD16  H  HCH3   0   0.224  -3.3149  -4.5199   3.6848
 0PJ  HD24  H  HCH3   0   0.230  -2.4892  -3.6478   0.1389
 0PJ  HD25  H  HCH3   0   0.225  -2.0396  -4.6395   1.5190
 0PJ  HD26  H  HCH3   0   0.211  -3.4757  -5.0434   0.5799

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
 0PJ  C1    O1    double    1.214  0.020  1.214
 0PJ  C1    O2    single    1.343  0.020  1.343
 0PJ  O2    C2    single    1.429  0.020  1.429
 0PJ  C2    C3    single    1.500  0.020  1.500
 0PJ  C2    H21   single    0.970  0.020  1.090
 0PJ  C2    H22   single    0.970  0.020  1.090
 0PJ  C3    C4    aromatic  1.394  0.020  1.394
 0PJ  C3    C8    aromatic  1.390  0.020  1.390
 0PJ  C4    C5    aromatic  1.386  0.020  1.386
 0PJ  C4    H41   single    0.930  0.020  1.080
 0PJ  C5    C6    aromatic  1.391  0.020  1.391
 0PJ  C5    H51   single    0.930  0.020  1.080
 0PJ  C6    C7    aromatic  1.387  0.020  1.387
 0PJ  C6    H61   single    0.930  0.020  1.080
 0PJ  C7    C8    aromatic  1.390  0.020  1.390
 0PJ  C7    H71   single    0.930  0.020  1.080
 0PJ  C8    H81   single    0.930  0.020  1.080
 0PJ  N     C     single    1.450  0.020  1.450
 0PJ  N     HN2   single    0.890  0.020  1.040
 0PJ  C     P     single    1.847  0.020  1.847
 0PJ  C     H1    single    0.970  0.020  1.090
 0PJ  C     H2    single    0.970  0.020  1.090
 0PJ  P     O11   deloc     1.512  0.020  1.512
 0PJ  P     O21   deloc     1.510  0.020  1.510
 0PJ  N1    CA    single    1.442  0.020  1.442
 0PJ  N1    H     single    0.890  0.020  1.040
 0PJ  CA    C9    single    1.526  0.020  1.526
 0PJ  CA    CB    single    1.521  0.033  1.521
 0PJ  CA    HA    single    0.970  0.020  0.970
 0PJ  C9    O     double    1.226  0.020  1.226
 0PJ  CB    CG    single    1.528  0.020  1.528
 0PJ  CB    HB2   single    0.970  0.020  1.090
 0PJ  CB    HB3   single    0.970  0.020  1.090
 0PJ  CG    CD1   single    1.526  0.020  1.526
 0PJ  CG    CD2   single    1.526  0.020  1.526
 0PJ  CG    HG    single    0.970  0.020  1.090
 0PJ  CD1   HD11  single    0.970  0.020  1.090
 0PJ  CD1   HD12  single    0.970  0.020  1.090
 0PJ  CD1   HD13  single    0.970  0.020  1.090
 0PJ  CD2   HD21  single    0.970  0.020  1.090
 0PJ  CD2   HD22  single    0.970  0.020  1.090
 0PJ  CD2   HD23  single    0.970  0.020  1.090
 0PJ  N2    CA1   single    1.443  0.020  1.443
 0PJ  N2    H3    single    0.890  0.020  1.040
 0PJ  CA1   CC    single    1.551  0.020  1.551
 0PJ  CA1   CB1   single    1.528  0.020  1.528
 0PJ  CA1   HA1   single    0.970  0.020  1.090
 0PJ  CC    O3    deloc     1.242  0.020  1.242
 0PJ  CC    OXT   deloc     1.248  0.020  1.248
 0PJ  CB1   CG1   single    1.531  0.020  1.531
 0PJ  CB1   HB21  single    0.970  0.020  1.090
 0PJ  CB1   HB31  single    0.970  0.020  1.090
 0PJ  CG1   CD11  single    1.526  0.020  1.526
 0PJ  CG1   CD21  single    1.524  0.020  1.524
 0PJ  CG1   HG1   single    0.970  0.020  1.090
 0PJ  CD11  HD14  single    0.970  0.020  1.090
 0PJ  CD11  HD15  single    0.970  0.020  1.090
 0PJ  CD11  HD16  single    0.970  0.020  1.090
 0PJ  CD21  HD24  single    0.970  0.020  1.090
 0PJ  CD21  HD25  single    0.970  0.020  1.090
 0PJ  CD21  HD26  single    0.970  0.020  1.090
 0PJ  C1    N     single    1.346  0.020  1.346
 0PJ  P     N1    single    1.706  0.020  1.706
 0PJ  C9    N2    single    1.339  0.020  1.339

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
 0PJ  N     C1    O2    110.72  3.000
 0PJ  N     C1    O1    125.77  3.000
 0PJ  O2    C1    O1    123.45  3.000
 0PJ  C2    O2    C1    117.05  3.000
 0PJ  H22   C2    H21   107.92  3.000
 0PJ  H22   C2    C3    110.71  3.000
 0PJ  H21   C2    C3    110.47  3.000
 0PJ  H22   C2    O2    110.34  3.000
 0PJ  H21   C2    O2    110.18  3.000
 0PJ  C3    C2    O2    107.22  3.000
 0PJ  C8    C3    C4    119.04  3.000
 0PJ  C8    C3    C2    120.92  3.000
 0PJ  C4    C3    C2    120.04  3.000
 0PJ  H41   C4    C5    119.65  3.000
 0PJ  H41   C4    C3    119.83  3.000
 0PJ  C5    C4    C3    120.52  3.000
 0PJ  H51   C5    C6    120.04  3.000
 0PJ  H51   C5    C4    119.88  3.000
 0PJ  C6    C5    C4    120.08  3.000
 0PJ  H61   C6    C7    120.15  3.000
 0PJ  H61   C6    C5    120.08  3.000
 0PJ  C7    C6    C5    119.77  3.000
 0PJ  H71   C7    C8    119.87  3.000
 0PJ  H71   C7    C6    120.13  3.000
 0PJ  C8    C7    C6    120.00  3.000
 0PJ  H81   C8    C7    119.75  3.000
 0PJ  H81   C8    C3    119.66  3.000
 0PJ  C7    C8    C3    120.60  3.000
 0PJ  HN2   N     C     115.96  3.000
 0PJ  HN2   N     C1    116.74  3.000
 0PJ  C     N     C1    121.32  3.000
 0PJ  H2    C     H1    106.91  3.000
 0PJ  H2    C     P     111.18  3.000
 0PJ  H1    C     P     110.61  3.000
 0PJ  H2    C     N     109.00  3.000
 0PJ  H1    C     N     109.07  3.000
 0PJ  P     C     N     109.99  3.000
 0PJ  N1    P     O21   111.74  3.000
 0PJ  N1    P     O11   108.20  3.000
 0PJ  O21   P     O11   119.63  3.000
 0PJ  N1    P     C     100.84  3.000
 0PJ  O21   P     C     106.68  3.000
 0PJ  O11   P     C     108.03  3.000
 0PJ  H     N1    CA    111.93  3.000
 0PJ  H     N1    P     114.15  3.000
 0PJ  CA    N1    P     121.38  3.000
 0PJ  HA    CA    CB    109.00  3.000
 0PJ  HA    CA    C9    108.26  3.000
 0PJ  CB    CA    C9    108.43  3.000
 0PJ  HA    CA    N1    107.34  3.000
 0PJ  CB    CA    N1    111.89  3.000
 0PJ  C9    CA    N1    111.99  3.000
 0PJ  N2    C9    O     123.31  3.000
 0PJ  N2    C9    CA    114.99  3.000
 0PJ  O     C9    CA    121.70  3.000
 0PJ  HB3   CB    HB2   105.99  3.000
 0PJ  HB3   CB    CG    109.57  3.000
 0PJ  HB2   CB    CG    109.10  3.000
 0PJ  HB3   CB    CA    108.77  3.000
 0PJ  HB2   CB    CA    108.90  3.000
 0PJ  CG    CB    CA    114.18  3.000
 0PJ  HG    CG    CD2   107.97  3.000
 0PJ  HG    CG    CD1   108.45  3.000
 0PJ  CD2   CG    CD1   110.51  3.000
 0PJ  HG    CG    CB    107.82  3.000
 0PJ  CD2   CG    CB    112.22  3.000
 0PJ  CD1   CG    CB    109.75  3.000
 0PJ  HD13  CD1   HD12  107.65  3.000
 0PJ  HD13  CD1   HD11  107.56  3.000
 0PJ  HD12  CD1   HD11  107.63  3.000
 0PJ  HD13  CD1   CG    111.63  3.000
 0PJ  HD12  CD1   CG    111.38  3.000
 0PJ  HD11  CD1   CG    110.80  3.000
 0PJ  HD23  CD2   HD22  107.55  3.000
 0PJ  HD23  CD2   HD21  107.77  3.000
 0PJ  HD22  CD2   HD21  107.43  3.000
 0PJ  HD23  CD2   CG    110.99  3.000
 0PJ  HD22  CD2   CG    110.91  3.000
 0PJ  HD21  CD2   CG    112.00  3.000
 0PJ  H3    N2    CA1   117.19  3.000
 0PJ  H3    N2    C9    117.12  3.000
 0PJ  CA1   N2    C9    122.96  3.000
 0PJ  HA1   CA1   CB1   108.47  3.000
 0PJ  HA1   CA1   CC    107.59  3.000
 0PJ  CB1   CA1   CC    110.45  3.000
 0PJ  HA1   CA1   N2    107.79  3.000
 0PJ  CB1   CA1   N2    109.72  3.000
 0PJ  CC    CA1   N2    112.67  3.000
 0PJ  OXT   CC    O3    127.23  3.000
 0PJ  OXT   CC    CA1   114.86  3.000
 0PJ  O3    CC    CA1   117.91  3.000
 0PJ  HB31  CB1   HB21  106.17  3.000
 0PJ  HB31  CB1   CG1   109.20  3.000
 0PJ  HB21  CB1   CG1   108.71  3.000
 0PJ  HB31  CB1   CA1   107.82  3.000
 0PJ  HB21  CB1   CA1   109.13  3.000
 0PJ  CG1   CB1   CA1   115.43  3.000
 0PJ  HG1   CG1   CD21  107.89  3.000
 0PJ  HG1   CG1   CD11  107.59  3.000
 0PJ  CD21  CG1   CD11  110.73  3.000
 0PJ  HG1   CG1   CB1   108.40  3.000
 0PJ  CD21  CG1   CB1   112.29  3.000
 0PJ  CD11  CG1   CB1   109.79  3.000
 0PJ  HD16  CD11  HD15  107.56  3.000
 0PJ  HD16  CD11  HD14  107.71  3.000
 0PJ  HD15  CD11  HD14  107.61  3.000
 0PJ  HD16  CD11  CG1   111.33  3.000
 0PJ  HD15  CD11  CG1   110.99  3.000
 0PJ  HD14  CD11  CG1   111.45  3.000
 0PJ  HD26  CD21  HD25  107.62  3.000
 0PJ  HD26  CD21  HD24  107.87  3.000
 0PJ  HD25  CD21  HD24  107.35  3.000
 0PJ  HD26  CD21  CG1   110.96  3.000
 0PJ  HD25  CD21  CG1   110.85  3.000
 0PJ  HD24  CD21  CG1   112.00  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
 0PJ  CONST_01  C6    C5    C4   C3      0.00   0.0  0
 0PJ  CONST_02  C6    C7    C8   C3      0.00   0.0  0
 0PJ  CONST_03  C7    C8    C3   C4      0.00   0.0  0
 0PJ  CONST_04  C7    C6    C5   C4      0.00   0.0  0
 0PJ  CONST_05  C8    C3    C4   C5      0.00   0.0  0
 0PJ  CONST_06  C8    C7    C6   C5      0.00   0.0  0
 0PJ  CONST_07  C5    C4    C3   C2    180.00   0.0  0
 0PJ  CONST_08  C7    C8    C3   C2    180.00   0.0  0
 0PJ  CONST_09  H51   C5    C4   C3    180.00   0.0  0
 0PJ  CONST_10  H71   C7    C8   C3    180.00   0.0  0
 0PJ  CONST_11  H81   C8    C3   C4    180.00   0.0  0
 0PJ  CONST_12  H61   C6    C5   C4    180.00   0.0  0
 0PJ  CONST_13  H41   C4    C5   C6    180.00   0.0  0
 0PJ  CONST_14  CA1   N2    C9   CA    180.00   0.0  0
 0PJ  CONST_15  CA1   N2    C9   O       0.00   0.0  0
 0PJ  CONST_16  H3    N2    C9   CA      0.00   0.0  0
 0PJ  Var_01    C4    C3    C2   O2     68.74  30.0  2
 0PJ  Var_02    C3    C2    O2   C1   -169.30  30.0  3
 0PJ  Var_03    P     C     N    C1     87.91  30.0  3
 0PJ  Var_04    C     N     C1   O1     21.01  30.0  2
 0PJ  Var_05    N     C1    O2   C2   -177.85  30.0  1
 0PJ  Var_06    O11   P     C    N      73.05  30.0  3
 0PJ  Var_07    CA    N1    P    C    -135.05  30.0  3
 0PJ  Var_08    CD1   CG    CB   CA    179.81  30.0  3
 0PJ  Var_09    CD11  CG1   CB1  CA1   179.28  30.0  3
 0PJ  Var_10    HD11  CD1   CG   CB     61.32  30.0  3
 0PJ  Var_11    HD21  CD2   CG   CB     63.65  30.0  3
 0PJ  Var_12    HD14  CD11  CG1  CB1   -57.35  30.0  3
 0PJ  Var_13    HD24  CD21  CG1  CB1    61.95  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
 0PJ  chir_02  CA   N1  C9   CB  positiv
 0PJ  chir_03  CA1  N2  CB1  CC  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
 0PJ  plan-1  C2   0.020
 0PJ  plan-1  C3   0.020
 0PJ  plan-1  C4   0.020
 0PJ  plan-1  C5   0.020
 0PJ  plan-1  C6   0.020
 0PJ  plan-1  C7   0.020
 0PJ  plan-1  C8   0.020
 0PJ  plan-1  H41  0.020
 0PJ  plan-1  H51  0.020
 0PJ  plan-1  H61  0.020
 0PJ  plan-1  H71  0.020
 0PJ  plan-1  H81  0.020
 0PJ  plan-2  CA   0.020
 0PJ  plan-2  C9   0.020
 0PJ  plan-2  O    0.020
 0PJ  plan-2  N2   0.020
 0PJ  plan-2  CA1  0.020
 0PJ  plan-2  H3   0.020
 0PJ  plan-3  CA1  0.020
 0PJ  plan-3  CC   0.020
 0PJ  plan-3  O3   0.020
 0PJ  plan-3  OXT  0.020
 0PJ  plan-4  C1   0.020
 0PJ  plan-4  O1   0.020
 0PJ  plan-4  O2   0.020
 0PJ  plan-4  N    0.020

