# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 13:25:44 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: L-gamma-glutamyl-S-(2-carboxyethyl)-L-cysteinylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)N[C@@H](CSCCC(O)=O)C(=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
 99T  99T  L-gamma-glutamyl-S-(2-carboxyethyl)-L-cysteinylglycine  ligand  43  25  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_99T
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
 99T  O32  O  O      0  -0.599  -2.5213  -4.6554   1.7731
 99T  C3   C  C      0   0.399  -2.2879  -5.2219   0.6885
 99T  O31  O  OC    -1  -0.609  -2.5678  -6.3888   0.3657
 99T  CA3  C  CH2    0  -0.410  -1.5664  -4.3950  -0.3958
 99T  N3   N  NH1    0  -0.628  -1.2880  -3.0624   0.0746
 99T  C2   C  C      0   0.552  -0.6998  -2.1170  -0.6553
 99T  O2   O  O      0  -0.501  -0.2932  -2.2841  -1.7960
 99T  CA2  C  CH1    0  -0.185  -0.6306  -0.7429   0.0255
 99T  CB2  C  CH2    0  -0.571  -1.9034   0.0227  -0.3186
 99T  SG2  S  S2     0  -0.041  -1.8823   1.6735   0.4381
 99T  N2   N  NH1    0  -0.637   0.5259  -0.0107  -0.4123
 99T  CD1  C  C      0   0.566   1.7725  -0.4532  -0.1642
 99T  OE1  O  O      0  -0.503   1.9722  -1.4538   0.5126
 99T  CG1  C  CH2    0  -0.568   2.8887   0.3576  -0.7741
 99T  CB1  C  CH2    0  -0.416   4.0310   0.6154   0.2001
 99T  CA1  C  CH1    0  -0.218   5.1940   1.3691  -0.4509
 99T  N1   N  NH2    0  -0.788   5.7545   0.5752  -1.5337
 99T  C1   C  C      0   0.387   6.2013   1.7942   0.6471
 99T  O01  O  OC    -1  -0.622   5.8064   2.6754   1.4390
 99T  O02  O  O      0  -0.607   7.3064   1.2169   0.6719
 99T  C08  C  CH2    0  -0.529  -3.5281   2.2472  -0.0843
 99T  C09  C  CH2    0  -0.585  -3.7434   3.6762   0.3771
 99T  C10  C  C      0   0.423  -5.1150   4.2638  -0.0156
 99T  O11  O  O      0  -0.604  -5.8710   3.5521  -0.7036
 99T  O12  O  OC    -1  -0.625  -5.3450   5.4188   0.3945
 99T  H2   H  HCH2   0   0.242  -0.6423  -4.9083  -0.6791
 99T  H3   H  HCH2   0   0.242  -2.1909  -4.3658  -1.2942
 99T  H4   H  HNH1   0   0.387  -1.5927  -2.8765   1.0202
 99T  H5   H  HCH1   0   0.276  -0.5877  -0.8773   1.1108
 99T  H6   H  HCH2   0   0.277  -2.0109   0.1202  -1.4019
 99T  H7   H  HCH2   0   0.289  -2.7649  -0.5315   0.0563
 99T  H8   H  HNH1   0   0.400   0.3966   0.7765  -1.0276
 99T  H9   H  HCH2   0   0.266   3.2690  -0.1964  -1.6370
 99T  H10  H  HCH2   0   0.241   2.5096   1.3077  -1.1602
 99T  H11  H  HCH2   0   0.229   3.6655   1.1954   1.0498
 99T  H12  H  HCH2   0   0.218   4.3963  -0.3353   0.6003
 99T  H13  H  HCH1   0   0.211   4.7856   2.2868  -0.8904
 99T  H14  H  HNH2   0   0.336   6.3588   1.1649  -2.0929
 99T  H15  H  HNH2   0   0.324   6.3813  -0.1048  -1.1176
 99T  H18  H  HCH2   0   0.255  -3.5926   2.1746  -1.1706
 99T  H19  H  HCH2   0   0.254  -4.2811   1.5823   0.3409
 99T  H20  H  HCH2   0   0.234  -3.6360   3.7414   1.4646
 99T  H21  H  HCH2   0   0.236  -2.9612   4.3228  -0.0344

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
 99T  O32  C3   deloc   1.246  0.020  1.246
 99T  O31  C3   deloc   1.243  0.020  1.243
 99T  C3   CA3  single  1.543  0.020  1.543
 99T  CA3  N3   single  1.440  0.020  1.440
 99T  N3   C2   single  1.331  0.020  1.331
 99T  C2   O2   double  1.222  0.020  1.222
 99T  C2   CA2  single  1.535  0.020  1.535
 99T  O11  C10  deloc   1.246  0.020  1.246
 99T  C10  C09  single  1.543  0.020  1.543
 99T  C10  O12  deloc   1.247  0.020  1.247
 99T  C09  C08  single  1.517  0.020  1.517
 99T  OE1  CD1  double  1.224  0.020  1.224
 99T  CA2  CB2  single  1.525  0.020  1.525
 99T  CA2  N2   single  1.437  0.020  1.437
 99T  CB2  SG2  single  1.816  0.020  1.816
 99T  CD1  N2   single  1.346  0.020  1.346
 99T  CD1  CG1  single  1.508  0.020  1.508
 99T  C08  SG2  single  1.819  0.020  1.819
 99T  CB1  CG1  single  1.523  0.020  1.523
 99T  CB1  CA1  single  1.531  0.020  1.531
 99T  N1   CA1  single  1.455  0.020  1.455
 99T  CA1  C1   single  1.550  0.020  1.550
 99T  C1   O02  deloc   1.247  0.020  1.247
 99T  C1   O01  deloc   1.249  0.020  1.249
 99T  CA3  H2   single  0.970  0.020  1.090
 99T  CA3  H3   single  0.970  0.020  1.090
 99T  N3   H4   single  0.860  0.020  1.020
 99T  CA2  H5   single  0.970  0.020  1.090
 99T  CB2  H6   single  0.970  0.020  1.090
 99T  CB2  H7   single  0.970  0.020  1.090
 99T  N2   H8   single  0.860  0.020  1.020
 99T  CG1  H9   single  0.970  0.020  1.090
 99T  CG1  H10  single  0.970  0.020  1.090
 99T  CB1  H11  single  0.970  0.020  1.090
 99T  CB1  H12  single  0.970  0.020  1.090
 99T  CA1  H13  single  0.970  0.020  1.090
 99T  N1   H14  single  0.890  0.020  1.040
 99T  N1   H15  single  0.890  0.020  1.040
 99T  C08  H18  single  0.970  0.020  1.090
 99T  C08  H19  single  0.970  0.020  1.090
 99T  C09  H20  single  0.970  0.020  1.090
 99T  C09  H21  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
 99T  CA3  C3   O31  115.22  3.000
 99T  CA3  C3   O32  117.12  3.000
 99T  O31  C3   O32  127.66  3.000
 99T  H3   CA3  H2   106.37  3.000
 99T  H3   CA3  N3   110.71  3.000
 99T  H2   CA3  N3   110.81  3.000
 99T  H3   CA3  C3   108.93  3.000
 99T  H2   CA3  C3   108.99  3.000
 99T  N3   CA3  C3   110.90  3.000
 99T  H4   N3   C2   121.03  3.000
 99T  H4   N3   CA3  114.67  3.000
 99T  C2   N3   CA3  124.29  3.000
 99T  CA2  C2   O2   121.41  3.000
 99T  CA2  C2   N3   114.36  3.000
 99T  O2   C2   N3   124.15  3.000
 99T  H5   CA2  N2   109.45  3.000
 99T  H5   CA2  CB2  108.55  3.000
 99T  N2   CA2  CB2  110.32  3.000
 99T  H5   CA2  C2   109.37  3.000
 99T  N2   CA2  C2   110.93  3.000
 99T  CB2  CA2  C2   108.17  3.000
 99T  H7   CB2  H6   107.96  3.000
 99T  H7   CB2  SG2  109.13  3.000
 99T  H6   CB2  SG2  109.45  3.000
 99T  H7   CB2  CA2  109.07  3.000
 99T  H6   CB2  CA2  110.52  3.000
 99T  SG2  CB2  CA2  110.65  3.000
 99T  C08  SG2  CB2   99.00  3.000
 99T  H8   N2   CD1  119.23  3.000
 99T  H8   N2   CA2  118.74  3.000
 99T  CD1  N2   CA2  121.45  3.000
 99T  CG1  CD1  OE1  122.82  3.000
 99T  CG1  CD1  N2   115.73  3.000
 99T  OE1  CD1  N2   121.45  3.000
 99T  H10  CG1  H9   106.39  3.000
 99T  H10  CG1  CB1  109.80  3.000
 99T  H9   CG1  CB1  109.24  3.000
 99T  H10  CG1  CD1  110.69  3.000
 99T  H9   CG1  CD1  107.71  3.000
 99T  CB1  CG1  CD1  112.79  3.000
 99T  H12  CB1  H11  106.77  3.000
 99T  H12  CB1  CA1  109.25  3.000
 99T  H11  CB1  CA1  108.88  3.000
 99T  H12  CB1  CG1  109.71  3.000
 99T  H11  CB1  CG1  109.67  3.000
 99T  CA1  CB1  CG1  112.40  3.000
 99T  H13  CA1  C1   107.25  3.000
 99T  H13  CA1  N1   107.57  3.000
 99T  C1   CA1  N1   115.25  3.000
 99T  H13  CA1  CB1  107.43  3.000
 99T  C1   CA1  CB1  109.12  3.000
 99T  N1   CA1  CB1  109.90  3.000
 99T  H15  N1   H14  104.37  3.000
 99T  H15  N1   CA1  107.38  3.000
 99T  H14  N1   CA1  108.85  3.000
 99T  O02  C1   O01  126.46  3.000
 99T  O01  C1   CA1  115.93  3.000
 99T  O02  C1   CA1  117.59  3.000
 99T  H19  C08  H18  107.87  3.000
 99T  H19  C08  C09  110.95  3.000
 99T  H18  C08  C09  110.93  3.000
 99T  H19  C08  SG2  108.69  3.000
 99T  H18  C08  SG2  108.57  3.000
 99T  C09  C08  SG2  109.76  3.000
 99T  H21  C09  H20  105.54  3.000
 99T  H21  C09  C10  108.33  3.000
 99T  H20  C09  C10  108.50  3.000
 99T  H21  C09  C08  109.91  3.000
 99T  H20  C09  C08  110.14  3.000
 99T  C10  C09  C08  114.05  3.000
 99T  O12  C10  O11  126.79  3.000
 99T  O12  C10  C09  115.66  3.000
 99T  O11  C10  C09  117.55  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
 99T  CONST_01  O2   C2   N3   CA3     0.00   0.0  0
 99T  CONST_02  CA2  C2   N3   CA3   180.00   0.0  0
 99T  CONST_03  OE1  CD1  N2   CA2     0.00   0.0  0
 99T  CONST_04  CG1  CD1  N2   CA2   180.00   0.0  0
 99T  CONST_05  H4   N3   C2   O2    180.00   0.0  0
 99T  CONST_06  H8   N2   CD1  OE1   180.00   0.0  0
 99T  Var_01    N3   CA3  C3   O32    -0.04  30.0  3
 99T  Var_02    C2   N3   CA3  C3   -178.46  30.0  3
 99T  Var_03    C09  C08  SG2  CB2  -177.22  30.0  1
 99T  Var_04    C10  C09  C08  SG2   179.99  30.0  1
 99T  Var_05    CB1  CG1  CD1  N2    135.14  30.0  3
 99T  Var_06    CA1  CB1  CG1  CD1   176.71  30.0  1
 99T  Var_07    O11  C10  C09  C08    -2.96  30.0  2
 99T  Var_08    H6   CB2  SG2  C08    60.84  30.0  1

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
 99T  chir_01  CA2  C2  CB2  N2  positiv
 99T  chir_02  CA1  N1  CB1  C1  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
 99T  plan-1  CA3  0.020
 99T  plan-1  N3   0.020
 99T  plan-1  C2   0.020
 99T  plan-1  O2   0.020
 99T  plan-1  CA2  0.020
 99T  plan-1  H4   0.020
 99T  plan-2  CA2  0.020
 99T  plan-2  N2   0.020
 99T  plan-2  CD1  0.020
 99T  plan-2  OE1  0.020
 99T  plan-2  CG1  0.020
 99T  plan-2  H8   0.020
 99T  plan-3  O32  0.020
 99T  plan-3  C3   0.020
 99T  plan-3  O31  0.020
 99T  plan-3  CA3  0.020
 99T  plan-4  CA1  0.020
 99T  plan-4  C1   0.020
 99T  plan-4  O01  0.020
 99T  plan-4  O02  0.020
 99T  plan-5  C09  0.020
 99T  plan-5  C10  0.020
 99T  plan-5  O11  0.020
 99T  plan-5  O12  0.020

