# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 16:38:18 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  L-gamma-glutamyl-S-(cis-2,4,6-trinitrocyclohexa-2,5-dien-1-yl)-L-cysteinylglycine  ligand  53  35  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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  -6.7619   1.8944   1.4500
 GTD  CA1   C  CH1    0  -0.214  -5.8901   2.7213   0.6295
 GTD  C1    C  C      0   0.385  -6.6130   3.6306  -0.3962
 GTD  O11   O  O      0  -0.607  -7.8061   3.3747  -0.6520
 GTD  O12   O  OC    -1  -0.624  -5.9221   4.5382  -0.9051
 GTD  CB1   C  CH2    0  -0.421  -4.8873   1.8393  -0.1187
 GTD  CG1   C  CH2    0  -0.577  -4.0338   0.9924   0.8160
 GTD  CD1   C  C      0   0.573  -3.0905   0.0709   0.0838
 GTD  OE1   O  O      0  -0.493  -3.3615  -0.4527  -0.9864
 GTD  N2    N  NH1    0  -0.642  -1.9059  -0.1517   0.6961
 GTD  CA2   C  CH1    0  -0.194  -0.9947  -1.1471   0.1999
 GTD  C2    C  C      0   0.552  -1.5613  -2.5629   0.3777
 GTD  O2    O  O      0  -0.497  -2.2989  -2.8389   1.3127
 GTD  CB2   C  CH2    0  -0.575   0.3271  -1.0437   0.9481
 GTD  SG2   S  S2     0   0.064   1.0401   0.6104   0.6776
 GTD  N3    N  NH1    0  -0.627  -1.1390  -3.4392  -0.5303
 GTD  CA3   C  CH2    0  -0.410  -1.4708  -4.8410  -0.5255
 GTD  C3    C  C      0   0.400  -0.8011  -5.5611  -1.7143
 GTD  O31   O  O      0  -0.597  -0.1210  -4.8603  -2.4883
 GTD  O32   O  OC    -1  -0.608  -1.0124  -6.7835  -1.7811
 GTD  C1'   C  CR16   0  -0.584   2.8364   0.2383   0.4907
 GTD  C2'   C  CR6    0   0.377   3.5803   0.9545   1.5618
 GTD  N2'   N  N      1   0.365   3.3374   0.4776   2.9231
 GTD  O21   O  O      0  -0.356   2.8147  -0.6047   3.0341
 GTD  O22   O  O     -1  -0.363   3.6809   1.1711   3.8461
 GTD  C3'   C  CR16   0  -0.241   4.4072   1.9746   1.3909
 GTD  C4'   C  CR16   0  -0.277   4.7160   2.4924   0.0299
 GTD  N4'   N  N      1   0.467   6.2277   2.5189  -0.1283
 GTD  O41   O  O      0  -0.347   6.7090   1.8738  -1.0195
 GTD  O42   O  O     -1  -0.356   6.8350   3.1899   0.6626
 GTD  C5'   C  CR16   0  -0.241   4.1012   1.7260  -1.0843
 GTD  C6'   C  CR6    0   0.365   3.2725   0.7201  -0.8489
 GTD  N6'   N  N      1   0.367   2.7008   0.0087  -1.9929
 GTD  O61   O  O      0  -0.358   2.1738  -1.0537  -1.7673
 GTD  O62   O  O     -1  -0.362   2.7968   0.5065  -3.0857
 GTD  HN11  H  HNH2   0   0.336  -7.3448   2.4996   2.0157
 GTD  HN12  H  HNH2   0   0.323  -7.4142   1.4248   0.8316
 GTD  HA1   H  HCH1   0   0.210  -5.3216   3.3715   1.3056
 GTD  HB11  H  HCH2   0   0.219  -5.4295   1.1870  -0.8101
 GTD  HB12  H  HCH2   0   0.231  -4.2445   2.4776  -0.7274
 GTD  HG11  H  HCH2   0   0.245  -3.4788   1.6371   1.5032
 GTD  HG12  H  HCH2   0   0.273  -4.6861   0.3731   1.4389
 GTD  HN2   H  HNH1   0   0.405  -1.8013   0.1523   1.6522
 GTD  HA2   H  HCH1   0   0.283  -0.8066  -0.9609  -0.8604
 GTD  HB21  H  HCH2   0   0.297   0.1859  -1.2141   2.0160
 GTD  HB22  H  HCH2   0   0.304   1.0255  -1.7893   0.5736
 GTD  HN3   H  HNH1   0   0.386  -0.5605  -3.1519  -1.3090
 GTD  HA31  H  HCH2   0   0.243  -1.1475  -5.3125   0.4072
 GTD  HA32  H  HCH2   0   0.244  -2.5539  -4.9846  -0.5881
 GTD  H1'   H  HCR6   0   0.371   2.9760  -0.8401   0.5811
 GTD  H3'   H  HCR6   0   0.346   4.8687   2.4726   2.2324
 GTD  H4'   H  HCR6   0   0.379   4.4205   3.5462  -0.0359
 GTD  H5'   H  HCR6   0   0.345   4.3160   2.0492  -2.0931

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  1.455  0.020  1.455
 GTD  N1   HN11  single  0.890  0.020  1.040
 GTD  N1   HN12  single  0.890  0.020  1.040
 GTD  CA1  C1    single  1.550  0.020  1.550
 GTD  CA1  CB1   single  1.531  0.020  1.531
 GTD  CA1  HA1   single  0.970  0.020  1.090
 GTD  C1   O11   deloc   1.247  0.020  1.247
 GTD  C1   O12   deloc   1.249  0.020  1.249
 GTD  CB1  CG1   single  1.523  0.020  1.523
 GTD  CB1  HB11  single  0.970  0.020  1.090
 GTD  CB1  HB12  single  0.970  0.020  1.090
 GTD  CG1  CD1   single  1.508  0.020  1.508
 GTD  CG1  HG11  single  0.970  0.020  1.090
 GTD  CG1  HG12  single  0.970  0.020  1.090
 GTD  CD1  OE1   double  1.222  0.020  1.222
 GTD  CD1  N2    single  1.352  0.020  1.352
 GTD  N2   CA2   single  1.438  0.020  1.438
 GTD  N2   HN2   single  0.890  0.020  1.040
 GTD  CA2  C2    single  1.535  0.020  1.535
 GTD  CA2  CB2   single  1.522  0.020  1.522
 GTD  CA2  HA2   single  0.970  0.020  1.090
 GTD  C2   O2    double  1.222  0.020  1.222
 GTD  C2   N3    single  1.331  0.020  1.331
 GTD  CB2  SG2   single  1.821  0.020  1.821
 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  1.440  0.020  1.440
 GTD  N3   HN3   single  0.860  0.020  1.020
 GTD  CA3  C3    single  1.543  0.020  1.543
 GTD  CA3  HA31  single  0.970  0.020  1.090
 GTD  CA3  HA32  single  0.970  0.020  1.090
 GTD  C3   O31   deloc   1.246  0.020  1.246
 GTD  C3   O32   deloc   1.242  0.020  1.242
 GTD  C1'  C2'   single  1.488  0.020  1.488
 GTD  C1'  C6'   single  1.489  0.020  1.489
 GTD  C1'  H1'   single  0.970  0.020  1.090
 GTD  C2'  N2'   single  1.463  0.020  1.463
 GTD  C2'  C3'   double  1.324  0.020  1.324
 GTD  N2'  O21   double  1.207  0.020  1.207
 GTD  N2'  O22   single  1.205  0.020  1.205
 GTD  C3'  C4'   single  1.489  0.020  1.489
 GTD  C3'  H3'   single  0.930  0.020  1.080
 GTD  C4'  N4'   single  1.520  0.020  1.520
 GTD  C4'  C5'   single  1.486  0.020  1.486
 GTD  C4'  H4'   single  0.970  0.020  1.090
 GTD  N4'  O41   double  1.201  0.020  1.201
 GTD  N4'  O42   single  1.202  0.020  1.202
 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  1.207  0.020  1.207
 GTD  N6'  O62   single  1.205  0.020  1.205

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  104.30  3.000
 GTD  HN12  N1   CA1   107.74  3.000
 GTD  HN11  N1   CA1   108.68  3.000
 GTD  HA1   CA1  CB1   107.66  3.000
 GTD  HA1   CA1  C1    107.57  3.000
 GTD  CB1   CA1  C1    108.68  3.000
 GTD  HA1   CA1  N1    107.44  3.000
 GTD  CB1   CA1  N1    109.92  3.000
 GTD  C1    CA1  N1    115.29  3.000
 GTD  O12   C1   O11   126.50  3.000
 GTD  O12   C1   CA1   115.98  3.000
 GTD  O11   C1   CA1   117.50  3.000
 GTD  HB12  CB1  HB11  106.74  3.000
 GTD  HB12  CB1  CG1   109.72  3.000
 GTD  HB11  CB1  CG1   109.51  3.000
 GTD  HB12  CB1  CA1   108.75  3.000
 GTD  HB11  CB1  CA1   109.13  3.000
 GTD  CG1   CB1  CA1   112.81  3.000
 GTD  HG12  CG1  HG11  106.17  3.000
 GTD  HG12  CG1  CD1   107.67  3.000
 GTD  HG11  CG1  CD1   110.35  3.000
 GTD  HG12  CG1  CB1   109.27  3.000
 GTD  HG11  CG1  CB1   110.02  3.000
 GTD  CD1   CG1  CB1   113.10  3.000
 GTD  N2    CD1  OE1   121.36  3.000
 GTD  N2    CD1  CG1   115.39  3.000
 GTD  OE1   CD1  CG1   123.25  3.000
 GTD  HN2   N2   CA2   118.04  3.000
 GTD  HN2   N2   CD1   118.06  3.000
 GTD  CA2   N2   CD1   120.87  3.000
 GTD  HA2   CA2  CB2   108.41  3.000
 GTD  HA2   CA2  C2    109.45  3.000
 GTD  CB2   CA2  C2    109.04  3.000
 GTD  HA2   CA2  N2    109.02  3.000
 GTD  CB2   CA2  N2    109.49  3.000
 GTD  C2    CA2  N2    111.38  3.000
 GTD  N3    C2   O2    124.38  3.000
 GTD  N3    C2   CA2   114.28  3.000
 GTD  O2    C2   CA2   121.29  3.000
 GTD  HB22  CB2  HB21  108.24  3.000
 GTD  HB22  CB2  SG2   108.66  3.000
 GTD  HB21  CB2  SG2   109.75  3.000
 GTD  HB22  CB2  CA2   109.98  3.000
 GTD  HB21  CB2  CA2   110.99  3.000
 GTD  SG2   CB2  CA2   109.18  3.000
 GTD  C1'   SG2  CB2   102.31  3.000
 GTD  HN3   N3   CA3   114.24  3.000
 GTD  HN3   N3   C2    121.31  3.000
 GTD  CA3   N3   C2    124.44  3.000
 GTD  HA32  CA3  HA31  106.54  3.000
 GTD  HA32  CA3  C3    108.92  3.000
 GTD  HA31  CA3  C3    109.12  3.000
 GTD  HA32  CA3  N3    110.82  3.000
 GTD  HA31  CA3  N3    110.74  3.000
 GTD  C3    CA3  N3    110.59  3.000
 GTD  O32   C3   O31   127.79  3.000
 GTD  O32   C3   CA3   115.27  3.000
 GTD  O31   C3   CA3   116.94  3.000
 GTD  H1'   C1'  C6'   110.91  3.000
 GTD  H1'   C1'  C2'   110.61  3.000
 GTD  C6'   C1'  C2'   110.21  3.000
 GTD  H1'   C1'  SG2   108.40  3.000
 GTD  C6'   C1'  SG2   108.13  3.000
 GTD  C2'   C1'  SG2   108.48  3.000
 GTD  C3'   C2'  N2'   118.36  3.000
 GTD  C3'   C2'  C1'   126.17  3.000
 GTD  N2'   C2'  C1'   115.47  3.000
 GTD  O22   N2'  O21   124.70  3.000
 GTD  O22   N2'  C2'   118.56  3.000
 GTD  O21   N2'  C2'   116.74  3.000
 GTD  H3'   C3'  C4'   117.57  3.000
 GTD  H3'   C3'  C2'   121.39  3.000
 GTD  C4'   C3'  C2'   121.03  3.000
 GTD  H4'   C4'  C5'   109.83  3.000
 GTD  H4'   C4'  N4'   104.19  3.000
 GTD  C5'   C4'  N4'   110.03  3.000
 GTD  H4'   C4'  C3'   109.47  3.000
 GTD  C5'   C4'  C3'   114.86  3.000
 GTD  N4'   C4'  C3'   107.91  3.000
 GTD  O42   N4'  O41   125.85  3.000
 GTD  O42   N4'  C4'   116.34  3.000
 GTD  O41   N4'  C4'   117.80  3.000
 GTD  H5'   C5'  C6'   121.15  3.000
 GTD  H5'   C5'  C4'   117.61  3.000
 GTD  C6'   C5'  C4'   121.17  3.000
 GTD  N6'   C6'  C5'   118.34  3.000
 GTD  N6'   C6'  C1'   115.57  3.000
 GTD  C5'   C6'  C1'   126.08  3.000
 GTD  O62   N6'  O61   124.61  3.000
 GTD  O62   N6'  C6'   118.50  3.000
 GTD  O61   N6'  C6'   116.89  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  HN3   N3   C2   CA2     0.00   0.0  0
 GTD  Var_01    C4'   C3'  C2'  C1'    -2.20  30.0  1
 GTD  Var_02    C4'   C5'  C6'  C1'     0.86  30.0  1
 GTD  Var_03    O21   N2'  C2'  C1'    15.92  30.0  2
 GTD  Var_04    O61   N6'  C6'  C1'   -15.30  30.0  2
 GTD  Var_05    HB21  CB2  SG2  C1'    97.61  30.0  1
 GTD  Var_06    CD1   CG1  CB1  CA1   177.17  30.0  3
 GTD  Var_07    OE1   CD1  CG1  CB1   -33.88  30.0  3
 GTD  Var_08    C3    CA3  N3   C2   -179.47  30.0  3
 GTD  Var_09    O31   C3   CA3  N3     -1.24  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
 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'  positiv

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-7  CA3  0.020
 GTD  plan-7  C3   0.020
 GTD  plan-7  O31  0.020
 GTD  plan-7  O32  0.020

