# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 15:51:27 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: S-(carboxymethyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSCC(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
 CCS  CCS  S-(carboxymethyl)-L-cysteine  L-peptide  18  11  .  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_CCS
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
 CCS  N    N  NH2    0  -0.798  -17.3638  11.7018  12.2023
 CCS  CA   C  CH1    0  -0.220  -16.3001  12.0324  11.2701
 CCS  CB   C  CH2    0  -0.509  -14.9953  11.4064  11.7369
 CCS  SG   S  S2     0  -0.061  -15.1912   9.6120  11.9418
 CCS  CD   C  CH2    0  -0.695  -13.4805   9.0691  11.7362
 CCS  CE   C  C      0   0.419  -12.4717   9.4562  12.8454
 CCS  OZ1  O  O      0  -0.588  -12.8969  10.0103  13.8718
 CCS  OZ2  O  OC    -1  -0.617  -11.2924   9.1454  12.5825
 CCS  C    C  C      0   0.411  -16.6696  11.6226   9.8199
 CCS  O    O  O      0  -0.607  -15.7433  11.6559   8.9872
 CCS  OXT  O  OC    -1  -0.602  -17.8652  11.3490   9.5967
 CCS  H    H  HNH2   0   0.334  -18.2518  11.9140  11.7689
 CCS  H2   H  HNH2   0   0.330  -17.2894  12.2725  13.0344
 CCS  HA   H  HCH1   0   0.209  -16.1104  13.1203  11.2239
 CCS  HB2  H  HCH2   0   0.242  -14.2115  11.5910  11.0026
 CCS  HB3  H  HCH2   0   0.240  -14.6748  11.8423  12.6846
 CCS  HD2  H  HCH2   0   0.262  -13.5213   7.9774  11.6718
 CCS  HD3  H  HCH2   0   0.248  -13.1044   9.4107  10.7677

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
 CCS  N   CA   single  1.458  0.019  1.458
 CCS  N   H    single  0.860  0.020  0.860
 CCS  N   H2   single  0.890  0.020  1.040
 CCS  CA  CB   single  1.530  0.020  1.530
 CCS  CA  C    single  1.525  0.021  1.525
 CCS  CA  HA   single  0.970  0.020  0.970
 CCS  CB  SG   single  1.817  0.020  1.817
 CCS  CB  HB2  single  0.970  0.020  1.090
 CCS  CB  HB3  single  0.970  0.020  1.090
 CCS  SG  CD   single  1.807  0.020  1.807
 CCS  CD  CE   single  1.548  0.020  1.548
 CCS  CD  HD2  single  0.970  0.020  1.090
 CCS  CD  HD3  single  0.970  0.020  1.090
 CCS  CE  OZ1  deloc   1.242  0.020  1.242
 CCS  CE  OZ2  deloc   1.248  0.020  1.248
 CCS  C   O    deloc   1.231  0.020  1.231
 CCS  C   OXT  deloc   1.247  0.020  1.247

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
 CCS  H2   N   H    107.38  3.000
 CCS  H2   N   CA   110.22  3.000
 CCS  H    N   CA   114.00  3.000
 CCS  HA   CA  C    109.00  3.000
 CCS  HA   CA  CB   109.00  3.000
 CCS  C    CA  CB   110.10  1.900
 CCS  HA   CA  N    110.00  3.000
 CCS  C    CA  N    111.00  2.800
 CCS  CB   CA  N    110.50  1.700
 CCS  HB3  CB  HB2  107.84  3.000
 CCS  HB3  CB  SG   109.16  3.000
 CCS  HB2  CB  SG   108.72  3.000
 CCS  HB3  CB  CA   110.75  3.000
 CCS  HB2  CB  CA   109.91  3.000
 CCS  SG   CB  CA   110.40  3.000
 CCS  CD   SG  CB   100.48  3.000
 CCS  HD3  CD  HD2  105.80  3.000
 CCS  HD3  CD  CE   109.41  3.000
 CCS  HD2  CD  CE   108.41  3.000
 CCS  HD3  CD  SG   109.43  3.000
 CCS  HD2  CD  SG   105.73  3.000
 CCS  CE   CD  SG   117.40  3.000
 CCS  OZ2  CE  OZ1  127.53  3.000
 CCS  OZ2  CE  CD   113.74  3.000
 CCS  OZ1  CE  CD   118.73  3.000
 CCS  OXT  C   O    126.81  3.000
 CCS  OXT  C   CA   116.98  3.000
 CCS  O    C   CA   120.80  1.700

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
 CCS  Var_01  CE   CD  SG  CB  68.49  30.0  3
 CCS  Var_02  OZ1  CE  CD  SG   6.32  30.0  3
 CCS  Var_03  HB2  CB  SG  CD  34.75  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
 CCS  chir_01  CA  N  CB  C  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
 CCS  plan-1  CD   0.020
 CCS  plan-1  CE   0.020
 CCS  plan-1  OZ1  0.020
 CCS  plan-1  OZ2  0.020
 CCS  plan-2  CA   0.020
 CCS  plan-2  C    0.020
 CCS  plan-2  O    0.020
 CCS  plan-2  OXT  0.020

