# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 05:45:23 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (2~{S})-2-azanyl-6-sulfanyl-hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCS)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
 QM8  QM8  "6-Sulfanyl-L-norleucine"  L-peptide  22  10  .  2022-08-10  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_QM8
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
 QM8  N    N  NH2    0  -0.785  31.5902  11.0435  69.6711
 QM8  CA   C  CH1    0  -0.215  30.6108   9.9759  69.5284
 QM8  CB   C  CH2    0  -0.435  30.7882   9.2837  68.1736
 QM8  CG   C  CH2    0  -0.403  30.7718  10.2127  66.9630
 QM8  CD   C  CH2    0  -0.434  29.4695  10.9892  66.8119
 QM8  CE   C  CH2    0  -0.542  29.3409  11.7383  65.4945
 QM8  SZ   S  S2     0  -0.272  30.6325  13.0280  65.3752
 QM8  C    C  C      0   0.386  30.6019   8.9133  70.6602
 QM8  O    O  O      0  -0.618  29.6915   8.0597  70.5959
 QM8  OXT  O  OC    -1  -0.603  31.4884   8.9891  71.5336
 QM8  H    H  HNH2   0   0.330  31.4898  11.4509  70.5927
 QM8  H2   H  HNH2   0   0.320  32.5157  10.6287  69.6815
 QM8  HA   H  HCH1   0   0.209  29.6192  10.4460  69.5353
 QM8  HB1  H  HCH2   0   0.215  30.0025   8.5341  68.0607
 QM8  HB2  H  HCH2   0   0.211  31.7371   8.7338  68.1786
 QM8  H7   H  HCH2   0   0.212  30.9296   9.6113  66.0615
 QM8  H8   H  HCH2   0   0.214  31.6157  10.9034  67.0210
 QM8  H9   H  HCH2   0   0.230  29.3456  11.6930  67.6392
 QM8  H10  H  HCH2   0   0.234  28.6262  10.2938  66.8735
 QM8  H11  H  HCH2   0   0.270  28.3649  12.2178  65.4265
 QM8  H12  H  HCH2   0   0.258  29.4425  11.0516  64.6533
 QM8  H13  H  HSH1   0   0.217  30.2164  13.5862  64.2334

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
 QM8  SZ  CE   single  1.829  0.020  1.829
 QM8  CE  CD   single  1.521  0.020  1.521
 QM8  CG  CD   single  1.524  0.020  1.524
 QM8  CG  CB   single  1.526  0.020  1.526
 QM8  CB  CA   single  1.521  0.033  1.521
 QM8  CA  N    single  1.458  0.019  1.458
 QM8  CA  C    single  1.525  0.021  1.525
 QM8  C   O    deloc   1.231  0.020  1.231
 QM8  C   OXT  deloc   1.247  0.020  1.247
 QM8  N   H    single  0.860  0.020  0.860
 QM8  N   H2   single  0.890  0.020  1.040
 QM8  CA  HA   single  0.970  0.020  0.970
 QM8  CB  HB1  single  0.970  0.020  1.090
 QM8  CB  HB2  single  0.970  0.020  1.090
 QM8  CG  H7   single  0.970  0.020  1.090
 QM8  CG  H8   single  0.970  0.020  1.090
 QM8  CD  H9   single  0.970  0.020  1.090
 QM8  CD  H10  single  0.970  0.020  1.090
 QM8  CE  H11  single  0.970  0.020  1.090
 QM8  CE  H12  single  0.970  0.020  1.090
 QM8  SZ  H13  single  1.200  0.020  1.300

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
 QM8  H2   N   H    104.22  3.000
 QM8  H2   N   CA   108.36  3.000
 QM8  H    N   CA   114.00  3.000
 QM8  HA   CA  C    109.00  3.000
 QM8  HA   CA  CB   109.00  3.000
 QM8  C    CA  CB   110.50  1.500
 QM8  HA   CA  N    110.00  3.000
 QM8  C    CA  N    111.00  2.800
 QM8  CB   CA  N    110.40  1.500
 QM8  HB2  CB  HB1  106.19  3.000
 QM8  HB2  CB  CG   108.55  3.000
 QM8  HB1  CB  CG   109.16  3.000
 QM8  HB2  CB  CA   108.83  3.000
 QM8  HB1  CB  CA   108.57  3.000
 QM8  CG   CB  CA   115.17  3.000
 QM8  H8   CG  H7   106.24  3.000
 QM8  H8   CG  CD   110.08  3.000
 QM8  H7   CG  CD   108.74  3.000
 QM8  H8   CG  CB   109.55  3.000
 QM8  H7   CG  CB   108.50  3.000
 QM8  CD   CG  CB   113.46  3.000
 QM8  H10  CD  H9   106.20  3.000
 QM8  H10  CD  CE   107.25  3.000
 QM8  H9   CD  CE   109.20  3.000
 QM8  H10  CD  CG   109.21  3.000
 QM8  H9   CD  CG   110.48  3.000
 QM8  CE   CD  CG   114.16  3.000
 QM8  H12  CE  H11  108.20  3.000
 QM8  H12  CE  SZ   109.14  3.000
 QM8  H11  CE  SZ   108.55  3.000
 QM8  H12  CE  CD   110.49  3.000
 QM8  H11  CE  CD   110.28  3.000
 QM8  SZ   CE  CD   110.13  3.000
 QM8  H13  SZ  CE    97.49  3.000
 QM8  OXT  C   O    126.56  3.000
 QM8  OXT  C   CA   117.71  3.000
 QM8  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
 QM8  Var_01  CD   CG  CB  CA   -60.34  30.0  1
 QM8  Var_02  CE   CD  CG  CB  -170.26  30.0  3
 QM8  Var_03  SZ   CE  CD  CG   -63.78  30.0  1
 QM8  Var_04  H7   CG  CB  CA   178.70  30.0  1
 QM8  Var_05  H8   CG  CB  CA    63.12  30.0  1
 QM8  Var_06  H9   CD  CG  CB    66.22  30.0  3
 QM8  Var_07  H10  CD  CG  CB   -50.23  30.0  3
 QM8  Var_08  H11  CE  CD  CG   176.44  30.0  1
 QM8  Var_09  H12  CE  CD  CG    56.87  30.0  1
 QM8  Var_10  HB1  CB  CG  CD    62.06  30.0  3
 QM8  Var_11  HB2  CB  CG  CD   177.39  30.0  3
 QM8  Var_12  H7   CG  CD  CE   -49.44  30.0  1
 QM8  Var_13  H8   CG  CD  CE    66.57  30.0  1
 QM8  Var_14  H9   CD  CE  SZ    60.43  30.0  3
 QM8  Var_15  H10  CD  CE  SZ   175.09  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
 QM8  chir_01  CA  CB  N  C  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
 QM8  plan-1  CA   0.020
 QM8  plan-1  C    0.020
 QM8  plan-1  O    0.020
 QM8  plan-1  OXT  0.020

