# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:53:49 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: L-gamma-glutamylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)NCC(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
 9R7  9R7  'L-gamma-glutamylglycine  '  L-peptide  24  14  .  2019-03-22  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_9R7
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
 9R7  N    N  NH2    0  -0.804  -1.3511   6.6383  29.7925
 9R7  CA   C  CH1    0  -0.165  -1.8418   7.9795  30.0929
 9R7  C    C  C      0   0.388  -3.2017   8.2565  29.4086
 9R7  O    O  O      0  -0.612  -3.9193   9.1202  29.9570
 9R7  CB   C  CH2    0  -0.424  -0.7830   8.9797  29.6124
 9R7  CG   C  CH2    0  -0.571  -1.0524  10.4289  30.0023
 9R7  CD   C  C      0   0.546   0.0499  11.3577  29.5402
 9R7  O01  O  O      0  -0.517   0.4838  11.3276  28.3915
 9R7  NE   N  NH1    0  -0.630   0.5029  12.2179  30.4581
 9R7  CZ   C  CH2    0  -0.409   1.5248  13.2023  30.2167
 9R7  CH   C  C      0   0.394   1.8162  14.0267  31.4906
 9R7  O02  O  OC    -1  -0.595   1.1565  13.7460  32.5103
 9R7  O03  O  O      0  -0.603   2.6922  14.8994  31.3664
 9R7  O1   O  OC    -1  -0.600  -3.4610   7.6254  28.3667
 9R7  H1   H  HNH2   0   0.328  -0.5818   6.4246  30.4163
 9R7  H2   H  HNH2   0   0.331  -2.0700   5.9569  30.0001
 9R7  H4   H  HCH1   0   0.175  -1.9838   8.1398  31.1730
 9R7  H5   H  HCH2   0   0.219   0.1831   8.6768  30.0318
 9R7  H6   H  HCH2   0   0.215  -0.6881   8.8947  28.5272
 9R7  H7   H  HCH2   0   0.232  -1.1954  10.5051  31.0831
 9R7  H8   H  HCH2   0   0.259  -1.9848  10.7695  29.5466
 9R7  H9   H  HNH1   0   0.381   0.1367  12.2125  31.3989
 9R7  H10  H  HCH2   0   0.232   2.4536  12.7268  29.8851
 9R7  H11  H  HCH2   0   0.232   1.2287  13.8859  29.4144

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
 9R7  O01  CD   double  1.228  0.020  1.228
 9R7  C    O    deloc   1.231  0.020  1.231
 9R7  C    CA   single  1.525  0.021  1.525
 9R7  CD   CG   single  1.514  0.020  1.514
 9R7  CD   NE   single  1.337  0.020  1.337
 9R7  N    CA   single  1.458  0.019  1.458
 9R7  CZ   NE   single  1.439  0.020  1.439
 9R7  CZ   CH   single  1.545  0.020  1.545
 9R7  CA   CB   single  1.521  0.033  1.521
 9R7  CB   CG   single  1.525  0.020  1.525
 9R7  O03  CH   deloc   1.243  0.020  1.243
 9R7  CH   O02  deloc   1.247  0.020  1.247
 9R7  C    O1   deloc   1.245  0.020  1.245
 9R7  N    H1   single  0.890  0.020  1.040
 9R7  N    H2   single  0.890  0.020  1.040
 9R7  CA   H4   single  0.970  0.020  1.090
 9R7  CB   H5   single  0.970  0.020  1.090
 9R7  CB   H6   single  0.970  0.020  1.090
 9R7  CG   H7   single  0.970  0.020  1.090
 9R7  CG   H8   single  0.970  0.020  1.090
 9R7  NE   H9   single  0.860  0.020  1.020
 9R7  CZ   H10  single  0.970  0.020  1.090
 9R7  CZ   H11  single  0.970  0.020  1.090

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
 9R7  H2   N   H1   105.73  3.000
 9R7  H2   N   CA   109.74  3.000
 9R7  H1   N   CA   108.80  3.000
 9R7  H4   CA  CB   107.54  3.000
 9R7  H4   CA  C    107.12  3.000
 9R7  CB   CA  C    110.50  1.500
 9R7  H4   CA  N    112.28  3.000
 9R7  CB   CA  N    110.40  1.500
 9R7  C    CA  N    111.00  2.800
 9R7  O1   C   O    126.71  3.000
 9R7  O1   C   CA   117.53  3.000
 9R7  O    C   CA   120.80  1.700
 9R7  H6   CB  H5   106.38  3.000
 9R7  H6   CB  CG   110.07  3.000
 9R7  H5   CB  CG   108.70  3.000
 9R7  H6   CB  CA   108.69  3.000
 9R7  H5   CB  CA   107.97  3.000
 9R7  CG   CB  CA   114.69  3.000
 9R7  H8   CG  H7   106.21  3.000
 9R7  H8   CG  CD   107.64  3.000
 9R7  H7   CG  CD   110.75  3.000
 9R7  H8   CG  CB   109.91  3.000
 9R7  H7   CG  CB   110.01  3.000
 9R7  CD   CG  CB   112.11  3.000
 9R7  NE   CD  O01  122.56  3.000
 9R7  NE   CD  CG   115.59  3.000
 9R7  O01  CD  CG   121.85  3.000
 9R7  H9   NE  CZ   114.67  3.000
 9R7  H9   NE  CD   120.90  3.000
 9R7  CZ   NE  CD   124.43  3.000
 9R7  H11  CZ  H10  106.18  3.000
 9R7  H11  CZ  CH   108.79  3.000
 9R7  H10  CZ  CH   108.76  3.000
 9R7  H11  CZ  NE   110.97  3.000
 9R7  H10  CZ  NE   110.86  3.000
 9R7  CH   CZ  NE   111.13  3.000
 9R7  O03  CH  O02  127.80  3.000
 9R7  O02  CH  CZ   117.03  3.000
 9R7  O03  CH  CZ   115.16  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
 9R7  CONST_01  CZ   NE  CD  CG    180.00   0.0  0
 9R7  CONST_02  CZ   NE  CD  O01     0.00   0.0  0
 9R7  CONST_03  H9   NE  CD  CG      0.00   0.0  0
 9R7  Var_01    CD   CG  CB  CA    178.06  30.0  3
 9R7  Var_02    O01  CD  CG  CB     48.30  30.0  1
 9R7  Var_03    CH   CZ  NE  CD   -179.70  30.0  1
 9R7  Var_04    O03  CH  CZ  NE    179.84  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
 9R7  chir_01  CA  C  N  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
 9R7  plan-1  CG   0.020
 9R7  plan-1  CD   0.020
 9R7  plan-1  O01  0.020
 9R7  plan-1  NE   0.020
 9R7  plan-1  CZ   0.020
 9R7  plan-1  H9   0.020
 9R7  plan-2  CA   0.020
 9R7  plan-2  C    0.020
 9R7  plan-2  O    0.020
 9R7  plan-2  O1   0.020
 9R7  plan-3  CZ   0.020
 9R7  plan-3  CH   0.020
 9R7  plan-3  O02  0.020
 9R7  plan-3  O03  0.020

