# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun May 31 21:07:51 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  38  15  .  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_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  -0.253   0.4292  -0.1779  -0.5951
 LAV  N     N  NH2    0  -0.792   1.9468  -1.7653   0.6329
 LAV  O     O  O      0  -0.612  -1.9563   1.8329   0.6894
 LAV  C1    C  C      0   0.387  -2.1786   1.2659  -0.3978
 LAV  N1    N  NH1    0  -0.623  -0.7214  -0.6434   0.1524
 LAV  C2    C  CH1    0  -0.254  -3.1482  -0.9462   0.3327
 LAV  C3    C  CH1    0  -0.099  -1.9987  -0.2705  -0.4330
 LAV  CA    C  CH1    0  -0.119   1.7349  -0.3985   0.1743
 LAV  CB    C  CH2    0  -0.397   2.9159   0.0436  -0.6867
 LAV  CG    C  CH1    0  -0.220   4.2795   0.0530   0.0045
 LAV  CD1   C  CH3    0  -0.653   5.3758   0.3831  -1.0044
 LAV  CD2   C  CH3    0  -0.662   4.3224   1.0350   1.1712
 LAV  H     H  HCH2   0   0.175   0.5093  -0.6524  -1.5894
 LAV  HA    H  HCH2   0   0.218   0.3249   0.8949  -0.7767
 LAV  HN    H  HNH2   0   0.342   1.2088  -2.0409   1.2686
 LAV  HNA   H  HNH2   0   0.332   1.9022  -2.4030  -0.1548
 LAV  OXT   O  OC    -1  -0.618  -2.5586   1.8114  -1.4546
 LAV  HN1   H  HNH1   0   0.328  -0.6691  -1.6529   0.1936
 LAV  H2    H  HCH1   0   0.207  -3.0478  -0.6510   1.3829
 LAV  H3    H  HCH1   0   0.157  -2.0709  -0.5919  -1.4879
 LAV  HAA   H  HCH1   0   0.216   1.6869   0.2327   1.0675
 LAV  HB    H  HCH2   0   0.210   2.9627  -0.6147  -1.5635
 LAV  HBA   H  HCH2   0   0.208   2.7096   1.0477  -1.0769
 LAV  HG    H  HCH1   0   0.212   4.4679  -0.9515   0.3957
 LAV  HD1   H  HCH3   0   0.209   5.2246   1.3752  -1.4377
 LAV  HD1A  H  HCH3   0   0.222   6.3615   0.3782  -0.5349
 LAV  HD1B  H  HCH3   0   0.221   5.3972  -0.3362  -1.8255
 LAV  HD2   H  HCH3   0   0.227   3.6248   0.7652   1.9649
 LAV  HD2A  H  HCH3   0   0.222   5.3187   1.0725   1.6160
 LAV  HD2B  H  HCH3   0   0.209   4.0716   2.0457   0.8381
 LAV  HG1   H  HCH3   0   0.211  -4.6265  -0.6770  -1.2387
 LAV  HG1A  H  HCH3   0   0.220  -5.3133  -1.0028   0.3500
 LAV  HG1B  H  HCH3   0   0.230  -4.6673   0.5897  -0.0140
 LAV  HG2   H  HCH3   0   0.221  -2.1718  -2.8884   0.6868
 LAV  HG2A  H  HCH3   0   0.230  -3.9184  -2.9221   0.7860
 LAV  HG2B  H  HCH3   0   0.214  -3.1362  -2.8078  -0.7884
 LAV  CG1   C  CH3    0  -0.659  -4.5115  -0.4772  -0.1709
 LAV  CG2   C  CH3    0  -0.668  -3.0809  -2.4714   0.2503

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  1.449  0.020  1.449
 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    deloc   1.246  0.020  1.246
 LAV  C1   C3    single  1.547  0.020  1.547
 LAV  C1   OXT   deloc   1.249  0.020  1.249
 LAV  N1   C3    single  1.454  0.020  1.454
 LAV  N1   HN1   single  0.890  0.020  1.040
 LAV  C2   C3    single  1.538  0.020  1.538
 LAV  C2   CG1   single  1.527  0.020  1.527
 LAV  C2   CG2   single  1.529  0.020  1.529
 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  1.526  0.020  1.526
 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

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     106.20  3.000
 LAV  HA    C    CA    110.00  3.000
 LAV  H     C    CA    109.18  3.000
 LAV  HA    C    N1    108.98  3.000
 LAV  H     C    N1    112.58  3.000
 LAV  CA    C    N1    111.81  3.000
 LAV  HNA   N    HN    106.52  3.000
 LAV  HNA   N    CA    109.81  3.000
 LAV  HN    N    CA    110.30  3.000
 LAV  OXT   C1   C3    116.74  3.000
 LAV  OXT   C1   O     126.44  3.000
 LAV  C3    C1   O     116.81  3.000
 LAV  HN1   N1   C3    108.52  3.000
 LAV  HN1   N1   C     107.49  3.000
 LAV  C3    N1   C     114.05  3.000
 LAV  H2    C2   CG2   108.44  3.000
 LAV  H2    C2   CG1   108.37  3.000
 LAV  CG2   C2   CG1   109.14  3.000
 LAV  H2    C2   C3    106.88  3.000
 LAV  CG2   C2   C3    112.25  3.000
 LAV  CG1   C2   C3    111.61  3.000
 LAV  H3    C3   C2    107.38  3.000
 LAV  H3    C3   N1    111.54  3.000
 LAV  C2    C3   N1    110.10  3.000
 LAV  H3    C3   C1    107.63  3.000
 LAV  C2    C3   C1    109.76  3.000
 LAV  N1    C3   C1    110.35  3.000
 LAV  HAA   CA   CB    109.09  3.000
 LAV  HAA   CA   N     106.88  3.000
 LAV  CB    CA   N     110.40  1.500
 LAV  HAA   CA   C     106.83  3.000
 LAV  CB    CA   C     110.50  1.500
 LAV  N     CA   C     111.00  2.800
 LAV  HBA   CB   HB    105.84  3.000
 LAV  HBA   CB   CG    108.85  3.000
 LAV  HB    CB   CG    109.08  3.000
 LAV  HBA   CB   CA    108.67  3.000
 LAV  HB    CB   CA    108.05  3.000
 LAV  CG    CB   CA    115.90  3.000
 LAV  HG    CG   CD2   108.22  3.000
 LAV  HG    CG   CD1   108.14  3.000
 LAV  CD2   CG   CD1   110.25  3.000
 LAV  HG    CG   CB    108.03  3.000
 LAV  CD2   CG   CB    112.01  3.000
 LAV  CD1   CG   CB    110.07  3.000
 LAV  HD1B  CD1  HD1A  107.62  3.000
 LAV  HD1B  CD1  HD1   107.61  3.000
 LAV  HD1A  CD1  HD1   107.42  3.000
 LAV  HD1B  CD1  CG    111.64  3.000
 LAV  HD1A  CD1  CG    111.30  3.000
 LAV  HD1   CD1  CG    111.05  3.000
 LAV  HD2B  CD2  HD2A  107.56  3.000
 LAV  HD2B  CD2  HD2   107.68  3.000
 LAV  HD2A  CD2  HD2   107.20  3.000
 LAV  HD2B  CD2  CG    110.83  3.000
 LAV  HD2A  CD2  CG    111.06  3.000
 LAV  HD2   CD2  CG    112.30  3.000
 LAV  HG1B  CG1  HG1A  107.33  3.000
 LAV  HG1B  CG1  HG1   107.74  3.000
 LAV  HG1A  CG1  HG1   107.52  3.000
 LAV  HG1B  CG1  C2    112.40  3.000
 LAV  HG1A  CG1  C2    110.53  3.000
 LAV  HG1   CG1  C2    111.11  3.000
 LAV  HG2B  CG2  HG2A  107.49  3.000
 LAV  HG2B  CG2  HG2   107.73  3.000
 LAV  HG2A  CG2  HG2   106.56  3.000
 LAV  HG2B  CG2  C2    110.85  3.000
 LAV  HG2A  CG2  C2    110.59  3.000
 LAV  HG2   CG2  C2    113.35  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  Var_01  CA   C    N1  C3  170.81  30.0  1
 LAV  Var_02  CD1  CG   CB  CA  174.59  30.0  3
 LAV  Var_03  HG1  CG1  C2  C3   57.96  30.0  3
 LAV  Var_04  HG2  CG2  C2  C3   61.48  30.0  3
 LAV  Var_05  HD1  CD1  CG  CB   61.35  30.0  3
 LAV  Var_06  HD2  CD2  CG  CB   63.32  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
 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

