# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 09:23:05 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  21  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  OC    -1  -0.624  -3.3514   0.5521   0.3148
 6L9  CD1  C  C      0   0.413  -2.2235   1.0024   0.0224
 6L9  O3   O  O      0  -0.608  -1.9993   2.0824  -0.5607
 6L9  CG   C  CH1    0  -0.477  -1.0196   0.1248   0.4302
 6L9  CD2  C  C      0   0.401  -1.2855  -1.3080  -0.0683
 6L9  O4   O  O      0  -0.625  -1.1028  -1.5068  -1.2905
 6L9  O5   O  OC    -1  -0.626  -1.6643  -2.1625   0.7586
 6L9  CB   C  CH2    0  -0.398   0.3096   0.6495  -0.0893
 6L9  CA   C  CH1    0  -0.225   1.5158  -0.1393   0.4406
 6L9  N    N  NH2    0  -0.777   1.6570   0.0434   1.8688
 6L9  C    C  C      0   0.488   2.7522   0.2753  -0.3582
 6L9  O    O  O      0  -0.495   3.5537   1.1041   0.0528
 6L9  N1   N  NH2    0  -0.796   2.8695  -0.3246  -1.5541
 6L9  H2   H  HCH1   0   0.204  -0.9688   0.1062   1.5253
 6L9  H4   H  HCH2   0   0.212   0.3049   0.6183  -1.1796
 6L9  H5   H  HCH2   0   0.210   0.4390   1.6994   0.1898
 6L9  H6   H  HCH1   0   0.246   1.3467  -1.2052   0.2536
 6L9  H7   H  HNH2   0   0.345   2.4177  -0.5264   2.2176
 6L9  H8   H  HNH2   0   0.335   1.9213   1.0029   2.0588
 6L9  H10  H  HNH2   0   0.400   2.1681  -0.9665  -1.8835
 6L9  H11  H  HNH2   0   0.396   3.5800  -0.0394  -2.2086

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  1.447  0.020  1.447
 6L9  CA   C    single  1.529  0.020  1.529
 6L9  CA   CB   single  1.536  0.020  1.536
 6L9  O3   CD1  deloc   1.248  0.020  1.248
 6L9  N1   C    single  1.343  0.020  1.343
 6L9  C    O    double  1.224  0.020  1.224
 6L9  CD1  O2   deloc   1.249  0.020  1.249
 6L9  CD1  CG   single  1.545  0.020  1.545
 6L9  CB   CG   single  1.521  0.020  1.521
 6L9  CG   CD2  single  1.540  0.020  1.540
 6L9  CD2  O4   deloc   1.252  0.020  1.252
 6L9  CD2  O5   deloc   1.248  0.020  1.248
 6L9  CG   H2   single  0.970  0.020  1.090
 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  CG   CD1  O3   118.37  3.000
 6L9  CG   CD1  O2   115.92  3.000
 6L9  O3   CD1  O2   125.71  3.000
 6L9  H2   CG   CB   107.85  3.000
 6L9  H2   CG   CD2  108.39  3.000
 6L9  CB   CG   CD2  111.18  3.000
 6L9  H2   CG   CD1  108.03  3.000
 6L9  CD2  CG   CD1  107.97  3.000
 6L9  CB   CG   CD1  113.27  3.000
 6L9  O5   CD2  O4   125.63  3.000
 6L9  O5   CD2  CG   118.35  3.000
 6L9  O4   CD2  CG   116.02  3.000
 6L9  H5   CB   H4   106.45  3.000
 6L9  H5   CB   CA   108.18  3.000
 6L9  H4   CB   CA   109.49  3.000
 6L9  H5   CB   CG   110.32  3.000
 6L9  H4   CB   CG   109.14  3.000
 6L9  CA   CB   CG   113.04  3.000
 6L9  H6   CA   C    107.42  3.000
 6L9  H6   CA   N    107.85  3.000
 6L9  C    CA   N    113.73  3.000
 6L9  H6   CA   CB   108.65  3.000
 6L9  C    CA   CB   108.39  3.000
 6L9  N    CA   CB   110.64  3.000
 6L9  H8   N    H7   105.81  3.000
 6L9  H8   N    CA   109.28  3.000
 6L9  H7   N    CA   110.03  3.000
 6L9  N1   C    O    122.98  3.000
 6L9  O    C    CA   122.51  3.000
 6L9  N1   C    CA   114.49  3.000
 6L9  H11  N1   H10  117.37  3.000
 6L9  H11  N1   C    120.91  3.000
 6L9  H10  N1   C    121.04  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  Var_01    CB   CG   CD1  O2   173.54  30.0  3
 6L9  Var_02    CA   CB   CG   CD1  173.90  30.0  1
 6L9  Var_03    O4   CD2  CG   CD1   77.21  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-3  CG   0.020
 6L9  plan-3  CD2  0.020
 6L9  plan-3  O4   0.020
 6L9  plan-3  O5   0.020

