# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 15:16:04 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: D-gamma-glutamyl-2-methyl-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(NC(=O)CC[C@@H](N)C(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
 9R4  9R4  D-gamma-glutamyl-2-methyl-L-alanine  L-peptide  30  16  .  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_9R4
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
 9R4  N    N  NH2    0  -0.800  85.2808  -2.8188  40.9286
 9R4  CA   C  CH1    0  -0.173  84.6809  -3.0895  39.6258
 9R4  C    C  C      0   0.402  85.8056  -3.2444  38.5754
 9R4  O    O  O      0  -0.609  86.7335  -4.0191  38.8913
 9R4  CB   C  CH2    0  -0.465  83.7961  -4.3436  39.6364
 9R4  CG   C  CH2    0  -0.557  83.0392  -4.6171  38.3351
 9R4  CD   C  C      0   0.513  82.0530  -3.5280  37.9399
 9R4  NE   N  NH1    0  -0.647  81.1114  -3.2847  38.8588
 9R4  CZ   C  CT     0  -0.009  80.0332  -2.3108  38.8145
 9R4  C01  C  CH3    0  -0.645  79.0805  -2.5946  37.6511
 9R4  C02  C  CH3    0  -0.647  80.5822  -0.8848  38.7233
 9R4  CH   C  C      0   0.435  79.2488  -2.4625  40.1600
 9R4  O01  O  OC    -1  -0.592  79.6788  -3.3056  40.9754
 9R4  O02  O  O      0  -0.589  78.2604  -1.7239  40.2989
 9R4  O03  O  O      0  -0.511  82.1300  -2.9510  36.8586
 9R4  H1   H  HNH2   0   0.328  84.5818  -2.9247  41.6549
 9R4  H2   H  HNH2   0   0.324  85.9781  -3.5331  41.1026
 9R4  H4   H  HCH1   0   0.194  84.0615  -2.2271  39.3553
 9R4  H6   H  HCH2   0   0.218  83.0899  -4.2642  40.4697
 9R4  H7   H  HCH2   0   0.222  84.4254  -5.2092  39.8621
 9R4  H8   H  HCH2   0   0.253  82.4915  -5.5587  38.4376
 9R4  H9   H  HCH2   0   0.244  83.7383  -4.7497  37.5093
 9R4  H10  H  HNH1   0   0.386  81.1015  -3.8135  39.7228
 9R4  H11  H  HCH3   0   0.220  78.2434  -1.8979  37.6655
 9R4  H12  H  HCH3   0   0.225  79.5882  -2.4922  36.6931
 9R4  H13  H  HCH3   0   0.217  78.6776  -3.6073  37.7143
 9R4  H14  H  HCH3   0   0.219  81.2744  -0.6806  39.5427
 9R4  H15  H  HCH3   0   0.225  81.1139  -0.7281  37.7856
 9R4  H16  H  HCH3   0   0.221  79.7695  -0.1619  38.7772
 9R4  O1   O  OC    -1  -0.604  85.6861  -2.6162  37.5067

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
 9R4  C01  CZ   single  1.530  0.020  1.530
 9R4  O    C    deloc   1.231  0.020  1.231
 9R4  C    CA   single  1.525  0.021  1.525
 9R4  O03  CD   double  1.228  0.020  1.228
 9R4  CD   CG   single  1.521  0.020  1.521
 9R4  CD   NE   single  1.338  0.020  1.338
 9R4  CZ   NE   single  1.454  0.020  1.454
 9R4  CZ   C02  single  1.531  0.020  1.531
 9R4  CZ   CH   single  1.565  0.020  1.565
 9R4  CG   CB   single  1.530  0.020  1.530
 9R4  O02  CH   deloc   1.242  0.020  1.242
 9R4  CA   CB   single  1.521  0.033  1.521
 9R4  CA   N    single  1.458  0.019  1.458
 9R4  CH   O01  deloc   1.249  0.020  1.249
 9R4  N    H1   single  0.890  0.020  1.040
 9R4  N    H2   single  0.890  0.020  1.040
 9R4  CA   H4   single  0.970  0.020  1.090
 9R4  CB   H6   single  0.970  0.020  1.090
 9R4  CB   H7   single  0.970  0.020  1.090
 9R4  CG   H8   single  0.970  0.020  1.090
 9R4  CG   H9   single  0.970  0.020  1.090
 9R4  NE   H10  single  0.860  0.020  1.020
 9R4  C01  H11  single  0.970  0.020  1.090
 9R4  C01  H12  single  0.970  0.020  1.090
 9R4  C01  H13  single  0.970  0.020  1.090
 9R4  C02  H14  single  0.970  0.020  1.090
 9R4  C02  H15  single  0.970  0.020  1.090
 9R4  C02  H16  single  0.970  0.020  1.090
 9R4  C    O1   deloc   1.245  0.020  1.245

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
 9R4  H2   N    H1   106.13  3.000
 9R4  H2   N    CA   107.78  3.000
 9R4  H1   N    CA   109.67  3.000
 9R4  H4   CA   CB   108.60  3.000
 9R4  H4   CA   C    108.80  3.000
 9R4  CB   CA   C    110.50  1.500
 9R4  H4   CA   N    107.86  3.000
 9R4  CB   CA   N    110.40  1.500
 9R4  C    CA   N    111.00  2.800
 9R4  O1   C    O    126.94  3.000
 9R4  O1   C    CA   117.55  3.000
 9R4  O    C    CA   120.80  1.700
 9R4  H7   CB   H6   105.75  3.000
 9R4  H7   CB   CG   108.59  3.000
 9R4  H6   CB   CG   109.94  3.000
 9R4  H7   CB   CA   108.44  3.000
 9R4  H6   CB   CA   108.52  3.000
 9R4  CG   CB   CA   115.18  3.000
 9R4  H9   CG   H8   106.70  3.000
 9R4  H9   CG   CD   107.82  3.000
 9R4  H8   CG   CD   108.41  3.000
 9R4  H9   CG   CB   110.41  3.000
 9R4  H8   CG   CB   108.78  3.000
 9R4  CD   CG   CB   114.43  3.000
 9R4  O03  CD   NE   124.28  3.000
 9R4  NE   CD   CG   114.07  3.000
 9R4  O03  CD   CG   121.64  3.000
 9R4  H10  NE   CZ   111.62  3.000
 9R4  H10  NE   CD   119.85  3.000
 9R4  CZ   NE   CD   128.53  3.000
 9R4  CH   CZ   C02  108.74  3.000
 9R4  CH   CZ   C01  108.88  3.000
 9R4  C02  CZ   C01  110.53  3.000
 9R4  CH   CZ   NE   106.30  3.000
 9R4  C02  CZ   NE   111.10  3.000
 9R4  C01  CZ   NE   111.14  3.000
 9R4  H13  C01  H12  108.07  3.000
 9R4  H13  C01  H11  108.00  3.000
 9R4  H12  C01  H11  108.05  3.000
 9R4  H13  C01  CZ   110.97  3.000
 9R4  H12  C01  CZ   111.17  3.000
 9R4  H11  C01  CZ   110.48  3.000
 9R4  H16  C02  H15  108.14  3.000
 9R4  H16  C02  H14  108.17  3.000
 9R4  H15  C02  H14  108.04  3.000
 9R4  H16  C02  CZ   110.35  3.000
 9R4  H15  C02  CZ   111.12  3.000
 9R4  H14  C02  CZ   110.90  3.000
 9R4  O02  CH   O01  127.05  3.000
 9R4  O01  CH   CZ   117.01  3.000
 9R4  O02  CH   CZ   115.95  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
 9R4  CONST_01  CZ   NE   CD  CG   180.00   0.0  0
 9R4  CONST_02  O03  CD   NE  CZ     0.00   0.0  0
 9R4  CONST_03  H10  NE   CD  CG     0.00   0.0  0
 9R4  Var_01    CD   CG   CB  CA   -61.83  30.0  1
 9R4  Var_02    O03  CD   CG  CB   122.53  30.0  1
 9R4  Var_03    C01  CZ   NE  CD    62.01  30.0  2
 9R4  Var_04    O02  CH   CZ  NE  -178.53  30.0  3
 9R4  Var_05    H11  C01  CZ  NE   176.42  30.0  3
 9R4  Var_06    H14  C02  CZ  NE   -55.29  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
 9R4  chir_01  CA  C  CB  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
 9R4  plan-1  CG   0.020
 9R4  plan-1  CD   0.020
 9R4  plan-1  NE   0.020
 9R4  plan-1  CZ   0.020
 9R4  plan-1  O03  0.020
 9R4  plan-1  H10  0.020
 9R4  plan-2  CA   0.020
 9R4  plan-2  C    0.020
 9R4  plan-2  O    0.020
 9R4  plan-2  O1   0.020
 9R4  plan-3  CZ   0.020
 9R4  plan-3  CH   0.020
 9R4  plan-3  O01  0.020
 9R4  plan-3  O02  0.020

