# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 03:50:34 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: [(2S)-2,3-diamino-3-oxopropyl]propanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(C(O)=O)C(O)=O)C(N)=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
 6L9  6L9  '[(2S)-2,3-diamino-3-oxopropyl]propanedioic acid'  ligand  23  13  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6L9
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
 6L9  O2   O  OH1   0  -0.590  -3.2611   0.4303   0.2098
 6L9  CD1  C  C     0   0.592  -2.0959   1.0266   0.0040
 6L9  O3   O  O     0  -0.423  -1.9806   2.1469  -0.4162
 6L9  CG   C  CH1   0  -0.507  -0.9386   0.1300   0.4015
 6L9  CD2  C  C     0   0.546  -1.2474  -1.2967  -0.0116
 6L9  O4   O  O     0  -0.430  -1.1644  -1.6840  -1.1497
 6L9  O5   O  OH1   0  -0.576  -1.6137  -2.0594   1.0036
 6L9  CB   C  CH2   0  -0.429   0.3757   0.6109  -0.2018
 6L9  CA   C  CH1   0  -0.230   1.5803  -0.1972   0.2974
 6L9  N    N  NH2   0  -0.775   1.6319  -0.1848   1.7403
 6L9  C    C  C     0   0.500   2.8329   0.3838  -0.3687
 6L9  O    O  O     0  -0.486   3.4838   1.2705   0.1644
 6L9  N1   N  NH2   0  -0.796   3.1262  -0.1273  -1.5715
 6L9  H1   H  HOH1  0   0.489  -3.9912   1.0241  -0.0244
 6L9  H2   H  HCH1  0   0.331  -0.8663   0.1786   1.4927
 6L9  H3   H  HOH1  0   0.485  -1.8192  -2.9546   0.6914
 6L9  H4   H  HCH2  0   0.261   0.3255   0.5699  -1.2912
 6L9  H5   H  HCH2  0   0.265   0.5192   1.6588   0.0697
 6L9  H6   H  HCH1  0   0.264   1.4709  -1.2378  -0.0238
 6L9  H7   H  HNH2  0   0.357   2.3465  -0.8223   2.0672
 6L9  H8   H  HNH2  0   0.344   1.9034   0.7357   2.0658
 6L9  H10  H  HNH2  0   0.407   2.5667  -0.8502  -1.9904
 6L9  H11  H  HNH2  0   0.402   3.8765   0.2533  -2.1256

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
 6L9  N    CA   single  1.444  0.020  1.444
 6L9  CA   C    single  1.533  0.020  1.533
 6L9  CA   CB   single  1.534  0.020  1.534
 6L9  O3   CD1  double  1.202  0.020  1.202
 6L9  N1   C    single  1.339  0.020  1.339
 6L9  C    O    double  1.222  0.020  1.222
 6L9  CD1  O2   single  1.325  0.020  1.325
 6L9  CD1  CG   single  1.517  0.020  1.517
 6L9  CB   CG   single  1.524  0.020  1.524
 6L9  CG   CD2  single  1.517  0.020  1.517
 6L9  CD2  O4   double  1.205  0.020  1.205
 6L9  CD2  O5   single  1.322  0.020  1.322
 6L9  O2   H1   single  0.850  0.020  0.980
 6L9  CG   H2   single  0.970  0.020  1.090
 6L9  O5   H3   single  0.850  0.020  0.980
 6L9  CB   H4   single  0.970  0.020  1.090
 6L9  CB   H5   single  0.970  0.020  1.090
 6L9  CA   H6   single  0.970  0.020  1.090
 6L9  N    H7   single  0.890  0.020  1.040
 6L9  N    H8   single  0.890  0.020  1.040
 6L9  N1   H10  single  0.860  0.020  1.020
 6L9  N1   H11  single  0.860  0.020  1.020

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
 6L9  H1   O2   CD1  110.42  3.000
 6L9  CG   CD1  O3   124.70  3.000
 6L9  CG   CD1  O2   111.36  3.000
 6L9  O3   CD1  O2   123.92  3.000
 6L9  H2   CG   CB   108.89  3.000
 6L9  H2   CG   CD2  109.06  3.000
 6L9  CB   CG   CD2  111.38  3.000
 6L9  H2   CG   CD1  106.58  3.000
 6L9  CD2  CG   CD1  109.22  3.000
 6L9  CB   CG   CD1  111.57  3.000
 6L9  O5   CD2  O4   123.99  3.000
 6L9  O5   CD2  CG   112.96  3.000
 6L9  O4   CD2  CG   123.05  3.000
 6L9  H3   O5   CD2  110.12  3.000
 6L9  H5   CB   H4   106.88  3.000
 6L9  H5   CB   CA   108.75  3.000
 6L9  H4   CB   CA   109.95  3.000
 6L9  H5   CB   CG   108.52  3.000
 6L9  H4   CB   CG   110.10  3.000
 6L9  CA   CB   CG   112.47  3.000
 6L9  H6   CA   C    108.32  3.000
 6L9  H6   CA   N    107.76  3.000
 6L9  C    CA   N    113.69  3.000
 6L9  H6   CA   CB   109.08  3.000
 6L9  C    CA   CB   107.49  3.000
 6L9  N    CA   CB   110.41  3.000
 6L9  H8   N    H7   106.22  3.000
 6L9  H8   N    CA   109.77  3.000
 6L9  H7   N    CA   110.04  3.000
 6L9  N1   C    O    123.49  3.000
 6L9  O    C    CA   121.37  3.000
 6L9  N1   C    CA   115.12  3.000
 6L9  H11  N1   H10  117.18  3.000
 6L9  H11  N1   C    120.86  3.000
 6L9  H10  N1   C    121.78  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
 6L9  CONST_01  H10  N1   C    CA     0.00   0.0  0
 6L9  CONST_02  H11  N1   C    CA   180.00   0.0  0
 6L9  CONST_03  H1   O2   CD1  O3     0.00   0.0  0
 6L9  CONST_04  H3   O5   CD2  CG   180.00   0.0  0
 6L9  Var_01    CB   CG   CD1  O2   162.94  30.0  3
 6L9  Var_02    CA   CB   CG   CD1  174.33  30.0  1
 6L9  Var_03    O4   CD2  CG   CD1   76.52  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
 6L9  chir_01  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
 6L9  plan-1  CA   0.020
 6L9  plan-1  C    0.020
 6L9  plan-1  O    0.020
 6L9  plan-1  N1   0.020
 6L9  plan-1  H10  0.020
 6L9  plan-1  H11  0.020
 6L9  plan-2  O2   0.020
 6L9  plan-2  CD1  0.020
 6L9  plan-2  O3   0.020
 6L9  plan-2  CG   0.020
 6L9  plan-2  H1   0.020
 6L9  plan-3  CG   0.020
 6L9  plan-3  CD2  0.020
 6L9  plan-3  O4   0.020
 6L9  plan-3  O5   0.020
 6L9  plan-3  H3   0.020

