# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 22:19:39 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: S-(3-oxo-3-thiophen-2-ylpropyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSCCC(=O)c1sccc1)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
 CS3  CS3  S-(3-oxo-3-thiophen-2-ylpropyl)-L-cysteine  L-peptide  28  16  .  2012-08-28  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_CS3
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
 CS3  OXT   O  OC    -1  -0.601  12.1495   9.6128   1.8518
 CS3  C     C  C      0   0.402  11.1544  10.0927   1.2754
 CS3  CA    C  CH1    0  -0.229  10.2192   9.0815   0.5539
 CS3  N     N  NH2    0  -0.784  10.2119   7.7407   1.1232
 CS3  CB    C  CH2    0  -0.537   8.8014   9.6126   0.4327
 CS3  SG    S  S2     0  -0.031   8.0955  10.0230   2.0669
 CS3  C1H   C  CH2    0  -0.575   6.6014   8.9973   2.0928
 CS3  C1I   C  CH2    0  -0.571   6.8859   7.5045   2.2783
 CS3  C1L   C  C      0   0.382   5.5907   6.7268   2.2582
 CS3  O1C   O  O      0  -0.387   5.1424   6.2674   1.2272
 CS3  C1M   C  CR5    0  -0.303   4.8428   6.5859   3.5142
 CS3  C1G   C  CR15   0  -0.180   3.5986   6.0236   3.6549
 CS3  S1K   S  S2     0   0.252   5.4368   7.1396   5.0366
 CS3  C1F   C  CR15   0  -0.443   4.0307   6.6190   5.8419
 CS3  C1E   C  CR15   0  -0.173   3.1335   6.0426   4.9863
 CS3  O     O  O      0  -0.602  10.8462  11.2988   1.1869
 CS3  HA    H  HCH1   0   0.233  10.5976   8.9910  -0.4748
 CS3  H     H  HNH2   0   0.335  11.1763   7.4709   1.2776
 CS3  H2    H  HNH2   0   0.329   9.8183   7.8036   2.0573
 CS3  HB2   H  HCH2   0   0.265   8.7812  10.5130  -0.1764
 CS3  HB3   H  HCH2   0   0.264   8.1542   8.8751  -0.0445
 CS3  H1H1  H  HCH2   0   0.278   6.0324   9.1701   1.1778
 CS3  H1H2  H  HCH2   0   0.280   6.0013   9.3804   2.9203
 CS3  H1I1  H  HCH2   0   0.259   7.4323   7.3550   3.2125
 CS3  H1I2  H  HCH2   0   0.279   7.5220   7.1416   1.4694
 CS3  H1G   H  HCR5   0   0.277   3.0406   5.6148   2.8247
 CS3  H1F   H  HCR5   0   0.308   3.9317   6.7576   6.9079
 CS3  H1E   H  HCR5   0   0.276   2.1798   5.6465   5.3030

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
 CS3  OXT  C     deloc     1.246  0.020  1.246
 CS3  C    O     deloc     1.231  0.020  1.231
 CS3  C    CA    single    1.525  0.021  1.525
 CS3  CA   CB    single    1.530  0.020  1.530
 CS3  CA   N     single    1.458  0.019  1.458
 CS3  CA   HA    single    0.970  0.020  0.970
 CS3  N    H     single    0.860  0.020  0.860
 CS3  N    H2    single    0.890  0.020  1.040
 CS3  CB   SG    single    1.827  0.020  1.827
 CS3  CB   HB2   single    0.970  0.020  1.090
 CS3  CB   HB3   single    0.970  0.020  1.090
 CS3  SG   C1H   single    1.812  0.020  1.812
 CS3  C1H  C1I   single    1.531  0.020  1.531
 CS3  C1H  H1H1  single    0.970  0.020  1.090
 CS3  C1H  H1H2  single    0.970  0.020  1.090
 CS3  C1I  C1L   single    1.511  0.020  1.511
 CS3  C1I  H1I1  single    0.970  0.020  1.090
 CS3  C1I  H1I2  single    0.970  0.020  1.090
 CS3  C1L  O1C   double    1.214  0.020  1.214
 CS3  C1L  C1M   single    1.469  0.020  1.469
 CS3  C1M  C1G   aromatic  1.373  0.020  1.373
 CS3  C1M  S1K   aromatic  1.725  0.020  1.725
 CS3  C1G  C1E   aromatic  1.410  0.020  1.410
 CS3  C1G  H1G   single    0.930  0.020  1.080
 CS3  S1K  C1F   aromatic  1.702  0.020  1.702
 CS3  C1F  C1E   aromatic  1.367  0.020  1.367
 CS3  C1F  H1F   single    0.930  0.020  1.080
 CS3  C1E  H1E   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
 CS3  O     C    CA    120.80  1.700
 CS3  CA    C    OXT   116.39  3.000
 CS3  O     C    OXT   127.03  3.000
 CS3  HA    CA   CB    109.00  3.000
 CS3  HA    CA   N     110.00  3.000
 CS3  CB    CA   N     110.50  1.700
 CS3  HA    CA   C     109.00  3.000
 CS3  N     CA   C     111.00  2.800
 CS3  CB    CA   C     110.10  1.900
 CS3  H2    N    H     104.20  3.000
 CS3  H2    N    CA    107.73  3.000
 CS3  H     N    CA    114.00  3.000
 CS3  HB3   CB   HB2   107.68  3.000
 CS3  HB3   CB   SG    108.29  3.000
 CS3  HB2   CB   SG    107.94  3.000
 CS3  HB3   CB   CA    110.62  3.000
 CS3  HB2   CB   CA    110.59  3.000
 CS3  SG    CB   CA    111.59  3.000
 CS3  C1H   SG   CB    101.78  3.000
 CS3  H1H2  C1H  H1H1  107.06  3.000
 CS3  H1H2  C1H  C1I   110.64  3.000
 CS3  H1H1  C1H  C1I   110.67  3.000
 CS3  H1H2  C1H  SG    105.39  3.000
 CS3  H1H1  C1H  SG    109.16  3.000
 CS3  C1I   C1H  SG    113.60  3.000
 CS3  H1I2  C1I  H1I1  107.27  3.000
 CS3  H1I2  C1I  C1L   108.58  3.000
 CS3  H1I1  C1I  C1L   111.69  3.000
 CS3  H1I2  C1I  C1H   110.05  3.000
 CS3  H1I1  C1I  C1H   109.27  3.000
 CS3  C1L   C1I  C1H   109.94  3.000
 CS3  C1M   C1L  O1C   120.12  3.000
 CS3  C1M   C1L  C1I   118.33  3.000
 CS3  O1C   C1L  C1I   121.49  3.000
 CS3  S1K   C1M  C1G   110.67  3.000
 CS3  S1K   C1M  C1L   123.26  3.000
 CS3  C1G   C1M  C1L   126.06  3.000
 CS3  H1G   C1G  C1E   124.06  3.000
 CS3  H1G   C1G  C1M   122.97  3.000
 CS3  C1E   C1G  C1M   112.97  3.000
 CS3  C1F   S1K  C1M    92.00  3.000
 CS3  H1F   C1F  C1E   127.72  3.000
 CS3  H1F   C1F  S1K   120.25  3.000
 CS3  C1E   C1F  S1K   112.03  3.000
 CS3  H1E   C1E  C1F   123.41  3.000
 CS3  H1E   C1E  C1G   124.26  3.000
 CS3  C1F   C1E  C1G   112.33  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
 CS3  CONST_01  C1F  C1E  C1G  C1M     0.00   0.0  0
 CS3  CONST_02  C1E  C1F  S1K  C1M     0.00   0.0  0
 CS3  CONST_03  C1F  S1K  C1M  C1G     0.00   0.0  0
 CS3  CONST_04  S1K  C1F  C1E  C1G     0.00   0.0  0
 CS3  CONST_05  C1E  C1G  C1M  S1K     0.00   0.0  0
 CS3  CONST_06  C1E  C1G  C1M  C1L   180.00   0.0  0
 CS3  CONST_07  C1F  S1K  C1M  C1L   180.00   0.0  0
 CS3  CONST_08  H1E  C1E  C1G  C1M   180.00   0.0  0
 CS3  CONST_09  H1F  C1F  S1K  C1M   180.00   0.0  0
 CS3  CONST_10  H1G  C1G  C1M  S1K   180.00   0.0  0
 CS3  Var_01    C1G  C1M  C1L  C1I   173.65  30.0  2
 CS3  Var_02    C1M  C1L  C1I  C1H   -85.89  30.0  3
 CS3  Var_03    C1I  C1H  SG   CB     72.87  30.0  3
 CS3  Var_04    C1L  C1I  C1H  SG   -178.80  30.0  3
 CS3  Var_05    HB2  CB   SG   C1H   115.33  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
 CS3  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
 CS3  plan-1  C1L  0.020
 CS3  plan-1  C1M  0.020
 CS3  plan-1  C1G  0.020
 CS3  plan-1  S1K  0.020
 CS3  plan-1  C1F  0.020
 CS3  plan-1  C1E  0.020
 CS3  plan-1  H1G  0.020
 CS3  plan-1  H1F  0.020
 CS3  plan-1  H1E  0.020
 CS3  plan-2  C1I  0.020
 CS3  plan-2  C1L  0.020
 CS3  plan-2  O1C  0.020
 CS3  plan-2  C1M  0.020
 CS3  plan-3  OXT  0.020
 CS3  plan-3  C    0.020
 CS3  plan-3  CA   0.020
 CS3  plan-3  O    0.020

