# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 16:11:51 2022
#   Inital geometry file: a 49 line input string
#   Ligand name: (2S,3S)-2-azanyl-3-methyl-4-oxo-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](C=O)[C@H](N)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
 LVN  LVN  '(2S,3S)-2-azanyl-3-methyl-4-oxo-butanoic acid'  L-peptide  17  9  .  2012-08-28  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LVN
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
 LVN  C     C  C      0   0.397  -44.0520  -30.0877  -30.5347
 LVN  N     N  NH2    0  -0.819  -44.4631  -28.0476  -29.2506
 LVN  O     O  O      0  -0.526  -43.5338  -30.4167  -31.6209
 LVN  CA    C  CH1    0  -0.143  -44.8129  -28.7361  -30.4869
 LVN  CB    C  CH1    0  -0.396  -44.4763  -27.8759  -31.6972
 LVN  CG1   C  C1     0   0.177  -44.8475  -28.5541  -32.9865
 LVN  OG1   O  O      0  -0.394  -45.8664  -29.1735  -33.1821
 LVN  CG2   C  CH3    0  -0.662  -45.1743  -26.5105  -31.6924
 LVN  OXT   O  OC    -1  -0.760  -44.0792  -30.7589  -29.4846
 LVN  H     H  HNH2   0   0.355  -45.1632  -27.3480  -29.0380
 LVN  H2    H  HNH2   0   0.350  -44.5167  -28.7246  -28.4992
 LVN  HA    H  HCH1   0   0.236  -45.8878  -28.9802  -30.5259
 LVN  HB    H  HCH1   0   0.268  -43.3970  -27.7041  -31.7238
 LVN  HG11  H  H      0   0.174  -44.1253  -28.3942  -33.8116
 LVN  HG21  H  HCH3   0   0.268  -44.9573  -25.9489  -32.6032
 LVN  HG22  H  HCH3   0   0.269  -46.2581  -26.6193  -31.6163
 LVN  HG23  H  HCH3   0   0.205  -44.8305  -25.9054  -30.8531

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
 LVN  C    O     deloc   1.231  0.020  1.231
 LVN  C    CA    single  1.525  0.021  1.525
 LVN  C    OXT   deloc   1.247  0.020  1.247
 LVN  N    CA    single  1.458  0.019  1.458
 LVN  CA   CB    single  1.540  0.027  1.540
 LVN  CB   CG1   single  1.503  0.020  1.503
 LVN  CB   CG2   single  1.533  0.020  1.533
 LVN  CG1  OG1   double  1.208  0.020  1.208
 LVN  N    H     single  0.860  0.020  0.860
 LVN  N    H2    single  0.890  0.020  1.040
 LVN  CA   HA    single  0.970  0.020  0.970
 LVN  CB   HB    single  0.970  0.020  1.090
 LVN  CG1  HG11  single  0.930  0.020  1.080
 LVN  CG2  HG21  single  0.970  0.020  1.090
 LVN  CG2  HG22  single  0.970  0.020  1.090
 LVN  CG2  HG23  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
 LVN  OXT   C    CA    115.61  3.000
 LVN  OXT   C    O     126.91  3.000
 LVN  CA    C    O     120.80  1.700
 LVN  H2    N    H     105.64  3.000
 LVN  H2    N    CA    107.50  3.000
 LVN  H     N    CA    114.00  3.000
 LVN  HA    CA   CB    109.00  3.000
 LVN  HA    CA   N     110.00  3.000
 LVN  CB    CA   N     111.50  1.700
 LVN  HA    CA   C     109.00  3.000
 LVN  CB    CA   C     111.40  1.900
 LVN  N     CA   C     111.00  2.800
 LVN  HB    CB   CG2   108.03  3.000
 LVN  HB    CB   CG1   107.09  3.000
 LVN  CG2   CB   CG1   106.98  3.000
 LVN  HB    CB   CA    109.05  3.000
 LVN  CG2   CB   CA    113.57  3.000
 LVN  CG1   CB   CA    111.85  3.000
 LVN  HG11  CG1  OG1   120.20  3.000
 LVN  HG11  CG1  CB    114.36  3.000
 LVN  OG1   CG1  CB    125.33  3.000
 LVN  HG23  CG2  HG22  108.35  3.000
 LVN  HG23  CG2  HG21  107.10  3.000
 LVN  HG22  CG2  HG21  107.86  3.000
 LVN  HG23  CG2  CB    110.67  3.000
 LVN  HG22  CG2  CB    111.30  3.000
 LVN  HG21  CG2  CB    111.40  3.000

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
 LVN  chir_01  CA  C   N    CB   negativ
 LVN  chir_02  CB  CA  CG1  CG2  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
 LVN  plan-1  C     0.020
 LVN  plan-1  O     0.020
 LVN  plan-1  CA    0.020
 LVN  plan-1  OXT   0.020
 LVN  plan-2  CB    0.020
 LVN  plan-2  CG1   0.020
 LVN  plan-2  OG1   0.020
 LVN  plan-2  HG11  0.020

