# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 21:32:02 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: S-methyl hexanethioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC(=O)SC
#
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
 QRL  QRL  'S-methyl hexanethioate   '  ligand  23  9  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_QRL
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
 QRL  CAA   C  CH3   0  -0.663   5.0949  -0.3629   0.0114
 QRL  CAB   C  CH2   0  -0.420   3.8215   0.4713   0.0044
 QRL  CAC   C  CH2   0  -0.411   2.5609  -0.3850   0.0198
 QRL  CAD   C  CH2   0  -0.416   1.2813   0.4424   0.0206
 QRL  CAE   C  CH2   0  -0.537   0.0431  -0.4419   0.0336
 QRL  CAF   C  C     0   0.250  -1.2575   0.3187   0.0353
 QRL  OAG   O  O     0  -0.388  -1.3542   1.5158   0.1153
 QRL  SAH   S  S2    0  -0.006  -2.6757  -0.7399  -0.0869
 QRL  CAI   C  CH3   0  -0.768  -4.0193   0.4629  -0.0328
 QRL  HAA   H  HCH3  0   0.216   5.1449  -0.9952   0.9000
 QRL  HAAA  H  HCH3  0   0.217   5.1407  -1.0176  -0.8611
 QRL  HAAB  H  HCH3  0   0.227   5.9876   0.2634   0.0011
 QRL  HAB   H  HCH2  0   0.213   3.8147   1.1404   0.8703
 QRL  HABA  H  HCH2  0   0.213   3.8091   1.1172  -0.8790
 QRL  HAC   H  HCH2  0   0.213   2.5660  -1.0515  -0.8498
 QRL  HACA  H  HCH2  0   0.213   2.5764  -1.0360   0.9011
 QRL  HAD   H  HCH2  0   0.227   1.2758   1.1029   0.8917
 QRL  HADA  H  HCH2  0   0.227   1.2656   1.0896  -0.8607
 QRL  HAE   H  HCH2  0   0.274   0.0442  -1.1178  -0.8278
 QRL  HAEA  H  HCH2  0   0.280   0.0467  -1.0936   0.9141
 QRL  HAI   H  HCH3  0   0.284  -4.9439  -0.1068  -0.0923
 QRL  HAIA  H  HCH3  0   0.278  -4.0069   1.0217   0.8995
 QRL  HAIB  H  HCH3  0   0.278  -3.9671   1.1448  -0.8775

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
 QRL  CAA  CAB   single  1.522  0.020  1.522
 QRL  CAB  CAC   single  1.524  0.020  1.524
 QRL  CAC  CAD   single  1.524  0.020  1.524
 QRL  CAD  CAE   single  1.522  0.020  1.522
 QRL  CAE  CAF   single  1.507  0.020  1.507
 QRL  CAF  OAG   double  1.204  0.020  1.204
 QRL  CAF  SAH   single  1.774  0.020  1.774
 QRL  SAH  CAI   single  1.804  0.020  1.804
 QRL  CAA  HAA   single  0.970  0.020  1.090
 QRL  CAA  HAAA  single  0.970  0.020  1.090
 QRL  CAA  HAAB  single  0.970  0.020  1.090
 QRL  CAB  HAB   single  0.970  0.020  1.090
 QRL  CAB  HABA  single  0.970  0.020  1.090
 QRL  CAC  HAC   single  0.970  0.020  1.090
 QRL  CAC  HACA  single  0.970  0.020  1.090
 QRL  CAD  HAD   single  0.970  0.020  1.090
 QRL  CAD  HADA  single  0.970  0.020  1.090
 QRL  CAE  HAE   single  0.970  0.020  1.090
 QRL  CAE  HAEA  single  0.970  0.020  1.090
 QRL  CAI  HAI   single  0.970  0.020  1.090
 QRL  CAI  HAIA  single  0.970  0.020  1.090
 QRL  CAI  HAIB  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
 QRL  HAAB  CAA  HAAA  107.61  3.000
 QRL  HAAB  CAA  HAA   107.63  3.000
 QRL  HAAA  CAA  HAA   107.54  3.000
 QRL  HAAB  CAA  CAB   111.71  3.000
 QRL  HAAA  CAA  CAB   111.10  3.000
 QRL  HAA   CAA  CAB   111.07  3.000
 QRL  HABA  CAB  HAB   106.13  3.000
 QRL  HABA  CAB  CAC   109.30  3.000
 QRL  HAB   CAB  CAC   109.29  3.000
 QRL  HABA  CAB  CAA   109.67  3.000
 QRL  HAB   CAB  CAA   109.67  3.000
 QRL  CAC   CAB  CAA   112.58  3.000
 QRL  HACA  CAC  HAC   106.07  3.000
 QRL  HACA  CAC  CAD   109.52  3.000
 QRL  HAC   CAC  CAD   109.55  3.000
 QRL  HACA  CAC  CAB   109.29  3.000
 QRL  HAC   CAC  CAB   109.26  3.000
 QRL  CAD   CAC  CAB   112.92  3.000
 QRL  HADA  CAD  HAD   106.54  3.000
 QRL  HADA  CAD  CAE   109.82  3.000
 QRL  HAD   CAD  CAE   109.89  3.000
 QRL  HADA  CAD  CAC   109.45  3.000
 QRL  HAD   CAD  CAC   109.44  3.000
 QRL  CAE   CAD  CAC   111.57  3.000
 QRL  HAEA  CAE  HAE   105.37  3.000
 QRL  HAEA  CAE  CAF   107.59  3.000
 QRL  HAE   CAE  CAF   108.27  3.000
 QRL  HAEA  CAE  CAD   110.48  3.000
 QRL  HAE   CAE  CAD   110.56  3.000
 QRL  CAF   CAE  CAD   114.14  3.000
 QRL  SAH   CAF  OAG   122.26  3.000
 QRL  SAH   CAF  CAE   112.88  3.000
 QRL  OAG   CAF  CAE   124.86  3.000
 QRL  CAI   SAH  CAF   101.27  3.000
 QRL  HAIB  CAI  HAIA  110.09  3.000
 QRL  HAIB  CAI  HAI   109.09  3.000
 QRL  HAIA  CAI  HAI   109.02  3.000
 QRL  HAIB  CAI  SAH   111.05  3.000
 QRL  HAIA  CAI  SAH   111.09  3.000
 QRL  HAI   CAI  SAH   106.39  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
 QRL  Var_01  CAD  CAC  CAB  CAA   179.69  30.0  3
 QRL  Var_02  CAE  CAD  CAC  CAB   179.89  30.0  3
 QRL  Var_03  CAF  CAE  CAD  CAC   179.98  30.0  3
 QRL  Var_04  OAG  CAF  CAE  CAD    -5.10  30.0  3
 QRL  Var_05  HAA  CAA  CAB  CAC   -59.77  30.0  3
 QRL  Var_06  HAI  CAI  SAH  CAF  -179.40  30.0  3

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
 QRL  plan-1  CAE  0.020
 QRL  plan-1  CAF  0.020
 QRL  plan-1  OAG  0.020
 QRL  plan-1  SAH  0.020

