# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 20:16:04 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: L-gamma-glutamyl-S-{(S)-hydroxy[(4-nitrobenzyl)oxy]methyl}-L-cysteinylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)N[C@@H](CS[C@@H](O)OCc1ccc(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
 GNB  GNB  L-gamma-glutamyl-S-{(S)-hydroxy[(4-nitrobenzyl)oxy]methyl}-L-cysteinylglycine  ligand  55  33  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GNB
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
 GNB  C     C  C      0   0.307  64.4039  34.3064  27.7669
 GNB  OT1   O  OC    -1  -0.641  65.1172  34.9118  28.5836
 GNB  OT2   O  O      0  -0.354  63.1859  34.0248  27.9379
 GNB  N     N  NH2    0  -0.777  66.0011  34.9419  26.0000
 GNB  CA    C  CH1    0  -0.181  65.0083  33.9569  26.3987
 GNB  CB    C  CH2    0  -0.411  65.5815  32.5289  26.4251
 GNB  CB2   C  CH2    0  -0.633  60.1588  32.8488  25.8132
 GNB  SG2   S  S2     0   0.027  59.7668  31.6302  27.1176
 GNB  CG    C  CH2    0  -0.627  64.6119  31.4011  26.8022
 GNB  CD    C  C      0   0.563  63.4648  31.2816  25.8220
 GNB  OE    O  O      0  -0.356  63.4576  30.4529  24.9178
 GNB  N2    N  NH1    0  -0.698  62.4798  32.1765  26.0112
 GNB  CA2   C  CH1    0  -0.169  61.3874  32.3279  25.0809
 GNB  C2    C  C      0   0.549  61.7915  33.2829  23.9475
 GNB  O2    O  O      0  -0.489  61.5660  34.4830  24.0119
 GNB  N3    N  NH1    0  -0.672  62.3893  32.6854  22.9158
 GNB  CA3   C  CH2    0  -0.372  63.0079  33.4247  21.8509
 GNB  C3    C  C      0   0.421  64.4369  33.9265  22.1496
 GNB  O31   O  O      0  -0.588  65.0007  33.4893  23.1648
 GNB  O32   O  OC    -1  -0.692  64.8791  34.7516  21.3194
 GNB  CD2   C  CH1    0   0.202  58.2879  32.0359  27.8215
 GNB  OZ1   O  OH1    0  -0.405  57.7720  33.1519  27.3877
 GNB  CG2   C  CR6    0   0.158  59.7391  29.1267  29.2797
 GNB  CL1   C  CR16   0  -0.304  59.3662  28.4338  28.1305
 GNB  CL2   C  CR16   0  -0.310  61.0909  29.3749  29.5039
 GNB  CM1   C  CR16   0  -0.231  60.3147  28.0115  27.2168
 GNB  CM2   C  CR16   0  -0.272  62.0550  28.9541  28.6079
 GNB  CZ    C  CR6    0   0.122  61.6533  28.2811  27.4637
 GNB  OH1   O  O2     0  -0.392  57.4774  29.9440  29.6695
 GNB  CH    C  CH2    0  -0.376  58.7026  29.6239  30.2598
 GNB  N7    N  N      1   0.299  62.6560  27.8329  26.5154
 GNB  O8    O  O     -1  -0.486  63.8187  27.8982  26.8425
 GNB  O9    O  O      0  -0.392  62.2835  27.4250  25.4401
 GNB  H11N  H  HNH2   0   0.319  66.3461  34.6821  25.0833
 GNB  H12N  H  HNH2   0   0.304  66.7882  34.9124  26.6365
 GNB  HA1   H  HCH1   0   0.141  64.2249  33.9929  25.6408
 GNB  HB1   H  HCH2   0   0.161  65.9922  32.3205  25.4342
 GNB  HB2   H  HCH2   0   0.157  66.4191  32.5031  27.1310
 GNB  HB21  H  HCH2   0   0.315  59.3124  32.9333  25.1326
 GNB  HB22  H  HCH2   0   0.318  60.3459  33.8227  26.2646
 GNB  HG1   H  HCH2   0   0.308  65.1524  30.4544  26.8027
 GNB  HG2   H  HCH2   0   0.258  64.2287  31.5546  27.8123
 GNB  HN21  H  HNH1   0   0.400  62.6427  32.9152  26.7187
 GNB  HA2   H  HCH1   0   0.298  61.1570  31.3479  24.6561
 GNB  HN3   H  HNH1   0   0.418  62.6744  31.7269  23.0417
 GNB  HA31  H  HCH2   0   0.195  63.0457  32.7743  20.9750
 GNB  HA32  H  HCH2   0   0.274  62.3732  34.2673  21.5789
 GNB  HD2   H  HCH1   0   0.079  57.6462  30.7007  29.0537
 GNB  HOZ1  H  HOH1   0   0.525  56.9371  33.3205  27.8475
 GNB  HL1   H  HCR6   0   0.238  58.3221  28.2364  27.9300
 GNB  HL2   H  HCR6   0   0.250  61.3982  29.9250  30.3849
 GNB  HM1   H  HCR6   0   0.278  60.0056  27.4830  26.3268
 GNB  HM2   H  HCR6   0   0.274  63.0968  29.1690  28.7970
 GNB  HC1   H  HCH2   0   0.330  58.5219  28.8393  31.0019
 GNB  HC2   H  HCH2   0   0.339  59.1326  30.4700  30.8136

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
 GNB  C    OT1   deloc     1.242  0.020  1.242
 GNB  C    OT2   deloc     1.262  0.020  1.262
 GNB  C    CA    single    1.536  0.020  1.536
 GNB  N    CA    single    1.454  0.020  1.454
 GNB  N    H11N  single    0.890  0.020  1.040
 GNB  N    H12N  single    0.890  0.020  1.040
 GNB  CA   CB    single    1.539  0.020  1.539
 GNB  CA   HA1   single    0.970  0.020  1.090
 GNB  CB   CG    single    1.534  0.020  1.534
 GNB  CB   HB1   single    0.970  0.020  1.090
 GNB  CB   HB2   single    0.970  0.020  1.090
 GNB  CB2  SG2   single    1.828  0.020  1.828
 GNB  CB2  CA2   single    1.522  0.020  1.522
 GNB  CB2  HB21  single    0.970  0.020  1.090
 GNB  CB2  HB22  single    0.970  0.020  1.090
 GNB  SG2  CD2   single    1.687  0.020  1.687
 GNB  CG   CD    single    1.514  0.020  1.514
 GNB  CG   HG1   single    0.970  0.020  1.090
 GNB  CG   HG2   single    0.970  0.020  1.090
 GNB  CD   OE    double    1.227  0.020  1.227
 GNB  CD   N2    single    1.344  0.020  1.344
 GNB  N2   CA2   single    1.443  0.020  1.443
 GNB  N2   HN21  single    0.860  0.020  1.020
 GNB  CA2  C2    single    1.536  0.020  1.536
 GNB  CA2  HA2   single    0.970  0.020  1.090
 GNB  C2   O2    double    1.223  0.020  1.223
 GNB  C2   N3    single    1.334  0.020  1.334
 GNB  N3   CA3   single    1.436  0.020  1.436
 GNB  N3   HN3   single    0.890  0.020  1.040
 GNB  CA3  C3    single    1.544  0.020  1.544
 GNB  CA3  HA31  single    0.970  0.020  1.090
 GNB  CA3  HA32  single    0.970  0.020  1.090
 GNB  C3   O31   deloc     1.241  0.020  1.241
 GNB  C3   O32   deloc     1.251  0.020  1.251
 GNB  CD2  OZ1   single    1.304  0.020  1.304
 GNB  CD2  OH1   single    2.906  0.020  2.906
 GNB  CD2  HD2   single    0.970  0.020  1.090
 GNB  OZ1  HOZ1  single    0.850  0.020  0.980
 GNB  CG2  CL1   aromatic  1.393  0.020  1.393
 GNB  CG2  CL2   aromatic  1.392  0.020  1.392
 GNB  CG2  CH    single    1.511  0.020  1.511
 GNB  CL1  CM1   aromatic  1.383  0.020  1.383
 GNB  CL1  HL1   single    0.930  0.020  1.080
 GNB  CL2  CM2   aromatic  1.382  0.020  1.382
 GNB  CL2  HL2   single    0.930  0.020  1.080
 GNB  CM1  CZ    aromatic  1.388  0.020  1.388
 GNB  CM1  HM1   single    0.930  0.020  1.080
 GNB  CM2  CZ    aromatic  1.387  0.020  1.387
 GNB  CM2  HM2   single    0.930  0.020  1.080
 GNB  CZ   N7    single    1.451  0.020  1.451
 GNB  OH1  CH    single    1.397  0.020  1.397
 GNB  CH   HC1   single    0.970  0.020  1.090
 GNB  CH   HC2   single    0.970  0.020  1.090
 GNB  N7   O8    single    1.210  0.020  1.210
 GNB  N7   O9    double    1.209  0.020  1.209

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
 GNB  CA    C    OT2   116.72  3.000
 GNB  CA    C    OT1   118.08  3.000
 GNB  OT2   C    OT1   125.04  3.000
 GNB  H12N  N    H11N  107.24  3.000
 GNB  H12N  N    CA    109.79  3.000
 GNB  H11N  N    CA    107.86  3.000
 GNB  HA1   CA   CB    108.06  3.000
 GNB  HA1   CA   N     106.11  3.000
 GNB  CB    CA   N     112.27  3.000
 GNB  HA1   CA   C     109.20  3.000
 GNB  CB    CA   C     110.02  3.000
 GNB  N     CA   C     111.02  3.000
 GNB  HB2   CB   HB1   107.00  3.000
 GNB  HB2   CB   CG    107.90  3.000
 GNB  HB1   CB   CG    108.67  3.000
 GNB  HB2   CB   CA    108.52  3.000
 GNB  HB1   CB   CA    107.55  3.000
 GNB  CG    CB   CA    116.80  3.000
 GNB  HB22  CB2  HB21  108.84  3.000
 GNB  HB22  CB2  CA2   111.50  3.000
 GNB  HB21  CB2  CA2   110.68  3.000
 GNB  HB22  CB2  SG2   109.70  3.000
 GNB  HB21  CB2  SG2   109.33  3.000
 GNB  CA2   CB2  SG2   106.76  3.000
 GNB  CD2   SG2  CB2   108.99  3.000
 GNB  HG2   CG   HG1   107.21  3.000
 GNB  HG2   CG   CD    110.15  3.000
 GNB  HG1   CG   CD    107.90  3.000
 GNB  HG2   CG   CB    110.25  3.000
 GNB  HG1   CG   CB    108.98  3.000
 GNB  CD    CG   CB    112.20  3.000
 GNB  N2    CD   OE    123.32  3.000
 GNB  N2    CD   CG    114.30  3.000
 GNB  OE    CD   CG    122.36  3.000
 GNB  HN21  N2   CA2   118.99  3.000
 GNB  HN21  N2   CD    117.11  3.000
 GNB  CA2   N2   CD    122.27  3.000
 GNB  HA2   CA2  C2    109.04  3.000
 GNB  HA2   CA2  N2    108.43  3.000
 GNB  C2    CA2  N2    109.98  3.000
 GNB  HA2   CA2  CB2   108.89  3.000
 GNB  C2    CA2  CB2   110.76  3.000
 GNB  N2    CA2  CB2   109.69  3.000
 GNB  N3    C2   O2    124.27  3.000
 GNB  N3    C2   CA2   114.21  3.000
 GNB  O2    C2   CA2   121.51  3.000
 GNB  HN3   N3   CA3   117.40  3.000
 GNB  HN3   N3   C2    117.15  3.000
 GNB  CA3   N3   C2    122.41  3.000
 GNB  HA32  CA3  HA31  106.31  3.000
 GNB  HA32  CA3  C3    109.65  3.000
 GNB  HA31  CA3  C3    108.47  3.000
 GNB  HA32  CA3  N3    109.40  3.000
 GNB  HA31  CA3  N3    107.64  3.000
 GNB  C3    CA3  N3    114.99  3.000
 GNB  O32   C3   O31   127.92  3.000
 GNB  O32   C3   CA3   114.40  3.000
 GNB  O31   C3   CA3   117.67  3.000
 GNB  HD2   CD2  OH1     3.47  3.000
 GNB  HD2   CD2  OZ1   132.39  3.000
 GNB  OH1   CD2  OZ1   135.83  3.000
 GNB  HD2   CD2  SG2   113.08  3.000
 GNB  OH1   CD2  SG2   109.67  3.000
 GNB  OZ1   CD2  SG2   114.44  3.000
 GNB  HOZ1  OZ1  CD2   109.41  3.000
 GNB  CH    CG2  CL2   120.19  3.000
 GNB  CH    CG2  CL1   121.02  3.000
 GNB  CL2   CG2  CL1   118.78  3.000
 GNB  HL1   CL1  CM1   118.94  3.000
 GNB  HL1   CL1  CG2   120.16  3.000
 GNB  CM1   CL1  CG2   120.89  3.000
 GNB  HL2   CL2  CM2   118.96  3.000
 GNB  HL2   CL2  CG2   119.80  3.000
 GNB  CM2   CL2  CG2   121.23  3.000
 GNB  HM1   CM1  CZ    121.17  3.000
 GNB  HM1   CM1  CL1   119.84  3.000
 GNB  CZ    CM1  CL1   118.99  3.000
 GNB  HM2   CM2  CZ    121.34  3.000
 GNB  HM2   CM2  CL2   119.91  3.000
 GNB  CZ    CM2  CL2   118.73  3.000
 GNB  N7    CZ   CM2   119.27  3.000
 GNB  N7    CZ   CM1   119.36  3.000
 GNB  CM2   CZ   CM1   121.36  3.000
 GNB  CH    OH1  CD2   100.90  3.000
 GNB  HC2   CH   HC1   105.95  3.000
 GNB  HC2   CH   OH1   112.32  3.000
 GNB  HC1   CH   OH1   107.81  3.000
 GNB  HC2   CH   CG2   108.17  3.000
 GNB  HC1   CH   CG2   108.48  3.000
 GNB  OH1   CH   CG2   113.76  3.000
 GNB  O9    N7   O8    123.70  3.000
 GNB  O9    N7   CZ    118.21  3.000
 GNB  O8    N7   CZ    118.09  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
 GNB  CONST_01  CZ    CM1  CL1  CG2    0.00   0.0  0
 GNB  CONST_02  CZ    CM2  CL2  CG2    0.00   0.0  0
 GNB  CONST_03  CM2   CL2  CG2  CL1    0.00   0.0  0
 GNB  CONST_04  CM2   CZ   CM1  CL1    0.00   0.0  0
 GNB  CONST_05  CM1   CL1  CG2  CL2    0.00   0.0  0
 GNB  CONST_06  CM1   CZ   CM2  CL2    0.00   0.0  0
 GNB  CONST_07  N7    CZ   CM1  CL1  180.00   0.0  0
 GNB  CONST_08  N7    CZ   CM2  CL2  180.00   0.0  0
 GNB  CONST_09  CH    CG2  CL1  CM1  180.00   0.0  0
 GNB  CONST_10  CH    CG2  CL2  CM2  180.00   0.0  0
 GNB  CONST_11  HM1   CM1  CL1  CG2  180.00   0.0  0
 GNB  CONST_12  HM2   CM2  CL2  CG2  180.00   0.0  0
 GNB  CONST_13  HL2   CL2  CG2  CL1  180.00   0.0  0
 GNB  CONST_14  HL1   CL1  CG2  CL2  180.00   0.0  0
 GNB  CONST_15  O8    N7   CZ   CM1  180.00   0.0  0
 GNB  CONST_16  O9    N7   CZ   CM1    0.00   0.0  0
 GNB  CONST_17  O8    N7   CZ   CM2    0.00   0.0  0
 GNB  CONST_18  O9    N7   CZ   CM2  180.00   0.0  0
 GNB  CONST_19  CA2   N2   CD   CG   180.00   0.0  0
 GNB  CONST_20  CA2   N2   CD   OE     0.00   0.0  0
 GNB  CONST_21  CA3   N3   C2   CA2  180.00   0.0  0
 GNB  CONST_22  CA3   N3   C2   O2     0.00   0.0  0
 GNB  CONST_23  HN21  N2   CD   CG     0.00   0.0  0
 GNB  CONST_24  HN3   N3   C2   CA2    0.00   0.0  0
 GNB  Var_01    OH1   CH   CG2  CL1  -30.31  30.0  2
 GNB  Var_02    CG2   CH   OH1  CD2  -60.46  30.0  3
 GNB  Var_03    CD    CG   CB   CA    61.81  30.0  3
 GNB  Var_04    OE    CD   CG   CB    98.60  30.0  3
 GNB  Var_05    C3    CA3  N3   C2    81.97  30.0  3
 GNB  Var_06    O31   C3   CA3  N3    10.82  30.0  3
 GNB  Var_07    HB21  CB2  SG2  CD2  -52.22  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
 GNB  chir_01  CA   C    N    CB   negativ
 GNB  chir_02  CA2  N2   CB2  C2   negativ
 GNB  chir_03  CD2  SG2  OH1  OZ1  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
 GNB  plan-1  CG2   0.020
 GNB  plan-1  CL1   0.020
 GNB  plan-1  CL2   0.020
 GNB  plan-1  CM1   0.020
 GNB  plan-1  CM2   0.020
 GNB  plan-1  CZ    0.020
 GNB  plan-1  CH    0.020
 GNB  plan-1  N7    0.020
 GNB  plan-1  HL1   0.020
 GNB  plan-1  HL2   0.020
 GNB  plan-1  HM1   0.020
 GNB  plan-1  HM2   0.020
 GNB  plan-2  CG    0.020
 GNB  plan-2  CD    0.020
 GNB  plan-2  OE    0.020
 GNB  plan-2  N2    0.020
 GNB  plan-2  CA2   0.020
 GNB  plan-2  HN21  0.020
 GNB  plan-3  CA2   0.020
 GNB  plan-3  C2    0.020
 GNB  plan-3  O2    0.020
 GNB  plan-3  N3    0.020
 GNB  plan-3  CA3   0.020
 GNB  plan-3  HN3   0.020
 GNB  plan-4  CZ    0.020
 GNB  plan-4  N7    0.020
 GNB  plan-4  O8    0.020
 GNB  plan-4  O9    0.020
 GNB  plan-5  C     0.020
 GNB  plan-5  OT1   0.020
 GNB  plan-5  OT2   0.020
 GNB  plan-5  CA    0.020
 GNB  plan-6  CA3   0.020
 GNB  plan-6  C3    0.020
 GNB  plan-6  O31   0.020
 GNB  plan-6  O32   0.020

