# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 12:58:00 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (3R,4S)-3-amino-4-methylhexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[C@H](N)CC(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
 BIL  BIL  '(3R,4S)-3-amino-4-methylhexanoic acid'  L-peptide  24  10  .  2022-03-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BIL
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
 BIL  C     C  C      0   0.412   2.4591   0.1309  -0.0409
 BIL  O     O  O      0  -0.624   2.5969  -0.0771  -1.2646
 BIL  CA    C  CH2    0  -0.555   1.0808   0.6279   0.4209
 BIL  CB    C  CH1    0  -0.058  -0.0697  -0.2215  -0.1108
 BIL  N     N  NH2    0  -0.793   0.1339  -1.5806   0.3817
 BIL  CG    C  CH1    0  -0.218  -1.4527   0.3909   0.2156
 BIL  CD2   C  CH3    0  -0.674  -1.6246   1.7483  -0.4648
 BIL  CD1   C  CH2    0  -0.415  -2.5955  -0.5531  -0.1742
 BIL  CE1   C  CH3    0  -0.669  -3.9832  -0.0690   0.2300
 BIL  HA    H  HCH2   0   0.190   1.0288   0.6528   1.5149
 BIL  HAA   H  HCH2   0   0.224   0.9706   1.6638   0.0868
 BIL  HB    H  HCH1   0   0.198   0.0211  -0.2629  -1.2024
 BIL  HN    H  HNH2   0   0.327  -0.0729  -1.6167   1.3743
 BIL  HG    H  HCH1   0   0.193  -1.5043   0.5396   1.3043
 BIL  H3D2  H  HCH3   0   0.211  -1.5014   1.6516  -1.5472
 BIL  H2D2  H  HCH3   0   0.231  -2.6122   2.1717  -0.2832
 BIL  H1D2  H  HCH3   0   0.230  -0.8994   2.4821  -0.1153
 BIL  H1D1  H  HCH2   0   0.205  -2.5666  -0.7237  -1.2567
 BIL  H2D1  H  HCH2   0   0.210  -2.4349  -1.5293   0.2892
 BIL  H3E1  H  HCH3   0   0.214  -4.0235   0.1660   1.2958
 BIL  H2E1  H  HCH3   0   0.220  -4.2910   0.8232  -0.3153
 BIL  H1E1  H  HCH3   0   0.227  -4.7331  -0.8371   0.0362
 BIL  OXT   O  OC    -1  -0.627   3.3474   0.0077   0.8284
 BIL  HNA   H  HNH2   0   0.343  -0.5148  -2.2210  -0.0568

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
 BIL  C     O     deloc   1.231  0.020  1.231
 BIL  C     OXT   deloc   1.249  0.020  1.249
 BIL  CA    C     single  1.525  0.021  1.525
 BIL  CA    CB    single  1.521  0.033  1.521
 BIL  CA    HA    single  0.970  0.020  0.970
 BIL  CB    HB    single  0.970  0.020  1.090
 BIL  N     CB    single  1.460  0.020  1.460
 BIL  N     HNA   single  0.890  0.020  1.040
 BIL  CG    CB    single  1.547  0.020  1.547
 BIL  CG    CD1   single  1.533  0.020  1.533
 BIL  CG    CD2   single  1.528  0.020  1.528
 BIL  CD2   H1D2  single  0.970  0.020  1.090
 BIL  CD2   H3D2  single  0.970  0.020  1.090
 BIL  CD1   CE1   single  1.524  0.020  1.524
 BIL  CE1   H2E1  single  0.970  0.020  1.090
 BIL  CE1   H3E1  single  0.970  0.020  1.090
 BIL  HAA   CA    single  0.970  0.020  1.090
 BIL  HN    N     single  0.890  0.020  1.040
 BIL  HG    CG    single  0.970  0.020  1.090
 BIL  H2D2  CD2   single  0.970  0.020  1.090
 BIL  H1D1  CD1   single  0.970  0.020  1.090
 BIL  H2D1  CD1   single  0.970  0.020  1.090
 BIL  H1E1  CE1   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
 BIL  OXT   C    CA    120.80  1.700
 BIL  CA    C    O     120.80  1.700
 BIL  OXT   C    O     125.95  3.000
 BIL  HAA   CA   HA    106.18  3.000
 BIL  HAA   CA   CB    110.16  3.000
 BIL  HA    CA   CB    109.00  3.000
 BIL  HAA   CA   C     107.75  3.000
 BIL  HA    CA   C     110.00  3.000
 BIL  CB    CA   C     110.50  1.500
 BIL  HB    CB   CG    107.40  3.000
 BIL  CG    CB   N     114.96  3.000
 BIL  HB    CB   N     106.81  3.000
 BIL  CG    CB   CA    112.35  3.000
 BIL  N     CB   CA    110.40  1.500
 BIL  HB    CB   CA    107.80  3.000
 BIL  HNA   N    HN    105.72  3.000
 BIL  HN    N    CB    109.55  3.000
 BIL  HNA   N    CB    110.71  3.000
 BIL  HG    CG   CD1   107.46  3.000
 BIL  HG    CG   CD2   108.38  3.000
 BIL  CD1   CG   CD2   110.49  3.000
 BIL  HG    CG   CB    107.71  3.000
 BIL  CD2   CG   CB    110.99  3.000
 BIL  CD1   CG   CB    111.66  3.000
 BIL  H1D2  CD2  H2D2  106.74  3.000
 BIL  H2D2  CD2  H3D2  107.54  3.000
 BIL  H1D2  CD2  H3D2  107.58  3.000
 BIL  H2D2  CD2  CG    111.89  3.000
 BIL  H3D2  CD2  CG    110.46  3.000
 BIL  H1D2  CD2  CG    112.37  3.000
 BIL  H2D1  CD1  H1D1  106.02  3.000
 BIL  H2D1  CD1  CE1   107.77  3.000
 BIL  H1D1  CD1  CE1   109.59  3.000
 BIL  H2D1  CD1  CG    109.44  3.000
 BIL  H1D1  CD1  CG    109.11  3.000
 BIL  CE1   CD1  CG    114.57  3.000
 BIL  H1E1  CE1  H2E1  107.06  3.000
 BIL  H1E1  CE1  H3E1  107.43  3.000
 BIL  H2E1  CE1  H3E1  107.56  3.000
 BIL  H1E1  CE1  CD1   110.80  3.000
 BIL  H3E1  CE1  CD1   111.14  3.000
 BIL  H2E1  CE1  CD1   112.60  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
 BIL  Var_01  CB    CA   C    O   50.25  30.0  2
 BIL  Var_02  H2E1  CE1  CD1  CG  67.14  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
 BIL  chir_01  CB  CA  N    CG   negativ
 BIL  chir_02  CG  CB  CD1  CD2  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
 BIL  plan-1  C    0.020
 BIL  plan-1  O    0.020
 BIL  plan-1  CA   0.020
 BIL  plan-1  OXT  0.020

