# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 15:22:54 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: 3-hydroxy-2-methyl-4H-pyran-4-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(O)C(=S)C=CO1
#
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
 TM4  TM4  3-hydroxy-2-methyl-4H-pyran-4-thione  ligand  15  9  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TM4
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
 TM4  C6  C  CH3   0  -0.741   2.6112  -1.1987  -0.0206
 TM4  C1  C  C     0   0.279   1.4456  -0.2789  -0.0146
 TM4  O1  O  O2    0  -0.374   1.7508   1.0252   0.0098
 TM4  C5  C  C1    0   0.075   0.8045   1.9531   0.0184
 TM4  C4  C  C1    0  -0.373  -0.5086   1.6427   0.0030
 TM4  C3  C  C     0  -0.075  -0.9216   0.2840  -0.0239
 TM4  S1  S  S1    0  -0.352  -2.5117  -0.2373  -0.0458
 TM4  C2  C  C     0   0.273   0.1419  -0.6751  -0.0318
 TM4  O2  O  OH1   0  -0.614  -0.1350  -1.9810  -0.0558
 TM4  H1  H  HCH3  0   0.274   3.5473  -0.6452  -0.0040
 TM4  H2  H  HCH3  0   0.275   2.5871  -1.8588   0.8473
 TM4  H3  H  HCH3  0   0.275   2.6011  -1.8300  -0.9101
 TM4  H5  H  H     0   0.322   1.2016   2.9575   0.0385
 TM4  H6  H  H     0   0.301  -1.2395   2.4375   0.0106
 TM4  H4  H  HOH1  0   0.454  -1.1098  -2.0632  -0.0680

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
 TM4  C6  C1  single  1.485  0.020  1.485
 TM4  C1  O1  single  1.339  0.020  1.339
 TM4  C1  C2  double  1.363  0.020  1.363
 TM4  O2  C2  single  1.335  0.020  1.335
 TM4  O1  C5  single  1.325  0.020  1.325
 TM4  C2  C3  single  1.432  0.020  1.432
 TM4  C5  C4  double  1.349  0.020  1.349
 TM4  C3  C4  single  1.420  0.020  1.420
 TM4  C3  S1  double  1.674  0.020  1.674
 TM4  C6  H1  single  0.970  0.020  1.090
 TM4  C6  H2  single  0.970  0.020  1.090
 TM4  C6  H3  single  0.970  0.020  1.090
 TM4  C5  H5  single  0.930  0.020  1.080
 TM4  C4  H6  single  0.930  0.020  1.080
 TM4  O2  H4  single  0.850  0.020  0.980

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
 TM4  H3  C6  H2  107.36  3.000
 TM4  H3  C6  H1  108.36  3.000
 TM4  H2  C6  H1  108.35  3.000
 TM4  H3  C6  C1  110.76  3.000
 TM4  H2  C6  C1  110.76  3.000
 TM4  H1  C6  C1  111.12  3.000
 TM4  C2  C1  O1  120.08  3.000
 TM4  C2  C1  C6  124.81  3.000
 TM4  O1  C1  C6  115.11  3.000
 TM4  C5  O1  C1  121.27  3.000
 TM4  H5  C5  C4  124.88  3.000
 TM4  H5  C5  O1  112.87  3.000
 TM4  C4  C5  O1  122.25  3.000
 TM4  H6  C4  C3  120.49  3.000
 TM4  H6  C4  C5  119.29  3.000
 TM4  C3  C4  C5  120.21  3.000
 TM4  C2  C3  S1  119.80  3.000
 TM4  S1  C3  C4  125.06  3.000
 TM4  C2  C3  C4  115.14  3.000
 TM4  O2  C2  C3  120.07  3.000
 TM4  C3  C2  C1  121.04  3.000
 TM4  O2  C2  C1  118.89  3.000
 TM4  H4  O2  C2  106.80  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
 TM4  Var_01  C4  C5  O1  C1  -0.01  30.0  1
 TM4  Var_02  C4  C3  C2  C1  -0.02  30.0  1
 TM4  Var_03  C3  C2  C1  O1  -0.01  30.0  1
 TM4  Var_04  C2  C1  O1  C5   0.02  30.0  1
 TM4  Var_05  C2  C3  C4  C5   0.03  30.0  1
 TM4  Var_06  H1  C6  C1  O1  -0.02  30.0  3

