# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 18:24:51 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  65  32  .  2022-09-22  2022-11-17
;
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   0.774   3.2047   0.3284  -0.7792
 0PI  O1    O  O     0  -0.521   2.4874  -0.1959  -1.6088
 0PI  O2    O  O2    0  -0.473   4.4088  -0.1206  -0.4322
 0PI  C2    C  CH2   0  -0.240   4.8948  -1.2818  -1.1209
 0PI  C3    C  CR6   0   0.074   6.2421  -1.5974  -0.5471
 0PI  C4    C  CR16  0  -0.297   6.3972  -2.6327   0.3682
 0PI  C5    C  CR16  0  -0.241   7.6444  -2.9132   0.9124
 0PI  C6    C  CR16  0  -0.261   8.7470  -2.1533   0.5483
 0PI  C7    C  CR16  0  -0.243   8.6000  -1.1157  -0.3652
 0PI  C8    C  CR16  0  -0.282   7.3545  -0.8415  -0.9101
 0PI  N     N  NH1   0  -0.659   2.8882   1.4472  -0.0976
 0PI  C     C  CH2   0  -0.582   1.6358   2.1206  -0.3048
 0PI  P     P  P     0   1.371   0.3329   1.4288   0.7639
 0PI  O11   O  O     0  -0.699   0.4630   1.6882   2.2159
 0PI  O21   O  OH1   0  -0.737   0.2928  -0.1562   0.5153
 0PI  OS    O  O2    0  -0.590  -0.9635   2.0586   0.0530
 0PI  CA    C  CH1   0  -0.102  -2.2789   1.6570   0.4122
 0PI  C9    C  C     0   0.552  -2.6213   0.3931  -0.3745
 0PI  O     O  O     0  -0.480  -2.0920   0.1265  -1.4389
 0PI  CB    C  CH2   0  -0.428  -3.2546   2.7762   0.0596
 0PI  CG    C  CH1   0  -0.241  -3.3576   3.9034   1.0899
 0PI  CD1   C  CH3   0  -0.656  -2.0338   4.6076   1.3734
 0PI  CD2   C  CH3   0  -0.656  -4.4091   4.9073   0.6264
 0PI  N1    N  NH1   0  -0.635  -3.5592  -0.3773   0.1970
 0PI  CA1   C  CH1   0  -0.198  -4.1131  -1.5179  -0.4783
 0PI  CC    C  C     0   0.555  -4.9897  -1.0689  -1.6383
 0PI  O3    O  O     0  -0.428  -5.4146   0.0469  -1.7817
 0PI  CB1   C  CH2   0  -0.455  -4.9241  -2.3797   0.4954
 0PI  CG1   C  CH1   0  -0.234  -4.1373  -2.8650   1.7157
 0PI  CD11  C  CH3   0  -0.653  -5.0501  -3.7119   2.5969
 0PI  CD21  C  CH3   0  -0.664  -2.8877  -3.6471   1.3265
 0PI  OXT   O  OH1   0  -0.591  -5.2453  -2.0748  -2.4624
 0PI  H21   H  HCH2  0   0.253   4.2071  -2.1181  -0.9829
 0PI  H22   H  HCH2  0   0.251   4.9665  -1.0729  -2.1905
 0PI  H41   H  HCR6  0   0.256   5.5394  -3.2290   0.6559
 0PI  H51   H  HCR6  0   0.259   7.7523  -3.7248   1.6199
 0PI  H61   H  HCR6  0   0.259   9.7194  -2.3686   0.9718
 0PI  H71   H  HCR6  0   0.259   9.4575  -0.5222  -0.6548
 0PI  H81   H  HCR6  0   0.256   7.2479  -0.0373  -1.6284
 0PI  HN2   H  HNH1  0   0.417   3.5277   1.8148   0.5885
 0PI  H1    H  HCH2  0   0.318   1.7533   3.1766  -0.0614
 0PI  H2    H  HCH2  0   0.300   1.3346   2.0646  -1.3513
 0PI  HO2   H  HOH1  0   0.483   0.2911  -0.4340  -0.4116
 0PI  HA    H  HCH1  0   0.268  -2.3368   1.4507   1.4887
 0PI  HB1   H  HCH2  0   0.245  -2.9787   3.1774  -0.9210
 0PI  HB2   H  HCH2  0   0.253  -4.2484   2.3357  -0.0629
 0PI  HG    H  HCH1  0   0.223  -3.7095   3.4579   2.0279
 0PI  HD11  H  HCH3  0   0.225  -2.1990   5.4625   2.0314
 0PI  HD12  H  HCH3  0   0.230  -1.3116   3.9586   1.8677
 0PI  HD13  H  HCH3  0   0.215  -1.5762   4.9802   0.4547
 0PI  HD21  H  HCH3  0   0.227  -5.3770   4.4290   0.4658
 0PI  HD22  H  HCH3  0   0.229  -4.5469   5.6988   1.3644
 0PI  HD23  H  HCH3  0   0.217  -4.1126   5.3791  -0.3134
 0PI  H     H  HNH1  0   0.409  -4.0127  -0.0592   1.0395
 0PI  HA1   H  HCH1  0   0.292  -3.2976  -2.1187  -0.8885
 0PI  HB21  H  HCH2  0   0.252  -5.8010  -1.8154   0.8303
 0PI  HB3   H  HCH2  0   0.256  -5.3027  -3.2481  -0.0494
 0PI  HG1   H  HCH1  0   0.225  -3.8240  -1.9947   2.3024
 0PI  HD14  H  HCH3  0   0.231  -4.5409  -4.0093   3.5144
 0PI  HD15  H  HCH3  0   0.228  -5.9536  -3.1685   2.8783
 0PI  HD16  H  HCH3  0   0.217  -5.3574  -4.6225   2.0778
 0PI  HD24  H  HCH3  0   0.229  -2.1582  -3.0319   0.7977
 0PI  HD25  H  HCH3  0   0.235  -2.3899  -4.0423   2.2132
 0PI  HD26  H  HCH3  0   0.220  -3.1398  -4.4943   0.6841
 0PI  HXT   H  HOH1  0   0.485  -5.8292  -1.7830  -3.1783

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    1.331  0.020  1.331
 0PI  O2    C2    single    1.435  0.020  1.435
 0PI  C2    C3    single    1.498  0.020  1.498
 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  1.393  0.020  1.393
 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  1.387  0.020  1.387
 0PI  C7    H71   single    0.930  0.020  1.080
 0PI  C8    H81   single    0.930  0.020  1.080
 0PI  N     C     single    1.437  0.020  1.437
 0PI  N     HN2   single    0.860  0.020  1.020
 0PI  C     P     single    1.822  0.020  1.822
 0PI  C     H1    single    0.970  0.020  1.090
 0PI  C     H2    single    0.970  0.020  1.090
 0PI  P     O11   double    1.481  0.020  1.481
 0PI  P     O21   single    1.605  0.020  1.605
 0PI  O21   HO2   single    0.850  0.020  0.980
 0PI  OS    CA    single    1.422  0.020  1.422
 0PI  CA    C9    single    1.528  0.020  1.528
 0PI  CA    CB    single    1.521  0.033  1.521
 0PI  CA    HA    single    0.970  0.020  0.970
 0PI  C9    O     double    1.218  0.020  1.218
 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    1.526  0.020  1.526
 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    1.437  0.020  1.437
 0PI  N1    H     single    0.860  0.020  1.020
 0PI  CA1   CC    single    1.522  0.020  1.522
 0PI  CA1   CB1   single    1.533  0.020  1.533
 0PI  CA1   HA1   single    0.970  0.020  1.090
 0PI  CC    O3    double    1.203  0.020  1.203
 0PI  CC    OXT   single    1.325  0.020  1.325
 0PI  CB1   CG1   single    1.531  0.020  1.531
 0PI  CB1   HB21  single    0.970  0.020  1.090
 0PI  CB1   HB3   single    0.970  0.020  1.090
 0PI  CG1   CD11  single    1.525  0.020  1.525
 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  OXT   HXT   single    0.850  0.020  0.980
 0PI  C1    N     single    1.348  0.020  1.348
 0PI  P     OS    single    1.607  0.020  1.607
 0PI  C9    N1    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
 0PI  N     C1    O2    111.13  3.000
 0PI  N     C1    O1    124.38  3.000
 0PI  O2    C1    O1    124.48  3.000
 0PI  C2    O2    C1    117.02  3.000
 0PI  H22   C2    H21   108.17  3.000
 0PI  H22   C2    C3    110.88  3.000
 0PI  H21   C2    C3    110.90  3.000
 0PI  H22   C2    O2    109.72  3.000
 0PI  H21   C2    O2    110.24  3.000
 0PI  C3    C2    O2    106.93  3.000
 0PI  C8    C3    C4    119.11  3.000
 0PI  C8    C3    C2    120.27  3.000
 0PI  C4    C3    C2    120.62  3.000
 0PI  H41   C4    C5    119.70  3.000
 0PI  H41   C4    C3    119.75  3.000
 0PI  C5    C4    C3    120.55  3.000
 0PI  H51   C5    C6    120.20  3.000
 0PI  H51   C5    C4    119.81  3.000
 0PI  C6    C5    C4    119.99  3.000
 0PI  H61   C6    C7    120.04  3.000
 0PI  H61   C6    C5    120.15  3.000
 0PI  C7    C6    C5    119.81  3.000
 0PI  H71   C7    C8    119.86  3.000
 0PI  H71   C7    C6    120.09  3.000
 0PI  C8    C7    C6    120.05  3.000
 0PI  H81   C8    C7    119.71  3.000
 0PI  H81   C8    C3    119.80  3.000
 0PI  C7    C8    C3    120.49  3.000
 0PI  HN2   N     C     118.71  3.000
 0PI  HN2   N     C1    119.89  3.000
 0PI  C     N     C1    121.38  3.000
 0PI  H2    C     H1    107.08  3.000
 0PI  H2    C     P     110.24  3.000
 0PI  H1    C     P     108.30  3.000
 0PI  H2    C     N     110.80  3.000
 0PI  H1    C     N     109.14  3.000
 0PI  P     C     N     111.15  3.000
 0PI  OS    P     O21   107.36  3.000
 0PI  OS    P     O11   115.85  3.000
 0PI  O21   P     O11   109.09  3.000
 0PI  OS    P     C      99.71  3.000
 0PI  O21   P     C     107.58  3.000
 0PI  O11   P     C     116.48  3.000
 0PI  HO2   O21   P     115.59  3.000
 0PI  CA    OS    P     121.60  3.000
 0PI  HA    CA    CB    109.00  3.000
 0PI  HA    CA    C9    109.74  3.000
 0PI  CB    CA    C9    110.15  3.000
 0PI  HA    CA    OS    110.47  3.000
 0PI  CB    CA    OS    109.03  3.000
 0PI  C9    CA    OS    108.12  3.000
 0PI  N1    C9    O     123.39  3.000
 0PI  N1    C9    CA    114.35  3.000
 0PI  O     C9    CA    122.25  3.000
 0PI  HB2   CB    HB1   106.03  3.000
 0PI  HB2   CB    CG    108.11  3.000
 0PI  HB1   CB    CG    110.49  3.000
 0PI  HB2   CB    CA    108.14  3.000
 0PI  HB1   CB    CA    108.33  3.000
 0PI  CG    CB    CA    115.31  3.000
 0PI  HG    CG    CD2   107.82  3.000
 0PI  HG    CG    CD1   107.88  3.000
 0PI  CD2   CG    CD1   110.53  3.000
 0PI  HG    CG    CB    107.35  3.000
 0PI  CD2   CG    CB    109.05  3.000
 0PI  CD1   CG    CB    113.99  3.000
 0PI  HD13  CD1   HD12  107.89  3.000
 0PI  HD13  CD1   HD11  107.66  3.000
 0PI  HD12  CD1   HD11  107.06  3.000
 0PI  HD13  CD1   CG    111.39  3.000
 0PI  HD12  CD1   CG    112.61  3.000
 0PI  HD11  CD1   CG    110.01  3.000
 0PI  HD23  CD2   HD22  107.63  3.000
 0PI  HD23  CD2   HD21  107.66  3.000
 0PI  HD22  CD2   HD21  107.78  3.000
 0PI  HD23  CD2   CG    111.00  3.000
 0PI  HD22  CD2   CG    111.03  3.000
 0PI  HD21  CD2   CG    111.56  3.000
 0PI  H     N1    CA1   118.02  3.000
 0PI  H     N1    C9    119.30  3.000
 0PI  CA1   N1    C9    121.68  3.000
 0PI  HA1   CA1   CB1   108.92  3.000
 0PI  HA1   CA1   CC    107.82  3.000
 0PI  CB1   CA1   CC    110.21  3.000
 0PI  HA1   CA1   N1    108.97  3.000
 0PI  CB1   CA1   N1    110.60  3.000
 0PI  CC    CA1   N1    110.26  3.000
 0PI  OXT   CC    O3    124.19  3.000
 0PI  OXT   CC    CA1   111.17  3.000
 0PI  O3    CC    CA1   124.63  3.000
 0PI  HB3   CB1   HB21  106.53  3.000
 0PI  HB3   CB1   CG1   108.88  3.000
 0PI  HB21  CB1   CG1   109.34  3.000
 0PI  HB3   CB1   CA1   108.26  3.000
 0PI  HB21  CB1   CA1   109.16  3.000
 0PI  CG1   CB1   CA1   114.38  3.000
 0PI  HG1   CG1   CD21  108.05  3.000
 0PI  HG1   CG1   CD11  107.63  3.000
 0PI  CD21  CG1   CD11  110.68  3.000
 0PI  HG1   CG1   CB1   108.78  3.000
 0PI  CD21  CG1   CB1   112.35  3.000
 0PI  CD11  CG1   CB1   109.20  3.000
 0PI  HD16  CD11  HD15  107.74  3.000
 0PI  HD16  CD11  HD14  107.69  3.000
 0PI  HD15  CD11  HD14  107.78  3.000
 0PI  HD16  CD11  CG1   110.90  3.000
 0PI  HD15  CD11  CG1   111.59  3.000
 0PI  HD14  CD11  CG1   110.97  3.000
 0PI  HD26  CD21  HD25  107.59  3.000
 0PI  HD26  CD21  HD24  107.85  3.000
 0PI  HD25  CD21  HD24  107.04  3.000
 0PI  HD26  CD21  CG1   111.02  3.000
 0PI  HD25  CD21  CG1   110.63  3.000
 0PI  HD24  CD21  CG1   112.49  3.000
 0PI  HXT   OXT   CC    110.31  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  CONST_17  HXT   OXT   CC   CA1   180.00   0.0  0
 0PI  Var_01    C4    C3    C2   O2    102.35  30.0  2
 0PI  Var_02    C3    C2    O2   C1   -179.24  30.0  3
 0PI  Var_03    P     C     N    C1     87.23  30.0  3
 0PI  Var_04    C     N     C1   O1      0.29  30.0  2
 0PI  Var_05    N     C1    O2   C2   -177.67  30.0  1
 0PI  Var_06    O11   P     C    N      69.18  30.0  3
 0PI  Var_07    CD1   CG    CB   CA     58.38  30.0  3
 0PI  Var_08    CD11  CG1   CB1  CA1  -179.74  30.0  3
 0PI  Var_09    HD11  CD1   CG   CB    174.01  30.0  3
 0PI  Var_10    HD21  CD2   CG   CB     56.75  30.0  3
 0PI  Var_11    HD14  CD11  CG1  CB1  -175.61  30.0  3
 0PI  Var_12    HD24  CD21  CG1  CB1    64.57  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
 0PI  chir_04  P    O11  O21  OS  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
 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-3  HXT  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

