# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 23:27:57 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: L-gamma-glutamyl-S-(4-nitrobenzyl)-L-cysteinylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)N[C@@H](CSCc1ccc(cc1)[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
 GTB  GTB  L-gamma-glutamyl-S-(4-nitrobenzyl)-L-cysteinylglycine  ligand  50  30  .  2022-07-25  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_GTB
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
 GTB  N1    N  NH2    0  -0.787  -4.5219   4.2073   1.5496
 GTB  CA1   C  CH1    0  -0.216  -3.5866   4.3470   0.4436
 GTB  C1    C  C      0   0.386  -4.0150   5.3462  -0.6603
 GTB  O11   O  O      0  -0.607  -5.2082   5.7084  -0.6763
 GTB  O12   O  OC    -1  -0.623  -3.1248   5.6877  -1.4667
 GTB  CB1   C  CH2    0  -0.418  -3.3315   2.9805  -0.1998
 GTB  CG1   C  CH2    0  -0.570  -2.7639   1.9683   0.7868
 GTB  CD1   C  C      0   0.570  -2.6140   0.5892   0.1944
 GTB  OE1   O  O      0  -0.501  -3.4576   0.0803  -0.5321
 GTB  N2    N  NH1    0  -0.640  -1.4865  -0.0676   0.5241
 GTB  CA2   C  CH1    0  -0.187  -1.2547  -1.4206   0.0985
 GTB  C2    C  C      0   0.553  -2.3244  -2.3664   0.6628
 GTB  O2    O  O      0  -0.500  -2.7904  -2.2046   1.7812
 GTB  CB2   C  CH2    0  -0.578   0.1053  -1.9011   0.5925
 GTB  SG2   S  S2     0   0.002   1.4254  -0.8550  -0.0891
 GTB  N3    N  NH1    0  -0.627  -2.6318  -3.3847  -0.1368
 GTB  CA3   C  CH2    0  -0.410  -3.5335  -4.4501   0.2184
 GTB  C3    C  C      0   0.399  -3.6360  -5.4858  -0.9200
 GTB  O31   O  O      0  -0.600  -2.9799  -5.2580  -1.9547
 GTB  O32   O  OC    -1  -0.609  -4.3764  -6.4564  -0.6886
 GTB  C'    C  CH2    0  -0.619   2.8471  -1.5962   0.7745
 GTB  C1'   C  CR6    0   0.123   4.0631  -0.7845   0.4546
 GTB  C2'   C  CR16   0  -0.272   4.2930   0.4218   1.1134
 GTB  C3'   C  CR16   0  -0.253   5.4051   1.1889   0.8210
 GTB  C4'   C  CR6    0   0.240   6.2899   0.7403  -0.1503
 GTB  N41   N  N      1   0.330   7.4659   1.5370  -0.4601
 GTB  O41   O  O     -1  -0.379   7.6404   2.5591   0.1612
 GTB  O42   O  O      0  -0.379   8.2122   1.1383  -1.3233
 GTB  C5'   C  CR16   0  -0.251   6.0814  -0.4507  -0.8291
 GTB  C6'   C  CR16   0  -0.284   4.9622  -1.2050  -0.5210
 GTB  HN11  H  HNH2   0   0.336  -4.5317   5.0707   2.0788
 GTB  HN12  H  HNH2   0   0.324  -5.4543   4.1444   1.1551
 GTB  HA1   H  HCH1   0   0.210  -2.6349   4.6990   0.8587
 GTB  HB11  H  HCH2   0   0.219  -4.2688   2.6009  -0.6181
 GTB  HB12  H  HCH2   0   0.230  -2.6420   3.1064  -1.0366
 GTB  HG11  H  HCH2   0   0.241  -1.8071   2.3251   1.1773
 GTB  HG12  H  HCH2   0   0.268  -3.4376   1.8927   1.6447
 GTB  HN2   H  HNH1   0   0.402  -0.8294   0.3651   1.1535
 GTB  HA2   H  HCH1   0   0.280  -1.2703  -1.4725  -0.9954
 GTB  HB21  H  HCH2   0   0.285   0.1484  -1.8672   1.6838
 GTB  HB22  H  HCH2   0   0.297   0.2611  -2.9330   0.2766
 GTB  HN3   H  HNH1   0   0.388  -2.2371  -3.4565  -1.0645
 GTB  HA31  H  HCH2   0   0.242  -3.1974  -4.9519   1.1305
 GTB  HA32  H  HCH2   0   0.243  -4.5332  -4.0584   0.4312
 GTB  H'1   H  HCH2   0   0.296   2.6484  -1.5873   1.8474
 GTB  H'2   H  HCH2   0   0.294   2.9720  -2.6307   0.4546
 GTB  H2'   H  HCR6   0   0.275   3.5980   0.7666   1.8682
 GTB  H3'   H  HCR6   0   0.299   5.5709   2.1184   1.3452
 GTB  H5'   H  HCR6   0   0.299   6.7722  -0.7973  -1.5837
 GTB  H6'   H  HCR6   0   0.276   4.7937  -2.1383  -1.0425

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
 GTB  N1   CA1   single    1.455  0.020  1.455
 GTB  N1   HN11  single    0.890  0.020  1.040
 GTB  N1   HN12  single    0.890  0.020  1.040
 GTB  CA1  C1    single    1.549  0.020  1.549
 GTB  CA1  CB1   single    1.532  0.020  1.532
 GTB  CA1  HA1   single    0.970  0.020  1.090
 GTB  C1   O11   deloc     1.247  0.020  1.247
 GTB  C1   O12   deloc     1.249  0.020  1.249
 GTB  CB1  CG1   single    1.523  0.020  1.523
 GTB  CB1  HB11  single    0.970  0.020  1.090
 GTB  CB1  HB12  single    0.970  0.020  1.090
 GTB  CG1  CD1   single    1.508  0.020  1.508
 GTB  CG1  HG11  single    0.970  0.020  1.090
 GTB  CG1  HG12  single    0.970  0.020  1.090
 GTB  CD1  OE1   double    1.224  0.020  1.224
 GTB  CD1  N2    single    1.346  0.020  1.346
 GTB  N2   CA2   single    1.437  0.020  1.437
 GTB  N2   HN2   single    0.860  0.020  1.020
 GTB  CA2  C2    single    1.535  0.020  1.535
 GTB  CA2  CB2   single    1.525  0.020  1.525
 GTB  CA2  HA2   single    0.970  0.020  1.090
 GTB  C2   O2    double    1.222  0.020  1.222
 GTB  C2   N3    single    1.331  0.020  1.331
 GTB  CB2  SG2   single    1.817  0.020  1.817
 GTB  CB2  HB21  single    0.970  0.020  1.090
 GTB  CB2  HB22  single    0.970  0.020  1.090
 GTB  SG2  C'    single    1.821  0.020  1.821
 GTB  N3   CA3   single    1.440  0.020  1.440
 GTB  N3   HN3   single    0.860  0.020  1.020
 GTB  CA3  C3    single    1.542  0.020  1.542
 GTB  CA3  HA31  single    0.970  0.020  1.090
 GTB  CA3  HA32  single    0.970  0.020  1.090
 GTB  C3   O31   deloc     1.246  0.020  1.246
 GTB  C3   O32   deloc     1.242  0.020  1.242
 GTB  C'   C1'   single    1.497  0.020  1.497
 GTB  C'   H'1   single    0.970  0.020  1.090
 GTB  C'   H'2   single    0.970  0.020  1.090
 GTB  C1'  C2'   aromatic  1.394  0.020  1.394
 GTB  C1'  C6'   aromatic  1.392  0.020  1.392
 GTB  C2'  C3'   aromatic  1.382  0.020  1.382
 GTB  C2'  H2'   single    0.930  0.020  1.080
 GTB  C3'  C4'   aromatic  1.388  0.020  1.388
 GTB  C3'  H3'   single    0.930  0.020  1.080
 GTB  C4'  N41   single    1.454  0.020  1.454
 GTB  C4'  C5'   aromatic  1.387  0.020  1.387
 GTB  N41  O41   single    1.209  0.020  1.209
 GTB  N41  O42   double    1.209  0.020  1.209
 GTB  C5'  C6'   aromatic  1.384  0.020  1.384
 GTB  C5'  H5'   single    0.930  0.020  1.080
 GTB  C6'  H6'   single    0.930  0.020  1.080

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
 GTB  HN12  N1   HN11  104.31  3.000
 GTB  HN12  N1   CA1   107.53  3.000
 GTB  HN11  N1   CA1   108.76  3.000
 GTB  HA1   CA1  CB1   107.51  3.000
 GTB  HA1   CA1  C1    107.62  3.000
 GTB  CB1   CA1  C1    108.79  3.000
 GTB  HA1   CA1  N1    107.52  3.000
 GTB  CB1   CA1  N1    109.91  3.000
 GTB  C1    CA1  N1    115.19  3.000
 GTB  O12   C1   O11   126.46  3.000
 GTB  O12   C1   CA1   116.06  3.000
 GTB  O11   C1   CA1   117.46  3.000
 GTB  HB12  CB1  HB11  106.74  3.000
 GTB  HB12  CB1  CG1   109.74  3.000
 GTB  HB11  CB1  CG1   109.65  3.000
 GTB  HB12  CB1  CA1   108.92  3.000
 GTB  HB11  CB1  CA1   109.11  3.000
 GTB  CG1   CB1  CA1   112.51  3.000
 GTB  HG12  CG1  HG11  106.35  3.000
 GTB  HG12  CG1  CD1   107.83  3.000
 GTB  HG11  CG1  CD1   110.59  3.000
 GTB  HG12  CG1  CB1   108.94  3.000
 GTB  HG11  CG1  CB1   109.91  3.000
 GTB  CD1   CG1  CB1   112.97  3.000
 GTB  N2    CD1  OE1   121.32  3.000
 GTB  N2    CD1  CG1   115.67  3.000
 GTB  OE1   CD1  CG1   123.00  3.000
 GTB  HN2   N2   CA2   118.95  3.000
 GTB  HN2   N2   CD1   119.33  3.000
 GTB  CA2   N2   CD1   121.47  3.000
 GTB  HA2   CA2  CB2   108.75  3.000
 GTB  HA2   CA2  C2    109.15  3.000
 GTB  CB2   CA2  C2    107.96  3.000
 GTB  HA2   CA2  N2    109.76  3.000
 GTB  CB2   CA2  N2    110.16  3.000
 GTB  C2    CA2  N2    111.02  3.000
 GTB  N3    C2   O2    124.27  3.000
 GTB  N3    C2   CA2   114.29  3.000
 GTB  O2    C2   CA2   121.36  3.000
 GTB  HB22  CB2  HB21  108.25  3.000
 GTB  HB22  CB2  SG2   109.41  3.000
 GTB  HB21  CB2  SG2   109.15  3.000
 GTB  HB22  CB2  CA2   109.38  3.000
 GTB  HB21  CB2  CA2   110.43  3.000
 GTB  SG2   CB2  CA2   110.19  3.000
 GTB  C'    SG2  CB2    98.92  3.000
 GTB  HN3   N3   CA3   114.73  3.000
 GTB  HN3   N3   C2    121.05  3.000
 GTB  CA3   N3   C2    124.22  3.000
 GTB  HA32  CA3  HA31  106.42  3.000
 GTB  HA32  CA3  C3    108.85  3.000
 GTB  HA31  CA3  C3    109.14  3.000
 GTB  HA32  CA3  N3    110.79  3.000
 GTB  HA31  CA3  N3    110.65  3.000
 GTB  C3    CA3  N3    110.87  3.000
 GTB  O32   C3   O31   127.67  3.000
 GTB  O32   C3   CA3   115.26  3.000
 GTB  O31   C3   CA3   117.07  3.000
 GTB  H'2   C'   H'1   108.49  3.000
 GTB  H'2   C'   C1'   111.03  3.000
 GTB  H'1   C'   C1'   110.72  3.000
 GTB  H'2   C'   SG2   109.66  3.000
 GTB  H'1   C'   SG2   108.71  3.000
 GTB  C1'   C'   SG2   108.19  3.000
 GTB  C6'   C1'  C2'   119.10  3.000
 GTB  C6'   C1'  C'    120.72  3.000
 GTB  C2'   C1'  C'    120.16  3.000
 GTB  H2'   C2'  C3'   119.16  3.000
 GTB  H2'   C2'  C1'   119.96  3.000
 GTB  C3'   C2'  C1'   120.87  3.000
 GTB  H3'   C3'  C4'   121.32  3.000
 GTB  H3'   C3'  C2'   119.91  3.000
 GTB  C4'   C3'  C2'   118.77  3.000
 GTB  C5'   C4'  N41   119.21  3.000
 GTB  C5'   C4'  C3'   121.61  3.000
 GTB  N41   C4'  C3'   119.18  3.000
 GTB  O42   N41  O41   123.84  3.000
 GTB  O42   N41  C4'   118.09  3.000
 GTB  O41   N41  C4'   118.07  3.000
 GTB  H5'   C5'  C6'   119.85  3.000
 GTB  H5'   C5'  C4'   121.43  3.000
 GTB  C6'   C5'  C4'   118.73  3.000
 GTB  H6'   C6'  C5'   119.24  3.000
 GTB  H6'   C6'  C1'   119.85  3.000
 GTB  C5'   C6'  C1'   120.91  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
 GTB  CONST_01  C4'   C3'  C2'  C1'     0.00   0.0  0
 GTB  CONST_02  C4'   C5'  C6'  C1'     0.00   0.0  0
 GTB  CONST_03  C5'   C6'  C1'  C2'     0.00   0.0  0
 GTB  CONST_04  C5'   C4'  C3'  C2'     0.00   0.0  0
 GTB  CONST_05  C6'   C1'  C2'  C3'     0.00   0.0  0
 GTB  CONST_06  C6'   C5'  C4'  C3'     0.00   0.0  0
 GTB  CONST_07  C3'   C2'  C1'  C'    180.00   0.0  0
 GTB  CONST_08  C5'   C6'  C1'  C'    180.00   0.0  0
 GTB  CONST_09  N41   C4'  C3'  C2'   180.00   0.0  0
 GTB  CONST_10  C6'   C5'  C4'  N41   180.00   0.0  0
 GTB  CONST_11  H3'   C3'  C2'  C1'   180.00   0.0  0
 GTB  CONST_12  H5'   C5'  C6'  C1'   180.00   0.0  0
 GTB  CONST_13  H6'   C6'  C1'  C2'   180.00   0.0  0
 GTB  CONST_14  H2'   C2'  C3'  C4'   180.00   0.0  0
 GTB  CONST_15  O41   N41  C4'  C3'     0.00   0.0  0
 GTB  CONST_16  O42   N41  C4'  C3'   180.00   0.0  0
 GTB  CONST_17  C5'   C4'  N41  O41   180.00   0.0  0
 GTB  CONST_18  C5'   C4'  N41  O42     0.00   0.0  0
 GTB  CONST_19  CA2   N2   CD1  CG1   180.00   0.0  0
 GTB  CONST_20  CA2   N2   CD1  OE1     0.00   0.0  0
 GTB  CONST_21  CA3   N3   C2   CA2   180.00   0.0  0
 GTB  CONST_22  CA3   N3   C2   O2      0.00   0.0  0
 GTB  CONST_23  HN2   N2   CD1  CG1     0.00   0.0  0
 GTB  CONST_24  HN3   N3   C2   CA2     0.00   0.0  0
 GTB  Var_01    C2'   C1'  C'   SG2    79.04  30.0  2
 GTB  Var_02    C1'   C'   SG2  CB2  -174.59  30.0  3
 GTB  Var_03    CD1   CG1  CB1  CA1   175.32  30.0  3
 GTB  Var_04    OE1   CD1  CG1  CB1   -41.59  30.0  3
 GTB  Var_05    C3    CA3  N3   C2   -178.42  30.0  3
 GTB  Var_06    O31   C3   CA3  N3     -1.45  30.0  3
 GTB  Var_07    HB21  CB2  SG2  C'     54.45  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
 GTB  chir_01  CA1  N1  C1  CB1  positiv
 GTB  chir_02  CA2  N2  C2  CB2  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
 GTB  plan-1  C'   0.020
 GTB  plan-1  C1'  0.020
 GTB  plan-1  C2'  0.020
 GTB  plan-1  C3'  0.020
 GTB  plan-1  C4'  0.020
 GTB  plan-1  N41  0.020
 GTB  plan-1  C5'  0.020
 GTB  plan-1  C6'  0.020
 GTB  plan-1  H2'  0.020
 GTB  plan-1  H3'  0.020
 GTB  plan-1  H5'  0.020
 GTB  plan-1  H6'  0.020
 GTB  plan-2  CG1  0.020
 GTB  plan-2  CD1  0.020
 GTB  plan-2  OE1  0.020
 GTB  plan-2  N2   0.020
 GTB  plan-2  CA2  0.020
 GTB  plan-2  HN2  0.020
 GTB  plan-3  CA2  0.020
 GTB  plan-3  C2   0.020
 GTB  plan-3  O2   0.020
 GTB  plan-3  N3   0.020
 GTB  plan-3  CA3  0.020
 GTB  plan-3  HN3  0.020
 GTB  plan-4  C4'  0.020
 GTB  plan-4  N41  0.020
 GTB  plan-4  O41  0.020
 GTB  plan-4  O42  0.020
 GTB  plan-5  CA1  0.020
 GTB  plan-5  C1   0.020
 GTB  plan-5  O11  0.020
 GTB  plan-5  O12  0.020
 GTB  plan-6  CA3  0.020
 GTB  plan-6  C3   0.020
 GTB  plan-6  O31  0.020
 GTB  plan-6  O32  0.020

