# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 21:26:21 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: D-glutamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCC(N)=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
 DGN  DGN  'D-glutamine              '  D-peptide  19  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_DGN
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
 DGN  N     N  NH2    0  -0.820  22.8769  33.3597  29.9755
 DGN  CA    C  CH1    0  -0.220  22.3758  33.5926  28.6271
 DGN  C     C  C      0   0.412  21.9441  32.2628  27.9490
 DGN  O     O  O      0  -0.604  21.3090  32.3716  26.8827
 DGN  OXT   O  OC    -1  -0.599  22.2942  31.2008  28.5029
 DGN  CB    C  CH2    0  -0.389  21.2303  34.6045  28.6460
 DGN  CG    C  CH2    0  -0.577  21.6601  35.9470  29.2198
 DGN  CD    C  C      0   0.520  20.5564  36.9836  29.2369
 DGN  OE1   O  O      0  -0.492  19.3766  36.6885  29.3675
 DGN  NE2   N  NH2    0  -0.806  20.9717  38.2576  29.1228
 DGN  H     H  HNH2   0   0.331  23.6533  33.9751  30.1752
 DGN  H2    H  HNH2   0   0.334  23.2317  32.4123  30.0086
 DGN  HA    H  HCH1   0   0.195  23.1614  34.0082  27.9721
 DGN  HB2   H  HCH2   0   0.213  20.8608  34.7423  27.6289
 DGN  HB3   H  HCH2   0   0.206  20.4040  34.2008  29.2370
 DGN  HG2   H  HCH2   0   0.262  21.9948  35.8173  30.2548
 DGN  HG3   H  HCH2   0   0.240  22.5260  36.3293  28.6708
 DGN  HE21  H  HNH2   0   0.401  21.9434  38.4937  29.0216
 DGN  HE22  H  HNH2   0   0.392  20.3132  39.0170  29.1837

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
 DGN  N    CA    single  1.458  0.019  1.458
 DGN  N    H     single  0.860  0.020  0.860
 DGN  N    H2    single  0.890  0.020  1.040
 DGN  CA   C     single  1.525  0.021  1.525
 DGN  CA   CB    single  1.521  0.033  1.521
 DGN  CA   HA    single  0.970  0.020  0.970
 DGN  C    O     deloc   1.231  0.020  1.231
 DGN  C    OXT   deloc   1.248  0.020  1.248
 DGN  CB   CG    single  1.522  0.020  1.522
 DGN  CB   HB2   single  0.970  0.020  1.090
 DGN  CB   HB3   single  0.970  0.020  1.090
 DGN  CG   CD    single  1.514  0.020  1.514
 DGN  CG   HG2   single  0.970  0.020  1.090
 DGN  CG   HG3   single  0.970  0.020  1.090
 DGN  CD   OE1   double  1.223  0.020  1.223
 DGN  CD   NE2   single  1.345  0.020  1.345
 DGN  NE2  HE21  single  0.860  0.020  1.020
 DGN  NE2  HE22  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
 DGN  H2    N    H     107.11  3.000
 DGN  H2    N    CA    107.48  3.000
 DGN  H     N    CA    114.00  3.000
 DGN  HA    CA   CB    109.00  3.000
 DGN  HA    CA   C     110.00  3.000
 DGN  CB    CA   C     110.50  1.500
 DGN  HA    CA   N     110.00  3.000
 DGN  CB    CA   N     110.40  1.500
 DGN  C     CA   N     111.00  2.800
 DGN  OXT   C    O     126.67  3.000
 DGN  OXT   C    CA    120.80  1.700
 DGN  O     C    CA    120.80  1.700
 DGN  HB3   CB   HB2   107.14  3.000
 DGN  HB3   CB   CG    109.59  3.000
 DGN  HB2   CB   CG    109.62  3.000
 DGN  HB3   CB   CA    109.19  3.000
 DGN  HB2   CB   CA    109.02  3.000
 DGN  CG    CB   CA    112.14  3.000
 DGN  HG3   CG   HG2   105.88  3.000
 DGN  HG3   CG   CD    110.08  3.000
 DGN  HG2   CG   CD    107.05  3.000
 DGN  HG3   CG   CB    110.03  3.000
 DGN  HG2   CG   CB    109.76  3.000
 DGN  CD    CG   CB    113.72  3.000
 DGN  NE2   CD   OE1   122.37  3.000
 DGN  NE2   CD   CG    114.99  3.000
 DGN  OE1   CD   CG    122.63  3.000
 DGN  HE22  NE2  HE21  117.46  3.000
 DGN  HE22  NE2  CD    120.50  3.000
 DGN  HE21  NE2  CD    121.98  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
 DGN  CONST_01  HE21  NE2  CD  CG    0.00   0.0  0
 DGN  CONST_02  HE22  NE2  CD  CG  180.00   0.0  0
 DGN  Var_01    CD    CG   CB  CA  179.17  30.0  3
 DGN  Var_02    OE1   CD   CG  CB   30.88  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
 DGN  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
 DGN  plan-1  CG    0.020
 DGN  plan-1  CD    0.020
 DGN  plan-1  OE1   0.020
 DGN  plan-1  NE2   0.020
 DGN  plan-1  HE21  0.020
 DGN  plan-1  HE22  0.020
 DGN  plan-2  CA    0.020
 DGN  plan-2  C     0.020
 DGN  plan-2  O     0.020
 DGN  plan-2  OXT   0.020

