# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 08:40:38 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (3S)-3-amino-5-methylhexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)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
 B3L  B3L  '(3S)-3-amino-5-methylhexanoic acid'  L-peptide  24  10  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B3L
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
 B3L  O     O  O      0  -0.624   2.6661  -0.7879  -0.9752
 B3L  C     C  C      0   0.407   2.5784   0.1378  -0.1413
 B3L  CA    C  CH2    0  -0.539   1.2333   0.8776  -0.0809
 B3L  CB    C  CH1    0  -0.100   0.0397  -0.0567   0.0814
 B3L  N     N  NH2    0  -0.791   0.1856  -0.7856   1.3376
 B3L  CG    C  CH2    0  -0.391  -1.2735   0.7234  -0.0514
 B3L  CD    C  CH1    0  -0.241  -2.5571  -0.0917   0.1116
 B3L  CE2   C  CH3    0  -0.647  -3.7731   0.8289   0.0621
 B3L  CE1   C  CH3    0  -0.657  -2.6752  -1.1908  -0.9402
 B3L  HA    H  HCH2   0   0.191   1.2323   1.6096   0.7339
 B3L  HAA   H  HCH2   0   0.216   1.1089   1.4499  -1.0078
 B3L  HB    H  HCH1   0   0.211   0.0955  -0.7955  -0.7231
 B3L  HN    H  HNH2   0   0.327   0.0634  -0.1438   2.1142
 B3L  HG    H  HCH2   0   0.205  -1.2734   1.5327   0.6906
 B3L  HGA   H  HCH2   0   0.200  -1.2939   1.2141  -1.0329
 B3L  HD    H  HCH1   0   0.202  -2.5419  -0.5643   1.1010
 B3L  H3E2  H  HCH3   0   0.222  -4.7021   0.2723   0.1989
 B3L  H2E2  H  HCH3   0   0.222  -3.7250   1.5932   0.8398
 B3L  H1E2  H  HCH3   0   0.210  -3.8348   1.3408  -0.9018
 B3L  H3E1  H  HCH3   0   0.224  -3.6015  -1.7554  -0.8197
 B3L  H2E1  H  HCH3   0   0.212  -2.6776  -0.7641  -1.9467
 B3L  H1E1  H  HCH3   0   0.226  -1.8511  -1.9030  -0.8881
 B3L  OXT   O  OC    -1  -0.625   3.4871   0.5284   0.6209
 B3L  HNA   H  HNH2   0   0.340  -0.5510  -1.4739   1.4349

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
 B3L  C     O     deloc   1.231  0.020  1.231
 B3L  C     OXT   deloc   1.249  0.020  1.249
 B3L  CA    C     single  1.525  0.021  1.525
 B3L  CB    CA    single  1.521  0.033  1.521
 B3L  CB    HB    single  0.970  0.020  1.090
 B3L  N     CB    single  1.460  0.020  1.460
 B3L  N     HNA   single  0.890  0.020  1.040
 B3L  CG    CB    single  1.533  0.020  1.533
 B3L  CG    HG    single  0.970  0.020  1.090
 B3L  CD    CG    single  1.529  0.020  1.529
 B3L  CD    CE1   single  1.526  0.020  1.526
 B3L  CE2   CD    single  1.526  0.020  1.526
 B3L  CE2   H1E2  single  0.970  0.020  1.090
 B3L  CE1   H1E1  single  0.970  0.020  1.090
 B3L  CE1   H3E1  single  0.970  0.020  1.090
 B3L  HA    CA    single  0.970  0.020  0.970
 B3L  HAA   CA    single  0.970  0.020  1.090
 B3L  HN    N     single  0.890  0.020  1.040
 B3L  HGA   CG    single  0.970  0.020  1.090
 B3L  HD    CD    single  0.970  0.020  1.090
 B3L  H3E2  CE2   single  0.970  0.020  1.090
 B3L  H2E2  CE2   single  0.970  0.020  1.090
 B3L  H2E1  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
 B3L  OXT   C    CA    117.55  3.000
 B3L  CA    C    O     120.80  1.700
 B3L  OXT   C    O     126.03  3.000
 B3L  HAA   CA   HA    106.26  3.000
 B3L  HAA   CA   CB    108.73  3.000
 B3L  HA    CA   CB    109.00  3.000
 B3L  HAA   CA   C     108.51  3.000
 B3L  HA    CA   C     110.00  3.000
 B3L  CB    CA   C     110.50  1.500
 B3L  HB    CB   CG    108.89  3.000
 B3L  CG    CB   N     114.47  3.000
 B3L  HB    CB   N     106.90  3.000
 B3L  CG    CB   CA    110.46  3.000
 B3L  N     CB   CA    110.40  1.500
 B3L  HB    CB   CA    107.20  3.000
 B3L  HNA   N    HN    105.59  3.000
 B3L  HN    N    CB    109.32  3.000
 B3L  HNA   N    CB    110.45  3.000
 B3L  HGA   CG   HG    105.95  3.000
 B3L  HGA   CG   CD    108.54  3.000
 B3L  HG    CG   CD    108.71  3.000
 B3L  HGA   CG   CB    108.72  3.000
 B3L  CD    CG   CB    116.01  3.000
 B3L  HG    CG   CB    108.45  3.000
 B3L  HD    CD   CE1   108.21  3.000
 B3L  HD    CD   CE2   107.48  3.000
 B3L  CE1   CD   CE2   110.52  3.000
 B3L  HD    CD   CG    108.32  3.000
 B3L  CE2   CD   CG    110.11  3.000
 B3L  CE1   CD   CG    112.05  3.000
 B3L  H1E2  CE2  H2E2  107.63  3.000
 B3L  H2E2  CE2  H3E2  107.77  3.000
 B3L  H1E2  CE2  H3E2  107.53  3.000
 B3L  H2E2  CE2  CD    111.36  3.000
 B3L  H3E2  CE2  CD    111.50  3.000
 B3L  H1E2  CE2  CD    110.86  3.000
 B3L  H1E1  CE1  H2E1  107.49  3.000
 B3L  H2E1  CE1  H3E1  107.56  3.000
 B3L  H1E1  CE1  H3E1  107.35  3.000
 B3L  H2E1  CE1  CD    110.71  3.000
 B3L  H3E1  CE1  CD    111.23  3.000
 B3L  H1E1  CE1  CD    112.27  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
 B3L  Var_01  CB    CA   C   O    52.27  30.0  2
 B3L  Var_02  CE1   CD   CG  CB  -60.90  30.0  2
 B3L  Var_03  H1E1  CE1  CD  CG   60.42  30.0  3
 B3L  Var_04  H1E2  CE2  CD  CG   61.51  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
 B3L  chir_01  CB  CA  N  CG  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
 B3L  plan-1  O    0.020
 B3L  plan-1  C    0.020
 B3L  plan-1  CA   0.020
 B3L  plan-1  OXT  0.020

