# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 10:40:59 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2S,4R)-2-amino-4-carboxypentanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](C[C@H](N)C([O-])=O)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
 SYM  SYM  (2S,4R)-2-amino-4-carboxypentanoate  ligand  20  11  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SYM
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
 SYM  CB    C  CH2    0  -0.393  -0.0254   0.5929   0.6511
 SYM  CG1   C  CH1    0  -0.319   1.4224   0.8089   0.2231
 SYM  CG2   C  CH3    0  -0.663   2.2461   1.3254   1.4044
 SYM  CD    C  C      0   0.405   2.0775  -0.4752  -0.3198
 SYM  OE1   O  OC    -1  -0.626   2.7662  -0.3741  -1.3577
 SYM  OE2   O  O      0  -0.622   1.9061  -1.5199   0.3441
 SYM  C     C  C      0   0.381  -2.3674  -0.1140   0.1573
 SYM  OT1   O  OC    -1  -0.626  -2.5001  -1.1885   0.7807
 SYM  OT2   O  O      0  -0.615  -3.2377   0.7722   0.0256
 SYM  N     N  NH2    0  -0.787  -0.9721   1.1347  -1.5447
 SYM  CA    C  CH1    0  -0.212  -0.9770   0.1560  -0.4654
 SYM  HB1   H  HCH2   0   0.204  -0.0542  -0.1545   1.4470
 SYM  HB2   H  HCH2   0   0.191  -0.4075   1.5254   1.0879
 SYM  HG1   H  HCH1   0   0.190   1.4427   1.5643  -0.5661
 SYM  HG21  H  HCH3   0   0.218   3.2807   1.5253   1.1174
 SYM  HG22  H  HCH3   0   0.214   1.8304   2.2553   1.7995
 SYM  HG23  H  HCH3   0   0.209   2.2623   0.5972   2.2178
 SYM  HA    H  HCH1   0   0.204  -0.6025  -0.7904  -0.8698
 SYM  HN1   H  HNH2   0   0.330  -1.5166   0.7676  -2.3165
 SYM  HN2   H  HNH2   0   0.318  -1.5037   1.9385  -1.2277

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
 SYM  CB   CG1   single  1.525  0.020  1.525
 SYM  CB   CA    single  1.531  0.020  1.531
 SYM  CB   HB1   single  0.970  0.020  1.090
 SYM  CB   HB2   single  0.970  0.020  1.090
 SYM  CG1  CG2   single  1.530  0.020  1.530
 SYM  CG1  CD    single  1.540  0.020  1.540
 SYM  CG1  HG1   single  0.970  0.020  1.090
 SYM  CG2  HG21  single  0.970  0.020  1.090
 SYM  CG2  HG22  single  0.970  0.020  1.090
 SYM  CG2  HG23  single  0.970  0.020  1.090
 SYM  CD   OE1   deloc   1.250  0.020  1.250
 SYM  CD   OE2   deloc   1.250  0.020  1.250
 SYM  C    OT1   deloc   1.249  0.020  1.249
 SYM  C    OT2   deloc   1.249  0.020  1.249
 SYM  C    CA    single  1.547  0.020  1.547
 SYM  N    CA    single  1.457  0.020  1.457
 SYM  N    HN1   single  0.890  0.020  1.040
 SYM  N    HN2   single  0.890  0.020  1.040
 SYM  CA   HA    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
 SYM  HB2   CB   HB1   106.38  3.000
 SYM  HB2   CB   CA    108.43  3.000
 SYM  HB1   CB   CA    108.65  3.000
 SYM  HB2   CB   CG1   108.76  3.000
 SYM  HB1   CB   CG1   109.06  3.000
 SYM  CA    CB   CG1   115.21  3.000
 SYM  HG1   CG1  CD    108.29  3.000
 SYM  HG1   CG1  CG2   108.32  3.000
 SYM  CD    CG1  CG2   108.94  3.000
 SYM  HG1   CG1  CB    108.56  3.000
 SYM  CD    CG1  CB    112.62  3.000
 SYM  CG2   CG1  CB    110.02  3.000
 SYM  HG23  CG2  HG22  107.69  3.000
 SYM  HG23  CG2  HG21  107.68  3.000
 SYM  HG22  CG2  HG21  107.44  3.000
 SYM  HG23  CG2  CG1   110.98  3.000
 SYM  HG22  CG2  CG1   111.21  3.000
 SYM  HG21  CG2  CG1   111.65  3.000
 SYM  OE2   CD   OE1   125.76  3.000
 SYM  OE2   CD   CG1   116.83  3.000
 SYM  OE1   CD   CG1   117.37  3.000
 SYM  CA    C    OT2   117.38  3.000
 SYM  CA    C    OT1   116.51  3.000
 SYM  OT2   C    OT1   126.07  3.000
 SYM  HN2   N    HN1   104.09  3.000
 SYM  HN2   N    CA    107.40  3.000
 SYM  HN1   N    CA    108.60  3.000
 SYM  HA    CA   N     107.81  3.000
 SYM  HA    CA   C     107.77  3.000
 SYM  N     CA   C     114.73  3.000
 SYM  HA    CA   CB    107.66  3.000
 SYM  N     CA   CB    110.27  3.000
 SYM  C     CA   CB    108.35  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
 SYM  chir_01  CG1  CB  CG2  CD  negativ
 SYM  chir_02  CA   N   C    CB  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
 SYM  plan-1  CG1  0.020
 SYM  plan-1  CD   0.020
 SYM  plan-1  OE1  0.020
 SYM  plan-1  OE2  0.020
 SYM  plan-2  C    0.020
 SYM  plan-2  OT1  0.020
 SYM  plan-2  OT2  0.020
 SYM  plan-2  CA   0.020

