# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Oct  1 00:19:36 2022
#   Inital geometry file: a 146 line input string
#   Ligand name: L-gamma-glutamyl-S-(cis-2,4,6-trinitrocyclohexa-2,5-dien-1-yl)-L-cysteinylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)N[C@@H](CS[C@@H]1C(=C[C@@H](C=C1[N+]([O-])=O)[N+]([O-])=O)[N+]([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
 GTD  GTD  "1-(S-GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE"  ligand  55  35  .  2022-09-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GTD
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
 GTD  N1    N  NH2    0  -0.786  17.6730  14.3235  13.6237
 GTD  CA1   C  CH1    0  -0.194  18.2752  14.0462  12.3295
 GTD  C1    C  C      0   0.538  17.5092  12.9270  11.6512
 GTD  O11   O  O      0  -0.437  17.0679  12.9770  10.5306
 GTD  O12   O  OH1    0  -0.590  17.3957  11.8572  12.4303
 GTD  CB1   C  CH2    0  -0.445  19.7765  13.7261  12.3838
 GTD  CG1   C  CH2    0  -0.608  20.4022  13.5336  11.0107
 GTD  CD1   C  C      0   0.585  21.9021  13.3354  11.0669
 GTD  OE1   O  O      0  -0.467  22.5893  13.7283  11.9916
 GTD  N2    N  NH1    0  -0.665  22.4211  12.7120   9.9777
 GTD  CA2   C  CH1    0  -0.198  23.7985  12.3123   9.8746
 GTD  C2    C  C      0   0.578  24.5103  12.8905   8.6508
 GTD  O2    O  O      0  -0.480  25.5880  12.4450   8.2906
 GTD  CB2   C  CH2    0  -0.574  23.9262  10.7874   9.8655
 GTD  SG2   S  S2     0   0.070  23.0269  10.0421  11.2576
 GTD  N3    N  NH1    0  -0.629  23.8912  13.8972   8.0203
 GTD  CA3   C  CH2    0  -0.420  24.4761  14.5224   6.8737
 GTD  C3    C  C      0   0.533  25.6739  15.3830   7.2209
 GTD  O31   O  O      0  -0.425  25.9865  15.7142   8.3323
 GTD  O32   O  OH1    0  -0.590  26.3197  15.7489   6.1214
 GTD  C1'   C  CH1    0  -0.592  24.3523   9.3749  12.3529
 GTD  C2'   C  C      0   0.379  24.1754   7.9001  12.4542
 GTD  N2'   N  N      1   0.363  24.5220   7.1321  11.2567
 GTD  O21   O  O      0  -0.355  25.0868   7.7269  10.3715
 GTD  O22   O  O     -1  -0.360  24.2345   5.9627  11.2215
 GTD  C3'   C  C1     0  -0.232  23.7173   7.2462  13.5111
 GTD  C4'   C  CH1    0  -0.296  23.3842   7.9652  14.7728
 GTD  N4'   N  N      1   0.468  21.8971   7.7858  15.0484
 GTD  O41   O  O      0  -0.353  21.4891   6.6561  15.0721
 GTD  O42   O  O     -1  -0.345  21.2418   8.7762  15.2262
 GTD  C5'   C  C1     0  -0.230  23.7285   9.4115  14.7804
 GTD  C6'   C  C      0   0.364  24.1972  10.0037  13.6934
 GTD  N6'   N  N      1   0.364  24.5968  11.4081  13.7841
 GTD  O61   O  O      0  -0.355  24.1501  12.0728  14.6830
 GTD  O62   O  O     -1  -0.358  25.3729  11.8080  12.9501
 GTD  HN11  H  HNH2   0   0.357  18.0428  15.1992  13.9716
 GTD  HN12  H  HNH2   0   0.348  17.9500  13.6182  14.2965
 GTD  HA1   H  HCH1   0   0.265  18.1353  14.9290  11.7015
 GTD  HO1   H  HOH1   0   0.479  16.9055  11.1595  11.9693
 GTD  HB11  H  HCH2   0   0.252  20.2604  14.5592  12.8969
 GTD  HB12  H  HCH2   0   0.240  19.9368  12.8402  13.0047
 GTD  HG11  H  HCH2   0   0.265  19.9498  12.6900  10.4834
 GTD  HG12  H  HCH2   0   0.282  20.2102  14.4131  10.3858
 GTD  HN2   H  HNH1   0   0.409  21.7792  12.3451   9.2893
 GTD  HA2   H  HCH1   0   0.306  24.3185  12.7085  10.7486
 GTD  HB21  H  HCH2   0   0.299  23.4861  10.3746   8.9560
 GTD  HB22  H  HCH2   0   0.308  24.9672  10.4758   9.8962
 GTD  HN3   H  HNH1   0   0.415  23.0244  14.2561   8.3861
 GTD  HA31  H  HCH2   0   0.288  24.7659  13.7803   6.1271
 GTD  HA32  H  HCH2   0   0.312  23.7235  15.1584   6.4037
 GTD  HO3   H  HOH1   0   0.482  27.0619  16.3306   6.3463
 GTD  H1'   H  HCH1   0   0.373  25.3213   9.6245  11.9197
 GTD  H3'   H  H      0   0.344  23.5964   6.1720  13.5027
 GTD  H4'   H  HCH1   0   0.375  23.8738   7.4634  15.6146
 GTD  H5'   H  H      0   0.341  23.6390   9.9429  15.7177

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
 GTD  N1   CA1   single  1.454  0.020  1.454
 GTD  N1   HN11  single  0.890  0.020  1.040
 GTD  N1   HN12  single  0.890  0.020  1.040
 GTD  CA1  C1    single  1.516  0.020  1.516
 GTD  CA1  CB1   single  1.536  0.020  1.536
 GTD  CA1  HA1   single  0.970  0.020  1.090
 GTD  C1   O11   double  1.205  0.020  1.205
 GTD  C1   O12   single  1.328  0.020  1.328
 GTD  O12  HO1   single  0.850  0.020  0.980
 GTD  CB1  CG1   single  1.521  0.020  1.521
 GTD  CB1  HB11  single  0.970  0.020  1.090
 GTD  CB1  HB12  single  0.970  0.020  1.090
 GTD  CG1  CD1   single  1.514  0.020  1.514
 GTD  CG1  HG11  single  0.970  0.020  1.090
 GTD  CG1  HG12  single  0.970  0.020  1.090
 GTD  CD1  OE1   double  1.217  0.020  1.217
 GTD  CD1  N2    single  1.358  0.020  1.358
 GTD  N2   CA2   single  1.438  0.020  1.438
 GTD  N2   HN2   single  0.860  0.020  1.020
 GTD  CA2  C2    single  1.529  0.020  1.529
 GTD  CA2  CB2   single  1.530  0.020  1.530
 GTD  CA2  HA2   single  0.970  0.020  1.090
 GTD  C2   O2    double  1.221  0.020  1.221
 GTD  C2   N3    single  1.339  0.020  1.339
 GTD  CB2  SG2   single  1.817  0.020  1.817
 GTD  CB2  HB21  single  0.970  0.020  1.090
 GTD  CB2  HB22  single  0.970  0.020  1.090
 GTD  SG2  C1'   single  1.844  0.020  1.844
 GTD  N3   CA3   single  1.431  0.020  1.431
 GTD  N3   HN3   single  0.860  0.020  1.020
 GTD  CA3  C3    single  1.515  0.020  1.515
 GTD  CA3  HA31  single  0.970  0.020  1.090
 GTD  CA3  HA32  single  0.970  0.020  1.090
 GTD  C3   O31   double  1.201  0.020  1.201
 GTD  C3   O32   single  1.327  0.020  1.327
 GTD  O32  HO3   single  0.850  0.020  0.980
 GTD  C1'  C2'   single  1.489  0.020  1.489
 GTD  C1'  C6'   single  1.489  0.020  1.489
 GTD  C1'  H1'   single  0.970  0.020  1.090
 GTD  C2'  N2'   single  1.464  0.020  1.464
 GTD  C2'  C3'   double  1.325  0.020  1.325
 GTD  N2'  O21   double  1.207  0.020  1.207
 GTD  N2'  O22   single  1.205  0.020  1.205
 GTD  C3'  C4'   single  1.490  0.020  1.490
 GTD  C3'  H3'   single  0.930  0.020  1.080
 GTD  C4'  N4'   single  1.523  0.020  1.523
 GTD  C4'  C5'   single  1.487  0.020  1.487
 GTD  C4'  H4'   single  0.970  0.020  1.090
 GTD  N4'  O41   double  1.201  0.020  1.201
 GTD  N4'  O42   single  1.201  0.020  1.201
 GTD  C5'  C6'   double  1.324  0.020  1.324
 GTD  C5'  H5'   single  0.930  0.020  1.080
 GTD  C6'  N6'   single  1.463  0.020  1.463
 GTD  N6'  O61   double  1.204  0.020  1.204
 GTD  N6'  O62   single  1.207  0.020  1.207

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
 GTD  HN12  N1   HN11  105.90  3.000
 GTD  HN12  N1   CA1   110.18  3.000
 GTD  HN11  N1   CA1   108.64  3.000
 GTD  HA1   CA1  CB1   108.30  3.000
 GTD  HA1   CA1  C1    105.94  3.000
 GTD  CB1   CA1  C1    110.84  3.000
 GTD  HA1   CA1  N1    107.73  3.000
 GTD  CB1   CA1  N1    114.39  3.000
 GTD  C1    CA1  N1    109.25  3.000
 GTD  O12   C1   O11   123.19  3.000
 GTD  O12   C1   CA1   112.04  3.000
 GTD  O11   C1   CA1   124.76  3.000
 GTD  HO1   O12  C1    110.12  3.000
 GTD  HB12  CB1  HB11  106.64  3.000
 GTD  HB12  CB1  CG1   110.47  3.000
 GTD  HB11  CB1  CG1   109.79  3.000
 GTD  HB12  CB1  CA1   109.40  3.000
 GTD  HB11  CB1  CA1   106.91  3.000
 GTD  CG1   CB1  CA1   113.36  3.000
 GTD  HG12  CG1  HG11  105.78  3.000
 GTD  HG12  CG1  CD1   107.45  3.000
 GTD  HG11  CG1  CD1   109.08  3.000
 GTD  HG12  CG1  CB1   109.94  3.000
 GTD  HG11  CG1  CB1   111.28  3.000
 GTD  CD1   CG1  CB1   112.99  3.000
 GTD  N2    CD1  OE1   122.80  3.000
 GTD  N2    CD1  CG1   114.14  3.000
 GTD  OE1   CD1  CG1   123.04  3.000
 GTD  HN2   N2   CA2   117.31  3.000
 GTD  HN2   N2   CD1   118.06  3.000
 GTD  CA2   N2   CD1   123.45  3.000
 GTD  HA2   CA2  CB2   109.07  3.000
 GTD  HA2   CA2  C2    106.36  3.000
 GTD  CB2   CA2  C2    109.46  3.000
 GTD  HA2   CA2  N2    107.34  3.000
 GTD  CB2   CA2  N2    110.94  3.000
 GTD  C2    CA2  N2    113.46  3.000
 GTD  N3    C2   O2    122.93  3.000
 GTD  N3    C2   CA2   116.47  3.000
 GTD  O2    C2   CA2   120.60  3.000
 GTD  HB22  CB2  HB21  107.54  3.000
 GTD  HB22  CB2  SG2   109.56  3.000
 GTD  HB21  CB2  SG2   106.48  3.000
 GTD  HB22  CB2  CA2   111.43  3.000
 GTD  HB21  CB2  CA2   110.38  3.000
 GTD  SG2   CB2  CA2   111.27  3.000
 GTD  C1'   SG2  CB2   104.34  3.000
 GTD  HN3   N3   CA3   119.16  3.000
 GTD  HN3   N3   C2    119.65  3.000
 GTD  CA3   N3   C2    121.10  3.000
 GTD  HA32  CA3  HA31  106.53  3.000
 GTD  HA32  CA3  C3    108.22  3.000
 GTD  HA31  CA3  C3    109.45  3.000
 GTD  HA32  CA3  N3    108.52  3.000
 GTD  HA31  CA3  N3    111.07  3.000
 GTD  C3    CA3  N3    112.81  3.000
 GTD  O32   C3   O31   124.35  3.000
 GTD  O32   C3   CA3   110.58  3.000
 GTD  O31   C3   CA3   125.06  3.000
 GTD  HO3   O32  C3    110.23  3.000
 GTD  H1'   C1'  C6'   110.71  3.000
 GTD  H1'   C1'  C2'   111.06  3.000
 GTD  C6'   C1'  C2'   110.17  3.000
 GTD  H1'   C1'  SG2   108.65  3.000
 GTD  C6'   C1'  SG2   107.88  3.000
 GTD  C2'   C1'  SG2   108.27  3.000
 GTD  C3'   C2'  N2'   118.39  3.000
 GTD  C3'   C2'  C1'   125.76  3.000
 GTD  N2'   C2'  C1'   115.84  3.000
 GTD  O22   N2'  O21   124.66  3.000
 GTD  O22   N2'  C2'   118.46  3.000
 GTD  O21   N2'  C2'   116.88  3.000
 GTD  H3'   C3'  C4'   117.47  3.000
 GTD  H3'   C3'  C2'   121.53  3.000
 GTD  C4'   C3'  C2'   120.98  3.000
 GTD  H4'   C4'  C5'   109.77  3.000
 GTD  H4'   C4'  N4'   104.09  3.000
 GTD  C5'   C4'  N4'   109.86  3.000
 GTD  H4'   C4'  C3'   109.25  3.000
 GTD  C5'   C4'  C3'   114.97  3.000
 GTD  N4'   C4'  C3'   108.34  3.000
 GTD  O42   N4'  O41   125.96  3.000
 GTD  O42   N4'  C4'   117.55  3.000
 GTD  O41   N4'  C4'   116.49  3.000
 GTD  H5'   C5'  C6'   121.42  3.000
 GTD  H5'   C5'  C4'   117.61  3.000
 GTD  C6'   C5'  C4'   120.87  3.000
 GTD  N6'   C6'  C5'   118.38  3.000
 GTD  N6'   C6'  C1'   115.65  3.000
 GTD  C5'   C6'  C1'   125.97  3.000
 GTD  O62   N6'  O61   124.85  3.000
 GTD  O62   N6'  C6'   116.78  3.000
 GTD  O61   N6'  C6'   118.36  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
 GTD  CONST_01  CA2   N2   CD1  CG1   180.00   0.0  0
 GTD  CONST_02  CA2   N2   CD1  OE1     0.00   0.0  0
 GTD  CONST_03  CA3   N3   C2   CA2   180.00   0.0  0
 GTD  CONST_04  CA3   N3   C2   O2      0.00   0.0  0
 GTD  CONST_05  HN2   N2   CD1  CG1     0.00   0.0  0
 GTD  CONST_06  HN2   N2   CD1  OE1   180.00   0.0  0
 GTD  CONST_07  HN3   N3   C2   CA2     0.00   0.0  0
 GTD  CONST_08  HN3   N3   C2   O2    180.00   0.0  0
 GTD  CONST_09  HO1   O12  C1   CA1   180.00   0.0  0
 GTD  CONST_10  HO1   O12  C1   O11     0.00   0.0  0
 GTD  CONST_11  HO3   O32  C3   CA3   180.00   0.0  0
 GTD  CONST_12  HO3   O32  C3   O31     0.00   0.0  0
 GTD  Var_01    C4'   C3'  C2'  C1'    -3.04  30.0  1
 GTD  Var_02    C4'   C5'  C6'  C1'     4.32  30.0  1
 GTD  Var_03    C4'   C3'  C2'  N2'   178.22  30.0  1
 GTD  Var_04    N6'   C6'  C5'  C4'  -176.24  30.0  1
 GTD  Var_05    H3'   C3'  C2'  C1'   178.67  30.0  1
 GTD  Var_06    H5'   C5'  C6'  C1'  -179.45  30.0  1
 GTD  Var_07    O21   N2'  C2'  C1'     9.92  30.0  2
 GTD  Var_08    O22   N2'  C2'  C1'  -170.41  30.0  2
 GTD  Var_09    O61   N6'  C6'  C1'   158.59  30.0  2
 GTD  Var_10    O62   N6'  C6'  C1'   -22.38  30.0  2
 GTD  Var_11    C3'   C2'  N2'  O21  -171.23  30.0  2
 GTD  Var_12    C3'   C2'  N2'  O22     8.45  30.0  2
 GTD  Var_13    O61   N6'  C6'  C5'   -20.90  30.0  2
 GTD  Var_14    O62   N6'  C6'  C5'   158.13  30.0  2
 GTD  Var_15    H3'   C3'  C2'  N2'    -0.06  30.0  1
 GTD  Var_16    H5'   C5'  C6'  N6'    -0.01  30.0  1
 GTD  Var_17    C1'   SG2  CB2  CA2  -111.24  30.0  3
 GTD  Var_18    HB21  CB2  SG2  C1'   128.44  30.0  1
 GTD  Var_19    HB22  CB2  SG2  C1'    12.42  30.0  1
 GTD  Var_20    CD1   CG1  CB1  CA1   175.12  30.0  3
 GTD  Var_21    OE1   CD1  CG1  CB1   -23.58  30.0  3
 GTD  Var_22    N2    CD1  CG1  CB1   158.11  30.0  3
 GTD  Var_23    C3    CA3  N3   C2    -71.80  30.0  3
 GTD  Var_24    O31   C3   CA3  N3    -12.29  30.0  3
 GTD  Var_25    O32   C3   CA3  N3    169.07  30.0  3
 GTD  Var_26    HG11  CG1  CB1  CA1   -61.77  30.0  3
 GTD  Var_27    HG12  CG1  CB1  CA1    55.08  30.0  3
 GTD  Var_28    HB11  CB1  CG1  CD1    55.64  30.0  1
 GTD  Var_29    HB12  CB1  CG1  CD1   -61.69  30.0  1
 GTD  Var_30    HG11  CG1  CD1  OE1  -147.90  30.0  1
 GTD  Var_31    HG12  CG1  CD1  OE1    97.88  30.0  1
 GTD  Var_32    HG11  CG1  CD1  N2     33.79  30.0  1
 GTD  Var_33    HG12  CG1  CD1  N2    -80.44  30.0  1
 GTD  Var_34    HA31  CA3  N3   C2     51.51  30.0  3
 GTD  Var_35    HA32  CA3  N3   C2    168.29  30.0  3
 GTD  Var_36    HN3   N3   CA3  C3    104.82  30.0  2
 GTD  Var_37    HA31  CA3  C3   O31  -136.49  30.0  1
 GTD  Var_38    HA32  CA3  C3   O31   107.79  30.0  1
 GTD  Var_39    HA31  CA3  C3   O32    44.88  30.0  1
 GTD  Var_40    HA32  CA3  C3   O32   -70.84  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
 GTD  chir_01  CA1  N1   C1   CB1  positiv
 GTD  chir_02  CA2  N2   C2   CB2  positiv
 GTD  chir_03  C1'  SG2  C2'  C6'  positiv
 GTD  chir_04  C4'  N4'  C3'  C5'  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
 GTD  plan-1  CG1  0.020
 GTD  plan-1  CD1  0.020
 GTD  plan-1  OE1  0.020
 GTD  plan-1  N2   0.020
 GTD  plan-1  CA2  0.020
 GTD  plan-1  HN2  0.020
 GTD  plan-2  C2'  0.020
 GTD  plan-2  N2'  0.020
 GTD  plan-2  O21  0.020
 GTD  plan-2  O22  0.020
 GTD  plan-3  C4'  0.020
 GTD  plan-3  N4'  0.020
 GTD  plan-3  O41  0.020
 GTD  plan-3  O42  0.020
 GTD  plan-4  C6'  0.020
 GTD  plan-4  N6'  0.020
 GTD  plan-4  O61  0.020
 GTD  plan-4  O62  0.020
 GTD  plan-5  CA2  0.020
 GTD  plan-5  C2   0.020
 GTD  plan-5  O2   0.020
 GTD  plan-5  N3   0.020
 GTD  plan-5  CA3  0.020
 GTD  plan-5  HN3  0.020
 GTD  plan-6  CA1  0.020
 GTD  plan-6  C1   0.020
 GTD  plan-6  O11  0.020
 GTD  plan-6  O12  0.020
 GTD  plan-6  HO1  0.020
 GTD  plan-7  CA3  0.020
 GTD  plan-7  C3   0.020
 GTD  plan-7  O31  0.020
 GTD  plan-7  O32  0.020
 GTD  plan-7  HO3  0.020

