# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 00:38:54 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: L-gamma-glutamyl-S-[2-(biphenyl-4-yl)-2-oxoethyl]-L-cysteinylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)N[C@@H](CSCC(=O)c1ccc(cc1)c2ccccc2)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
 48T  48T  L-gamma-glutamyl-S-[2-(biphenyl-4-yl)-2-oxoethyl]-L-cysteinylglycine  ligand  60  35  .  2022-07-23  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_48T
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
 48T  N1    N  NH2    0  -0.786  -6.8984   3.2283   1.9600
 48T  CA1   C  CH1    0  -0.215  -6.0902   3.5474   0.7941
 48T  C1    C  C      0   0.385  -6.7675   4.4535  -0.2668
 48T  O11   O  OC    -1  -0.623  -6.0234   4.8665  -1.1814
 48T  CB1   C  CH2    0  -0.423  -5.6069   2.2603   0.1243
 48T  CG1   C  CH2    0  -0.563  -4.7729   1.3843   1.0528
 48T  CD1   C  C      0   0.565  -4.2922   0.1298   0.3673
 48T  OE1   O  O      0  -0.503  -5.0324  -0.5943  -0.2861
 48T  O12   O  O      0  -0.606  -7.9841   4.6900  -0.1371
 48T  N2    N  NH1    0  -0.636  -2.9829  -0.1476   0.5060
 48T  CA2   C  CH1    0  -0.193  -2.4028  -1.3351  -0.0577
 48T  C2    C  C      0   0.554  -2.9816  -2.5980   0.5953
 48T  O2    O  O      0  -0.499  -3.3195  -2.6129   1.7698
 48T  CB2   C  CH2    0  -0.577  -0.8927  -1.3310   0.1563
 48T  SG2   S  S2     0   0.018  -0.1662   0.1286  -0.6471
 48T  CZ4   C  CR16   0  -0.308   8.9931   1.3198  -0.7277
 48T  CE4   C  CR16   0  -0.239  10.3613   1.3042  -0.5024
 48T  CD4   C  CR16   0  -0.263  10.8672   0.8053   0.6909
 48T  CG4   C  CR16   0  -0.240   9.9936   0.3207   1.6558
 48T  CB4   C  CR16   0  -0.307   8.6255   0.3338   1.4295
 48T  CH4   C  CR6    0   0.091   8.1051   0.8344   0.2344
 48T  CH5   C  CR6    0   0.094   6.6500   0.8503  -0.0079
 48T  CB5   C  CR16   0  -0.298   6.0534   1.8906  -0.7265
 48T  CG5   C  CR16   0  -0.243   4.6913   1.9063  -0.9543
 48T  CD5   C  CR6    0  -0.017   3.8767   0.8812  -0.4708
 48T  CE5   C  CR16   0  -0.274   4.4664  -0.1585   0.2474
 48T  CZ5   C  CR16   0  -0.292   5.8316  -0.1730   0.4731
 48T  O5    O  O      0  -0.383   1.9212   1.8465  -1.3610
 48T  N3    N  NH1    0  -0.628  -3.0201  -3.6573  -0.2097
 48T  CA3   C  CH2    0  -0.411  -3.4384  -4.9736   0.1978
 48T  C3    C  C      0   0.400  -3.3090  -5.9754  -0.9682
 48T  C13   C  CH2    0  -0.700   1.5571  -0.1820  -0.2026
 48T  O31   O  O      0  -0.599  -2.8979  -5.5287  -2.0564
 48T  C14   C  C      0   0.389   2.4186   0.9353  -0.7356
 48T  O32   O  OC    -1  -0.609  -3.6340  -7.1444  -0.7007
 48T  H11N  H  HNH2   0   0.336  -7.1450   4.0912   2.4295
 48T  H12N  H  HNH2   0   0.323  -7.7848   2.8548   1.6389
 48T  HA1   H  HCH1   0   0.212  -5.2021   4.0842   1.1512
 48T  HB11  H  HCH2   0   0.219  -6.4711   1.6935  -0.2366
 48T  HB12  H  HCH2   0   0.232  -5.0193   2.5265  -0.7560
 48T  HG11  H  HCH2   0   0.240  -3.9279   1.9573   1.4434
 48T  HG12  H  HCH2   0   0.265  -5.3725   1.0908   1.9182
 48T  H2    H  HNH1   0   0.402  -2.4153   0.4345   1.1010
 48T  HA2   H  HCH1   0   0.280  -2.6045  -1.3647  -1.1337
 48T  HB21  H  HCH2   0   0.283  -0.6598  -1.3199   1.2240
 48T  HB22  H  HCH2   0   0.296  -0.4642  -2.2368  -0.2744
 48T  H3    H  HNH1   0   0.388  -2.7514  -3.5813  -1.1811
 48T  H131  H  HCH2   0   0.308   1.6615  -0.2468   0.8839
 48T  H132  H  HCH2   0   0.308   1.8922  -1.1383  -0.6137
 48T  HD4   H  HCR6   0   0.260  11.9347   0.7933   0.8681
 48T  HE4   H  HCR6   0   0.260  11.0330   1.6766  -1.2649
 48T  HZ4   H  HCR6   0   0.258   8.6177   1.6937  -1.6719
 48T  HZ5   H  HCR6   0   0.265   6.2656  -1.0044   1.0130
 48T  HB5   H  HCR6   0   0.263   6.6553   2.7108  -1.0958
 48T  HE5   H  HCR6   0   0.268   3.8737  -0.9760   0.6366
 48T  HG5   H  HCR6   0   0.267   4.2549   2.7289  -1.5048
 48T  HA31  H  HCH2   0   0.243  -2.8380  -5.3276   1.0412
 48T  HA32  H  HCH2   0   0.243  -4.4774  -4.9615   0.5412
 48T  HB4   H  HCR6   0   0.258   7.9581  -0.0311   2.2003
 48T  HG4   H  HCR6   0   0.261  10.3778  -0.0659   2.5907

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
 48T  N1   CA1   single    1.454  0.020  1.454
 48T  CA1  C1    single    1.551  0.020  1.551
 48T  CA1  CB1   single    1.529  0.020  1.529
 48T  C1   O11   deloc     1.249  0.020  1.249
 48T  C1   O12   deloc     1.246  0.020  1.246
 48T  CB1  CG1   single    1.525  0.020  1.525
 48T  CG1  CD1   single    1.508  0.020  1.508
 48T  CD1  OE1   double    1.224  0.020  1.224
 48T  CD1  N2    single    1.346  0.020  1.346
 48T  N2   CA2   single    1.437  0.020  1.437
 48T  CA2  C2    single    1.535  0.020  1.535
 48T  CA2  CB2   single    1.525  0.020  1.525
 48T  C2   O2    double    1.222  0.020  1.222
 48T  C2   N3    single    1.331  0.020  1.331
 48T  CB2  SG2   single    1.818  0.020  1.818
 48T  SG2  C13   single    1.807  0.020  1.807
 48T  CB4  CG4   aromatic  1.387  0.020  1.387
 48T  CB4  CH4   aromatic  1.396  0.020  1.396
 48T  CG4  CD4   aromatic  1.389  0.020  1.389
 48T  CD4  CE4   aromatic  1.389  0.020  1.389
 48T  CE4  CZ4   aromatic  1.387  0.020  1.387
 48T  CZ4  CH4   aromatic  1.396  0.020  1.396
 48T  CH4  CH5   single    1.475  0.020  1.475
 48T  CH5  CZ5   aromatic  1.396  0.020  1.396
 48T  CH5  CB5   aromatic  1.398  0.020  1.398
 48T  CZ5  CE5   aromatic  1.384  0.020  1.384
 48T  CE5  CD5   aromatic  1.394  0.020  1.394
 48T  CD5  CG5   aromatic  1.396  0.020  1.396
 48T  CD5  C14   single    1.483  0.020  1.483
 48T  CG5  CB5   aromatic  1.381  0.020  1.381
 48T  O5   C14   double    1.212  0.020  1.212
 48T  N3   CA3   single    1.440  0.020  1.440
 48T  CA3  C3    single    1.543  0.020  1.543
 48T  C3   O31   deloc     1.246  0.020  1.246
 48T  C3   O32   deloc     1.242  0.020  1.242
 48T  C13  C14   single    1.508  0.020  1.508
 48T  N1   H11N  single    0.890  0.020  1.040
 48T  N1   H12N  single    0.890  0.020  1.040
 48T  CA1  HA1   single    0.970  0.020  1.090
 48T  CB1  HB11  single    0.970  0.020  1.090
 48T  CB1  HB12  single    0.970  0.020  1.090
 48T  CG1  HG11  single    0.970  0.020  1.090
 48T  CG1  HG12  single    0.970  0.020  1.090
 48T  N2   H2    single    0.860  0.020  1.020
 48T  CA2  HA2   single    0.970  0.020  1.090
 48T  CB2  HB21  single    0.970  0.020  1.090
 48T  CB2  HB22  single    0.970  0.020  1.090
 48T  N3   H3    single    0.860  0.020  1.020
 48T  C13  H131  single    0.970  0.020  1.090
 48T  C13  H132  single    0.970  0.020  1.090
 48T  CB4  HB4   single    0.930  0.020  1.080
 48T  CG4  HG4   single    0.930  0.020  1.080
 48T  CD4  HD4   single    0.930  0.020  1.080
 48T  CE4  HE4   single    0.930  0.020  1.080
 48T  CZ4  HZ4   single    0.930  0.020  1.080
 48T  CZ5  HZ5   single    0.930  0.020  1.080
 48T  CB5  HB5   single    0.930  0.020  1.080
 48T  CE5  HE5   single    0.930  0.020  1.080
 48T  CG5  HG5   single    0.930  0.020  1.080
 48T  CA3  HA31  single    0.970  0.020  1.090
 48T  CA3  HA32  single    0.970  0.020  1.090

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
 48T  H12N  N1   H11N  104.34  3.000
 48T  H12N  N1   CA1   108.23  3.000
 48T  H11N  N1   CA1   108.67  3.000
 48T  HA1   CA1  CB1   107.36  3.000
 48T  HA1   CA1  C1    106.87  3.000
 48T  CB1   CA1  C1    109.28  3.000
 48T  HA1   CA1  N1    107.23  3.000
 48T  CB1   CA1  N1    110.00  3.000
 48T  C1    CA1  N1    115.72  3.000
 48T  O12   C1   O11   126.51  3.000
 48T  O12   C1   CA1   117.78  3.000
 48T  O11   C1   CA1   115.71  3.000
 48T  HB12  CB1  HB11  106.59  3.000
 48T  HB12  CB1  CG1   109.69  3.000
 48T  HB11  CB1  CG1   109.58  3.000
 48T  HB12  CB1  CA1   108.55  3.000
 48T  HB11  CB1  CA1   109.31  3.000
 48T  CG1   CB1  CA1   112.93  3.000
 48T  HG12  CG1  HG11  106.37  3.000
 48T  HG12  CG1  CD1   108.14  3.000
 48T  HG11  CG1  CD1   110.61  3.000
 48T  HG12  CG1  CB1   109.66  3.000
 48T  HG11  CG1  CB1   109.83  3.000
 48T  CD1   CG1  CB1   112.05  3.000
 48T  N2    CD1  OE1   121.42  3.000
 48T  N2    CD1  CG1   115.77  3.000
 48T  OE1   CD1  CG1   122.81  3.000
 48T  H2    N2   CA2   118.80  3.000
 48T  H2    N2   CD1   119.34  3.000
 48T  CA2   N2   CD1   121.52  3.000
 48T  HA2   CA2  CB2   108.68  3.000
 48T  HA2   CA2  C2    109.04  3.000
 48T  CB2   CA2  C2    108.41  3.000
 48T  HA2   CA2  N2    109.48  3.000
 48T  CB2   CA2  N2    110.03  3.000
 48T  C2    CA2  N2    111.15  3.000
 48T  N3    C2   O2    124.29  3.000
 48T  N3    C2   CA2   114.11  3.000
 48T  O2    C2   CA2   121.54  3.000
 48T  HB22  CB2  HB21  108.09  3.000
 48T  HB22  CB2  SG2   109.59  3.000
 48T  HB21  CB2  SG2   109.79  3.000
 48T  HB22  CB2  CA2   109.35  3.000
 48T  HB21  CB2  CA2   110.37  3.000
 48T  SG2   CB2  CA2   109.63  3.000
 48T  C13   SG2  CB2    97.73  3.000
 48T  HZ4   CZ4  CH4   120.03  3.000
 48T  HZ4   CZ4  CE4   119.19  3.000
 48T  CH4   CZ4  CE4   120.77  3.000
 48T  HE4   CE4  CD4   120.19  3.000
 48T  HE4   CE4  CZ4   119.60  3.000
 48T  CD4   CE4  CZ4   120.20  3.000
 48T  HD4   CD4  CG4   120.19  3.000
 48T  HD4   CD4  CE4   120.26  3.000
 48T  CG4   CD4  CE4   119.55  3.000
 48T  HG4   CG4  CB4   119.64  3.000
 48T  HG4   CG4  CD4   120.10  3.000
 48T  CB4   CG4  CD4   120.25  3.000
 48T  HB4   CB4  CH4   120.02  3.000
 48T  HB4   CB4  CG4   119.26  3.000
 48T  CH4   CB4  CG4   120.71  3.000
 48T  CH5   CH4  CB4   120.80  3.000
 48T  CH5   CH4  CZ4   120.69  3.000
 48T  CB4   CH4  CZ4   118.51  3.000
 48T  CZ5   CH5  CB5   118.20  3.000
 48T  CB5   CH5  CH4   120.88  3.000
 48T  CZ5   CH5  CH4   120.92  3.000
 48T  HB5   CB5  CG5   118.92  3.000
 48T  HB5   CB5  CH5   120.13  3.000
 48T  CG5   CB5  CH5   120.93  3.000
 48T  HG5   CG5  CD5   119.96  3.000
 48T  HG5   CG5  CB5   119.37  3.000
 48T  CD5   CG5  CB5   120.67  3.000
 48T  C14   CD5  CE5   122.34  3.000
 48T  C14   CD5  CG5   119.02  3.000
 48T  CE5   CD5  CG5   118.63  3.000
 48T  HE5   CE5  CZ5   118.27  3.000
 48T  HE5   CE5  CD5   121.13  3.000
 48T  CZ5   CE5  CD5   120.60  3.000
 48T  HZ5   CZ5  CE5   119.02  3.000
 48T  HZ5   CZ5  CH5   120.00  3.000
 48T  CE5   CZ5  CH5   120.97  3.000
 48T  H3    N3   CA3   114.71  3.000
 48T  H3    N3   C2    120.91  3.000
 48T  CA3   N3   C2    124.38  3.000
 48T  HA32  CA3  HA31  106.42  3.000
 48T  HA32  CA3  C3    108.91  3.000
 48T  HA31  CA3  C3    109.05  3.000
 48T  HA32  CA3  N3    110.76  3.000
 48T  HA31  CA3  N3    110.76  3.000
 48T  C3    CA3  N3    110.82  3.000
 48T  O32   C3   O31   127.70  3.000
 48T  O32   C3   CA3   115.24  3.000
 48T  O31   C3   CA3   117.06  3.000
 48T  H132  C13  H131  107.01  3.000
 48T  H132  C13  C14   109.88  3.000
 48T  H131  C13  C14   109.90  3.000
 48T  H132  C13  SG2   110.50  3.000
 48T  H131  C13  SG2   110.23  3.000
 48T  C14   C13  SG2   109.30  3.000
 48T  C13   C14  O5    120.33  3.000
 48T  C13   C14  CD5   118.13  3.000
 48T  O5    C14  CD5   121.54  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
 48T  CONST_01  CG4   CD4  CE4  CZ4     0.00   0.0  0
 48T  CONST_02  CG4   CB4  CH4  CZ4     0.00   0.0  0
 48T  CONST_05  CB4   CG4  CD4  CE4     0.00   0.0  0
 48T  CONST_06  CB4   CH4  CZ4  CE4     0.00   0.0  0
 48T  CONST_07  CH5   CH4  CZ4  CE4   180.00   0.0  0
 48T  CONST_08  CH4   CB4  CG4  CD4     0.00   0.0  0
 48T  CONST_09  CH4   CZ4  CE4  CD4     0.00   0.0  0
 48T  CONST_10  CH5   CH4  CB4  CG4   180.00   0.0  0
 48T  CONST_13  CE5   CZ5  CH5  CH4   180.00   0.0  0
 48T  CONST_14  CG5   CB5  CH5  CH4   180.00   0.0  0
 48T  CONST_15  CD5   CE5  CZ5  CH5     0.00   0.0  0
 48T  CONST_16  CD5   CG5  CB5  CH5     0.00   0.0  0
 48T  CONST_17  CE5   CZ5  CH5  CB5     0.00   0.0  0
 48T  CONST_18  CE5   CD5  CG5  CB5     0.00   0.0  0
 48T  CONST_19  CZ5   CE5  CD5  CG5     0.00   0.0  0
 48T  CONST_20  CZ5   CH5  CB5  CG5     0.00   0.0  0
 48T  CONST_21  C14   CD5  CG5  CB5   180.00   0.0  0
 48T  CONST_22  C14   CD5  CE5  CZ5   180.00   0.0  0
 48T  CONST_23  HD4   CD4  CE4  CZ4   180.00   0.0  0
 48T  CONST_24  HB4   CB4  CH4  CZ4   180.00   0.0  0
 48T  CONST_25  HG4   CG4  CD4  CE4   180.00   0.0  0
 48T  CONST_26  HZ4   CZ4  CE4  CD4   180.00   0.0  0
 48T  CONST_27  HE4   CE4  CD4  CG4   180.00   0.0  0
 48T  CONST_28  HZ5   CZ5  CH5  CH4     0.00   0.0  0
 48T  CONST_29  HB5   CB5  CH5  CH4     0.00   0.0  0
 48T  CONST_30  HE5   CE5  CZ5  CH5   180.00   0.0  0
 48T  CONST_31  HG5   CG5  CB5  CH5   180.00   0.0  0
 48T  CONST_32  CA2   N2   CD1  CG1   180.00   0.0  0
 48T  CONST_33  CA2   N2   CD1  OE1     0.00   0.0  0
 48T  CONST_34  CA3   N3   C2   CA2   180.00   0.0  0
 48T  CONST_35  CA3   N3   C2   O2      0.00   0.0  0
 48T  CONST_36  H2    N2   CD1  CG1     0.00   0.0  0
 48T  CONST_37  H3    N3   C2   CA2     0.00   0.0  0
 48T  Var_01    O5    C14  CD5  CG5     0.05  30.0  2
 48T  Var_02    CD5   C14  C13  SG2   179.53  30.0  3
 48T  Var_03    CD1   CG1  CB1  CA1  -179.27  30.0  3
 48T  Var_04    OE1   CD1  CG1  CB1   -48.20  30.0  3
 48T  Var_05    C3    CA3  N3   C2   -177.78  30.0  3
 48T  Var_06    C14   C13  SG2  CB2  -178.73  30.0  3
 48T  Var_07    O31   C3   CA3  N3     -0.92  30.0  3
 48T  Var_08    HB21  CB2  SG2  C13    58.48  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
 48T  chir_01  CA1  N1  C1  CB1  positiv
 48T  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
 48T  plan-1  CZ4  0.020
 48T  plan-1  CE4  0.020
 48T  plan-1  CD4  0.020
 48T  plan-1  CG4  0.020
 48T  plan-1  CB4  0.020
 48T  plan-1  CH4  0.020
 48T  plan-1  CH5  0.020
 48T  plan-1  HD4  0.020
 48T  plan-1  HE4  0.020
 48T  plan-1  HZ4  0.020
 48T  plan-1  HB4  0.020
 48T  plan-1  HG4  0.020
 48T  plan-2  CH4  0.020
 48T  plan-2  CH5  0.020
 48T  plan-2  CB5  0.020
 48T  plan-2  CG5  0.020
 48T  plan-2  CD5  0.020
 48T  plan-2  CE5  0.020
 48T  plan-2  CZ5  0.020
 48T  plan-2  C14  0.020
 48T  plan-2  HZ5  0.020
 48T  plan-2  HB5  0.020
 48T  plan-2  HE5  0.020
 48T  plan-2  HG5  0.020
 48T  plan-3  CG1  0.020
 48T  plan-3  CD1  0.020
 48T  plan-3  OE1  0.020
 48T  plan-3  N2   0.020
 48T  plan-3  CA2  0.020
 48T  plan-3  H2   0.020
 48T  plan-4  CA2  0.020
 48T  plan-4  C2   0.020
 48T  plan-4  O2   0.020
 48T  plan-4  N3   0.020
 48T  plan-4  CA3  0.020
 48T  plan-4  H3   0.020
 48T  plan-5  CD5  0.020
 48T  plan-5  O5   0.020
 48T  plan-5  C13  0.020
 48T  plan-5  C14  0.020
 48T  plan-6  CA1  0.020
 48T  plan-6  C1   0.020
 48T  plan-6  O11  0.020
 48T  plan-6  O12  0.020
 48T  plan-7  CA3  0.020
 48T  plan-7  C3   0.020
 48T  plan-7  O31  0.020
 48T  plan-7  O32  0.020

