# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:02:26 2022
#   Inital geometry file: a 44 line input string
#   Ligand name: methyl L-cysteinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](N)CS
#
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
 CMT  CMT  'methyl L-cysteinate      '  L-peptide  17  8  .  2012-08-28  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CMT
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
 CMT  N    N  NH2   0  -0.780  64.8298  18.2731  40.4783
 CMT  CA   C  CH1   0  -0.226  63.9666  19.4316  40.5296
 CMT  C    C  C     0   0.617  64.4955  20.4782  41.5070
 CMT  O    O  O     0  -0.438  65.8121  20.5792  41.4819
 CMT  CB   C  CH2   0  -0.553  62.4971  19.1475  40.8475
 CMT  SG   S  S2    0  -0.259  61.8670  17.9314  39.6396
 CMT  OXT  O  O2    0  -0.444  63.7870  21.1684  42.1966
 CMT  C1   C  CH3   0  -0.424  66.4061  21.5749  42.3148
 CMT  H    H  HNH2  0   0.362  64.6535  17.7330  39.6421
 CMT  H2   H  HNH2  0   0.352  64.6641  17.6630  41.2695
 CMT  HA   H  HCH1  0   0.289  64.0084  19.9098  39.5431
 CMT  HB2  H  HCH2  0   0.269  62.3920  18.7486  41.8574
 CMT  HB3  H  HCH2  0   0.280  61.8993  20.0532  40.7706
 CMT  HG   H  HSH1  0   0.227  60.5677  18.2033  39.7959
 CMT  H11  H  HCH3  0   0.238  66.1857  21.3983  43.3673
 CMT  H12  H  HCH3  0   0.250  67.4773  21.4976  42.1532
 CMT  H13  H  HCH3  0   0.238  66.0710  22.5756  42.0422

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
 CMT  N    CA   single  1.458  0.019  1.458
 CMT  N    H    single  0.860  0.020  0.860
 CMT  N    H2   single  0.890  0.020  1.040
 CMT  CA   C    single  1.525  0.021  1.525
 CMT  CA   CB   single  1.530  0.020  1.530
 CMT  CA   HA   single  0.970  0.020  0.970
 CMT  C    O    double  1.231  0.020  1.231
 CMT  C    OXT  single  1.206  0.020  1.206
 CMT  CB   SG   single  1.826  0.020  1.826
 CMT  CB   HB2  single  0.970  0.020  1.090
 CMT  CB   HB3  single  0.970  0.020  1.090
 CMT  SG   HG   single  1.200  0.020  1.300
 CMT  OXT  C1   single  2.653  0.020  2.653
 CMT  C1   H11  single  0.970  0.020  1.090
 CMT  C1   H12  single  0.970  0.020  1.090
 CMT  C1   H13  single  0.970  0.020  1.090

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
 CMT  H2   N    H    107.21  3.000
 CMT  H2   N    CA   110.94  3.000
 CMT  H    N    CA   114.00  3.000
 CMT  HA   CA   CB   109.00  3.000
 CMT  HA   CA   C    109.00  3.000
 CMT  CB   CA   C    110.10  1.900
 CMT  HA   CA   N    110.00  3.000
 CMT  CB   CA   N    110.50  1.700
 CMT  C    CA   N    111.00  2.800
 CMT  OXT  C    O    123.56  3.000
 CMT  OXT  C    CA   123.72  3.000
 CMT  O    C    CA   120.80  1.700
 CMT  HB3  CB   HB2  108.47  3.000
 CMT  HB3  CB   SG   108.55  3.000
 CMT  HB2  CB   SG   109.61  3.000
 CMT  HB3  CB   CA   111.01  3.000
 CMT  HB2  CB   CA   110.65  3.000
 CMT  SG   CB   CA   108.52  3.000
 CMT  HG   SG   CB    97.04  3.000
 CMT  C1   OXT  C     62.17  3.000
 CMT  H13  C1   H12  109.35  3.000
 CMT  H13  C1   H11  109.16  3.000
 CMT  H12  C1   H11  109.37  3.000
 CMT  H13  C1   OXT   79.98  3.000
 CMT  H12  C1   OXT  162.97  3.000
 CMT  H11  C1   OXT   79.54  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
 CMT  Var_01  H11  C1  OXT  C  -124.59  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
 CMT  chir_01  CA  N  C  CB  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
 CMT  plan-1  CA   0.020
 CMT  plan-1  C    0.020
 CMT  plan-1  O    0.020
 CMT  plan-1  OXT  0.020

