# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 19:08:50 2021
#   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  57  33  .  2021-08-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.577  66.2012  34.5306  24.8418
 GNB  OT1   O  OH1    0  -0.546  66.8582  35.6430  25.0657
 GNB  OT2   O  O      0  -0.545  65.8881  33.7776  25.7358
 GNB  N     N  NH2    0  -0.824  66.4657  35.4009  22.6066
 GNB  CA    C  CH1    0  -0.222  65.8516  34.3178  23.3656
 GNB  CB    C  CH2    0  -0.443  66.2379  32.9320  22.8393
 GNB  CB2   C  CH2    0  -0.572  61.5592  31.7826  26.1405
 GNB  SG2   S  S2     0   0.054  61.9418  29.9939  26.1389
 GNB  CG    C  CH2    0  -0.595  65.5271  31.7435  23.4896
 GNB  CD    C  C      0   0.587  64.0268  31.9185  23.4556
 GNB  OE    O  O      0  -0.533  63.3871  31.8636  22.4135
 GNB  N2    N  NH1    0  -0.635  63.4531  32.1629  24.6511
 GNB  CA2   C  CH1    0  -0.184  62.0354  32.3795  24.8260
 GNB  C2    C  C      0   0.539  61.7024  33.8772  24.7736
 GNB  O2    O  O      0  -0.366  61.3755  34.5116  25.7594
 GNB  N3    N  NH1    0  -0.657  61.7994  34.4288  23.5529
 GNB  CA3   C  CH2    0  -0.424  61.5201  35.8179  23.3469
 GNB  C3    C  C      0   0.511  62.5478  36.7260  23.9903
 GNB  O31   O  O      0  -0.387  63.6202  36.3775  24.4048
 GNB  O32   O  OH1    0  -0.587  62.1152  37.9801  24.0108
 GNB  CD2   C  CH1    0   0.249  61.4282  29.3510  27.6153
 GNB  OZ1   O  OH1    0  -0.507  60.8768  30.2233  28.4075
 GNB  CG2   C  CR6    0  -0.018  59.6817  27.2155  29.7194
 GNB  CL1   C  CR16   0  -0.264  60.4130  27.9261  30.6716
 GNB  CL2   C  CR16   0  -0.278  58.2947  27.3499  29.7050
 GNB  CM1   C  CR16   0  -0.240  59.7797  28.7547  31.5849
 GNB  CM2   C  CR16   0  -0.234  57.6444  28.1672  30.6111
 GNB  CZ    C  CR6    0   0.172  58.3979  28.8682  31.5432
 GNB  OH1   O  O2     0  -0.497  61.7090  26.5987  28.5154
 GNB  CH    C  CH2    0  -0.305  60.3632  26.3048  28.7261
 GNB  N7    N  N      1   0.211  57.7263  29.7403  32.4927
 GNB  O8    O  O     -1  -0.519  56.5202  29.8068  32.4468
 GNB  O9    O  O      0  -0.515  58.4077  30.3540  33.2798
 GNB  HOT1  H  HOH1   0   0.498  66.9524  36.0461  24.1558
 GNB  H11N  H  HNH2   0   0.377  65.8169  35.8307  21.9637
 GNB  H12N  H  HNH2   0   0.355  67.2629  35.0831  22.0702
 GNB  HA1   H  HCH1   0   0.301  64.7664  34.4334  23.3076
 GNB  HB1   H  HCH2   0   0.231  66.0139  32.9282  21.7708
 GNB  HB2   H  HCH2   0   0.257  67.3174  32.7906  22.9338
 GNB  HB21  H  HCH2   0   0.306  60.4833  31.9126  26.2451
 GNB  HB22  H  HCH2   0   0.269  62.0495  32.2501  26.9941
 GNB  HG1   H  HCH2   0   0.294  65.7692  30.8469  22.9164
 GNB  HG2   H  HCH2   0   0.241  65.8848  31.5794  24.5037
 GNB  HN21  H  HNH1   0   0.433  64.0628  32.3508  25.4344
 GNB  HA2   H  HCH1   0   0.320  61.5216  31.8880  23.9965
 GNB  HN3   H  HNH1   0   0.392  62.0455  33.8571  22.7599
 GNB  HA31  H  HCH2   0   0.270  61.5213  36.0131  22.2733
 GNB  HA32  H  HCH2   0   0.315  60.5249  36.0828  23.7105
 GNB  HO31  H  HOH1   0   0.491  62.7941  38.5579  24.3890
 GNB  HD2   H  HCH1   0   0.366  61.7371  27.5032  28.1214
 GNB  HOZ1  H  HOH1   0   0.530  60.6151  29.7847  29.2340
 GNB  HL1   H  HCR6   0   0.276  61.4903  27.8288  30.7107
 GNB  HL2   H  HCR6   0   0.277  57.7102  26.8157  28.9663
 GNB  HM1   H  HCR6   0   0.277  60.3654  29.2954  32.3140
 GNB  HM2   H  HCR6   0   0.284  56.5688  28.2613  30.5774
 GNB  HC1   H  HCH2   0   0.387  60.3003  25.2811  29.1094
 GNB  HC2   H  HCH2   0   0.249  59.7786  26.3159  27.7958

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   single    1.311  0.020  1.311
 GNB  C    OT2   double    1.210  0.020  1.210
 GNB  C    CA    single    1.532  0.020  1.532
 GNB  OT1  HOT1  single    0.850  0.020  0.980
 GNB  N    CA    single    1.458  0.020  1.458
 GNB  N    H11N  single    0.890  0.020  1.040
 GNB  N    H12N  single    0.890  0.020  1.040
 GNB  CA   CB    single    1.532  0.020  1.532
 GNB  CA   HA1   single    0.970  0.020  1.090
 GNB  CB   CG    single    1.530  0.020  1.530
 GNB  CB   HB1   single    0.970  0.020  1.090
 GNB  CB   HB2   single    0.970  0.020  1.090
 GNB  CB2  SG2   single    1.829  0.020  1.829
 GNB  CB2  CA2   single    1.520  0.020  1.520
 GNB  CB2  HB21  single    0.970  0.020  1.090
 GNB  CB2  HB22  single    0.970  0.020  1.090
 GNB  SG2  CD2   single    1.690  0.020  1.690
 GNB  CG   CD    single    1.511  0.020  1.511
 GNB  CG   HG1   single    0.970  0.020  1.090
 GNB  CG   HG2   single    0.970  0.020  1.090
 GNB  CD   OE    double    1.224  0.020  1.224
 GNB  CD   N2    single    1.348  0.020  1.348
 GNB  N2   CA2   single    1.445  0.020  1.445
 GNB  N2   HN21  single    0.860  0.020  1.020
 GNB  CA2  C2    single    1.535  0.020  1.535
 GNB  CA2  HA2   single    0.970  0.020  1.090
 GNB  C2   O2    double    1.217  0.020  1.217
 GNB  C2   N3    single    1.343  0.020  1.343
 GNB  N3   CA3   single    1.432  0.020  1.432
 GNB  N3   HN3   single    0.860  0.020  1.020
 GNB  CA3  C3    single    1.515  0.020  1.515
 GNB  CA3  HA31  single    0.970  0.020  1.090
 GNB  CA3  HA32  single    0.970  0.020  1.090
 GNB  C3   O31   double    1.201  0.020  1.201
 GNB  C3   O32   single    1.327  0.020  1.327
 GNB  O32  HO31  single    0.850  0.020  0.980
 GNB  CD2  OZ1   single    1.301  0.020  1.301
 GNB  CD2  OH1   single    2.909  0.020  2.909
 GNB  CD2  HD2   single    0.970  0.020  1.090
 GNB  OZ1  HOZ1  single    0.850  0.020  0.980
 GNB  CG2  CL1   aromatic  1.395  0.020  1.395
 GNB  CG2  CL2   aromatic  1.394  0.020  1.394
 GNB  CG2  CH    single    1.510  0.020  1.510
 GNB  CL1  CM1   aromatic  1.386  0.020  1.386
 GNB  CL1  HL1   single    0.930  0.020  1.080
 GNB  CL2  CM2   aromatic  1.383  0.020  1.383
 GNB  CL2  HL2   single    0.930  0.020  1.080
 GNB  CM1  CZ    aromatic  1.387  0.020  1.387
 GNB  CM1  HM1   single    0.930  0.020  1.080
 GNB  CM2  CZ    aromatic  1.389  0.020  1.389
 GNB  CM2  HM2   single    0.930  0.020  1.080
 GNB  CZ   N7    single    1.454  0.020  1.454
 GNB  OH1  CH    single    1.394  0.020  1.394
 GNB  CH   HC1   single    0.970  0.020  1.090
 GNB  CH   HC2   single    0.970  0.020  1.090
 GNB  N7   O8    single    1.209  0.020  1.209
 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   124.50  3.000
 GNB  CA    C    OT1   113.38  3.000
 GNB  OT2   C    OT1   122.10  3.000
 GNB  HOT1  OT1  C     103.52  3.000
 GNB  H12N  N    H11N  107.60  3.000
 GNB  H12N  N    CA    111.98  3.000
 GNB  H11N  N    CA    112.15  3.000
 GNB  HA1   CA   CB    109.14  3.000
 GNB  HA1   CA   N     108.18  3.000
 GNB  CB    CA   N     112.76  3.000
 GNB  HA1   CA   C     105.26  3.000
 GNB  CB    CA   C     113.53  3.000
 GNB  N     CA   C     107.59  3.000
 GNB  HB2   CB   HB1   106.67  3.000
 GNB  HB2   CB   CG    108.76  3.000
 GNB  HB1   CB   CG    108.54  3.000
 GNB  HB2   CB   CA    109.66  3.000
 GNB  HB1   CB   CA    106.72  3.000
 GNB  CG    CB   CA    116.08  3.000
 GNB  HB22  CB2  HB21  108.55  3.000
 GNB  HB22  CB2  CA2   111.58  3.000
 GNB  HB21  CB2  CA2   110.23  3.000
 GNB  HB22  CB2  SG2   109.03  3.000
 GNB  HB21  CB2  SG2   108.88  3.000
 GNB  CA2   CB2  SG2   108.53  3.000
 GNB  CD2   SG2  CB2   107.92  3.000
 GNB  HG2   CG   HG1   107.02  3.000
 GNB  HG2   CG   CD    111.40  3.000
 GNB  HG1   CG   CD    107.67  3.000
 GNB  HG2   CG   CB    111.15  3.000
 GNB  HG1   CG   CB    108.18  3.000
 GNB  CD    CG   CB    111.21  3.000
 GNB  N2    CD   OE    122.72  3.000
 GNB  N2    CD   CG    115.06  3.000
 GNB  OE    CD   CG    122.20  3.000
 GNB  HN21  N2   CA2   118.06  3.000
 GNB  HN21  N2   CD    117.67  3.000
 GNB  CA2   N2   CD    123.51  3.000
 GNB  HA2   CA2  C2    108.12  3.000
 GNB  HA2   CA2  N2    107.58  3.000
 GNB  C2    CA2  N2    110.79  3.000
 GNB  HA2   CA2  CB2   109.42  3.000
 GNB  C2    CA2  CB2   110.16  3.000
 GNB  N2    CA2  CB2   110.68  3.000
 GNB  N3    C2   O2    122.79  3.000
 GNB  N3    C2   CA2   114.58  3.000
 GNB  O2    C2   CA2   122.63  3.000
 GNB  HN3   N3   CA3   118.99  3.000
 GNB  HN3   N3   C2    119.98  3.000
 GNB  CA3   N3   C2    121.01  3.000
 GNB  HA32  CA3  HA31  106.57  3.000
 GNB  HA32  CA3  C3    109.35  3.000
 GNB  HA31  CA3  C3    108.05  3.000
 GNB  HA32  CA3  N3    111.41  3.000
 GNB  HA31  CA3  N3    108.35  3.000
 GNB  C3    CA3  N3    112.84  3.000
 GNB  O32   C3   O31   124.04  3.000
 GNB  O32   C3   CA3   110.61  3.000
 GNB  O31   C3   CA3   125.33  3.000
 GNB  HO31  O32  C3    109.97  3.000
 GNB  HD2   CD2  OH1     4.56  3.000
 GNB  HD2   CD2  OZ1   123.17  3.000
 GNB  OH1   CD2  OZ1   119.13  3.000
 GNB  HD2   CD2  SG2   122.79  3.000
 GNB  OH1   CD2  SG2   126.93  3.000
 GNB  OZ1   CD2  SG2   113.93  3.000
 GNB  HOZ1  OZ1  CD2   109.24  3.000
 GNB  CH    CG2  CL2   120.04  3.000
 GNB  CH    CG2  CL1   121.30  3.000
 GNB  CL2   CG2  CL1   118.66  3.000
 GNB  HL1   CL1  CM1   118.99  3.000
 GNB  HL1   CL1  CG2   120.04  3.000
 GNB  CM1   CL1  CG2   120.97  3.000
 GNB  HL2   CL2  CM2   119.00  3.000
 GNB  HL2   CL2  CG2   119.78  3.000
 GNB  CM2   CL2  CG2   121.22  3.000
 GNB  HM1   CM1  CZ    121.30  3.000
 GNB  HM1   CM1  CL1   119.74  3.000
 GNB  CZ    CM1  CL1   118.96  3.000
 GNB  HM2   CM2  CZ    121.15  3.000
 GNB  HM2   CM2  CL2   119.96  3.000
 GNB  CZ    CM2  CL2   118.89  3.000
 GNB  N7    CZ   CM2   119.38  3.000
 GNB  N7    CZ   CM1   119.32  3.000
 GNB  CM2   CZ   CM1   121.30  3.000
 GNB  CH    OH1  CD2    98.81  3.000
 GNB  HC2   CH   HC1   105.98  3.000
 GNB  HC2   CH   OH1   112.56  3.000
 GNB  HC1   CH   OH1   107.79  3.000
 GNB  HC2   CH   CG2   108.10  3.000
 GNB  HC1   CH   CG2   107.92  3.000
 GNB  OH1   CH   CG2   114.08  3.000
 GNB  O9    N7   O8    124.01  3.000
 GNB  O9    N7   CZ    118.00  3.000
 GNB  O8    N7   CZ    117.98  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  CONST_25  HOT1  OT1  C    OT2  180.00   0.0  0
 GNB  CONST_26  HO31  O32  C3   CA3  180.00   0.0  0
 GNB  Var_01    OH1   CH   CG2  CL1  -22.16  30.0  2
 GNB  Var_02    CG2   CH   OH1  CD2  -58.38  30.0  3
 GNB  Var_03    CD    CG   CB   CA    52.78  30.0  3
 GNB  Var_04    OE    CD   CG   CB    69.44  30.0  3
 GNB  Var_05    C3    CA3  N3   C2    68.40  30.0  3
 GNB  Var_06    O31   C3   CA3  N3    13.98  30.0  3
 GNB  Var_07    HB21  CB2  SG2  CD2  -60.86  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  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
 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-5  HOT1  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
 GNB  plan-6  HO31  0.020

