# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 05:44:29 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (3R)-3-amino-4-methylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(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
 1VR  1VR  '(3R)-3-amino-4-methylpentanoic acid'  L-peptide  21  9  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1VR
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
 1VR  O    O  O      0  -0.515   2.1230  -0.1095  -1.2649
 1VR  C    C  C      0   0.404   2.0140   0.1156  -0.0415
 1VR  CA   C  CH2    0  -0.579   0.6381   0.5890   0.4514
 1VR  CB   C  CH1    0  -0.060  -0.5157  -0.2636  -0.0648
 1VR  N    N  NH2    0  -0.784  -0.3038  -1.6273   0.4126
 1VR  CG   C  CH1    0  -0.276  -1.8932   0.3352   0.2921
 1VR  CD2  C  CH3    0  -0.657  -2.1312   1.6651  -0.4203
 1VR  CD1  C  CH3    0  -0.680  -3.0314  -0.6280  -0.0389
 1VR  OXT  O  OC    -1  -0.801   2.9282   0.0291   0.8050
 1VR  HA1  H  HCH2   0   0.250   0.6089   0.6041   1.5464
 1VR  HA2  H  HCH2   0   0.259   0.5089   1.6275   0.1305
 1VR  HB   H  HCH1   0   0.235  -0.4461  -0.2979  -1.1583
 1VR  H    H  HNH2   0   0.317  -0.4737  -1.6650   1.4124
 1VR  H1   H  HNH2   0   0.328  -0.9810  -2.2545  -0.0024
 1VR  HG   H  HCH1   0   0.209  -1.9117   0.5165   1.3754
 1VR  H3   H  HCH3   0   0.269  -3.1156   2.0693  -0.1775
 1VR  H4   H  HCH3   0   0.203  -1.3968   2.4236  -0.1500
 1VR  H5   H  HCH3   0   0.212  -2.0884   1.5356  -1.5051
 1VR  H6   H  HCH3   0   0.215  -3.0083  -0.9175  -1.0932
 1VR  H7   H  HCH3   0   0.208  -2.9904  -1.5402   0.5579
 1VR  H8   H  HCH3   0   0.241  -4.0004  -0.1645   0.1528

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
 1VR  CD1  CG   single  1.527  0.020  1.527
 1VR  CG   CD2  single  1.527  0.020  1.527
 1VR  CG   CB   single  1.544  0.020  1.544
 1VR  N    CB   single  1.460  0.020  1.460
 1VR  CA   CB   single  1.521  0.033  1.521
 1VR  CA   C    single  1.525  0.021  1.525
 1VR  C    O    deloc   1.231  0.020  1.231
 1VR  C    OXT  deloc   1.249  0.020  1.249
 1VR  CA   HA1  single  0.970  0.020  1.090
 1VR  CA   HA2  single  0.970  0.020  1.090
 1VR  CB   HB   single  0.970  0.020  1.090
 1VR  N    H    single  0.860  0.020  0.860
 1VR  N    H1   single  0.890  0.020  1.040
 1VR  CG   HG   single  0.970  0.020  1.090
 1VR  CD2  H3   single  0.970  0.020  1.090
 1VR  CD2  H4   single  0.970  0.020  1.090
 1VR  CD2  H5   single  0.970  0.020  1.090
 1VR  CD1  H6   single  0.970  0.020  1.090
 1VR  CD1  H7   single  0.970  0.020  1.090
 1VR  CD1  H8   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
 1VR  OXT  C    CA   117.35  3.000
 1VR  OXT  C    O    125.99  3.000
 1VR  CA   C    O    120.80  1.700
 1VR  HA2  CA   HA1  106.07  3.000
 1VR  HA2  CA   CB   110.00  3.000
 1VR  HA1  CA   CB   109.03  3.000
 1VR  HA2  CA   C    107.70  3.000
 1VR  HA1  CA   C    110.41  3.000
 1VR  CB   CA   C    110.50  1.500
 1VR  HB   CB   CG   107.42  3.000
 1VR  HB   CB   N    106.72  3.000
 1VR  CG   CB   N    114.58  3.000
 1VR  HB   CB   CA   107.89  3.000
 1VR  N    CB   CA   110.40  1.500
 1VR  CG   CB   CA   112.33  3.000
 1VR  H1   N    H    105.61  3.000
 1VR  H1   N    CB   110.34  3.000
 1VR  H    N    CB   109.42  3.000
 1VR  HG   CG   CD1  107.77  3.000
 1VR  HG   CG   CD2  108.28  3.000
 1VR  CD1  CG   CD2  109.38  3.000
 1VR  HG   CG   CB   107.88  3.000
 1VR  CD2  CG   CB   111.65  3.000
 1VR  CD1  CG   CB   111.73  3.000
 1VR  H5   CD2  H4   107.58  3.000
 1VR  H5   CD2  H3   107.45  3.000
 1VR  H4   CD2  H3   107.15  3.000
 1VR  H5   CD2  CG   110.70  3.000
 1VR  H4   CD2  CG   112.66  3.000
 1VR  H3   CD2  CG   111.06  3.000
 1VR  H8   CD1  H7   107.00  3.000
 1VR  H8   CD1  H6   107.49  3.000
 1VR  H7   CD1  H6   107.78  3.000
 1VR  H8   CD1  CG   110.84  3.000
 1VR  H7   CD1  CG   112.38  3.000
 1VR  H6   CD1  CG   111.11  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
 1VR  Var_01  CB  CA   C   O    48.46  30.0  2
 1VR  Var_02  H6  CD1  CG  CB  -56.55  30.0  3
 1VR  Var_03  H3  CD2  CG  CB  178.82  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
 1VR  chir_01  CB  CG  N  CA  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
 1VR  plan-1  O    0.020
 1VR  plan-1  C    0.020
 1VR  plan-1  CA   0.020
 1VR  plan-1  OXT  0.020

