# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 20:25:12 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (2R,4S,5S)-5-amino-4-hydroxy-7-methyl-2-(2-methylpropyl)octanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)[C@@H](O)C[C@@H](CC(C)C)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
 LPL  LPL  '(2R,4S,5S)-5-amino-4-hydroxy-7-methyl-2-(2-methylpropyl)octanoic acid'  L-peptide  43  17  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LPL
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
 LPL  N     N  NH2    0  -0.805  -1.9267  -0.4091   1.8254
 LPL  CA    C  CH1    0  -0.111  -0.5387   0.0391   1.8882
 LPL  CB    C  CH2    0  -0.408   0.1890  -0.3778   3.1692
 LPL  CG    C  CH1    0  -0.236  -0.4171   0.1421   4.4736
 LPL  CD1   C  CH3    0  -0.649   0.3280  -0.4448   5.6684
 LPL  CD2   C  CH3    0  -0.658  -0.4198   1.6665   4.5397
 LPL  CH    C  CH1    0   0.057   0.2182  -0.4460   0.6427
 LPL  OH    O  OH1    0  -0.678   0.1415  -1.8576   0.5202
 LPL  CM    C  CH2    0  -0.446  -0.2522   0.2583  -0.6248
 LPL  CA1   C  CH1    0  -0.341   0.5019  -0.1474  -1.8867
 LPL  CB1   C  CH2    0  -0.397  -0.0491   0.5655  -3.1304
 LPL  CG1   C  CH1    0  -0.237  -1.5100   0.2857  -3.4921
 LPL  CD3   C  CH3    0  -0.648  -1.8994   1.0887  -4.7306
 LPL  CD4   C  CH3    0  -0.657  -1.7710  -1.1986  -3.7215
 LPL  C     C  C      0   0.412   2.0119   0.1599  -1.8072
 LPL  O     O  O      0  -0.616   2.3524   1.2127  -1.2270
 LPL  OXT   O  OC    -1  -0.622   2.7822  -0.6454  -2.3720
 LPL  H     H  HNH2   0   0.350  -2.5010   0.1489   2.4434
 LPL  H2    H  HNH2   0   0.336  -1.9952  -1.3573   2.1777
 LPL  HA    H  HCH1   0   0.220  -0.5491   1.1327   1.8297
 LPL  HB2   H  HCH2   0   0.204   1.2320  -0.0428   3.1098
 LPL  HB3   H  HCH2   0   0.214   0.2258  -1.4726   3.2069
 LPL  HG    H  HCH1   0   0.203  -1.4569  -0.2013   4.5341
 LPL  HD11  H  HCH3   0   0.222  -0.0974  -0.0991   6.6124
 LPL  HD12  H  HCH3   0   0.222   0.2881  -1.5358   5.6645
 LPL  HD13  H  HCH3   0   0.211   1.3816  -0.1545   5.6541
 LPL  HD21  H  HCH3   0   0.212   0.5952   2.0615   4.4461
 LPL  HD22  H  HCH3   0   0.226  -1.0221   2.1132   3.7470
 LPL  HD23  H  HCH3   0   0.225  -0.8242   2.0158   5.4914
 LPL  HH    H  HCH1   0   0.213   1.2784  -0.2200   0.7924
 LPL  HO    H  HOH1   0   0.435  -0.7562  -2.0726   0.2440
 LPL  HM1   H  HCH2   0   0.215  -1.3246   0.0704  -0.7399
 LPL  HM2   H  HCH2   0   0.205  -0.1472   1.3373  -0.4803
 LPL  HA1   H  HCH1   0   0.195   0.3919  -1.2253  -2.0363
 LPL  HB11  H  HCH2   0   0.207   0.0790   1.6460  -2.9969
 LPL  HB12  H  HCH2   0   0.206   0.5689   0.2895  -3.9939
 LPL  HG1   H  HCH1   0   0.212  -2.1495   0.6213  -2.6685
 LPL  HD31  H  HCH3   0   0.221  -2.9544   0.9543  -4.9774
 LPL  HD32  H  HCH3   0   0.220  -1.7248   2.1569  -4.5866
 LPL  HD33  H  HCH3   0   0.209  -1.3151   0.7732  -5.5991
 LPL  HD41  H  HCH3   0   0.210  -1.1308  -1.5850  -4.5193
 LPL  HD42  H  HCH3   0   0.224  -1.5789  -1.7950  -2.8287
 LPL  HD43  H  HCH3   0   0.223  -2.8072  -1.3740  -4.0165

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
 LPL  N    CA    single  1.458  0.019  1.458
 LPL  N    H     single  0.860  0.020  0.860
 LPL  N    H2    single  0.890  0.020  1.040
 LPL  CA   CB    single  1.521  0.033  1.521
 LPL  CA   CH    single  1.536  0.020  1.536
 LPL  CA   HA    single  0.970  0.020  0.970
 LPL  CB   CG    single  1.529  0.020  1.529
 LPL  CB   HB2   single  0.970  0.020  1.090
 LPL  CB   HB3   single  0.970  0.020  1.090
 LPL  CG   CD1   single  1.526  0.020  1.526
 LPL  CG   CD2   single  1.526  0.020  1.526
 LPL  CG   HG    single  0.970  0.020  1.090
 LPL  CD1  HD11  single  0.970  0.020  1.090
 LPL  CD1  HD12  single  0.970  0.020  1.090
 LPL  CD1  HD13  single  0.970  0.020  1.090
 LPL  CD2  HD21  single  0.970  0.020  1.090
 LPL  CD2  HD22  single  0.970  0.020  1.090
 LPL  CD2  HD23  single  0.970  0.020  1.090
 LPL  CH   OH    single  1.419  0.020  1.419
 LPL  CH   CM    single  1.524  0.020  1.524
 LPL  CH   HH    single  0.970  0.020  1.090
 LPL  OH   HO    single  0.850  0.020  0.980
 LPL  CM   CA1   single  1.525  0.020  1.525
 LPL  CM   HM1   single  0.970  0.020  1.090
 LPL  CM   HM2   single  0.970  0.020  1.090
 LPL  CA1  CB1   single  1.536  0.020  1.536
 LPL  CA1  C     single  1.543  0.020  1.543
 LPL  CA1  HA1   single  0.970  0.020  1.090
 LPL  CB1  CG1   single  1.531  0.020  1.531
 LPL  CB1  HB11  single  0.970  0.020  1.090
 LPL  CB1  HB12  single  0.970  0.020  1.090
 LPL  CG1  CD3   single  1.526  0.020  1.526
 LPL  CG1  CD4   single  1.524  0.020  1.524
 LPL  CG1  HG1   single  0.970  0.020  1.090
 LPL  CD3  HD31  single  0.970  0.020  1.090
 LPL  CD3  HD32  single  0.970  0.020  1.090
 LPL  CD3  HD33  single  0.970  0.020  1.090
 LPL  CD4  HD41  single  0.970  0.020  1.090
 LPL  CD4  HD42  single  0.970  0.020  1.090
 LPL  CD4  HD43  single  0.970  0.020  1.090
 LPL  C    O     deloc   1.231  0.020  1.231
 LPL  C    OXT   deloc   1.249  0.020  1.249

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
 LPL  H2    N    H     105.39  3.000
 LPL  H2    N    CA    109.66  3.000
 LPL  H     N    CA    114.00  3.000
 LPL  HA    CA   CH    106.06  3.000
 LPL  HA    CA   CB    109.00  3.000
 LPL  CH    CA   CB    110.99  3.000
 LPL  HA    CA   N     110.00  3.000
 LPL  CH    CA   N     109.67  3.000
 LPL  CB    CA   N     110.40  1.500
 LPL  HB3   CB   HB2   105.96  3.000
 LPL  HB3   CB   CG    108.88  3.000
 LPL  HB2   CB   CG    108.61  3.000
 LPL  HB3   CB   CA    108.46  3.000
 LPL  HB2   CB   CA    108.87  3.000
 LPL  CG    CB   CA    115.63  3.000
 LPL  HG    CG   CD2   107.99  3.000
 LPL  HG    CG   CD1   107.42  3.000
 LPL  CD2   CG   CD1   110.57  3.000
 LPL  HG    CG   CB    108.45  3.000
 LPL  CD2   CG   CB    112.17  3.000
 LPL  CD1   CG   CB    110.09  3.000
 LPL  HD13  CD1  HD12  107.50  3.000
 LPL  HD13  CD1  HD11  107.63  3.000
 LPL  HD12  CD1  HD11  107.78  3.000
 LPL  HD13  CD1  CG    111.00  3.000
 LPL  HD12  CD1  CG    111.34  3.000
 LPL  HD11  CD1  CG    111.41  3.000
 LPL  HD23  CD2  HD22  107.33  3.000
 LPL  HD23  CD2  HD21  107.64  3.000
 LPL  HD22  CD2  HD21  107.60  3.000
 LPL  HD23  CD2  CG    110.99  3.000
 LPL  HD22  CD2  CG    112.24  3.000
 LPL  HD21  CD2  CG    110.83  3.000
 LPL  HH    CH   CM    108.50  3.000
 LPL  HH    CH   OH    105.64  3.000
 LPL  CM    CH   OH    111.79  3.000
 LPL  HH    CH   CA    107.53  3.000
 LPL  CM    CH   CA    112.10  3.000
 LPL  OH    CH   CA    110.95  3.000
 LPL  HO    OH   CH    107.28  3.000
 LPL  HM2   CM   HM1   106.09  3.000
 LPL  HM2   CM   CA1   108.92  3.000
 LPL  HM1   CM   CA1   110.59  3.000
 LPL  HM2   CM   CH    108.44  3.000
 LPL  HM1   CM   CH    108.09  3.000
 LPL  CA1   CM   CH    114.36  3.000
 LPL  HA1   CA1  C     107.56  3.000
 LPL  HA1   CA1  CB1   108.10  3.000
 LPL  C     CA1  CB1   107.48  3.000
 LPL  HA1   CA1  CM    109.00  3.000
 LPL  C     CA1  CM    112.85  3.000
 LPL  CB1   CA1  CM    111.67  3.000
 LPL  HB12  CB1  HB11  106.14  3.000
 LPL  HB12  CB1  CG1   107.80  3.000
 LPL  HB11  CB1  CG1   108.69  3.000
 LPL  HB12  CB1  CA1   108.57  3.000
 LPL  HB11  CB1  CA1   108.48  3.000
 LPL  CG1   CB1  CA1   116.67  3.000
 LPL  HG1   CG1  CD4   108.15  3.000
 LPL  HG1   CG1  CD3   107.45  3.000
 LPL  CD4   CG1  CD3   110.27  3.000
 LPL  HG1   CG1  CB1   108.88  3.000
 LPL  CD4   CG1  CB1   112.14  3.000
 LPL  CD3   CG1  CB1   109.81  3.000
 LPL  HD33  CD3  HD32  107.55  3.000
 LPL  HD33  CD3  HD31  107.53  3.000
 LPL  HD32  CD3  HD31  107.74  3.000
 LPL  HD33  CD3  CG1   110.88  3.000
 LPL  HD32  CD3  CG1   111.53  3.000
 LPL  HD31  CD3  CG1   111.42  3.000
 LPL  HD43  CD4  HD42  107.49  3.000
 LPL  HD43  CD4  HD41  107.56  3.000
 LPL  HD42  CD4  HD41  107.51  3.000
 LPL  HD43  CD4  CG1   111.08  3.000
 LPL  HD42  CD4  CG1   112.28  3.000
 LPL  HD41  CD4  CG1   110.71  3.000
 LPL  OXT   C    O     125.81  3.000
 LPL  OXT   C    CA1   116.85  3.000
 LPL  O     C    CA1   117.29  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
 LPL  Var_01  CD1   CG   CB   CA    175.04  30.0  3
 LPL  Var_02  CD3   CG1  CB1  CA1   178.97  30.0  3
 LPL  Var_03  HD11  CD1  CG   CB   -179.14  30.0  3
 LPL  Var_04  HD21  CD2  CG   CB    -58.49  30.0  3
 LPL  Var_05  HD31  CD3  CG1  CB1  -176.63  30.0  3
 LPL  Var_06  HD41  CD4  CG1  CB1   -58.32  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
 LPL  chir_01  CA   N   CB   CH  negativ
 LPL  chir_02  CH   OH  CA   CM  positiv
 LPL  chir_03  CA1  CM  CB1  C   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
 LPL  plan-1  CA1  0.020
 LPL  plan-1  C    0.020
 LPL  plan-1  O    0.020
 LPL  plan-1  OXT  0.020

