# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 17:41:21 2022
#   Inital geometry file: a 44 line input string
#   Ligand name: 2-methyl-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](N)(CS)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
 03Y  03Y  '2-methyl-L-cysteine      '  L-peptide  16  8  .  2012-08-28  2022-03-09
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_03Y
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
 03Y  CB    C  CH2    0  -0.514  -2.3161  -41.0256  21.0635
 03Y  C     C  C      0   0.405  -0.7165  -39.2439  21.8008
 03Y  CA    C  CT     0  -0.053  -1.9997  -39.5307  20.9549
 03Y  CM    C  CH3    0  -0.637  -3.1925  -38.7649  21.5273
 03Y  N     N  NH2    0  -0.781  -1.8837  -39.1843  19.5427
 03Y  O     O  O      0  -0.603  -0.8385  -39.3519  23.0375
 03Y  SG    S  S2     0  -0.274  -0.9077  -42.0402  20.4725
 03Y  HB2   H  HCH2   0   0.257  -2.5314  -41.2890  22.0977
 03Y  HB3   H  HCH2   0   0.261  -3.1879  -41.2605  20.4522
 03Y  H21   H  HCH3   0   0.222  -3.0238  -37.6867  21.4706
 03Y  H21A  H  HCH3   0   0.215  -4.0990  -38.9887  20.9616
 03Y  H21B  H  HCH3   0   0.223  -3.3660  -39.0196  22.5704
 03Y  H     H  HNH2   0   0.329  -1.7248  -38.1851  19.4745
 03Y  H2    H  HNH2   0   0.329  -1.0325  -39.5962  19.1788
 03Y  HG    H  HSH1   0   0.214  -1.5836  -43.1831  20.3122
 03Y  OXT   O  OC    -1  -0.592   0.3229  -38.9624  21.1741

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
 03Y  CB  HB2   single  0.970  0.020  1.090
 03Y  CB  HB3   single  0.970  0.020  1.090
 03Y  C   O     deloc   1.231  0.020  1.231
 03Y  CA  CB    single  1.530  0.020  1.530
 03Y  CA  C     single  1.525  0.021  1.525
 03Y  CA  CM    single  1.529  0.020  1.529
 03Y  CM  H21   single  0.970  0.020  1.090
 03Y  CM  H21A  single  0.970  0.020  1.090
 03Y  CM  H21B  single  0.970  0.020  1.090
 03Y  N   CA    single  1.458  0.019  1.458
 03Y  N   H     single  0.860  0.020  0.860
 03Y  N   H2    single  0.890  0.020  1.040
 03Y  SG  CB    single  1.834  0.020  1.834
 03Y  SG  HG    single  1.200  0.020  1.300
 03Y  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
 03Y  HB3   CB  HB2   108.81  3.000
 03Y  HB3   CB  SG    108.31  3.000
 03Y  HB2   CB  SG    108.92  3.000
 03Y  SG    CB  CA    111.00  3.000
 03Y  HB3   CB  CA    109.61  3.000
 03Y  HB2   CB  CA    110.13  3.000
 03Y  OXT   C   O     126.86  3.000
 03Y  OXT   C   CA    117.00  3.000
 03Y  O     C   CA    120.80  1.700
 03Y  N     CA  CM    107.79  3.000
 03Y  N     CA  C     111.00  2.800
 03Y  CM    CA  C     110.24  3.000
 03Y  N     CA  CB    110.50  1.700
 03Y  CM    CA  CB    107.53  3.000
 03Y  C     CA  CB    110.10  1.900
 03Y  H21B  CM  H21A  108.45  3.000
 03Y  H21B  CM  H21   107.79  3.000
 03Y  H21A  CM  H21   107.67  3.000
 03Y  H21B  CM  CA    111.48  3.000
 03Y  H21A  CM  CA    110.56  3.000
 03Y  H21   CM  CA    110.76  3.000
 03Y  H2    N   H     104.17  3.000
 03Y  H2    N   CA    108.54  3.000
 03Y  H     N   CA    114.00  3.000
 03Y  HG    SG  CB     97.08  3.000

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
 03Y  chir_01  CA  C  CM  N  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
 03Y  plan-1  C    0.020
 03Y  plan-1  CA   0.020
 03Y  plan-1  O    0.020
 03Y  plan-1  OXT  0.020

