# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 14:10:16 2021
#   Inital geometry file: a 145 line input string
#   Ligand name: D-gamma-glutamyl-(Z)-N-(carboxymethylidene)-S-[(2R)-2-hydroxy-4-phenylbutyl]-L-cysteinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCC(=O)N[C@@H](CSC[C@H](O)CCc1ccccc1)C(=O)N=CC(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
 1JP  1JP  D-gamma-glutamyl-(Z)-N-(carboxymethylidene)-S-[(2R)-2-hydroxy-4-phenylbutyl]-L-cysteinamide  ligand  58  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1JP
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
 1JP  O    O  O     0  -0.438  15.1618  -7.7550  -64.5332
 1JP  C    C  C     0   0.525  15.7536  -6.7159  -64.6779
 1JP  OXT  O  OH1   0  -0.612  15.3275  -5.5542  -64.1983
 1JP  CA   C  CH1   0  -0.170  17.0616  -6.5521  -65.4262
 1JP  N    N  NH2   0  -0.799  17.2160  -7.6429  -66.3665
 1JP  CB   C  CH2   0  -0.449  18.2523  -6.5762  -64.4540
 1JP  CG   C  CH2   0  -0.590  18.2965  -5.4569  -63.4253
 1JP  CD   C  C     0   0.591  17.3701  -5.6646  -62.2463
 1JP  OE1  O  O     0  -0.488  17.0210  -6.7759  -61.8822
 1JP  NE2  N  NH1   0  -0.630  17.0198  -4.5322  -61.5996
 1JP  CBE  C  CH1   0  -0.205  16.1971  -4.5148  -60.4267
 1JP  CBA  C  C     0   0.489  14.9121  -3.7363  -60.6956
 1JP  OAE  O  O     0  -0.391  14.8186  -2.8715  -61.5290
 1JP  NAU  N  N     0  -0.322  13.9280  -3.9545  -59.7464
 1JP  CAO  C  C1    0  -0.093  12.9719  -4.7629  -59.8234
 1JP  CAX  C  C     0   0.539  12.7736  -5.6595  -61.0174
 1JP  OAF  O  OH1   0  -0.560  11.6640  -6.3460  -60.9243
 1JP  OAB  O  O     0  -0.422  13.5728  -5.7097  -61.9170
 1JP  CAT  C  CH2   0  -0.544  16.9215  -3.8835  -59.2304
 1JP  S1   S  S2    0   0.014  18.5429  -4.6824  -59.0704
 1JP  CAS  C  CH2   0  -0.570  18.8563  -4.3700  -57.3076
 1JP  CBD  C  CH1   0   0.058  20.0891  -5.1305  -56.8231
 1JP  OAH  O  OH1   0  -0.658  21.0815  -4.9954  -57.8159
 1JP  CAR  C  CH2   0  -0.496  19.8300  -6.5782  -56.4072
 1JP  CAP  C  CH2   0  -0.503  19.3390  -7.5697  -57.4628
 1JP  CBB  C  CR6   0   0.148  20.3151  -7.8885  -58.5665
 1JP  CAL  C  CR16  0  -0.312  19.9271  -7.8201  -59.9020
 1JP  CAJ  C  CR16  0  -0.251  20.8130  -8.1418  -60.9225
 1JP  CAI  C  CR16  0  -0.276  22.1088  -8.5416  -60.6255
 1JP  CAK  C  CR16  0  -0.242  22.5048  -8.6276  -59.2963
 1JP  CAM  C  CR16  0  -0.328  21.6146  -8.3082  -58.2799
 1JP  H1   H  HOH1  0   0.483  14.5716  -5.6839  -63.5996
 1JP  H2   H  HCH1  0   0.241  17.0435  -5.5605  -65.9021
 1JP  H3   H  HNH2  0   0.351  16.4879  -7.6077  -67.0686
 1JP  H4   H  HNH2  0   0.352  18.0879  -7.5209  -66.8662
 1JP  H6   H  HCH2  0   0.245  18.2878  -7.5477  -63.9579
 1JP  H7   H  HCH2  0   0.257  19.1532  -6.5068  -65.0681
 1JP  H8   H  HCH2  0   0.286  19.3083  -5.4065  -63.0093
 1JP  H9   H  HCH2  0   0.262  18.1207  -4.4848  -63.8914
 1JP  H10  H  HNH1  0   0.402  17.3197  -3.6472  -61.9777
 1JP  H11  H  HCH1  0   0.296  15.9523  -5.5463  -60.1729
 1JP  H12  H  H     0   0.313  12.2607  -4.8349  -59.0059
 1JP  H13  H  HOH1  0   0.503  11.5385  -6.9256  -61.6931
 1JP  H14  H  HCH2  0   0.273  17.0398  -2.8066  -59.3708
 1JP  H15  H  HCH2  0   0.284  16.3358  -4.0435  -58.3242
 1JP  H16  H  HCH2  0   0.274  19.0001  -3.2977  -57.1603
 1JP  H17  H  HCH2  0   0.269  17.9861  -4.6682  -56.7196
 1JP  H18  H  HCH1  0   0.222  20.4022  -4.6191  -55.9001
 1JP  H19  H  HOH1  0   0.452  21.8038  -5.5995  -57.6170
 1JP  H20  H  HCH2  0   0.244  19.0991  -6.5515  -55.5942
 1JP  H21  H  HCH2  0   0.239  20.7476  -6.9616  -55.9465
 1JP  H22  H  HCH2  0   0.246  18.4020  -7.2195  -57.8980
 1JP  H23  H  HCH2  0   0.250  19.0992  -8.5002  -56.9381
 1JP  H24  H  HCR6  0   0.252  18.9233  -7.5007  -60.1494
 1JP  H25  H  HCR6  0   0.242  20.4883  -8.0762  -61.9540
 1JP  H26  H  HCR6  0   0.248  22.8020  -8.7878  -61.4198
 1JP  H27  H  HCR6  0   0.249  23.5087  -8.9487  -59.0481
 1JP  H28  H  HCR6  0   0.248  21.9390  -8.3941  -57.2487

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
 1JP  N    CA   single    1.448  0.020  1.448
 1JP  CA   CB   single    1.537  0.020  1.537
 1JP  CA   C    single    1.516  0.020  1.516
 1JP  O    C    double    1.205  0.020  1.205
 1JP  CB   CG   single    1.521  0.020  1.521
 1JP  C    OXT  single    1.327  0.020  1.327
 1JP  CG   CD   single    1.514  0.020  1.514
 1JP  CD   OE1  double    1.220  0.020  1.220
 1JP  CD   NE2  single    1.350  0.020  1.350
 1JP  NE2  CBE  single    1.433  0.020  1.433
 1JP  OAB  CAX  double    1.204  0.020  1.204
 1JP  OAE  CBA  double    1.205  0.020  1.205
 1JP  CBE  CBA  single    1.526  0.020  1.526
 1JP  CBE  CAT  single    1.534  0.020  1.534
 1JP  CBA  NAU  single    1.385  0.020  1.385
 1JP  CAX  CAO  single    1.506  0.020  1.506
 1JP  CAX  OAF  single    1.308  0.020  1.308
 1JP  NAU  CAO  double    1.254  0.020  1.254
 1JP  CAT  S1   single    1.815  0.020  1.815
 1JP  S1   CAS  single    1.818  0.020  1.818
 1JP  OAH  CBD  single    1.410  0.020  1.410
 1JP  CAL  CAJ  aromatic  1.389  0.020  1.389
 1JP  CAL  CBB  aromatic  1.392  0.020  1.392
 1JP  CAP  CBB  single    1.507  0.020  1.507
 1JP  CAP  CAR  single    1.529  0.020  1.529
 1JP  CAS  CBD  single    1.527  0.020  1.527
 1JP  CAJ  CAI  aromatic  1.388  0.020  1.388
 1JP  CBB  CAM  aromatic  1.395  0.020  1.395
 1JP  CBD  CAR  single    1.528  0.020  1.528
 1JP  CAI  CAK  aromatic  1.390  0.020  1.390
 1JP  CAM  CAK  aromatic  1.388  0.020  1.388
 1JP  OXT  H1   single    0.850  0.020  0.980
 1JP  CA   H2   single    0.970  0.020  1.090
 1JP  N    H3   single    0.890  0.020  1.040
 1JP  N    H4   single    0.890  0.020  1.040
 1JP  CB   H6   single    0.970  0.020  1.090
 1JP  CB   H7   single    0.970  0.020  1.090
 1JP  CG   H8   single    0.970  0.020  1.090
 1JP  CG   H9   single    0.970  0.020  1.090
 1JP  NE2  H10  single    0.860  0.020  1.020
 1JP  CBE  H11  single    0.970  0.020  1.090
 1JP  CAO  H12  single    0.930  0.020  1.080
 1JP  OAF  H13  single    0.850  0.020  0.980
 1JP  CAT  H14  single    0.970  0.020  1.090
 1JP  CAT  H15  single    0.970  0.020  1.090
 1JP  CAS  H16  single    0.970  0.020  1.090
 1JP  CAS  H17  single    0.970  0.020  1.090
 1JP  CBD  H18  single    0.970  0.020  1.090
 1JP  OAH  H19  single    0.850  0.020  0.980
 1JP  CAR  H20  single    0.970  0.020  1.090
 1JP  CAR  H21  single    0.970  0.020  1.090
 1JP  CAP  H22  single    0.970  0.020  1.090
 1JP  CAP  H23  single    0.970  0.020  1.090
 1JP  CAL  H24  single    0.930  0.020  1.080
 1JP  CAJ  H25  single    0.930  0.020  1.080
 1JP  CAI  H26  single    0.930  0.020  1.080
 1JP  CAK  H27  single    0.930  0.020  1.080
 1JP  CAM  H28  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
 1JP  CA   C    OXT  111.15  3.000
 1JP  OXT  C    O    123.65  3.000
 1JP  CA   C    O    125.20  3.000
 1JP  H1   OXT  C    110.80  3.000
 1JP  H2   CA   CB   107.49  3.000
 1JP  H2   CA   N    113.57  3.000
 1JP  CB   CA   N    108.43  3.000
 1JP  H2   CA   C    107.26  3.000
 1JP  CB   CA   C    110.76  3.000
 1JP  N    CA   C    109.33  3.000
 1JP  H4   N    H3   105.84  3.000
 1JP  H4   N    CA   108.75  3.000
 1JP  H3   N    CA   110.33  3.000
 1JP  H7   CB   H6   106.57  3.000
 1JP  H7   CB   CG   108.03  3.000
 1JP  H6   CB   CG   110.28  3.000
 1JP  H7   CB   CA   106.39  3.000
 1JP  H6   CB   CA   109.07  3.000
 1JP  CG   CB   CA   116.02  3.000
 1JP  H9   CG   H8   105.66  3.000
 1JP  H9   CG   CD   110.85  3.000
 1JP  H8   CG   CD   106.01  3.000
 1JP  H9   CG   CB   111.20  3.000
 1JP  H8   CG   CB   108.52  3.000
 1JP  CD   CG   CB   114.08  3.000
 1JP  NE2  CD   OE1  123.13  3.000
 1JP  NE2  CD   CG   114.63  3.000
 1JP  OE1  CD   CG   122.16  3.000
 1JP  H10  NE2  CBE  117.85  3.000
 1JP  H10  NE2  CD   118.65  3.000
 1JP  CBE  NE2  CD   123.45  3.000
 1JP  H11  CBE  CAT  108.29  3.000
 1JP  H11  CBE  CBA  109.55  3.000
 1JP  CAT  CBE  CBA  108.96  3.000
 1JP  H11  CBE  NE2  107.94  3.000
 1JP  CAT  CBE  NE2  111.85  3.000
 1JP  CBA  CBE  NE2  110.21  3.000
 1JP  NAU  CBA  OAE  122.16  3.000
 1JP  NAU  CBA  CBE  113.41  3.000
 1JP  OAE  CBA  CBE  123.60  3.000
 1JP  CAO  NAU  CBA  126.96  3.000
 1JP  H12  CAO  CAX  118.10  3.000
 1JP  H12  CAO  NAU  119.71  3.000
 1JP  CAX  CAO  NAU  122.18  3.000
 1JP  OAB  CAX  OAF  126.45  3.000
 1JP  OAF  CAX  CAO  111.57  3.000
 1JP  OAB  CAX  CAO  121.98  3.000
 1JP  H13  OAF  CAX  111.50  3.000
 1JP  H15  CAT  H14  108.03  3.000
 1JP  H15  CAT  S1   110.00  3.000
 1JP  H14  CAT  S1   110.40  3.000
 1JP  H15  CAT  CBE  109.51  3.000
 1JP  H14  CAT  CBE  110.88  3.000
 1JP  S1   CAT  CBE  108.03  3.000
 1JP  CAS  S1   CAT   99.44  3.000
 1JP  H17  CAS  H16  107.50  3.000
 1JP  H17  CAS  CBD  109.66  3.000
 1JP  H16  CAS  CBD  109.87  3.000
 1JP  H17  CAS  S1   109.76  3.000
 1JP  H16  CAS  S1   108.81  3.000
 1JP  CBD  CAS  S1   111.18  3.000
 1JP  H18  CBD  CAR  105.07  3.000
 1JP  H18  CBD  OAH  110.23  3.000
 1JP  CAR  CBD  OAH  113.68  3.000
 1JP  H18  CBD  CAS  105.32  3.000
 1JP  CAR  CBD  CAS  114.91  3.000
 1JP  OAH  CBD  CAS  107.28  3.000
 1JP  H19  OAH  CBD  108.82  3.000
 1JP  H21  CAR  H20  104.81  3.000
 1JP  H21  CAR  CAP  109.40  3.000
 1JP  H20  CAR  CAP  108.32  3.000
 1JP  H21  CAR  CBD  107.69  3.000
 1JP  H20  CAR  CBD  107.01  3.000
 1JP  CAP  CAR  CBD  118.73  3.000
 1JP  H23  CAP  H22  106.02  3.000
 1JP  H23  CAP  CBB  108.24  3.000
 1JP  H22  CAP  CBB  109.39  3.000
 1JP  H23  CAP  CAR  106.89  3.000
 1JP  H22  CAP  CAR  110.06  3.000
 1JP  CBB  CAP  CAR  115.76  3.000
 1JP  CAM  CBB  CAL  118.12  3.000
 1JP  CAM  CBB  CAP  121.09  3.000
 1JP  CAL  CBB  CAP  120.75  3.000
 1JP  H24  CAL  CAJ  119.47  3.000
 1JP  H24  CAL  CBB  119.49  3.000
 1JP  CAJ  CAL  CBB  121.03  3.000
 1JP  H25  CAJ  CAI  120.05  3.000
 1JP  H25  CAJ  CAL  119.63  3.000
 1JP  CAI  CAJ  CAL  120.32  3.000
 1JP  H26  CAI  CAK  120.35  3.000
 1JP  H26  CAI  CAJ  120.42  3.000
 1JP  CAK  CAI  CAJ  119.24  3.000
 1JP  H27  CAK  CAM  119.66  3.000
 1JP  H27  CAK  CAI  120.12  3.000
 1JP  CAM  CAK  CAI  120.22  3.000
 1JP  H28  CAM  CAK  119.08  3.000
 1JP  H28  CAM  CBB  119.85  3.000
 1JP  CAK  CAM  CBB  121.07  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
 1JP  CONST_01  CAI  CAJ  CAL  CBB     0.00   0.0  0
 1JP  CONST_02  CAI  CAK  CAM  CBB     0.00   0.0  0
 1JP  CONST_03  CAK  CAI  CAJ  CAL     0.00   0.0  0
 1JP  CONST_04  CAK  CAM  CBB  CAL     0.00   0.0  0
 1JP  CONST_05  CAM  CBB  CAL  CAJ     0.00   0.0  0
 1JP  CONST_06  CAM  CAK  CAI  CAJ     0.00   0.0  0
 1JP  CONST_07  CAJ  CAL  CBB  CAP   180.00   0.0  0
 1JP  CONST_08  CAK  CAM  CBB  CAP   180.00   0.0  0
 1JP  CONST_09  H25  CAJ  CAL  CBB   180.00   0.0  0
 1JP  CONST_10  H27  CAK  CAM  CBB   180.00   0.0  0
 1JP  CONST_11  H26  CAI  CAJ  CAL   180.00   0.0  0
 1JP  CONST_12  H28  CAM  CBB  CAL   180.00   0.0  0
 1JP  CONST_13  H24  CAL  CAJ  CAI   180.00   0.0  0
 1JP  CONST_14  CBE  NE2  CD   CG    180.00   0.0  0
 1JP  CONST_15  CBE  NE2  CD   OE1     0.00   0.0  0
 1JP  CONST_18  H10  NE2  CD   CG      0.00   0.0  0
 1JP  CONST_19  H1   OXT  C    O       0.00   0.0  0
 1JP  CONST_20  H13  OAF  CAX  CAO   180.00   0.0  0
 1JP  Var_01    CAL  CBB  CAP  CAR  -130.00  30.0  2
 1JP  Var_02    CBB  CAP  CAR  CBD    66.29  30.0  2
 1JP  Var_03    CAX  CAO  NAU  CBA     0.82   0.0  2
 1JP  Var_04    CD   CG   CB   CA     78.87  30.0  3
 1JP  Var_05    OE1  CD   CG   CB     26.13  30.0  3
 1JP  Var_06    OAB  CAX  CAO  NAU     5.12  30.0  1
 1JP  Var_07    CBD  CAS  S1   CAT   171.25  30.0  3
 1JP  Var_08    H14  CAT  S1   CAS    82.50  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
 1JP  chir_01  CA   N    CB   C    positiv
 1JP  chir_02  CBE  NE2  CBA  CAT  positiv
 1JP  chir_03  CBD  OAH  CAS  CAR  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
 1JP  plan-1  CAP  0.020
 1JP  plan-1  CBB  0.020
 1JP  plan-1  CAL  0.020
 1JP  plan-1  CAJ  0.020
 1JP  plan-1  CAI  0.020
 1JP  plan-1  CAK  0.020
 1JP  plan-1  CAM  0.020
 1JP  plan-1  H24  0.020
 1JP  plan-1  H25  0.020
 1JP  plan-1  H26  0.020
 1JP  plan-1  H27  0.020
 1JP  plan-1  H28  0.020
 1JP  plan-2  CG   0.020
 1JP  plan-2  CD   0.020
 1JP  plan-2  OE1  0.020
 1JP  plan-2  NE2  0.020
 1JP  plan-2  CBE  0.020
 1JP  plan-2  H10  0.020
 1JP  plan-3  CBE  0.020
 1JP  plan-3  CBA  0.020
 1JP  plan-3  OAE  0.020
 1JP  plan-3  NAU  0.020
 1JP  plan-3  CAO  0.020
 1JP  plan-3  CAX  0.020
 1JP  plan-3  H12  0.020
 1JP  plan-4  O    0.020
 1JP  plan-4  C    0.020
 1JP  plan-4  OXT  0.020
 1JP  plan-4  CA   0.020
 1JP  plan-4  H1   0.020
 1JP  plan-5  CAO  0.020
 1JP  plan-5  CAX  0.020
 1JP  plan-5  OAF  0.020
 1JP  plan-5  OAB  0.020
 1JP  plan-5  H13  0.020

