# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 20:37:16 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: S-[3-(3,4-dichlorophenyl)-3-oxopropyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSCCC(=O)c1ccc(Cl)c(Cl)c1)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
 CS4  CS4  S-[3-(3,4-dichlorophenyl)-3-oxopropyl]-L-cysteine  L-peptide  31  19  .  2016-04-22  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_CS4
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
 CS4  OXT   O   OC    -1  -0.606  12.4856  15.5597  28.2536
 CS4  C     C   C      0   0.418  11.9109  16.1524  27.3176
 CS4  CA    C   CH1    0  -0.185  12.1668  17.6746  27.2438
 CS4  N     N   NH2    0  -0.790  11.8578  18.2740  28.5367
 CS4  CB    C   CH2    0  -0.581  13.6109  17.9696  26.8273
 CS4  SG    S   S2     0  -0.037  14.1798  17.1792  25.2920
 CS4  C1J   C   CH2    0  -0.583  12.8969  17.6615  24.1050
 CS4  C1K   C   CH2    0  -0.583  12.7247  19.1700  23.9471
 CS4  C1N   C   C      0   0.395  14.0296  19.8823  23.6938
 CS4  O1C   O   O      0  -0.376  14.4859  20.6706  24.4922
 CS4  C1Q   C   CR6    0  -0.017  14.7722  19.5883  22.4314
 CS4  C1I   C   CR16   0  -0.232  16.1209  19.9278  22.3628
 CS4  C1H   C   CR16   0  -0.288  14.1569  19.0266  21.3159
 CS4  C1G   C   CR16   0  -0.197  14.8726  18.8125  20.1508
 CS4  C1O   C   CR6    0  -0.002  16.2161  19.1465  20.0916
 CS4  CL1D  CL  CL     0  -0.079  17.0919  18.8740  18.6405
 CS4  C1P   C   CR6    0   0.019  16.8426  19.7008  21.2062
 CS4  CL1E  CL  CL     0  -0.088  18.5125  20.1143  21.1544
 CS4  O     O   O      0  -0.599  11.1671  15.6510  26.4529
 CS4  HA    H   HCH1   0   0.212  11.4901  18.1140  26.5059
 CS4  H     H   HNH2   0   0.329  12.4213  17.8124  29.2412
 CS4  H2    H   HNH2   0   0.335  12.1347  19.2489  28.5418
 CS4  HB2   H   HCH2   0   0.265  14.2929  17.5909  27.5921
 CS4  HB3   H   HCH2   0   0.258  13.7678  19.0488  26.7579
 CS4  H1J1  H   HCH2   0   0.289  11.9485  17.2089  24.3927
 CS4  H1J2  H   HCH2   0   0.286  13.1991  17.1947  23.1665
 CS4  H1K1  H   HCH2   0   0.282  12.2783  19.5953  24.8466
 CS4  H1K2  H   HCH2   0   0.284  12.0207  19.3609  23.1312
 CS4  H1I   H   HCR6   0   0.293  16.6152  20.3656  23.2197
 CS4  H1H   H   HCR6   0   0.282  13.1082  18.7634  21.3278
 CS4  H1G   H   HCR6   0   0.296  14.3871  18.3863  19.2838

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
 CS4  OXT  C     deloc     1.248  0.020  1.248
 CS4  C    CA    single    1.525  0.021  1.525
 CS4  C    O     deloc     1.231  0.020  1.231
 CS4  CA   CB    single    1.530  0.020  1.530
 CS4  CA   N     single    1.458  0.019  1.458
 CS4  CA   HA    single    0.970  0.020  0.970
 CS4  N    H     single    0.860  0.020  0.860
 CS4  N    H2    single    0.890  0.020  1.040
 CS4  CB   SG    single    1.818  0.020  1.818
 CS4  CB   HB2   single    0.970  0.020  1.090
 CS4  CB   HB3   single    0.970  0.020  1.090
 CS4  SG   C1J   single    1.813  0.020  1.813
 CS4  C1J  C1K   single    1.527  0.020  1.527
 CS4  C1J  H1J1  single    0.970  0.020  1.090
 CS4  C1J  H1J2  single    0.970  0.020  1.090
 CS4  C1K  C1N   single    1.508  0.020  1.508
 CS4  C1K  H1K1  single    0.970  0.020  1.090
 CS4  C1K  H1K2  single    0.970  0.020  1.090
 CS4  C1N  C1Q   single    1.494  0.020  1.494
 CS4  C1N  O1C   double    1.211  0.020  1.211
 CS4  C1Q  C1H   aromatic  1.392  0.020  1.392
 CS4  C1Q  C1I   aromatic  1.392  0.020  1.392
 CS4  C1I  C1P   aromatic  1.382  0.020  1.382
 CS4  C1I  H1I   single    0.930  0.020  1.080
 CS4  C1H  C1G   aromatic  1.384  0.020  1.384
 CS4  C1H  H1H   single    0.930  0.020  1.080
 CS4  C1G  C1O   aromatic  1.386  0.020  1.386
 CS4  C1G  H1G   single    0.930  0.020  1.080
 CS4  C1O  CL1D  single    1.717  0.020  1.717
 CS4  C1O  C1P   aromatic  1.394  0.020  1.394
 CS4  C1P  CL1E  single    1.721  0.020  1.721

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
 CS4  O     C    CA    120.80  1.700
 CS4  O     C    OXT   127.17  3.000
 CS4  CA    C    OXT   115.30  3.000
 CS4  HA    CA   CB    109.00  3.000
 CS4  HA    CA   N     110.00  3.000
 CS4  CB    CA   N     110.50  1.700
 CS4  HA    CA   C     109.00  3.000
 CS4  N     CA   C     111.00  2.800
 CS4  CB    CA   C     110.10  1.900
 CS4  H2    N    H     106.42  3.000
 CS4  H2    N    CA    110.00  3.000
 CS4  H     N    CA    114.00  3.000
 CS4  HB3   CB   HB2   107.29  3.000
 CS4  HB3   CB   SG    109.32  3.000
 CS4  HB2   CB   SG    104.19  3.000
 CS4  HB3   CB   CA    110.05  3.000
 CS4  HB2   CB   CA    109.35  3.000
 CS4  SG    CB   CA    116.16  3.000
 CS4  C1J   SG   CB    102.47  3.000
 CS4  H1J2  C1J  H1J1  106.90  3.000
 CS4  H1J2  C1J  C1K   111.41  3.000
 CS4  H1J1  C1J  C1K   109.85  3.000
 CS4  H1J2  C1J  SG    104.68  3.000
 CS4  H1J1  C1J  SG    109.42  3.000
 CS4  C1K   C1J  SG    114.23  3.000
 CS4  H1K2  C1K  H1K1  106.47  3.000
 CS4  H1K2  C1K  C1N   110.43  3.000
 CS4  H1K1  C1K  C1N   107.97  3.000
 CS4  H1K2  C1K  C1J   108.79  3.000
 CS4  H1K1  C1K  C1J   110.26  3.000
 CS4  C1N   C1K  C1J   112.74  3.000
 CS4  C1Q   C1N  O1C   119.86  3.000
 CS4  O1C   C1N  C1K   121.51  3.000
 CS4  C1Q   C1N  C1K   118.63  3.000
 CS4  C1H   C1Q  C1I   119.14  3.000
 CS4  C1I   C1Q  C1N   118.37  3.000
 CS4  C1H   C1Q  C1N   122.46  3.000
 CS4  H1I   C1I  C1P   119.39  3.000
 CS4  H1I   C1I  C1Q   120.15  3.000
 CS4  C1P   C1I  C1Q   120.46  3.000
 CS4  H1H   C1H  C1G   118.24  3.000
 CS4  H1H   C1H  C1Q   121.20  3.000
 CS4  C1G   C1H  C1Q   120.55  3.000
 CS4  H1G   C1G  C1O   119.74  3.000
 CS4  H1G   C1G  C1H   120.25  3.000
 CS4  C1O   C1G  C1H   120.00  3.000
 CS4  C1P   C1O  CL1D  120.66  3.000
 CS4  C1P   C1O  C1G   119.84  3.000
 CS4  CL1D  C1O  C1G   119.50  3.000
 CS4  CL1E  C1P  C1O   120.51  3.000
 CS4  CL1E  C1P  C1I   119.50  3.000
 CS4  C1O   C1P  C1I   119.99  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
 CS4  CONST_01  C1O   C1G  C1H  C1Q    0.00   0.0  0
 CS4  CONST_02  C1O   C1P  C1I  C1Q    0.00   0.0  0
 CS4  CONST_03  C1G   C1H  C1Q  C1I    0.00   0.0  0
 CS4  CONST_04  C1G   C1O  C1P  C1I    0.00   0.0  0
 CS4  CONST_05  C1P   C1I  C1Q  C1H    0.00   0.0  0
 CS4  CONST_06  C1P   C1O  C1G  C1H    0.00   0.0  0
 CS4  CONST_07  C1G   C1H  C1Q  C1N  180.00   0.0  0
 CS4  CONST_08  C1P   C1I  C1Q  C1N  180.00   0.0  0
 CS4  CONST_09  CL1E  C1P  C1I  C1Q  180.00   0.0  0
 CS4  CONST_10  CL1D  C1O  C1P  C1I  180.00   0.0  0
 CS4  CONST_11  CL1D  C1O  C1G  C1H  180.00   0.0  0
 CS4  CONST_12  CL1E  C1P  C1O  C1G  180.00   0.0  0
 CS4  CONST_13  H1G   C1G  C1H  C1Q  180.00   0.0  0
 CS4  CONST_14  H1H   C1H  C1Q  C1I  180.00   0.0  0
 CS4  CONST_15  H1I   C1I  C1Q  C1H  180.00   0.0  0
 CS4  Var_01    C1H   C1Q  C1N  C1K   20.08  30.0  2
 CS4  Var_02    C1Q   C1N  C1K  C1J   64.51  30.0  3
 CS4  Var_03    C1K   C1J  SG   CB    58.43  30.0  3
 CS4  Var_04    C1N   C1K  C1J  SG    50.47  30.0  3
 CS4  Var_05    HB2   CB   SG   C1J  172.88  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
 CS4  chir_01  CA  C  CB  N  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
 CS4  plan-1  C1N   0.020
 CS4  plan-1  C1Q   0.020
 CS4  plan-1  C1I   0.020
 CS4  plan-1  C1H   0.020
 CS4  plan-1  C1G   0.020
 CS4  plan-1  C1O   0.020
 CS4  plan-1  CL1D  0.020
 CS4  plan-1  C1P   0.020
 CS4  plan-1  CL1E  0.020
 CS4  plan-1  H1I   0.020
 CS4  plan-1  H1H   0.020
 CS4  plan-1  H1G   0.020
 CS4  plan-2  C1K   0.020
 CS4  plan-2  C1N   0.020
 CS4  plan-2  O1C   0.020
 CS4  plan-2  C1Q   0.020
 CS4  plan-3  OXT   0.020
 CS4  plan-3  C     0.020
 CS4  plan-3  CA    0.020
 CS4  plan-3  O     0.020

