# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 08:03:49 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: S-methyl-L-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
 CYM  CYM  'S-methyl-L-cysteine      '  L-peptide  16  8  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CYM
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
 CYM  N    N  NH2    0  -0.791  -1.8092   0.1002  -0.5277
 CYM  CA   C  CH1    0  -0.217  -0.3975   0.4233  -0.6070
 CYM  CB   C  CH2    0  -0.545   0.4573  -0.1732   0.5197
 CYM  SG   S  S2     0  -0.061  -0.0645   0.4837   2.1339
 CYM  CD   C  CH3    0  -0.762   0.9011  -0.5769   3.2308
 CYM  C    C  C      0   0.412   0.2124  -0.0483  -1.9532
 CYM  O    O  O      0  -0.598  -0.4294  -0.8917  -2.6059
 CYM  OXT  O  OC    -1  -0.615   1.3203   0.4415  -2.2457
 CYM  HN1  H  HNH2   0   0.330  -2.1320   0.1652   0.4306
 CYM  HN2  H  HNH2   0   0.329  -1.9346  -0.8634  -0.8115
 CYM  HA   H  HCH1   0   0.219  -0.2856   1.5133  -0.5617
 CYM  HB1  H  HCH2   0   0.258   1.5101   0.0650   0.3653
 CYM  HB2  H  HCH2   0   0.251   0.3497  -1.2620   0.5345
 CYM  HD1  H  HCH3   0   0.272   0.6582  -0.3059   4.2566
 CYM  HD2  H  HCH3   0   0.260   0.6533  -1.6268   3.0794
 CYM  HD3  H  HCH3   0   0.259   1.9698  -0.4341   3.0773

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
 CYM  N   CA   single  1.458  0.019  1.458
 CYM  N   HN1  single  0.890  0.020  1.040
 CYM  N   HN2  single  0.890  0.020  1.040
 CYM  CA  CB   single  1.530  0.020  1.530
 CYM  CA  C    single  1.525  0.021  1.525
 CYM  CA  HA   single  0.970  0.020  0.970
 CYM  CB  SG   single  1.819  0.020  1.819
 CYM  CB  HB1  single  0.970  0.020  1.090
 CYM  CB  HB2  single  0.970  0.020  1.090
 CYM  SG  CD   single  1.806  0.020  1.806
 CYM  CD  HD1  single  0.970  0.020  1.090
 CYM  CD  HD2  single  0.970  0.020  1.090
 CYM  CD  HD3  single  0.970  0.020  1.090
 CYM  C   O    deloc   1.231  0.020  1.231
 CYM  C   OXT  deloc   1.246  0.020  1.246

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
 CYM  HN2  N   HN1  106.67  3.000
 CYM  HN2  N   CA   108.50  3.000
 CYM  HN1  N   CA   110.33  3.000
 CYM  HA   CA  C    109.00  3.000
 CYM  HA   CA  CB   109.00  3.000
 CYM  C    CA  CB   110.10  1.900
 CYM  HA   CA  N    110.00  3.000
 CYM  C    CA  N    111.00  2.800
 CYM  CB   CA  N    110.50  1.700
 CYM  HB2  CB  HB1  108.32  3.000
 CYM  HB2  CB  SG   108.61  3.000
 CYM  HB1  CB  SG   108.88  3.000
 CYM  HB2  CB  CA   110.00  3.000
 CYM  HB1  CB  CA   110.42  3.000
 CYM  SG   CB  CA   110.57  3.000
 CYM  CD   SG  CB   100.00  3.000
 CYM  HD3  CD  HD2  109.27  3.000
 CYM  HD3  CD  HD1  108.61  3.000
 CYM  HD2  CD  HD1  108.68  3.000
 CYM  HD3  CD  SG   111.23  3.000
 CYM  HD2  CD  SG   111.11  3.000
 CYM  HD1  CD  SG   107.88  3.000
 CYM  OXT  C   O    126.99  3.000
 CYM  OXT  C   CA   115.70  3.000
 CYM  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
 CYM  Var_01  HD1  CD  SG  CB  -178.35  30.0  3
 CYM  Var_02  HB1  CB  SG  CD   -67.40  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
 CYM  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
 CYM  plan-1  CA   0.020
 CYM  plan-1  C    0.020
 CYM  plan-1  O    0.020
 CYM  plan-1  OXT  0.020

