# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 21:49:15 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: D-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCC(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
 DGL  DGL  'D-glutamic acid          '  D-peptide  17  10  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_DGL
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
 DGL  N    N  NH2    0  -0.849  15.9200  -4.6948  28.5022
 DGL  CA   C  CH1    0  -0.179  14.8391  -5.6271  28.7987
 DGL  C    C  C      0   0.392  14.9368  -6.1553  30.2553
 DGL  O    O  O      0  -0.613  14.2770  -7.1823  30.5125
 DGL  CB   C  CH2    0  -0.430  13.4276  -5.0648  28.5577
 DGL  CG   C  CH2    0  -0.574  13.0491  -4.8699  27.0911
 DGL  CD   C  C      0   0.412  13.6169  -3.6572  26.3246
 DGL  OE1  O  O      0  -0.606  14.0925  -2.7077  26.9873
 DGL  OE2  O  OC    -1  -0.612  13.5134  -3.7055  25.0829
 DGL  OXT  O  OC    -1  -0.600  15.6441  -5.5065  31.0546
 DGL  H    H  HNH2   0   0.338  15.5542  -3.9071  27.9797
 DGL  H2   H  HNH2   0   0.319  16.2301  -4.3292  29.3956
 DGL  HA   H  HCH1   0   0.172  14.9302  -6.5090  28.1471
 DGL  HB2  H  HCH2   0   0.203  12.7134  -5.7688  28.9923
 DGL  HB3  H  HCH2   0   0.197  13.3094  -4.1254  29.1070
 DGL  HG2  H  HCH2   0   0.205  13.2872  -5.7814  26.5326
 DGL  HG3  H  HCH2   0   0.225  11.9574  -4.7797  27.0254

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
 DGL  N   CA   single  1.458  0.019  1.458
 DGL  N   H    single  0.860  0.020  0.860
 DGL  N   H2   single  0.890  0.020  1.040
 DGL  CA  C    single  1.525  0.021  1.525
 DGL  CA  CB   single  1.521  0.033  1.521
 DGL  CA  HA   single  0.970  0.020  0.970
 DGL  C   O    deloc   1.231  0.020  1.231
 DGL  C   OXT  deloc   1.249  0.020  1.249
 DGL  CB  CG   single  1.527  0.020  1.527
 DGL  CB  HB2  single  0.970  0.020  1.090
 DGL  CB  HB3  single  0.970  0.020  1.090
 DGL  CG  CD   single  1.543  0.020  1.543
 DGL  CG  HG2  single  0.970  0.020  1.090
 DGL  CG  HG3  single  0.970  0.020  1.090
 DGL  CD  OE1  deloc   1.252  0.020  1.252
 DGL  CD  OE2  deloc   1.247  0.020  1.247

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
 DGL  H2   N   H    106.52  3.000
 DGL  H2   N   CA   106.15  3.000
 DGL  H    N   CA   114.00  3.000
 DGL  HA   CA  CB   109.00  3.000
 DGL  HA   CA  C    110.00  3.000
 DGL  CB   CA  C    110.50  1.500
 DGL  HA   CA  N    110.00  3.000
 DGL  CB   CA  N    110.40  1.500
 DGL  C    CA  N    111.00  2.800
 DGL  OXT  C   O    126.53  3.000
 DGL  OXT  C   CA   120.80  1.700
 DGL  O    C   CA   120.80  1.700
 DGL  HB3  CB  HB2  106.42  3.000
 DGL  HB3  CB  CG   110.22  3.000
 DGL  HB2  CB  CG   107.58  3.000
 DGL  HB3  CB  CA   109.52  3.000
 DGL  HB2  CB  CA   107.57  3.000
 DGL  CG   CB  CA   115.12  3.000
 DGL  HG3  CG  HG2  104.72  3.000
 DGL  HG3  CG  CD   105.77  3.000
 DGL  HG2  CG  CD   108.71  3.000
 DGL  HG3  CG  CB   108.34  3.000
 DGL  HG2  CG  CB   109.25  3.000
 DGL  CD   CG  CB   119.09  3.000
 DGL  OE2  CD  OE1  126.02  3.000
 DGL  OE2  CD  CG   115.70  3.000
 DGL  OE1  CD  CG   118.23  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
 DGL  Var_01  CD   CG  CB  CA  -76.93  30.0  3
 DGL  Var_02  OE1  CD  CG  CB  -17.14  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
 DGL  chir_01  CA  N  C  CB  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
 DGL  plan-1  CA   0.020
 DGL  plan-1  C    0.020
 DGL  plan-1  O    0.020
 DGL  plan-1  OXT  0.020
 DGL  plan-2  CG   0.020
 DGL  plan-2  CD   0.020
 DGL  plan-2  OE1  0.020
 DGL  plan-2  OE2  0.020

