# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 04:52:54 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: S-(2-{[(2',4'-difluorobiphenyl-4-yl)methyl]amino}-2-oxoethyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSCC(=O)NCc1ccc(cc1)c2ccc(F)cc2F)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
 4J4  4J4  S-(2-{[(2',4'-difluorobiphenyl-4-yl)methyl]amino}-2-oxoethyl)-L-cysteine  L-peptide  43  26  .  2022-07-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_4J4
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
 4J4  N    N  NH2    0  -0.762   7.7195   0.6151  -0.1938
 4J4  CA   C  CH1    0  -0.220   7.1662  -0.5937   0.3889
 4J4  C    C  C      0   0.375   7.9251  -1.9128   0.0781
 4J4  O    O  O      0  -0.621   8.9727  -1.8266  -0.5877
 4J4  CB   C  CH2    0  -0.540   5.7067  -0.7335  -0.0201
 4J4  CAP  C  CH2    0  -0.329  -0.0056   2.2478  -0.3920
 4J4  CAQ  C  CR6    0   0.100  -1.3363   1.5525  -0.2571
 4J4  CAS  C  CR16   0  -0.258  -2.7573  -0.0860   0.8016
 4J4  CAR  C  CR16   0  -0.253  -1.5262   0.5362   0.6752
 4J4  CAM  C  CH2    0  -0.659   3.1300   0.1876   0.1363
 4J4  CAL  C  CR16   0  -0.385  -6.3808  -2.5029   0.2276
 4J4  CAN  C  C      0   0.567   2.1512   1.3194   0.3672
 4J4  OAF  O  O      0  -0.479   2.3233   2.1438   1.2520
 4J4  SG   S  S2     0   0.001   4.8202   0.8128   0.3352
 4J4  NAO  N  NH1    0  -0.617   1.0934   1.3140  -0.4595
 4J4  CAG  C  CR16   0  -0.279  -2.4095   1.9254  -1.0581
 4J4  CAH  C  CR16   0  -0.273  -3.6451   1.3075  -0.9319
 4J4  CAI  C  CR6    0   0.082  -3.8356   0.2890  -0.0007
 4J4  CAJ  C  CR6    0  -0.158  -5.1255  -0.4201   0.1208
 4J4  CAB  C  CR6    0   0.527  -6.3326   0.2515   0.2751
 4J4  FAA  F  F      0  -0.302  -6.3302   1.5895   0.3303
 4J4  CAC  C  CR16   0  -0.541  -7.5484  -0.3919   0.4003
 4J4  CAD  C  CR6    0   0.549  -7.5441  -1.7726   0.3704
 4J4  FAE  F  F      0  -0.299  -8.7115  -2.4174   0.4882
 4J4  CAK  C  CR16   0  -0.247  -5.1845  -1.8138   0.1058
 4J4  H    H  HNH2   0   0.327   8.6976   0.6769   0.0608
 4J4  H1   H  HNH2   0   0.312   7.7265   0.5175  -1.2033
 4J4  HA   H  HCH1   0   0.224   7.1881  -0.4660   1.4785
 4J4  HB1  H  HCH2   0   0.235   5.6214  -0.9598  -1.0873
 4J4  HB2  H  HCH2   0   0.280   5.2404  -1.5482   0.5323
 4J4  HAP  H  HCH2   0   0.249  -0.0109   2.8806  -1.2826
 4J4  HAQ  H  HCH2   0   0.273   0.1630   2.9065   0.4602
 4J4  HAS  H  HCR6   0   0.240  -2.8839  -0.8666   1.5416
 4J4  HAR  H  HCR6   0   0.240  -0.7084   0.2233   1.3132
 4J4  HAM  H  HCH2   0   0.286   2.9326  -0.5938   0.8758
 4J4  HAN  H  HCH2   0   0.252   3.0083  -0.2584  -0.8523
 4J4  HAO  H  HNH1   0   0.380   1.0552   0.6177  -1.1864
 4J4  HAG  H  HCR6   0   0.231  -2.2805   2.7036  -1.8008
 4J4  HAH  H  HCR6   0   0.232  -4.4504   1.6031  -1.5916
 4J4  HAC  H  HCR6   0   0.288  -8.4650   0.1693   0.5278
 4J4  HAK  H  HCR6   0   0.254  -4.2686  -2.3762  -0.0211
 4J4  OXT  O  OC    -1  -0.549   7.4182  -2.9530   0.5474
 4J4  HAL  H  HCR6   0   0.269  -6.4048  -3.5838   0.2051

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
 4J4  N    CA   single    1.458  0.019  1.458
 4J4  CA   C    single    1.525  0.021  1.525
 4J4  CA   CB   single    1.530  0.020  1.530
 4J4  C    O    deloc     1.231  0.020  1.231
 4J4  CB   SG   single    1.817  0.020  1.817
 4J4  CAP  CAQ  single    1.507  0.020  1.507
 4J4  CAP  NAO  single    1.444  0.020  1.444
 4J4  CAQ  CAR  aromatic  1.392  0.020  1.392
 4J4  CAQ  CAG  aromatic  1.390  0.020  1.390
 4J4  CAS  CAR  aromatic  1.385  0.020  1.385
 4J4  CAS  CAI  aromatic  1.395  0.020  1.395
 4J4  CAM  CAN  single    1.514  0.020  1.514
 4J4  CAM  SG   single    1.813  0.020  1.813
 4J4  CAL  CAD  aromatic  1.381  0.020  1.381
 4J4  CAL  CAK  aromatic  1.386  0.020  1.386
 4J4  CAN  OAF  double    1.222  0.020  1.222
 4J4  CAN  NAO  single    1.343  0.020  1.343
 4J4  CAG  CAH  aromatic  1.387  0.020  1.387
 4J4  CAH  CAI  aromatic  1.393  0.020  1.393
 4J4  CAI  CAJ  single    1.477  0.020  1.477
 4J4  CAJ  CAB  aromatic  1.390  0.020  1.390
 4J4  CAJ  CAK  aromatic  1.395  0.020  1.395
 4J4  CAB  FAA  single    1.339  0.020  1.339
 4J4  CAB  CAC  aromatic  1.381  0.020  1.381
 4J4  CAC  CAD  aromatic  1.381  0.020  1.381
 4J4  CAD  FAE  single    1.339  0.020  1.339
 4J4  N    H    single    0.860  0.020  0.860
 4J4  N    H1   single    0.890  0.020  1.040
 4J4  CA   HA   single    0.970  0.020  0.970
 4J4  CB   HB1  single    0.970  0.020  1.090
 4J4  CB   HB2  single    0.970  0.020  1.090
 4J4  CAP  HAP  single    0.970  0.020  1.090
 4J4  CAP  HAQ  single    0.970  0.020  1.090
 4J4  CAS  HAS  single    0.930  0.020  1.080
 4J4  CAR  HAR  single    0.930  0.020  1.080
 4J4  CAM  HAM  single    0.970  0.020  1.090
 4J4  CAM  HAN  single    0.970  0.020  1.090
 4J4  CAL  HAL  single    0.930  0.020  1.080
 4J4  NAO  HAO  single    0.860  0.020  1.020
 4J4  CAG  HAG  single    0.930  0.020  1.080
 4J4  CAH  HAH  single    0.930  0.020  1.080
 4J4  CAC  HAC  single    0.930  0.020  1.080
 4J4  CAK  HAK  single    0.930  0.020  1.080
 4J4  C    OXT  deloc     1.249  0.020  1.249

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
 4J4  H1   N    H    104.45  3.000
 4J4  H1   N    CA   108.79  3.000
 4J4  H    N    CA   114.00  3.000
 4J4  HA   CA   CB   109.00  3.000
 4J4  HA   CA   C    109.00  3.000
 4J4  CB   CA   C    110.10  1.900
 4J4  HA   CA   N    110.00  3.000
 4J4  CB   CA   N    110.50  1.700
 4J4  C    CA   N    111.00  2.800
 4J4  OXT  C    O    126.92  3.000
 4J4  OXT  C    CA   115.71  3.000
 4J4  O    C    CA   120.80  1.700
 4J4  HB2  CB   HB1  107.85  3.000
 4J4  HB2  CB   SG   109.17  3.000
 4J4  HB1  CB   SG   109.18  3.000
 4J4  HB2  CB   CA   110.06  3.000
 4J4  HB1  CB   CA   110.84  3.000
 4J4  SG   CB   CA   109.69  3.000
 4J4  HAQ  CAP  HAP  106.74  3.000
 4J4  HAQ  CAP  NAO  108.03  3.000
 4J4  HAP  CAP  NAO  109.89  3.000
 4J4  HAQ  CAP  CAQ  110.20  3.000
 4J4  HAP  CAP  CAQ  109.63  3.000
 4J4  NAO  CAP  CAQ  112.20  3.000
 4J4  CAG  CAQ  CAR  118.45  3.000
 4J4  CAG  CAQ  CAP  120.41  3.000
 4J4  CAR  CAQ  CAP  121.14  3.000
 4J4  HAS  CAS  CAI  119.75  3.000
 4J4  HAS  CAS  CAR  119.34  3.000
 4J4  CAI  CAS  CAR  120.91  3.000
 4J4  HAR  CAR  CAS  119.17  3.000
 4J4  HAR  CAR  CAQ  120.15  3.000
 4J4  CAS  CAR  CAQ  120.68  3.000
 4J4  HAN  CAM  HAM  107.48  3.000
 4J4  HAN  CAM  SG   110.13  3.000
 4J4  HAM  CAM  SG   109.91  3.000
 4J4  HAN  CAM  CAN  111.81  3.000
 4J4  HAM  CAM  CAN  108.32  3.000
 4J4  SG   CAM  CAN  109.16  3.000
 4J4  HAL  CAL  CAK  120.95  3.000
 4J4  HAL  CAL  CAD  120.81  3.000
 4J4  CAK  CAL  CAD  118.24  3.000
 4J4  NAO  CAN  OAF  124.04  3.000
 4J4  NAO  CAN  CAM  114.36  3.000
 4J4  OAF  CAN  CAM  121.59  3.000
 4J4  CAM  SG   CB    98.04  3.000
 4J4  HAO  NAO  CAN  118.49  3.000
 4J4  HAO  NAO  CAP  116.87  3.000
 4J4  CAN  NAO  CAP  124.64  3.000
 4J4  HAG  CAG  CAH  119.23  3.000
 4J4  HAG  CAG  CAQ  119.72  3.000
 4J4  CAH  CAG  CAQ  121.05  3.000
 4J4  HAH  CAH  CAI  120.35  3.000
 4J4  HAH  CAH  CAG  119.06  3.000
 4J4  CAI  CAH  CAG  120.55  3.000
 4J4  CAJ  CAI  CAH  121.70  3.000
 4J4  CAJ  CAI  CAS  119.91  3.000
 4J4  CAH  CAI  CAS  118.36  3.000
 4J4  CAK  CAJ  CAB  116.56  3.000
 4J4  CAK  CAJ  CAI  121.05  3.000
 4J4  CAB  CAJ  CAI  122.39  3.000
 4J4  CAC  CAB  FAA  117.60  3.000
 4J4  CAC  CAB  CAJ  123.33  3.000
 4J4  FAA  CAB  CAJ  119.06  3.000
 4J4  HAC  CAC  CAD  121.57  3.000
 4J4  HAC  CAC  CAB  120.98  3.000
 4J4  CAD  CAC  CAB  117.45  3.000
 4J4  FAE  CAD  CAC  118.49  3.000
 4J4  FAE  CAD  CAL  119.27  3.000
 4J4  CAC  CAD  CAL  122.25  3.000
 4J4  HAK  CAK  CAJ  118.99  3.000
 4J4  HAK  CAK  CAL  118.84  3.000
 4J4  CAJ  CAK  CAL  122.16  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
 4J4  CONST_01  CAI  CAS  CAR  CAQ     0.00   0.0  0
 4J4  CONST_02  CAI  CAH  CAG  CAQ     0.00   0.0  0
 4J4  CONST_03  CAG  CAQ  CAR  CAS     0.00   0.0  0
 4J4  CONST_04  CAG  CAH  CAI  CAS     0.00   0.0  0
 4J4  CONST_07  CAH  CAG  CAQ  CAR     0.00   0.0  0
 4J4  CONST_08  CAH  CAI  CAS  CAR     0.00   0.0  0
 4J4  CONST_09  CAJ  CAI  CAS  CAR   180.00   0.0  0
 4J4  CONST_10  CAB  CAC  CAD  CAL     0.00   0.0  0
 4J4  CONST_11  CAI  CAJ  CAK  CAL   180.00   0.0  0
 4J4  CONST_12  CAB  CAJ  CAK  CAL     0.00   0.0  0
 4J4  CONST_13  CAJ  CAI  CAH  CAG   180.00   0.0  0
 4J4  CONST_16  CAC  CAB  CAJ  CAI   180.00   0.0  0
 4J4  CONST_17  CAD  CAC  CAB  CAJ     0.00   0.0  0
 4J4  CONST_18  CAD  CAL  CAK  CAJ     0.00   0.0  0
 4J4  CONST_19  CAK  CAJ  CAB  CAC     0.00   0.0  0
 4J4  CONST_20  CAK  CAL  CAD  CAC     0.00   0.0  0
 4J4  CONST_21  CAS  CAR  CAQ  CAP   180.00   0.0  0
 4J4  CONST_22  CAH  CAG  CAQ  CAP   180.00   0.0  0
 4J4  CONST_23  FAA  CAB  CAJ  CAI     0.00   0.0  0
 4J4  CONST_24  FAE  CAD  CAC  CAB   180.00   0.0  0
 4J4  CONST_25  CAK  CAJ  CAB  FAA   180.00   0.0  0
 4J4  CONST_26  CAD  CAC  CAB  FAA   180.00   0.0  0
 4J4  CONST_27  CAK  CAL  CAD  FAE   180.00   0.0  0
 4J4  CONST_28  HAS  CAS  CAR  CAQ   180.00   0.0  0
 4J4  CONST_29  HAH  CAH  CAG  CAQ   180.00   0.0  0
 4J4  CONST_30  HAG  CAG  CAQ  CAR   180.00   0.0  0
 4J4  CONST_31  HAC  CAC  CAD  CAL   180.00   0.0  0
 4J4  CONST_32  HAR  CAR  CAQ  CAG   180.00   0.0  0
 4J4  CONST_33  HAK  CAK  CAJ  CAI     0.00   0.0  0
 4J4  CONST_34  HAL  CAL  CAK  CAJ   180.00   0.0  0
 4J4  CONST_35  CAM  CAN  NAO  CAP   180.00   0.0  0
 4J4  CONST_36  OAF  CAN  NAO  CAP     0.00   0.0  0
 4J4  CONST_37  HAO  NAO  CAN  CAM     0.00   0.0  0
 4J4  Var_01    NAO  CAP  CAQ  CAR    47.79  30.0  2
 4J4  Var_02    CAN  NAO  CAP  CAQ  -124.14  30.0  3
 4J4  Var_03    CAN  CAM  SG   CB   -179.21  30.0  1
 4J4  Var_04    SG   CAM  CAN  OAF   -40.11  30.0  1
 4J4  Var_05    HB1  CB   SG   CAM    71.49  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
 4J4  chir_01  CA  N  C  CB  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
 4J4  plan-1  CAP  0.020
 4J4  plan-1  CAQ  0.020
 4J4  plan-1  CAS  0.020
 4J4  plan-1  CAR  0.020
 4J4  plan-1  CAG  0.020
 4J4  plan-1  CAH  0.020
 4J4  plan-1  CAI  0.020
 4J4  plan-1  CAJ  0.020
 4J4  plan-1  HAS  0.020
 4J4  plan-1  HAR  0.020
 4J4  plan-1  HAG  0.020
 4J4  plan-1  HAH  0.020
 4J4  plan-2  CAL  0.020
 4J4  plan-2  CAI  0.020
 4J4  plan-2  CAJ  0.020
 4J4  plan-2  CAB  0.020
 4J4  plan-2  FAA  0.020
 4J4  plan-2  CAC  0.020
 4J4  plan-2  CAD  0.020
 4J4  plan-2  FAE  0.020
 4J4  plan-2  CAK  0.020
 4J4  plan-2  HAC  0.020
 4J4  plan-2  HAK  0.020
 4J4  plan-2  HAL  0.020
 4J4  plan-3  CAP  0.020
 4J4  plan-3  CAM  0.020
 4J4  plan-3  CAN  0.020
 4J4  plan-3  OAF  0.020
 4J4  plan-3  NAO  0.020
 4J4  plan-3  HAO  0.020
 4J4  plan-4  CA   0.020
 4J4  plan-4  C    0.020
 4J4  plan-4  O    0.020
 4J4  plan-4  OXT  0.020

