# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 20:40:11 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  66  32  .  2022-03-09  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.767   3.4542   0.8196  -1.0342
 0PJ  O1    O  O     0  -0.515   2.9396   0.3648  -2.0341
 0PJ  O2    O  O2    0  -0.477   4.6392   0.4333  -0.5560
 0PJ  C2    C  CH2   0  -0.240   5.3418  -0.5709  -1.2996
 0PJ  C3    C  CR6   0   0.076   6.6128  -0.8525  -0.5581
 0PJ  C4    C  CR16  0  -0.292   6.6679  -1.8725   0.3871
 0PJ  C5    C  CR16  0  -0.242   7.8379  -2.1180   1.0931
 0PJ  C6    C  CR16  0  -0.261   8.9654  -1.3413   0.8609
 0PJ  C7    C  CR16  0  -0.242   8.9194  -0.3215  -0.0819
 0PJ  C8    C  CR16  0  -0.288   7.7479  -0.0792  -0.7854
 0PJ  N     N  NH1   0  -0.657   2.9262   1.7969  -0.2690
 0PJ  C     C  CH2   0  -0.571   1.5977   2.2992  -0.4882
 0PJ  P     P  P     0   1.307   0.3790   1.3502   0.4847
 0PJ  O11   O  O     0  -0.715   0.5041   1.5016   1.9590
 0PJ  O21   O  OH1   0  -0.749   0.6347  -0.2045   0.1171
 0PJ  N1    N  NH1   0  -0.760  -1.0731   1.8539  -0.1435
 0PJ  CA    C  CH1   0  -0.251  -2.3170   1.2944   0.3351
 0PJ  C9    C  C     0   0.590  -2.6363  -0.0230  -0.3758
 0PJ  O     O  O     0  -0.491  -2.0423  -0.3811  -1.3822
 0PJ  CB    C  CH2   0  -0.413  -3.4687   2.2899   0.1510
 0PJ  CG    C  CH1   0  -0.222  -3.2218   3.6551   0.7925
 0PJ  CD1   C  CH3   0  -0.654  -4.4277   4.5574   0.5516
 0PJ  CD2   C  CH3   0  -0.672  -2.9166   3.5424   2.2821
 0PJ  N2    N  NH1   0  -0.632  -3.6118  -0.7523   0.1866
 0PJ  CA1   C  CH1   0  -0.201  -4.1249  -1.9419  -0.4345
 0PJ  CC    C  C     0   0.555  -4.9504  -1.5813  -1.6614
 0PJ  O3    O  O     0  -0.428  -5.3394  -0.4739  -1.9228
 0PJ  CB1   C  CH2   0  -0.453  -4.9633  -2.7532   0.5586
 0PJ  CG1   C  CH1   0  -0.233  -4.2144  -3.1579   1.8308
 0PJ  CD11  C  CH3   0  -0.653  -5.1539  -3.9475   2.7367
 0PJ  CD21  C  CH3   0  -0.663  -2.9578  -3.9664   1.5274
 0PJ  OXT   O  OH1   0  -0.592  -5.2023  -2.6518  -2.4013
 0PJ  H21   H  HCH2  0   0.249   4.7329  -1.4732  -1.3810
 0PJ  H22   H  HCH2  0   0.249   5.5521  -0.2095  -2.3084
 0PJ  H41   H  HCR6  0   0.255   5.7920  -2.4839   0.5703
 0PJ  H51   H  HCR6  0   0.259   7.8693  -2.9165   1.8227
 0PJ  H61   H  HCR6  0   0.259   9.8790  -1.5325   1.4091
 0PJ  H71   H  HCR6  0   0.258   9.7968   0.2836  -0.2704
 0PJ  H81   H  HCR6  0   0.256   7.7184   0.7148  -1.5222
 0PJ  HN2   H  HNH1  0   0.411   3.4096   2.0802   0.5684
 0PJ  H1    H  HCH2  0   0.307   1.5481   3.3437  -0.1791
 0PJ  H2    H  HCH2  0   0.291   1.3533   2.2696  -1.5506
 0PJ  HO2   H  HOH1  0   0.478   0.2701  -0.4701  -0.7381
 0PJ  H     H  HNH1  0   0.398  -1.0793   2.0805  -1.1303
 0PJ  HA    H  HCH1  0   0.284  -2.2033   1.0846   1.4029
 0PJ  HB2   H  HCH2  0   0.242  -3.6574   2.4201  -0.9199
 0PJ  HB3   H  HCH2  0   0.234  -4.3828   1.8571   0.5700
 0PJ  HG    H  HCH1  0   0.226  -2.3556   4.1081   0.3005
 0PJ  HD11  H  HCH3  0   0.214  -5.3199   4.1640   1.0448
 0PJ  HD12  H  HCH3  0   0.227  -4.2508   5.5613   0.9410
 0PJ  HD13  H  HCH3  0   0.225  -4.6518   4.6489  -0.5128
 0PJ  HD21  H  HCH3  0   0.232  -1.9843   3.0079   2.4722
 0PJ  HD22  H  HCH3  0   0.230  -2.8174   4.5316   2.7327
 0PJ  HD23  H  HCH3  0   0.214  -3.7185   3.0185   2.8091
 0PJ  H3    H  HNH1  0   0.408  -4.1274  -0.3650   0.9622
 0PJ  HA1   H  HCH1  0   0.292  -3.2851  -2.5545  -0.7736
 0PJ  HB21  H  HCH2  0   0.251  -5.8556  -2.1798   0.8314
 0PJ  HB31  H  HCH2  0   0.255  -5.3164  -3.6562   0.0545
 0PJ  HG1   H  HCH1  0   0.224  -3.9159  -2.2513   2.3680
 0PJ  HD14  H  HCH3  0   0.228  -6.0590  -3.3832   2.9679
 0PJ  HD15  H  HCH3  0   0.217  -5.4574  -4.8825   2.2603
 0PJ  HD16  H  HCH3  0   0.231  -4.6670  -4.1990   3.6797
 0PJ  HD24  H  HCH3  0   0.229  -2.2143  -3.3918   0.9735
 0PJ  HD25  H  HCH3  0   0.235  -2.4829  -4.3006   2.4512
 0PJ  HD26  H  HCH3  0   0.219  -3.1995  -4.8558   0.9404
 0PJ  HXT   H  HOH1  0   0.485  -5.7535  -2.4126  -3.1616

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    1.213  0.020  1.213
 0PJ  C1    O2    single    1.335  0.020  1.335
 0PJ  O2    C2    single    1.434  0.020  1.434
 0PJ  C2    C3    single    1.498  0.020  1.498
 0PJ  C2    H21   single    0.970  0.020  1.090
 0PJ  C2    H22   single    0.970  0.020  1.090
 0PJ  C3    C4    aromatic  1.392  0.020  1.392
 0PJ  C3    C8    aromatic  1.392  0.020  1.392
 0PJ  C4    C5    aromatic  1.388  0.020  1.388
 0PJ  C4    H41   single    0.930  0.020  1.080
 0PJ  C5    C6    aromatic  1.389  0.020  1.389
 0PJ  C5    H51   single    0.930  0.020  1.080
 0PJ  C6    C7    aromatic  1.390  0.020  1.390
 0PJ  C6    H61   single    0.930  0.020  1.080
 0PJ  C7    C8    aromatic  1.388  0.020  1.388
 0PJ  C7    H71   single    0.930  0.020  1.080
 0PJ  C8    H81   single    0.930  0.020  1.080
 0PJ  N     C     single    1.437  0.020  1.437
 0PJ  N     HN2   single    0.860  0.020  1.020
 0PJ  C     P     single    1.825  0.020  1.825
 0PJ  C     H1    single    0.970  0.020  1.090
 0PJ  C     H2    single    0.970  0.020  1.090
 0PJ  P     O11   double    1.487  0.020  1.487
 0PJ  P     O21   single    1.618  0.020  1.618
 0PJ  O21   HO2   single    0.850  0.020  0.980
 0PJ  N1    CA    single    1.446  0.020  1.446
 0PJ  N1    H     single    0.890  0.020  1.040
 0PJ  CA    C9    single    1.531  0.020  1.531
 0PJ  CA    CB    single    1.521  0.033  1.521
 0PJ  CA    HA    single    0.970  0.020  0.970
 0PJ  C9    O     double    1.222  0.020  1.222
 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    1.525  0.020  1.525
 0PJ  CG    CD2   single    1.525  0.020  1.525
 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    1.437  0.020  1.437
 0PJ  N2    H3    single    0.860  0.020  1.020
 0PJ  CA1   CC    single    1.522  0.020  1.522
 0PJ  CA1   CB1   single    1.532  0.020  1.532
 0PJ  CA1   HA1   single    0.970  0.020  1.090
 0PJ  CC    O3    double    1.203  0.020  1.203
 0PJ  CC    OXT   single    1.325  0.020  1.325
 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    1.525  0.020  1.525
 0PJ  CG1   CD21  single    1.525  0.020  1.525
 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  OXT   HXT   single    0.850  0.020  0.980
 0PJ  C1    N     single    1.349  0.020  1.349
 0PJ  P     N1    single    1.660  0.020  1.660
 0PJ  C9    N2    single    1.342  0.020  1.342

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    124.97  3.000
 0PJ  O2    C1    O1    124.29  3.000
 0PJ  C2    O2    C1    116.87  3.000
 0PJ  H22   C2    H21   108.18  3.000
 0PJ  H22   C2    C3    110.86  3.000
 0PJ  H21   C2    C3    110.78  3.000
 0PJ  H22   C2    O2    109.98  3.000
 0PJ  H21   C2    O2    110.14  3.000
 0PJ  C3    C2    O2    106.90  3.000
 0PJ  C8    C3    C4    119.06  3.000
 0PJ  C8    C3    C2    120.43  3.000
 0PJ  C4    C3    C2    120.50  3.000
 0PJ  H41   C4    C5    119.69  3.000
 0PJ  H41   C4    C3    119.76  3.000
 0PJ  C5    C4    C3    120.55  3.000
 0PJ  H51   C5    C6    120.13  3.000
 0PJ  H51   C5    C4    119.85  3.000
 0PJ  C6    C5    C4    120.02  3.000
 0PJ  H61   C6    C7    120.07  3.000
 0PJ  H61   C6    C5    120.12  3.000
 0PJ  C7    C6    C5    119.81  3.000
 0PJ  H71   C7    C8    119.89  3.000
 0PJ  H71   C7    C6    120.11  3.000
 0PJ  C8    C7    C6    120.00  3.000
 0PJ  H81   C8    C7    119.71  3.000
 0PJ  H81   C8    C3    119.73  3.000
 0PJ  C7    C8    C3    120.56  3.000
 0PJ  HN2   N     C     118.17  3.000
 0PJ  HN2   N     C1    119.17  3.000
 0PJ  C     N     C1    121.91  3.000
 0PJ  H2    C     H1    106.97  3.000
 0PJ  H2    C     P     110.83  3.000
 0PJ  H1    C     P     108.46  3.000
 0PJ  H2    C     N     110.26  3.000
 0PJ  H1    C     N     109.49  3.000
 0PJ  P     C     N     110.74  3.000
 0PJ  N1    P     O21   110.10  3.000
 0PJ  N1    P     O11   114.69  3.000
 0PJ  O21   P     O11   108.04  3.000
 0PJ  N1    P     C     102.97  3.000
 0PJ  O21   P     C     105.84  3.000
 0PJ  O11   P     C     114.79  3.000
 0PJ  HO2   O21   P     113.91  3.000
 0PJ  H     N1    CA    113.83  3.000
 0PJ  H     N1    P     116.23  3.000
 0PJ  CA    N1    P     120.66  3.000
 0PJ  HA    CA    CB    109.00  3.000
 0PJ  HA    CA    C9    108.06  3.000
 0PJ  CB    CA    C9    110.26  3.000
 0PJ  HA    CA    N1    107.93  3.000
 0PJ  CB    CA    N1    110.81  3.000
 0PJ  C9    CA    N1    111.03  3.000
 0PJ  N2    C9    O     122.63  3.000
 0PJ  N2    C9    CA    115.14  3.000
 0PJ  O     C9    CA    122.22  3.000
 0PJ  HB3   CB    HB2   106.10  3.000
 0PJ  HB3   CB    CG    109.11  3.000
 0PJ  HB2   CB    CG    109.39  3.000
 0PJ  HB3   CB    CA    108.94  3.000
 0PJ  HB2   CB    CA    108.91  3.000
 0PJ  CG    CB    CA    114.09  3.000
 0PJ  HG    CG    CD2   108.14  3.000
 0PJ  HG    CG    CD1   108.05  3.000
 0PJ  CD2   CG    CD1   110.87  3.000
 0PJ  HG    CG    CB    107.99  3.000
 0PJ  CD2   CG    CB    112.11  3.000
 0PJ  CD1   CG    CB    109.53  3.000
 0PJ  HD13  CD1   HD12  107.70  3.000
 0PJ  HD13  CD1   HD11  107.62  3.000
 0PJ  HD12  CD1   HD11  107.61  3.000
 0PJ  HD13  CD1   CG    111.47  3.000
 0PJ  HD12  CD1   CG    111.08  3.000
 0PJ  HD11  CD1   CG    111.18  3.000
 0PJ  HD23  CD2   HD22  107.58  3.000
 0PJ  HD23  CD2   HD21  107.93  3.000
 0PJ  HD22  CD2   HD21  107.12  3.000
 0PJ  HD23  CD2   CG    111.07  3.000
 0PJ  HD22  CD2   CG    110.76  3.000
 0PJ  HD21  CD2   CG    112.17  3.000
 0PJ  H3    N2    CA1   117.90  3.000
 0PJ  H3    N2    C9    119.03  3.000
 0PJ  CA1   N2    C9    121.91  3.000
 0PJ  HA1   CA1   CB1   108.95  3.000
 0PJ  HA1   CA1   CC    107.42  3.000
 0PJ  CB1   CA1   CC    110.56  3.000
 0PJ  HA1   CA1   N2    108.88  3.000
 0PJ  CB1   CA1   N2    110.71  3.000
 0PJ  CC    CA1   N2    110.24  3.000
 0PJ  OXT   CC    O3    124.12  3.000
 0PJ  OXT   CC    CA1   111.20  3.000
 0PJ  O3    CC    CA1   124.67  3.000
 0PJ  HB31  CB1   HB21  106.51  3.000
 0PJ  HB31  CB1   CG1   108.85  3.000
 0PJ  HB21  CB1   CG1   109.27  3.000
 0PJ  HB31  CB1   CA1   108.38  3.000
 0PJ  HB21  CB1   CA1   109.27  3.000
 0PJ  CG1   CB1   CA1   114.27  3.000
 0PJ  HG1   CG1   CD21  108.17  3.000
 0PJ  HG1   CG1   CD11  107.76  3.000
 0PJ  CD21  CG1   CD11  110.57  3.000
 0PJ  HG1   CG1   CB1   108.79  3.000
 0PJ  CD21  CG1   CB1   112.21  3.000
 0PJ  CD11  CG1   CB1   109.22  3.000
 0PJ  HD16  CD11  HD15  107.68  3.000
 0PJ  HD16  CD11  HD14  107.83  3.000
 0PJ  HD15  CD11  HD14  107.73  3.000
 0PJ  HD16  CD11  CG1   110.97  3.000
 0PJ  HD15  CD11  CG1   110.81  3.000
 0PJ  HD14  CD11  CG1   111.65  3.000
 0PJ  HD26  CD21  HD25  107.56  3.000
 0PJ  HD26  CD21  HD24  107.86  3.000
 0PJ  HD25  CD21  HD24  107.14  3.000
 0PJ  HD26  CD21  CG1   110.87  3.000
 0PJ  HD25  CD21  CG1   110.65  3.000
 0PJ  HD24  CD21  CG1   112.55  3.000
 0PJ  HXT   OXT   CC    110.28  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  CONST_17  HXT   OXT   CC   CA1   180.00   0.0  0
 0PJ  Var_01    C4    C3    C2   O2     92.29  30.0  2
 0PJ  Var_02    C3    C2    O2   C1   -178.87  30.0  3
 0PJ  Var_03    P     C     N    C1     89.99  30.0  3
 0PJ  Var_04    C     N     C1   O1      7.38  30.0  2
 0PJ  Var_05    N     C1    O2   C2   -177.84  30.0  1
 0PJ  Var_06    O11   P     C    N      66.26  30.0  3
 0PJ  Var_07    CA    N1    P    C     177.92  30.0  3
 0PJ  Var_08    CD1   CG    CB   CA   -179.82  30.0  3
 0PJ  Var_09    CD11  CG1   CB1  CA1   179.62  30.0  3
 0PJ  Var_10    HD11  CD1   CG   CB     64.03  30.0  3
 0PJ  Var_11    HD21  CD2   CG   CB     64.57  30.0  3
 0PJ  Var_12    HD14  CD11  CG1  CB1   -56.24  30.0  3
 0PJ  Var_13    HD24  CD21  CG1  CB1    64.15  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
 0PJ  chir_04  P    O11  O21  N1  both

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-3  HXT  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

