# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 18:37:09 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: N-[(2S)-2-amino-4-methylpentyl]-L-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)CN[C@@H](C(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
 LAV  LAV  N-[(2S)-2-amino-4-methylpentyl]-L-valine  peptide  39  15  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LAV
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
 LAV  C     C  CH2   0  -0.262   0.4177  -0.1518  -0.5261
 LAV  N     N  NH2   0  -0.792   1.9579  -1.7224   0.6858
 LAV  O     O  O     0  -0.435  -2.0376   1.9074   0.7365
 LAV  C1    C  C     0   0.520  -2.2280   1.2461  -0.2524
 LAV  N1    N  NH1   0  -0.615  -0.7248  -0.5551   0.2749
 LAV  C2    C  CH1   0  -0.266  -3.1499  -0.9777   0.4016
 LAV  C3    C  CH1   0  -0.117  -2.0018  -0.2552  -0.3349
 LAV  CA    C  CH1   0  -0.123   1.7352  -0.3593   0.2257
 LAV  CB    C  CH2   0  -0.396   2.8976   0.0898  -0.6568
 LAV  CG    C  CH1   0  -0.217   4.2836   0.0270  -0.0148
 LAV  CD1   C  CH3   0  -0.652   5.3405   0.4746  -1.0204
 LAV  CD2   C  CH3   0  -0.665   4.3683   0.8644   1.2571
 LAV  CG2   C  CH3   0  -0.668  -3.0368  -2.4922   0.2376
 LAV  H     H  HCH2  0   0.192   0.4595  -0.6850  -1.4906
 LAV  HA    H  HCH2  0   0.223   0.3255   0.9120  -0.7649
 LAV  HN    H  HNH2  0   0.346   1.2612  -1.9924   1.3679
 LAV  HNA   H  HNH2  0   0.335   1.8787  -2.3711  -0.0896
 LAV  OXT   O  OH1   0  -0.589  -2.6855   1.7533  -1.3914
 LAV  HN1   H  HNH1  0   0.342  -0.6683  -1.5535   0.4253
 LAV  H2    H  HCH1  0   0.237  -3.0527  -0.7299   1.4638
 LAV  H3    H  HCH1  0   0.225  -2.0435  -0.5504  -1.3963
 LAV  HAA   H  HCH1  0   0.224   1.6999   0.2770   1.1154
 LAV  HB    H  HCH2  0   0.212   2.9005  -0.5241  -1.5660
 LAV  HBA   H  HCH2  0   0.210   2.7069   1.1179  -0.9867
 LAV  HG    H  HCH1  0   0.212   4.4860  -1.0142   0.2532
 LAV  HD1   H  HCH3  0   0.210   5.1755   1.5102  -1.3291
 LAV  HD1A  H  HCH3  0   0.222   6.3443   0.4144  -0.5955
 LAV  HD1B  H  HCH3  0   0.221   5.3263  -0.1443  -1.9198
 LAV  HD2   H  HCH3  0   0.227   3.7121   0.4851   2.0411
 LAV  HD2A  H  HCH3  0   0.223   5.3839   0.8652   1.6574
 LAV  HD2B  H  HCH3  0   0.210   4.0887   1.9037   1.0637
 LAV  HG1   H  HCH3  0   0.225  -4.6386  -0.6699  -1.1565
 LAV  HG1A  H  HCH3  0   0.238  -5.3052  -1.0877   0.4183
 LAV  HG1B  H  HCH3  0   0.235  -4.7160   0.5357   0.1315
 LAV  HG2   H  HCH3  0   0.231  -2.1195  -2.9065   0.6578
 LAV  HG2A  H  HCH3  0   0.241  -3.8643  -2.9875   0.7469
 LAV  HG2B  H  HCH3  0   0.225  -3.0798  -2.7751  -0.8167
 LAV  HXT   H  HOH1  0   0.479  -2.8624   2.7006  -1.2845
 LAV  CG1   C  CH3   0  -0.668  -4.5231  -0.5161  -0.0817

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
 LAV  C    N1    single  1.452  0.020  1.452
 LAV  C    CA    single  1.525  0.021  1.525
 LAV  C    H     single  0.970  0.020  1.090
 LAV  C    HA    single  0.970  0.020  1.090
 LAV  N    CA    single  1.458  0.019  1.458
 LAV  N    HN    single  0.890  0.020  1.040
 LAV  N    HNA   single  0.890  0.020  1.040
 LAV  O    C1    double  1.205  0.020  1.205
 LAV  C1   C3    single  1.520  0.020  1.520
 LAV  C1   OXT   single  1.328  0.020  1.328
 LAV  N1   C3    single  1.447  0.020  1.447
 LAV  N1   HN1   single  0.890  0.020  1.040
 LAV  C2   C3    single  1.544  0.020  1.544
 LAV  C2   CG1   single  1.527  0.020  1.527
 LAV  C2   CG2   single  1.528  0.020  1.528
 LAV  C2   H2    single  0.970  0.020  1.090
 LAV  C3   H3    single  0.970  0.020  1.090
 LAV  CA   CB    single  1.521  0.033  1.521
 LAV  CA   HAA   single  0.970  0.020  1.090
 LAV  CB   CG    single  1.529  0.020  1.529
 LAV  CB   HB    single  0.970  0.020  1.090
 LAV  CB   HBA   single  0.970  0.020  1.090
 LAV  CG   CD1   single  1.526  0.020  1.526
 LAV  CG   CD2   single  1.525  0.020  1.525
 LAV  CG   HG    single  0.970  0.020  1.090
 LAV  CD1  HD1   single  0.970  0.020  1.090
 LAV  CD1  HD1A  single  0.970  0.020  1.090
 LAV  CD1  HD1B  single  0.970  0.020  1.090
 LAV  CD2  HD2   single  0.970  0.020  1.090
 LAV  CD2  HD2A  single  0.970  0.020  1.090
 LAV  CD2  HD2B  single  0.970  0.020  1.090
 LAV  CG1  HG1   single  0.970  0.020  1.090
 LAV  CG1  HG1A  single  0.970  0.020  1.090
 LAV  CG1  HG1B  single  0.970  0.020  1.090
 LAV  CG2  HG2   single  0.970  0.020  1.090
 LAV  CG2  HG2A  single  0.970  0.020  1.090
 LAV  CG2  HG2B  single  0.970  0.020  1.090
 LAV  OXT  HXT   single  0.850  0.020  0.980

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
 LAV  HA    C    H     106.40  3.000
 LAV  HA    C    CA    110.00  3.000
 LAV  H     C    CA    109.35  3.000
 LAV  HA    C    N1    108.91  3.000
 LAV  H     C    N1    112.20  3.000
 LAV  CA    C    N1    111.63  3.000
 LAV  HNA   N    HN    106.92  3.000
 LAV  HNA   N    CA    110.20  3.000
 LAV  HN    N    CA    110.96  3.000
 LAV  OXT   C1   C3    112.44  3.000
 LAV  OXT   C1   O     123.29  3.000
 LAV  C3    C1   O     124.26  3.000
 LAV  HN1   N1   C3    108.47  3.000
 LAV  HN1   N1   C     108.19  3.000
 LAV  C3    N1   C     113.85  3.000
 LAV  H2    C2   CG2   108.78  3.000
 LAV  H2    C2   CG1   108.56  3.000
 LAV  CG2   C2   CG1   109.41  3.000
 LAV  H2    C2   C3    106.91  3.000
 LAV  CG2   C2   C3    110.97  3.000
 LAV  CG1   C2   C3    112.11  3.000
 LAV  H3    C3   C2    107.81  3.000
 LAV  H3    C3   N1    112.57  3.000
 LAV  C2    C3   N1    111.00  3.000
 LAV  H3    C3   C1    108.12  3.000
 LAV  C2    C3   C1    109.00  3.000
 LAV  N1    C3   C1    108.25  3.000
 LAV  HAA   CA   CB    108.87  3.000
 LAV  HAA   CA   N     107.00  3.000
 LAV  CB    CA   N     110.40  1.500
 LAV  HAA   CA   C     107.01  3.000
 LAV  CB    CA   C     110.50  1.500
 LAV  N     CA   C     111.00  2.800
 LAV  HBA   CB   HB    106.00  3.000
 LAV  HBA   CB   CG    108.82  3.000
 LAV  HB    CB   CG    108.83  3.000
 LAV  HBA   CB   CA    108.50  3.000
 LAV  HB    CB   CA    108.45  3.000
 LAV  CG    CB   CA    115.81  3.000
 LAV  HG    CG   CD2   107.94  3.000
 LAV  HG    CG   CD1   108.21  3.000
 LAV  CD2   CG   CD1   110.49  3.000
 LAV  HG    CG   CB    108.04  3.000
 LAV  CD2   CG   CB    112.21  3.000
 LAV  CD1   CG   CB    109.82  3.000
 LAV  HD1B  CD1  HD1A  107.53  3.000
 LAV  HD1B  CD1  HD1   107.60  3.000
 LAV  HD1A  CD1  HD1   107.52  3.000
 LAV  HD1B  CD1  CG    111.57  3.000
 LAV  HD1A  CD1  CG    111.36  3.000
 LAV  HD1   CD1  CG    111.07  3.000
 LAV  HD2B  CD2  HD2A  107.58  3.000
 LAV  HD2B  CD2  HD2   107.69  3.000
 LAV  HD2A  CD2  HD2   107.24  3.000
 LAV  HD2B  CD2  CG    111.11  3.000
 LAV  HD2A  CD2  CG    110.97  3.000
 LAV  HD2   CD2  CG    112.04  3.000
 LAV  HG2B  CG2  HG2A  107.65  3.000
 LAV  HG2B  CG2  HG2   107.85  3.000
 LAV  HG2A  CG2  HG2   106.60  3.000
 LAV  HG2B  CG2  C2    110.94  3.000
 LAV  HG2A  CG2  C2    110.12  3.000
 LAV  HG2   CG2  C2    113.42  3.000
 LAV  HXT   OXT  C1    109.96  3.000
 LAV  HG1B  CG1  HG1A  106.81  3.000
 LAV  HG1B  CG1  HG1   108.04  3.000
 LAV  HG1A  CG1  HG1   107.57  3.000
 LAV  HG1B  CG1  C2    112.88  3.000
 LAV  HG1A  CG1  C2    109.96  3.000
 LAV  HG1   CG1  C2    111.35  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
 LAV  CONST_01  HXT  OXT  C1  O     0.00   0.0  0
 LAV  Var_01    CA   C    N1  C3  174.11  30.0  1
 LAV  Var_02    CD1  CG   CB  CA  178.78  30.0  3
 LAV  Var_03    HG1  CG1  C2  C3   57.62  30.0  3
 LAV  Var_04    HG2  CG2  C2  C3   61.71  30.0  3
 LAV  Var_05    HD1  CD1  CG  CB   61.70  30.0  3
 LAV  Var_06    HD2  CD2  CG  CB   64.37  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
 LAV  chir_01  C3  C1  N1  C2  negativ
 LAV  chir_02  CA  N   C   CB  positiv

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
 LAV  plan-1  O    0.020
 LAV  plan-1  C1   0.020
 LAV  plan-1  C3   0.020
 LAV  plan-1  OXT  0.020
 LAV  plan-1  HXT  0.020

