# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 18:05:42 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: S-methyl-D-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSC[C@@H](N)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
 060  060  'S-methyl-D-cysteine      '  D-peptide  17  8  .  2022-08-09  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_060
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
 060  C    C  CH3   0  -0.762   3.1932   0.8109   0.5939
 060  N    N  NH2   0  -0.775  -0.6453  -1.8350  -0.1656
 060  S    S  S2    0  -0.042   2.0841  -0.2015  -0.4074
 060  C1   C  CH2   0  -0.551   0.4911   0.3834   0.2372
 060  C2   C  CH1   0  -0.227  -0.6526  -0.4133  -0.4162
 060  C13  C  C     0   0.554  -1.9740   0.1691   0.0554
 060  H    H  HCH3  0   0.264   3.0574   0.6092   1.6555
 060  HA   H  HCH3  0   0.277   4.2135   0.5527   0.3173
 060  HB   H  HCH3  0   0.264   3.0381   1.8718   0.4036
 060  HN   H  HNH2  0   0.358   0.1877  -2.2484  -0.5635
 060  H1   H  HCH2  0   0.270   0.4696   0.2440   1.3215
 060  H1A  H  HCH2  0   0.277   0.3983   1.4499   0.0290
 060  H2   H  HCH1  0   0.285  -0.5971  -0.2580  -1.4988
 060  HO4  H  HOH1  0   0.484  -2.9951   1.7593  -0.0670
 060  H3   H  HNH2  0   0.348  -0.6066  -2.0172   0.8301
 060  O4   O  OH1   0  -0.592  -2.1649   1.3965  -0.4111
 060  O5   O  O     0  -0.431  -2.7495  -0.3970   0.7807

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
 060  C    S    single  1.805  0.020  1.805
 060  C    H    single  0.970  0.020  1.090
 060  C    HA   single  0.970  0.020  1.090
 060  C    HB   single  0.970  0.020  1.090
 060  C2   N    single  1.444  0.020  1.444
 060  N    HN   single  0.890  0.020  1.040
 060  S    C1   single  1.815  0.020  1.815
 060  C1   C2   single  1.539  0.020  1.539
 060  C1   H1   single  0.970  0.020  1.090
 060  C1   H1A  single  0.970  0.020  1.090
 060  C2   C13  single  1.519  0.020  1.519
 060  C2   H2   single  0.970  0.020  1.090
 060  C13  O4   single  1.327  0.020  1.327
 060  O4   HO4  single  0.850  0.020  0.980
 060  O5   C13  double  1.203  0.020  1.203
 060  N    H3   single  0.890  0.020  1.040

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
 060  HB   C    HA   108.68  3.000
 060  HB   C    H    109.45  3.000
 060  HA   C    H    108.71  3.000
 060  HB   C    S    111.22  3.000
 060  HA   C    S    107.58  3.000
 060  H    C    S    111.12  3.000
 060  H3   N    HN   106.36  3.000
 060  H3   N    C2   110.37  3.000
 060  HN   N    C2   109.77  3.000
 060  C1   S    C     99.29  3.000
 060  H1A  C1   H1   108.20  3.000
 060  H1A  C1   C2   111.21  3.000
 060  H1   C1   C2   109.90  3.000
 060  H1A  C1   S    108.78  3.000
 060  H1   C1   S    109.17  3.000
 060  C2   C1   S    109.54  3.000
 060  H2   C2   C13  107.26  3.000
 060  H2   C2   C1   107.97  3.000
 060  C13  C2   C1   108.42  3.000
 060  H2   C2   N    108.12  3.000
 060  C13  C2   N    109.15  3.000
 060  C1   C2   N    115.61  3.000
 060  O5   C13  O4   123.67  3.000
 060  O5   C13  C2   124.56  3.000
 060  O4   C13  C2   111.75  3.000
 060  HO4  O4   C13  110.17  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
 060  CONST_01  HO4  O4  C13  C2   180.00   0.0  0
 060  Var_01    C2   C1  S    C   -176.50  30.0  3
 060  Var_02    H    C   S    C1    60.45  30.0  3

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
 060  chir_01  C2  N  C1  C13  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
 060  plan-1  C2   0.020
 060  plan-1  C13  0.020
 060  plan-1  HO4  0.020
 060  plan-1  O4   0.020
 060  plan-1  O5   0.020

