# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 09:37:18 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  16  8  .  2022-08-09  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_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   3.2289   0.7626   0.6550
 060  N    N  NH2    0  -0.791  -0.5725  -1.7947  -0.1691
 060  S    S  S2     0  -0.061   2.1092  -0.0671  -0.4938
 060  C1   C  CH2    0  -0.546   0.5072   0.4432   0.2006
 060  C2   C  CH1    0  -0.215  -0.6376  -0.3679  -0.4232
 060  C13  C  C      0   0.412  -1.9636   0.2341   0.1086
 060  H    H  HCH3   0   0.260   3.0569   0.4303   1.6780
 060  HA   H  HCH3   0   0.272   4.2481   0.5064   0.3718
 060  HB   H  HCH3   0   0.259   3.1157   1.8447   0.6046
 060  HN   H  HNH2   0   0.331   0.3743  -2.1305  -0.3012
 060  H1   H  HCH2   0   0.252   0.5304   0.2812   1.2824
 060  H1A  H  HCH2   0   0.258   0.3639   1.5088   0.0167
 060  H2   H  HCH1   0   0.219  -0.6080  -0.2045  -1.5065
 060  H3   H  HNH2   0   0.328  -0.8040  -1.9565   0.8031
 060  O4   O  OC    -1  -0.614  -2.3039   1.3253  -0.3874
 060  O5   O  O      0  -0.601  -2.5498  -0.3948   1.0095

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  1.806  0.020  1.806
 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  1.451  0.020  1.451
 060  N    HN   single  0.890  0.020  1.040
 060  S    C1   single  1.819  0.020  1.819
 060  C1   C2   single  1.535  0.020  1.535
 060  C1   H1   single  0.970  0.020  1.090
 060  C1   H1A  single  0.970  0.020  1.090
 060  C2   C13  single  1.550  0.020  1.550
 060  C2   H2   single  0.970  0.020  1.090
 060  C13  O4   deloc   1.246  0.020  1.246
 060  O5   C13  deloc   1.245  0.020  1.245
 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   108.62  3.000
 060  HB   C    H    109.27  3.000
 060  HA   C    H    108.69  3.000
 060  HB   C    S    111.26  3.000
 060  HA   C    S    107.87  3.000
 060  H    C    S    111.06  3.000
 060  H3   N    HN   106.61  3.000
 060  H3   N    C2   108.37  3.000
 060  HN   N    C2   110.18  3.000
 060  C1   S    C    100.04  3.000
 060  H1A  C1   H1   108.31  3.000
 060  H1A  C1   C2   110.47  3.000
 060  H1   C1   C2   109.84  3.000
 060  H1A  C1   S    108.98  3.000
 060  H1   C1   S    108.49  3.000
 060  C2   C1   S    110.69  3.000
 060  H2   C2   C13  107.71  3.000
 060  H2   C2   C1   107.62  3.000
 060  C13  C2   C1   107.05  3.000
 060  H2   C2   N    108.57  3.000
 060  C13  C2   N    111.11  3.000
 060  C1   C2   N    114.52  3.000
 060  O5   C13  O4   127.00  3.000
 060  O5   C13  C2   117.04  3.000
 060  O4   C13  C2   115.92  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  Var_01  C2  C1  S  C   -168.21  30.0  3
 060  Var_02  H   C   S  C1    58.90  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  O4   0.020
 060  plan-1  O5   0.020

