# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 14:08:34 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (2~{S})-2-(2-azanylethylamino)butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCN[C@@H](CC(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
 EKN  EKN  '(2~{S})-2-(2-azanylethylamino)butanedioic acid'  ligand  22  12  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_EKN
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
 EKN  OD1  O  O      0  -0.627   2.1698  -1.7426   1.0750
 EKN  CG   C  C      0   0.407   2.2107  -1.2955  -0.0907
 EKN  OD2  O  OC    -1  -0.626   2.5706  -1.9283  -1.1056
 EKN  CB   C  CH2    0  -0.560   1.8147   0.1775  -0.2755
 EKN  CA   C  CH1    0  -0.182   0.4427   0.5020   0.3149
 EKN  C    C  C      0   0.391   0.1988   2.0256   0.2105
 EKN  OXT  O  OC    -1  -0.625   0.7124   2.7351   1.1016
 EKN  O    O  O      0  -0.614  -0.4493   2.4336  -0.7757
 EKN  N    N  NH1    0  -0.589  -0.5630  -0.3200  -0.3345
 EKN  CAG  C  CH2    0  -0.259  -1.8524  -0.2848   0.3247
 EKN  CAF  C  CH2    0  -0.298  -2.8440  -1.2014  -0.3741
 EKN  NAA  N  NH2    0  -0.803  -4.1376  -1.1543   0.2927
 EKN  H2   H  HCH2   0   0.217   2.5644   0.8063   0.2172
 EKN  H3   H  HCH2   0   0.192   1.8282   0.4480  -1.3364
 EKN  H4   H  HCH1   0   0.195   0.4674   0.2249   1.3733
 EKN  H6   H  HNH1   0   0.317  -0.6825   0.0394  -1.2762
 EKN  H8   H  HCH2   0   0.204  -1.7272  -0.6275   1.3565
 EKN  H9   H  HCH2   0   0.180  -2.2811   0.7287   0.3841
 EKN  H10  H  HCH2   0   0.186  -2.8917  -0.9310  -1.4401
 EKN  H11  H  HCH2   0   0.212  -2.4676  -2.2265  -0.3323
 EKN  H12  H  HNH2   0   0.337  -4.5553  -0.2440   0.1438
 EKN  H13  H  HNH2   0   0.346  -4.7672  -1.8153  -0.1435

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
 EKN  OD1  CG   deloc   1.249  0.020  1.249
 EKN  CG   CB   single  1.536  0.020  1.536
 EKN  CG   OD2  deloc   1.249  0.020  1.249
 EKN  CB   CA   single  1.529  0.020  1.529
 EKN  O    C    deloc   1.249  0.020  1.249
 EKN  CA   C    single  1.547  0.020  1.547
 EKN  CA   N    single  1.452  0.020  1.452
 EKN  C    OXT  deloc   1.249  0.020  1.249
 EKN  N    CAG  single  1.449  0.020  1.449
 EKN  CAG  CAF  single  1.520  0.020  1.520
 EKN  CAF  NAA  single  1.456  0.020  1.456
 EKN  CB   H2   single  0.970  0.020  1.090
 EKN  CB   H3   single  0.970  0.020  1.090
 EKN  CA   H4   single  0.970  0.020  1.090
 EKN  N    H6   single  0.890  0.020  1.040
 EKN  CAG  H8   single  0.970  0.020  1.090
 EKN  CAG  H9   single  0.970  0.020  1.090
 EKN  CAF  H10  single  0.970  0.020  1.090
 EKN  CAF  H11  single  0.970  0.020  1.090
 EKN  NAA  H12  single  0.890  0.020  1.040
 EKN  NAA  H13  single  0.890  0.020  1.040

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
 EKN  CB   CG   OD2  117.54  3.000
 EKN  OD2  CG   OD1  125.90  3.000
 EKN  CB   CG   OD1  116.54  3.000
 EKN  H3   CB   H2   106.59  3.000
 EKN  H3   CB   CA   109.44  3.000
 EKN  H2   CB   CA   108.58  3.000
 EKN  H3   CB   CG   110.50  3.000
 EKN  H2   CB   CG   108.65  3.000
 EKN  CA   CB   CG   112.86  3.000
 EKN  H4   CA   N    107.75  3.000
 EKN  H4   CA   C    108.56  3.000
 EKN  N    CA   C    114.73  3.000
 EKN  H4   CA   CB   107.43  3.000
 EKN  N    CA   CB   109.19  3.000
 EKN  C    CA   CB   108.94  3.000
 EKN  O    C    OXT  126.23  3.000
 EKN  OXT  C    CA   116.52  3.000
 EKN  O    C    CA   117.20  3.000
 EKN  H6   N    CAG  107.99  3.000
 EKN  H6   N    CA   107.21  3.000
 EKN  CAG  N    CA   113.53  3.000
 EKN  H9   CAG  H8   106.36  3.000
 EKN  H9   CAG  CAF  109.00  3.000
 EKN  H8   CAG  CAF  108.61  3.000
 EKN  H9   CAG  N    113.15  3.000
 EKN  H8   CAG  N    108.64  3.000
 EKN  CAF  CAG  N    110.90  3.000
 EKN  H11  CAF  H10  106.40  3.000
 EKN  H11  CAF  NAA  108.59  3.000
 EKN  H10  CAF  NAA  113.39  3.000
 EKN  H11  CAF  CAG  108.87  3.000
 EKN  H10  CAF  CAG  108.98  3.000
 EKN  NAA  CAF  CAG  110.45  3.000
 EKN  H13  NAA  H12  105.50  3.000
 EKN  H13  NAA  CAF  109.53  3.000
 EKN  H12  NAA  CAF  109.16  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
 EKN  Var_01  CA   CB   CG   OD1   -53.75  30.0  3
 EKN  Var_02  CAF  CAG  N    CA   -178.01  30.0  3
 EKN  Var_03  NAA  CAF  CAG  N    -179.76  30.0  3
 EKN  Var_04  H12  NAA  CAF  CAG    68.80  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
 EKN  chir_01  CA  CB  C  N  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
 EKN  plan-1  OD1  0.020
 EKN  plan-1  CG   0.020
 EKN  plan-1  OD2  0.020
 EKN  plan-1  CB   0.020
 EKN  plan-2  CA   0.020
 EKN  plan-2  C    0.020
 EKN  plan-2  OXT  0.020
 EKN  plan-2  O    0.020

