# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 17:10:11 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: N-[(2R,4S)-4-hydroxy-2-(2-methylpropyl)-4-oxido-7-oxo-9-phenyl-3,8-dioxa-6-aza-4-phosphanonan-1-oyl]-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)O[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
 0PI  0PI  N-[(2R,4S)-4-hydroxy-2-(2-methylpropyl)-4-oxido-7-oxo-9-phenyl-3,8-dioxa-6-aza-4-phosphanonan-1-oyl]-L-leucine  peptide  63  32  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_0PI
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
 0PI  C1    C  C      0   0.761   2.4414  -0.8240  -0.5758
 0PI  O1    O  O      0  -0.523   1.9403  -1.4216  -1.5086
 0PI  O2    O  O2     0  -0.484   3.6460  -1.1235  -0.0656
 0PI  C2    C  CH2    0  -0.236   4.3606  -2.1928  -0.6930
 0PI  C3    C  C      0   0.076   5.6506  -2.3543   0.0524
 0PI  C4    C  C1     0  -0.295   5.7678  -3.2934   1.0721
 0PI  C5    C  C1     0  -0.242   6.9576  -3.4268   1.7760
 0PI  C6    C  C1     0  -0.262   8.0423  -2.6173   1.4667
 0PI  C7    C  C1     0  -0.243   7.9334  -1.6757   0.4505
 0PI  C8    C  C1     0  -0.287   6.7434  -1.5464  -0.2513
 0PI  N     N  NH1    0  -0.664   1.8784   0.1974   0.0869
 0PI  C     C  CH2    0  -0.568   0.5998   0.7566  -0.2914
 0PI  P     P  P      0   1.281  -0.1174   1.6441   1.1545
 0PI  O11   O  O      0  -0.790   0.9232   2.6240   1.6246
 0PI  O21   O  OP    -1  -0.781  -0.7469   0.6752   2.1149
 0PI  OS    O  O2     0  -0.622  -1.2985   2.5211   0.4025
 0PI  CA    C  CH1    0  -0.039  -2.6618   2.2046   0.5602
 0PI  C9    C  C      0   0.521  -2.9825   0.9078  -0.1849
 0PI  O     O  O      0  -0.510  -2.5333   0.7082  -1.3078
 0PI  CB    C  CH2    0  -0.425  -3.5112   3.3343  -0.0166
 0PI  CG    C  CH1    0  -0.238  -3.6258   4.5904   0.8513
 0PI  CD1   C  CH3    0  -0.647  -2.3057   5.3306   1.0496
 0PI  CD2   C  CH3    0  -0.655  -4.6637   5.5304   0.2425
 0PI  N1    N  NH1    0  -0.603  -3.8026   0.0804   0.4636
 0PI  CA1   C  CH1    0  -0.228  -4.2996  -1.1830  -0.0308
 0PI  CC    C  C      0   0.423  -5.8096  -1.3250   0.2761
 0PI  O3    O  O      0  -0.603  -6.2772  -0.5962   1.1722
 0PI  CB1   C  CH2    0  -0.395  -3.5573  -2.3627   0.6169
 0PI  CG1   C  CH1    0  -0.258  -2.0400  -2.3895   0.4302
 0PI  CD11  C  CH3    0  -0.648  -1.4270  -3.4711   1.3157
 0PI  CD21  C  CH3    0  -0.675  -1.6400  -2.6167  -1.0239
 0PI  OXT   O  OC    -1  -0.611  -6.4141  -2.1958  -0.3771
 0PI  H21   H  HCH2   0   0.245   3.7752  -3.1139  -0.6565
 0PI  H22   H  HCH2   0   0.243   4.5490  -1.9541  -1.7424
 0PI  H41   H  H      0   0.255   4.9260  -3.9311   1.3157
 0PI  H51   H  H      0   0.258   7.0363  -4.1638   2.5645
 0PI  H61   H  H      0   0.258   8.9712  -2.7215   2.0126
 0PI  H71   H  H      0   0.258   8.7769  -1.0443   0.2023
 0PI  H81   H  H      0   0.255   6.6648  -0.8153  -1.0471
 0PI  HN2   H  HNH1   0   0.390   2.4361   0.7051   0.7565
 0PI  H1    H  HCH2   0   0.236   0.7022   1.4514  -1.1321
 0PI  H2    H  HCH2   0   0.277  -0.0694  -0.0406  -0.6112
 0PI  HA    H  HCH1   0   0.221  -2.9120   2.0847   1.6214
 0PI  HB1   H  HCH2   0   0.224  -3.1343   3.5955  -1.0112
 0PI  HB2   H  HCH2   0   0.234  -4.5229   2.9417  -0.1663
 0PI  HG    H  HCH1   0   0.213  -3.9935   4.2774   1.8361
 0PI  HD11  H  HCH3   0   0.213  -2.4699   6.2489   1.6172
 0PI  HD12  H  HCH3   0   0.237  -1.5648   4.7376   1.5820
 0PI  HD13  H  HCH3   0   0.207  -1.8715   5.6129   0.0873
 0PI  HD21  H  HCH3   0   0.223  -5.6316   5.0394   0.1257
 0PI  HD22  H  HCH3   0   0.225  -4.8103   6.4140   0.8656
 0PI  HD23  H  HCH3   0   0.213  -4.3455   5.8735  -0.7453
 0PI  H     H  HNH1   0   0.377  -4.1460   0.3501   1.3721
 0PI  HA1   H  HCH1   0   0.236  -4.1537  -1.2038  -1.1119
 0PI  HB21  H  HCH2   0   0.210  -3.7796  -2.3483   1.6910
 0PI  HB3   H  HCH2   0   0.212  -3.9877  -3.2915   0.2279
 0PI  HG1   H  HCH1   0   0.250  -1.6330  -1.4289   0.7628
 0PI  HD14  H  HCH3   0   0.218  -0.3389  -3.4816   1.2241
 0PI  HD15  H  HCH3   0   0.218  -1.6684  -3.3138   2.3689
 0PI  HD16  H  HCH3   0   0.206  -1.7902  -4.4640   1.0370
 0PI  HD24  H  HCH3   0   0.231  -2.0356  -1.8411  -1.6785
 0PI  HD25  H  HCH3   0   0.225  -0.5539  -2.6062  -1.1329
 0PI  HD26  H  HCH3   0   0.202  -2.0029  -3.5846  -1.3817

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
 0PI  C1    O1    double    1.216  0.020  1.216
 0PI  C1    O2    single    1.342  0.020  1.342
 0PI  O2    C2    single    1.431  0.020  1.431
 0PI  C2    C3    single    1.499  0.020  1.499
 0PI  C2    H21   single    0.970  0.020  1.090
 0PI  C2    H22   single    0.970  0.020  1.090
 0PI  C3    C4    aromatic  1.391  0.020  1.391
 0PI  C3    C8    aromatic  1.392  0.020  1.392
 0PI  C4    C5    aromatic  1.389  0.020  1.389
 0PI  C4    H41   single    0.930  0.020  1.080
 0PI  C5    C6    aromatic  1.388  0.020  1.388
 0PI  C5    H51   single    0.930  0.020  1.080
 0PI  C6    C7    aromatic  1.390  0.020  1.390
 0PI  C6    H61   single    0.930  0.020  1.080
 0PI  C7    C8    aromatic  1.388  0.020  1.388
 0PI  C7    H71   single    0.930  0.020  1.080
 0PI  C8    H81   single    0.930  0.020  1.080
 0PI  N     C     single    1.446  0.020  1.446
 0PI  N     HN2   single    0.860  0.020  1.020
 0PI  C     P     single    1.842  0.020  1.842
 0PI  C     H1    single    0.970  0.020  1.090
 0PI  C     H2    single    0.970  0.020  1.090
 0PI  P     O11   deloc     1.505  0.020  1.505
 0PI  P     O21   deloc     1.502  0.020  1.502
 0PI  OS    CA    single    1.408  0.020  1.408
 0PI  CA    C9    single    1.530  0.020  1.530
 0PI  CA    CB    single    1.521  0.033  1.521
 0PI  CA    HA    single    0.970  0.020  0.970
 0PI  C9    O     double    1.226  0.020  1.226
 0PI  CB    CG    single    1.531  0.020  1.531
 0PI  CB    HB1   single    0.970  0.020  1.090
 0PI  CB    HB2   single    0.970  0.020  1.090
 0PI  CG    CD1   single    1.526  0.020  1.526
 0PI  CG    CD2   single    1.527  0.020  1.527
 0PI  CG    HG    single    0.970  0.020  1.090
 0PI  CD1   HD11  single    0.970  0.020  1.090
 0PI  CD1   HD12  single    0.970  0.020  1.090
 0PI  CD1   HD13  single    0.970  0.020  1.090
 0PI  CD2   HD21  single    0.970  0.020  1.090
 0PI  CD2   HD22  single    0.970  0.020  1.090
 0PI  CD2   HD23  single    0.970  0.020  1.090
 0PI  N1    CA1   single    1.445  0.020  1.445
 0PI  N1    H     single    0.860  0.020  1.020
 0PI  CA1   CC    single    1.547  0.020  1.547
 0PI  CA1   CB1   single    1.537  0.020  1.537
 0PI  CA1   HA1   single    0.970  0.020  1.090
 0PI  CC    O3    deloc     1.246  0.020  1.246
 0PI  CC    OXT   deloc     1.245  0.020  1.245
 0PI  CB1   CG1   single    1.529  0.020  1.529
 0PI  CB1   HB21  single    0.970  0.020  1.090
 0PI  CB1   HB3   single    0.970  0.020  1.090
 0PI  CG1   CD11  single    1.526  0.020  1.526
 0PI  CG1   CD21  single    1.525  0.020  1.525
 0PI  CG1   HG1   single    0.970  0.020  1.090
 0PI  CD11  HD14  single    0.970  0.020  1.090
 0PI  CD11  HD15  single    0.970  0.020  1.090
 0PI  CD11  HD16  single    0.970  0.020  1.090
 0PI  CD21  HD24  single    0.970  0.020  1.090
 0PI  CD21  HD25  single    0.970  0.020  1.090
 0PI  CD21  HD26  single    0.970  0.020  1.090
 0PI  C1    N     single    1.341  0.020  1.341
 0PI  P     OS    single    1.652  0.020  1.652
 0PI  C9    N1    single    1.333  0.020  1.333

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
 0PI  N     C1    O2    111.03  3.000
 0PI  N     C1    O1    125.48  3.000
 0PI  O2    C1    O1    123.49  3.000
 0PI  C2    O2    C1    116.64  3.000
 0PI  H22   C2    H21   107.99  3.000
 0PI  H22   C2    C3    110.66  3.000
 0PI  H21   C2    C3    110.73  3.000
 0PI  H22   C2    O2    110.12  3.000
 0PI  H21   C2    O2    110.36  3.000
 0PI  C3    C2    O2    107.00  3.000
 0PI  C8    C3    C4    119.04  3.000
 0PI  C8    C3    C2    120.30  3.000
 0PI  C4    C3    C2    120.65  3.000
 0PI  H41   C4    C5    119.67  3.000
 0PI  H41   C4    C3    119.77  3.000
 0PI  C5    C4    C3    120.56  3.000
 0PI  H51   C5    C6    120.17  3.000
 0PI  H51   C5    C4    119.80  3.000
 0PI  C6    C5    C4    120.02  3.000
 0PI  H61   C6    C7    120.09  3.000
 0PI  H61   C6    C5    120.12  3.000
 0PI  C7    C6    C5    119.79  3.000
 0PI  H71   C7    C8    119.87  3.000
 0PI  H71   C7    C6    120.12  3.000
 0PI  C8    C7    C6    120.01  3.000
 0PI  H81   C8    C7    119.77  3.000
 0PI  H81   C8    C3    119.65  3.000
 0PI  C7    C8    C3    120.58  3.000
 0PI  HN2   N     C     117.91  3.000
 0PI  HN2   N     C1    118.64  3.000
 0PI  C     N     C1    122.43  3.000
 0PI  H2    C     H1    107.24  3.000
 0PI  H2    C     P     110.12  3.000
 0PI  H1    C     P     109.46  3.000
 0PI  H2    C     N     109.71  3.000
 0PI  H1    C     N     111.31  3.000
 0PI  P     C     N     108.98  3.000
 0PI  OS    P     O21   109.50  3.000
 0PI  OS    P     O11   106.91  3.000
 0PI  O21   P     O11   120.66  3.000
 0PI  OS    P     C     100.19  3.000
 0PI  O21   P     C     110.74  3.000
 0PI  O11   P     C     106.85  3.000
 0PI  CA    OS    P     121.45  3.000
 0PI  HA    CA    CB    109.00  3.000
 0PI  HA    CA    C9    109.31  3.000
 0PI  CB    CA    C9    109.07  3.000
 0PI  HA    CA    OS    110.71  3.000
 0PI  CB    CA    OS    109.27  3.000
 0PI  C9    CA    OS    109.81  3.000
 0PI  N1    C9    O     124.74  3.000
 0PI  N1    C9    CA    114.72  3.000
 0PI  O     C9    CA    120.49  3.000
 0PI  HB2   CB    HB1   106.21  3.000
 0PI  HB2   CB    CG    107.60  3.000
 0PI  HB1   CB    CG    110.18  3.000
 0PI  HB2   CB    CA    107.48  3.000
 0PI  HB1   CB    CA    109.15  3.000
 0PI  CG    CB    CA    115.76  3.000
 0PI  HG    CG    CD2   107.81  3.000
 0PI  HG    CG    CD1   108.16  3.000
 0PI  CD2   CG    CD1   109.95  3.000
 0PI  HG    CG    CB    107.45  3.000
 0PI  CD2   CG    CB    109.26  3.000
 0PI  CD1   CG    CB    114.00  3.000
 0PI  HD13  CD1   HD12  107.52  3.000
 0PI  HD13  CD1   HD11  107.47  3.000
 0PI  HD12  CD1   HD11  107.84  3.000
 0PI  HD13  CD1   CG    110.77  3.000
 0PI  HD12  CD1   CG    112.84  3.000
 0PI  HD11  CD1   CG    110.20  3.000
 0PI  HD23  CD2   HD22  107.52  3.000
 0PI  HD23  CD2   HD21  107.61  3.000
 0PI  HD22  CD2   HD21  107.83  3.000
 0PI  HD23  CD2   CG    110.84  3.000
 0PI  HD22  CD2   CG    111.23  3.000
 0PI  HD21  CD2   CG    111.62  3.000
 0PI  H     N1    CA1   115.16  3.000
 0PI  H     N1    C9    118.81  3.000
 0PI  CA1   N1    C9    126.00  3.000
 0PI  HA1   CA1   CB1   109.78  3.000
 0PI  HA1   CA1   CC    108.98  3.000
 0PI  CB1   CA1   CC    108.50  3.000
 0PI  HA1   CA1   N1    108.04  3.000
 0PI  CB1   CA1   N1    111.16  3.000
 0PI  CC    CA1   N1    110.36  3.000
 0PI  OXT   CC    O3    127.16  3.000
 0PI  OXT   CC    CA1   115.71  3.000
 0PI  O3    CC    CA1   117.07  3.000
 0PI  HB3   CB1   HB21  106.22  3.000
 0PI  HB3   CB1   CG1   109.38  3.000
 0PI  HB21  CB1   CG1   108.72  3.000
 0PI  HB3   CB1   CA1   108.15  3.000
 0PI  HB21  CB1   CA1   107.74  3.000
 0PI  CG1   CB1   CA1   116.18  3.000
 0PI  HG1   CG1   CD21  108.83  3.000
 0PI  HG1   CG1   CD11  107.22  3.000
 0PI  CD21  CG1   CD11  110.01  3.000
 0PI  HG1   CG1   CB1   108.45  3.000
 0PI  CD21  CG1   CB1   112.29  3.000
 0PI  CD11  CG1   CB1   109.88  3.000
 0PI  HD16  CD11  HD15  107.66  3.000
 0PI  HD16  CD11  HD14  107.51  3.000
 0PI  HD15  CD11  HD14  107.62  3.000
 0PI  HD16  CD11  CG1   111.24  3.000
 0PI  HD15  CD11  CG1   111.63  3.000
 0PI  HD14  CD11  CG1   111.00  3.000
 0PI  HD26  CD21  HD25  107.81  3.000
 0PI  HD26  CD21  HD24  108.25  3.000
 0PI  HD25  CD21  HD24  107.13  3.000
 0PI  HD26  CD21  CG1   110.89  3.000
 0PI  HD25  CD21  CG1   110.77  3.000
 0PI  HD24  CD21  CG1   111.81  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
 0PI  CONST_01  C6    C5    C4   C3      0.00   0.0  0
 0PI  CONST_02  C6    C7    C8   C3      0.00   0.0  0
 0PI  CONST_03  C7    C8    C3   C4      0.00   0.0  0
 0PI  CONST_04  C7    C6    C5   C4      0.00   0.0  0
 0PI  CONST_05  C8    C3    C4   C5      0.00   0.0  0
 0PI  CONST_06  C8    C7    C6   C5      0.00   0.0  0
 0PI  CONST_07  C5    C4    C3   C2    180.00   0.0  0
 0PI  CONST_08  C7    C8    C3   C2    180.00   0.0  0
 0PI  CONST_09  H51   C5    C4   C3    180.00   0.0  0
 0PI  CONST_10  H71   C7    C8   C3    180.00   0.0  0
 0PI  CONST_11  H81   C8    C3   C4    180.00   0.0  0
 0PI  CONST_12  H61   C6    C5   C4    180.00   0.0  0
 0PI  CONST_13  H41   C4    C5   C6    180.00   0.0  0
 0PI  CONST_14  CA1   N1    C9   CA    180.00   0.0  0
 0PI  CONST_15  CA1   N1    C9   O       0.00   0.0  0
 0PI  CONST_16  H     N1    C9   CA      0.00   0.0  0
 0PI  Var_01    C4    C3    C2   O2     95.31  30.0  2
 0PI  Var_02    C3    C2    O2   C1   -179.18  30.0  3
 0PI  Var_03    P     C     N    C1    158.71  30.0  3
 0PI  Var_04    C     N     C1   O1     -3.12  30.0  2
 0PI  Var_05    N     C1    O2   C2   -179.47  30.0  1
 0PI  Var_06    O11   P     C    N      53.71  30.0  3
 0PI  Var_07    CD1   CG    CB   CA     64.96  30.0  3
 0PI  Var_08    CD11  CG1   CB1  CA1   170.49  30.0  3
 0PI  Var_09    HD11  CD1   CG   CB    176.12  30.0  3
 0PI  Var_10    HD21  CD2   CG   CB     56.47  30.0  3
 0PI  Var_11    HD14  CD11  CG1  CB1  -177.92  30.0  3
 0PI  Var_12    HD24  CD21  CG1  CB1    59.16  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
 0PI  chir_02  CA   OS  C9   CB  positiv
 0PI  chir_03  CA1  N1  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
 0PI  plan-1  C2   0.020
 0PI  plan-1  C3   0.020
 0PI  plan-1  C4   0.020
 0PI  plan-1  C5   0.020
 0PI  plan-1  C6   0.020
 0PI  plan-1  C7   0.020
 0PI  plan-1  C8   0.020
 0PI  plan-1  H41  0.020
 0PI  plan-1  H51  0.020
 0PI  plan-1  H61  0.020
 0PI  plan-1  H71  0.020
 0PI  plan-1  H81  0.020
 0PI  plan-2  CA   0.020
 0PI  plan-2  C9   0.020
 0PI  plan-2  O    0.020
 0PI  plan-2  N1   0.020
 0PI  plan-2  CA1  0.020
 0PI  plan-2  H    0.020
 0PI  plan-3  CA1  0.020
 0PI  plan-3  CC   0.020
 0PI  plan-3  O3   0.020
 0PI  plan-3  OXT  0.020
 0PI  plan-4  C1   0.020
 0PI  plan-4  O1   0.020
 0PI  plan-4  O2   0.020
 0PI  plan-4  N    0.020

