# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 19:05:34 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: S-[(2R)-2-hydroxypropanoyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)C(=O)SC[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
 CYW  CYW  S-[(2R)-2-hydroxypropanoyl]-L-cysteine  L-peptide  22  12  .  2012-08-28  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_CYW
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
 CYW  C    C  C      0   0.420   1.2800  14.4038  5.3299
 CYW  N    N  NH2    0  -0.801   1.1137  11.9871  5.8176
 CYW  O    O  O      0  -0.596   2.4806  14.3275  5.6526
 CYW  CA   C  CH1    0  -0.219   0.5662  13.0624  5.0141
 CYW  CB   C  CH2    0  -0.553  -0.9442  13.1498  5.1792
 CYW  SG   S  S2     0  -0.006  -1.3595  13.7681  6.8438
 CYW  HN   H  HNH2   0   0.334   0.9651  11.0972  5.3606
 CYW  C1   C  C      0   0.264  -2.5978  12.7856  7.6204
 CYW  O1   O  O      0  -0.399  -2.9596  13.1662  8.7096
 CYW  C2   C  CH1    0  -0.051  -3.2444  11.5703  6.9700
 CYW  O2   O  OH1    0  -0.652  -2.2335  10.6916  6.5475
 CYW  C3   C  CH3    0  -0.710  -4.1882  12.0062  5.8556
 CYW  OXT  O  OC    -1  -0.594   0.5988  15.4374  5.1928
 CYW  HNA  H  HNH2   0   0.337   2.1134  12.1245  5.8838
 CYW  HA   H  HCH1   0   0.225   0.7207  12.8954  3.9325
 CYW  HB   H  HCH2   0   0.264  -1.3713  13.8458  4.4606
 CYW  HBA  H  HCH2   0   0.283  -1.3959  12.1754  5.0246
 CYW  H2   H  HCH1   0   0.245  -3.8473  11.1139  7.7660
 CYW  HO2  H  HOH1   0   0.460  -2.6480   9.9555  6.0847
 CYW  H3   H  HCH3   0   0.253  -4.6994  11.1340  5.4446
 CYW  H3A  H  HCH3   0   0.246  -4.9522  12.6802  6.2434
 CYW  H3B  H  HCH3   0   0.249  -3.6671  12.5102  5.0426

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
 CYW  C   CA   single  1.525  0.021  1.525
 CYW  C   O    deloc   1.231  0.020  1.231
 CYW  C   OXT  deloc   1.245  0.020  1.245
 CYW  N   HN   single  0.890  0.020  1.040
 CYW  N   HNA  single  0.890  0.020  1.040
 CYW  CA  N    single  1.458  0.019  1.458
 CYW  CA  HA   single  0.970  0.020  0.970
 CYW  CB  CA   single  1.530  0.020  1.530
 CYW  CB  SG   single  1.824  0.020  1.824
 CYW  CB  HB   single  0.970  0.020  1.090
 CYW  CB  HBA  single  0.970  0.020  1.090
 CYW  SG  C1   single  1.761  0.020  1.761
 CYW  C1  O1   double  1.209  0.020  1.209
 CYW  C2  C1   single  1.523  0.020  1.523
 CYW  C2  H2   single  0.970  0.020  1.090
 CYW  O2  C2   single  1.404  0.020  1.404
 CYW  O2  HO2  single  0.850  0.020  0.980
 CYW  C3  C2   single  1.524  0.020  1.524
 CYW  C3  H3   single  0.970  0.020  1.090
 CYW  C3  H3A  single  0.970  0.020  1.090
 CYW  C3  H3B  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
 CYW  OXT  C   CA   116.32  3.000
 CYW  OXT  C   O    127.34  3.000
 CYW  CA   C   O    120.80  1.700
 CYW  HNA  N   HN   107.12  3.000
 CYW  HNA  N   CA   108.00  3.000
 CYW  HN   N   CA   110.29  3.000
 CYW  HA   CA  CB   109.00  3.000
 CYW  CB   CA  N    110.50  1.700
 CYW  HA   CA  N    110.00  3.000
 CYW  CB   CA  C    110.10  1.900
 CYW  HA   CA  C    109.00  3.000
 CYW  N    CA  C    111.00  2.800
 CYW  HBA  CB  HB   108.48  3.000
 CYW  HBA  CB  SG   109.86  3.000
 CYW  HB   CB  SG   107.26  3.000
 CYW  HBA  CB  CA   110.25  3.000
 CYW  HB   CB  CA   110.78  3.000
 CYW  SG   CB  CA   110.15  3.000
 CYW  C1   SG  CB   111.93  3.000
 CYW  C2   C1  O1   120.60  3.000
 CYW  C2   C1  SG   123.74  3.000
 CYW  O1   C1  SG   115.59  3.000
 CYW  H2   C2  C3   108.00  3.000
 CYW  C3   C2  O2   113.88  3.000
 CYW  H2   C2  O2   110.68  3.000
 CYW  C3   C2  C1   110.31  3.000
 CYW  O2   C2  C1   108.80  3.000
 CYW  H2   C2  C1   104.79  3.000
 CYW  HO2  O2  C2   108.24  3.000
 CYW  H3B  C3  H3A  108.34  3.000
 CYW  H3B  C3  H3   108.23  3.000
 CYW  H3A  C3  H3   107.45  3.000
 CYW  H3B  C3  C2   112.45  3.000
 CYW  H3A  C3  C2   110.54  3.000
 CYW  H3   C3  C2   109.69  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
 CYW  Var_01  O1  C1  SG  CB  -177.37  30.0  3
 CYW  Var_02  HB  CB  SG  C1   107.16  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
 CYW  chir_01  CA  C   N   CB  negativ
 CYW  chir_02  C2  O2  C1  C3  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
 CYW  plan-1  C    0.020
 CYW  plan-1  O    0.020
 CYW  plan-1  CA   0.020
 CYW  plan-1  OXT  0.020
 CYW  plan-2  SG   0.020
 CYW  plan-2  C1   0.020
 CYW  plan-2  O1   0.020
 CYW  plan-2  C2   0.020

