# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 21:35:09 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: D-gamma-glutamyl-S-(4-phenylbutyl)-L-cysteinylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCC(=O)N[C@@H](CSCCCCc1ccccc1)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
 1JO  1JO  D-gamma-glutamyl-S-(4-phenylbutyl)-L-cysteinylglycine  ligand  57  30  .  2022-07-22  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_1JO
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
 1JO  OXT  O  OC     0  -0.623  -6.8971  -2.6781  -2.4878
 1JO  C    C  C      0   0.387  -6.8422  -3.2929  -1.4018
 1JO  O    O  O     -1  -0.606  -7.8022  -3.8008  -0.7899
 1JO  CA   C  CH1    0  -0.220  -5.4372  -3.4055  -0.7565
 1JO  N    N  NH2    0  -0.787  -5.3461  -4.3071   0.3815
 1JO  CB   C  CH2    0  -0.417  -4.9533  -2.0085  -0.3599
 1JO  CG   C  CH2    0  -0.564  -3.5177  -2.0095   0.1537
 1JO  CD   C  C      0   0.568  -3.0538  -0.6323   0.5571
 1JO  OE1  O  O      0  -0.505  -3.7366   0.1217   1.2385
 1JO  NE2  N  NH1    0  -0.632  -1.8210  -0.2836   0.1441
 1JO  CBD  C  CH1    0  -0.197  -1.2872   1.0251   0.4011
 1JO  CBA  C  C      0   0.552  -2.0701   2.0946  -0.3752
 1JO  OAE  O  O      0  -0.497  -2.5821   1.8482  -1.4573
 1JO  NAU  N  NH1    0  -0.629  -2.0913   3.2924   0.2057
 1JO  CAQ  C  CH2    0  -0.410  -2.6877   4.4657  -0.3793
 1JO  CAX  C  C      0   0.400  -2.4872   5.6951   0.5309
 1JO  OAF  O  O      0  -0.600  -1.8614   5.5170   1.5937
 1JO  OAB  O  OC    -1  -0.608  -2.9759   6.7547   0.1046
 1JO  CAT  C  CH2    0  -0.568   0.1756   1.0920  -0.0235
 1JO  SAW  S  S2     0  -0.024   1.1522  -0.1266   0.9019
 1JO  CAO  C  CH2    0  -0.544   2.7714   0.1312   0.1219
 1JO  CAM  C  CH2    0  -0.426   3.8054  -0.7718   0.7777
 1JO  CAN  C  CH2    0  -0.408   5.1704  -0.6483   0.1106
 1JO  CAR  C  CH2    0  -0.506   6.2237  -1.5291   0.7850
 1JO  CBB  C  CR6    0   0.137   7.5652  -1.4229   0.1159
 1JO  CAK  C  CR16   0  -0.310   7.8652  -2.1964  -1.0042
 1JO  CAI  C  CR16   0  -0.239   9.0890  -2.0756  -1.6485
 1JO  CAH  C  CR16   0  -0.275  10.0376  -1.1744  -1.1813
 1JO  CAJ  C  CR16   0  -0.240   9.7505  -0.3969  -0.0671
 1JO  CAL  C  CR16   0  -0.316   8.5244  -0.5223   0.5737
 1JO  H2   H  HCH1   0   0.213  -4.7542  -3.7826  -1.5273
 1JO  H3   H  HNH2   0   0.324  -6.1588  -4.1502   0.9675
 1JO  H4   H  HNH2   0   0.336  -5.4562  -5.2585   0.0527
 1JO  H6   H  HCH2   0   0.229  -5.0362  -1.3478  -1.2244
 1JO  H7   H  HCH2   0   0.217  -5.6151  -1.6012   0.4108
 1JO  H8   H  HCH2   0   0.266  -3.4518  -2.6615   1.0283
 1JO  H9   H  HCH2   0   0.238  -2.8522  -2.4399  -0.5995
 1JO  H10  H  HNH1   0   0.400  -1.3270  -0.8882  -0.4924
 1JO  H11  H  HCH1   0   0.278  -1.3531   1.2387   1.4725
 1JO  H12  H  HNH1   0   0.387  -1.6659   3.4457   1.1100
 1JO  H13  H  HCH2   0   0.242  -2.2499   4.6761  -1.3598
 1JO  H14  H  HCH2   0   0.242  -3.7591   4.3159  -0.5444
 1JO  H16  H  HCH2   0   0.279   0.2711   0.8984  -1.0949
 1JO  H17  H  HCH2   0   0.291   0.5614   2.0928   0.1741
 1JO  H18  H  HCH2   0   0.261   2.6883  -0.0908  -0.9443
 1JO  H19  H  HCH2   0   0.261   3.0584   1.1798   0.2265
 1JO  H20  H  HCH2   0   0.232   3.8909  -0.5200   1.8387
 1JO  H21  H  HCH2   0   0.231   3.4702  -1.8121   0.7265
 1JO  H22  H  HCH2   0   0.227   5.0867  -0.9238  -0.9452
 1JO  H23  H  HCH2   0   0.227   5.5021   0.3943   0.1345
 1JO  H24  H  HCH2   0   0.239   6.3128  -1.2419   1.8361
 1JO  H25  H  HCH2   0   0.239   5.8852  -2.5689   0.7716
 1JO  H26  H  HCR6   0   0.244   7.1338  -2.9056  -1.3749
 1JO  H27  H  HCR6   0   0.252   9.3033  -2.6886  -2.5149
 1JO  H28  H  HCR6   0   0.252  10.9945  -1.0827  -1.6789
 1JO  H29  H  HCR6   0   0.252  10.4837   0.3058   0.3080
 1JO  H30  H  HCR6   0   0.245   8.3128   0.0843   1.4470

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
 1JO  CAI  CAH  aromatic  1.389  0.020  1.389
 1JO  CAI  CAK  aromatic  1.388  0.020  1.388
 1JO  CAH  CAJ  aromatic  1.389  0.020  1.389
 1JO  CAK  CBB  aromatic  1.394  0.020  1.394
 1JO  CAJ  CAL  aromatic  1.389  0.020  1.389
 1JO  CBB  CAL  aromatic  1.393  0.020  1.393
 1JO  CBB  CAR  single    1.503  0.020  1.503
 1JO  CAR  CAN  single    1.530  0.020  1.530
 1JO  CB   CG   single    1.525  0.020  1.525
 1JO  CB   CA   single    1.531  0.020  1.531
 1JO  CG   CD   single    1.508  0.020  1.508
 1JO  N    CA   single    1.455  0.020  1.455
 1JO  OAE  CBA  double    1.222  0.020  1.222
 1JO  O    C    deloc     1.247  0.020  1.247
 1JO  CBA  CBD  single    1.536  0.020  1.536
 1JO  CBA  NAU  single    1.331  0.020  1.331
 1JO  CA   C    single    1.550  0.020  1.550
 1JO  OAF  CAX  deloc     1.246  0.020  1.246
 1JO  CBD  CAT  single    1.525  0.020  1.525
 1JO  CBD  NE2  single    1.437  0.020  1.437
 1JO  CAQ  NAU  single    1.440  0.020  1.440
 1JO  CAQ  CAX  single    1.543  0.020  1.543
 1JO  CAN  CAM  single    1.524  0.020  1.524
 1JO  C    OXT  deloc     1.249  0.020  1.249
 1JO  CD   NE2  single    1.346  0.020  1.346
 1JO  CD   OE1  double    1.224  0.020  1.224
 1JO  CAT  SAW  single    1.815  0.020  1.815
 1JO  CAX  OAB  deloc     1.242  0.020  1.242
 1JO  SAW  CAO  single    1.816  0.020  1.816
 1JO  CAM  CAO  single    1.521  0.020  1.521
 1JO  CA   H2   single    0.970  0.020  1.090
 1JO  N    H3   single    0.890  0.020  1.040
 1JO  N    H4   single    0.890  0.020  1.040
 1JO  CB   H6   single    0.970  0.020  1.090
 1JO  CB   H7   single    0.970  0.020  1.090
 1JO  CG   H8   single    0.970  0.020  1.090
 1JO  CG   H9   single    0.970  0.020  1.090
 1JO  NE2  H10  single    0.860  0.020  1.020
 1JO  CBD  H11  single    0.970  0.020  1.090
 1JO  NAU  H12  single    0.860  0.020  1.020
 1JO  CAQ  H13  single    0.970  0.020  1.090
 1JO  CAQ  H14  single    0.970  0.020  1.090
 1JO  CAT  H16  single    0.970  0.020  1.090
 1JO  CAT  H17  single    0.970  0.020  1.090
 1JO  CAO  H18  single    0.970  0.020  1.090
 1JO  CAO  H19  single    0.970  0.020  1.090
 1JO  CAM  H20  single    0.970  0.020  1.090
 1JO  CAM  H21  single    0.970  0.020  1.090
 1JO  CAN  H22  single    0.970  0.020  1.090
 1JO  CAN  H23  single    0.970  0.020  1.090
 1JO  CAR  H24  single    0.970  0.020  1.090
 1JO  CAR  H25  single    0.970  0.020  1.090
 1JO  CAK  H26  single    0.930  0.020  1.080
 1JO  CAI  H27  single    0.930  0.020  1.080
 1JO  CAH  H28  single    0.930  0.020  1.080
 1JO  CAJ  H29  single    0.930  0.020  1.080
 1JO  CAL  H30  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
 1JO  CA   C    O    117.65  3.000
 1JO  CA   C    OXT  115.94  3.000
 1JO  O    C    OXT  126.40  3.000
 1JO  H2   CA   CB   107.40  3.000
 1JO  H2   CA   N    107.32  3.000
 1JO  CB   CA   N    110.07  3.000
 1JO  H2   CA   C    107.27  3.000
 1JO  N    CA   C    115.30  3.000
 1JO  CB   CA   C    109.15  3.000
 1JO  H4   N    H3   104.23  3.000
 1JO  H4   N    CA   108.76  3.000
 1JO  H3   N    CA   107.82  3.000
 1JO  H7   CB   H6   106.66  3.000
 1JO  H7   CB   CG   109.41  3.000
 1JO  H6   CB   CG   109.80  3.000
 1JO  H7   CB   CA   109.33  3.000
 1JO  H6   CB   CA   108.86  3.000
 1JO  CG   CB   CA   112.60  3.000
 1JO  H9   CG   H8   106.24  3.000
 1JO  H9   CG   CD   110.88  3.000
 1JO  H8   CG   CD   108.19  3.000
 1JO  H9   CG   CB   109.96  3.000
 1JO  H8   CG   CB   109.07  3.000
 1JO  CD   CG   CB   112.28  3.000
 1JO  NE2  CD   OE1  121.47  3.000
 1JO  OE1  CD   CG   122.66  3.000
 1JO  NE2  CD   CG   115.86  3.000
 1JO  H10  NE2  CBD  118.53  3.000
 1JO  H10  NE2  CD   119.18  3.000
 1JO  CBD  NE2  CD   121.42  3.000
 1JO  H11  CBD  CAT  108.77  3.000
 1JO  H11  CBD  CBA  109.16  3.000
 1JO  CAT  CBD  CBA  108.53  3.000
 1JO  H11  CBD  NE2  109.30  3.000
 1JO  CAT  CBD  NE2  110.28  3.000
 1JO  CBA  CBD  NE2  110.76  3.000
 1JO  NAU  CBA  OAE  124.12  3.000
 1JO  NAU  CBA  CBD  114.46  3.000
 1JO  OAE  CBA  CBD  121.37  3.000
 1JO  H12  NAU  CAQ  114.46  3.000
 1JO  H12  NAU  CBA  121.33  3.000
 1JO  CAQ  NAU  CBA  124.21  3.000
 1JO  H14  CAQ  H13  106.43  3.000
 1JO  H14  CAQ  CAX  108.99  3.000
 1JO  H13  CAQ  CAX  108.87  3.000
 1JO  H14  CAQ  NAU  110.81  3.000
 1JO  H13  CAQ  NAU  110.79  3.000
 1JO  CAX  CAQ  NAU  110.83  3.000
 1JO  OAB  CAX  OAF  127.74  3.000
 1JO  OAB  CAX  CAQ  115.22  3.000
 1JO  OAF  CAX  CAQ  117.04  3.000
 1JO  H17  CAT  H16  108.01  3.000
 1JO  H17  CAT  SAW  109.47  3.000
 1JO  H16  CAT  SAW  109.50  3.000
 1JO  H17  CAT  CBD  109.22  3.000
 1JO  H16  CAT  CBD  110.43  3.000
 1JO  SAW  CAT  CBD  110.17  3.000
 1JO  CAO  SAW  CAT   99.52  3.000
 1JO  H19  CAO  H18  107.98  3.000
 1JO  H19  CAO  CAM  110.49  3.000
 1JO  H18  CAO  CAM  110.60  3.000
 1JO  H19  CAO  SAW  109.23  3.000
 1JO  H18  CAO  SAW  108.83  3.000
 1JO  CAM  CAO  SAW  109.67  3.000
 1JO  H21  CAM  H20  106.75  3.000
 1JO  H21  CAM  CAN  109.32  3.000
 1JO  H20  CAM  CAN  109.62  3.000
 1JO  H21  CAM  CAO  109.63  3.000
 1JO  H20  CAM  CAO  109.55  3.000
 1JO  CAN  CAM  CAO  111.83  3.000
 1JO  H23  CAN  H22  106.51  3.000
 1JO  H23  CAN  CAR  109.29  3.000
 1JO  H22  CAN  CAR  109.45  3.000
 1JO  H23  CAN  CAM  109.82  3.000
 1JO  H22  CAN  CAM  109.47  3.000
 1JO  CAR  CAN  CAM  112.14  3.000
 1JO  H25  CAR  H24  106.67  3.000
 1JO  H25  CAR  CBB  109.76  3.000
 1JO  H24  CAR  CBB  109.68  3.000
 1JO  H25  CAR  CAN  109.21  3.000
 1JO  H24  CAR  CAN  109.19  3.000
 1JO  CBB  CAR  CAN  112.18  3.000
 1JO  CAL  CBB  CAK  118.33  3.000
 1JO  CAL  CBB  CAR  120.93  3.000
 1JO  CAK  CBB  CAR  120.71  3.000
 1JO  H26  CAK  CAI  119.53  3.000
 1JO  H26  CAK  CBB  119.51  3.000
 1JO  CAI  CAK  CBB  120.96  3.000
 1JO  H27  CAI  CAH  120.08  3.000
 1JO  H27  CAI  CAK  119.77  3.000
 1JO  CAH  CAI  CAK  120.15  3.000
 1JO  H28  CAH  CAJ  120.28  3.000
 1JO  H28  CAH  CAI  120.26  3.000
 1JO  CAJ  CAH  CAI  119.46  3.000
 1JO  H29  CAJ  CAL  119.77  3.000
 1JO  H29  CAJ  CAH  120.10  3.000
 1JO  CAL  CAJ  CAH  120.14  3.000
 1JO  H30  CAL  CAJ  119.56  3.000
 1JO  H30  CAL  CBB  119.47  3.000
 1JO  CAJ  CAL  CBB  120.97  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
 1JO  CONST_01  CAH  CAI  CAK  CBB     0.00   0.0  0
 1JO  CONST_02  CAH  CAJ  CAL  CBB     0.00   0.0  0
 1JO  CONST_03  CAJ  CAH  CAI  CAK     0.00   0.0  0
 1JO  CONST_04  CAJ  CAL  CBB  CAK     0.00   0.0  0
 1JO  CONST_05  CAL  CAJ  CAH  CAI     0.00   0.0  0
 1JO  CONST_06  CAL  CBB  CAK  CAI     0.00   0.0  0
 1JO  CONST_07  CAI  CAK  CBB  CAR   180.00   0.0  0
 1JO  CONST_08  CAJ  CAL  CBB  CAR   180.00   0.0  0
 1JO  CONST_09  H27  CAI  CAK  CBB   180.00   0.0  0
 1JO  CONST_10  H29  CAJ  CAL  CBB   180.00   0.0  0
 1JO  CONST_11  H28  CAH  CAI  CAK   180.00   0.0  0
 1JO  CONST_12  H30  CAL  CBB  CAK   180.00   0.0  0
 1JO  CONST_13  H26  CAK  CAI  CAH   180.00   0.0  0
 1JO  CONST_14  CBD  NE2  CD   CG    180.00   0.0  0
 1JO  CONST_15  CBD  NE2  CD   OE1     0.00   0.0  0
 1JO  CONST_16  CAQ  NAU  CBA  CBD   180.00   0.0  0
 1JO  CONST_17  CAQ  NAU  CBA  OAE     0.00   0.0  0
 1JO  CONST_18  H10  NE2  CD   CG      0.00   0.0  0
 1JO  CONST_19  H12  NAU  CBA  CBD     0.00   0.0  0
 1JO  Var_01    CAK  CBB  CAR  CAN   -84.28  30.0  2
 1JO  Var_02    CBB  CAR  CAN  CAM   179.19  30.0  1
 1JO  Var_03    CD   CG   CB   CA   -179.35  30.0  3
 1JO  Var_04    NE2  CD   CG   CB   -135.45  30.0  3
 1JO  Var_05    CAX  CAQ  NAU  CBA  -177.73  30.0  1
 1JO  Var_06    OAF  CAX  CAQ  NAU     0.33  30.0  3
 1JO  Var_07    CAM  CAO  SAW  CAT   178.10  30.0  3
 1JO  Var_08    CAN  CAM  CAO  SAW   177.02  30.0  1
 1JO  Var_09    CAR  CAN  CAM  CAO   178.67  30.0  1
 1JO  Var_10    H16  CAT  SAW  CAO    55.31  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
 1JO  chir_01  CA   CB   N    C    negativ
 1JO  chir_02  CBD  NE2  CBA  CAT  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
 1JO  plan-1  CAR  0.020
 1JO  plan-1  CBB  0.020
 1JO  plan-1  CAK  0.020
 1JO  plan-1  CAI  0.020
 1JO  plan-1  CAH  0.020
 1JO  plan-1  CAJ  0.020
 1JO  plan-1  CAL  0.020
 1JO  plan-1  H26  0.020
 1JO  plan-1  H27  0.020
 1JO  plan-1  H28  0.020
 1JO  plan-1  H29  0.020
 1JO  plan-1  H30  0.020
 1JO  plan-2  CG   0.020
 1JO  plan-2  CD   0.020
 1JO  plan-2  OE1  0.020
 1JO  plan-2  NE2  0.020
 1JO  plan-2  CBD  0.020
 1JO  plan-2  H10  0.020
 1JO  plan-3  CBD  0.020
 1JO  plan-3  CBA  0.020
 1JO  plan-3  OAE  0.020
 1JO  plan-3  NAU  0.020
 1JO  plan-3  CAQ  0.020
 1JO  plan-3  H12  0.020
 1JO  plan-4  OXT  0.020
 1JO  plan-4  C    0.020
 1JO  plan-4  O    0.020
 1JO  plan-4  CA   0.020
 1JO  plan-5  CAQ  0.020
 1JO  plan-5  CAX  0.020
 1JO  plan-5  OAF  0.020
 1JO  plan-5  OAB  0.020

