# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 13:05:04 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: (2S)-2-amino-3-[(2S)-oxiran-2-yl]propanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[C@H]1CO1)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
 LIS  LIS  '(2S)-2-amino-3-[(2S)-oxiran-2-yl]propanoic acid (non-preferred name)'  ligand  18  9  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LIS
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
 LIS  N     N  NH2   0  -0.787   1.7157   0.7565   0.6542
 LIS  CA    C  CH1   0  -0.216   0.3077   0.4515   0.5379
 LIS  CB    C  CH2   0  -0.491  -0.0523  -0.6395  -0.4933
 LIS  CG    C  CH1   0  -0.002   0.4223  -0.2799  -1.8721
 LIS  C     C  C     0   0.546  -0.2301   0.0444   1.8955
 LIS  CD    C  CH2   0  -0.245  -0.3856  -0.5524  -3.0551
 LIS  OXT   O  OH1   0  -0.595  -1.5581   0.0461   1.9184
 LIS  O     O  O     0  -0.436   0.4491  -0.2697   2.8389
 LIS  OD1   O  O2    0  -0.489  -0.2822   0.7634  -2.5303
 LIS  HN1   H  HNH2  0   0.347   2.2553  -0.0920   0.7765
 LIS  HN2   H  HNH2  0   0.361   2.0457   1.1876  -0.1990
 LIS  HA    H  HCH1  0   0.281  -0.2122   1.3699   0.2470
 LIS  HBC1  H  HCH2  0   0.251   0.4171  -1.5840  -0.2007
 LIS  HBC2  H  HCH2  0   0.256  -1.1312  -0.8077  -0.5079
 LIS  HG    H  HCH1  0   0.256   1.5026  -0.2387  -2.0037
 LIS  HDC1  H  HCH2  0   0.241   0.0990  -0.7215  -4.0127
 LIS  HDC2  H  HCH2  0   0.239  -1.3544  -1.0327  -2.9422
 LIS  H     H  HOH1  0   0.482  -1.8776  -0.2570   2.7815

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
 LIS  N    CA    single  1.445  0.020  1.445
 LIS  N    HN1   single  0.890  0.020  1.040
 LIS  N    HN2   single  0.890  0.020  1.040
 LIS  CA   CB    single  1.544  0.020  1.544
 LIS  CA   C     single  1.516  0.020  1.516
 LIS  CA   HA    single  0.970  0.020  1.090
 LIS  CB   CG    single  1.502  0.020  1.502
 LIS  CB   HBC1  single  0.970  0.020  1.090
 LIS  CB   HBC2  single  0.970  0.020  1.090
 LIS  CG   CD    single  1.458  0.020  1.458
 LIS  CG   OD1   single  1.421  0.020  1.421
 LIS  CG   HG    single  0.970  0.020  1.090
 LIS  C    OXT   single  1.328  0.020  1.328
 LIS  C    O     double  1.204  0.020  1.204
 LIS  CD   OD1   single  1.420  0.020  1.420
 LIS  CD   HDC1  single  0.970  0.020  1.090
 LIS  CD   HDC2  single  0.970  0.020  1.090
 LIS  OXT  H     single  0.850  0.020  0.980

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
 LIS  HN2   N    HN1   106.57  3.000
 LIS  HN2   N    CA    109.88  3.000
 LIS  HN1   N    CA    110.60  3.000
 LIS  HA    CA   C     107.15  3.000
 LIS  HA    CA   CB    107.73  3.000
 LIS  C     CA   CB    109.01  3.000
 LIS  HA    CA   N     107.88  3.000
 LIS  C     CA   N     109.28  3.000
 LIS  CB    CA   N     115.47  3.000
 LIS  HBC2  CB   HBC1  107.12  3.000
 LIS  HBC2  CB   CG    109.68  3.000
 LIS  HBC1  CB   CG    108.45  3.000
 LIS  HBC2  CB   CA    110.37  3.000
 LIS  HBC1  CB   CA    109.34  3.000
 LIS  CG    CB   CA    111.74  3.000
 LIS  HG    CG   OD1   114.10  3.000
 LIS  HG    CG   CD    117.30  3.000
 LIS  OD1   CG   CD     59.11  3.000
 LIS  HG    CG   CB    115.68  3.000
 LIS  OD1   CG   CB    116.39  3.000
 LIS  CD    CG   CB    121.66  3.000
 LIS  O     C    OXT   123.42  3.000
 LIS  O     C    CA    124.86  3.000
 LIS  OXT   C    CA    111.71  3.000
 LIS  HDC2  CD   HDC1  114.84  3.000
 LIS  HDC2  CD   OD1   115.84  3.000
 LIS  HDC1  CD   OD1   115.94  3.000
 LIS  HDC2  CD   CG    119.48  3.000
 LIS  HDC1  CD   CG    119.80  3.000
 LIS  OD1   CD   CG     59.12  3.000
 LIS  H     OXT  C     110.16  3.000
 LIS  CD    OD1  CG     61.77  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
 LIS  CONST_01  H     OXT  C    CA   180.00   0.0  0
 LIS  Var_01    OD1   CD   CG   CB   103.86  30.0  1
 LIS  Var_02    HDC1  CD   OD1  CG  -110.68  30.0  1
 LIS  Var_03    CD    CG   CB   CA  -140.35  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
 LIS  chir_01  CA  N   CB  C    negativ
 LIS  chir_02  CG  CB  CD  OD1  both

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
 LIS  plan-1  CA   0.020
 LIS  plan-1  C    0.020
 LIS  plan-1  OXT  0.020
 LIS  plan-1  O    0.020
 LIS  plan-1  H    0.020

