# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 15:44:47 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: 5-hydroxy-2-methyl-4H-pyran-4-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=S)C(=CO1)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
 TM7  TM7  5-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_TM7
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
 TM7  S   S  S1    0  -0.339  -2.1481   1.2322  -0.3500
 TM7  O1  O  O2    0  -0.385   1.7072  -0.9424   0.1607
 TM7  C1  C  C1    0  -0.076   0.5509  -1.6182   0.1454
 TM7  C2  C  C     0   0.251  -0.6492  -1.0128  -0.0037
 TM7  C3  C  C     0  -0.036  -0.7107   0.4197  -0.1586
 TM7  C4  C  C1    0  -0.393   0.5575   1.0657  -0.1320
 TM7  C5  C  C     0   0.395   1.7177   0.3823   0.0247
 TM7  C6  C  CH3   0  -0.732   3.0762   0.9772   0.0685
 TM7  H1  H  HOH1  0   0.481  -1.6648  -2.6269   0.0894
 TM7  H2  H  H     0   0.320   0.6913  -2.6845   0.2648
 TM7  H3  H  H     0   0.290   0.6004   2.1402  -0.2384
 TM7  H4  H  HCH3  0   0.275   3.7077   0.5630  -0.7189
 TM7  H5  H  HCH3  0   0.270   3.0203   2.0544  -0.0644
 TM7  H6  H  HCH3  0   0.275   3.5600   0.7707   1.0243
 TM7  O2  O  OH1   0  -0.595  -1.8095  -1.6789  -0.0185

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
 TM7  O1  C1  single  1.339  0.020  1.339
 TM7  O1  C5  single  1.332  0.020  1.332
 TM7  C1  C2  double  1.352  0.020  1.352
 TM7  C6  C5  single  1.484  0.020  1.484
 TM7  C5  C4  double  1.356  0.020  1.356
 TM7  C2  O2  single  1.338  0.020  1.338
 TM7  C2  C3  single  1.442  0.020  1.442
 TM7  C4  C3  single  1.424  0.020  1.424
 TM7  C3  S   double  1.662  0.020  1.662
 TM7  O2  H1  single  0.850  0.020  0.980
 TM7  C1  H2  single  0.930  0.020  1.080
 TM7  C4  H3  single  0.930  0.020  1.080
 TM7  C6  H4  single  0.970  0.020  1.090
 TM7  C6  H5  single  0.970  0.020  1.090
 TM7  C6  H6  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
 TM7  C5  O1  C1  120.51  3.000
 TM7  H2  C1  C2  124.64  3.000
 TM7  H2  C1  O1  112.58  3.000
 TM7  C2  C1  O1  122.78  3.000
 TM7  C3  C2  C1  119.63  3.000
 TM7  C3  C2  O2  117.15  3.000
 TM7  C1  C2  O2  123.22  3.000
 TM7  C4  C3  C2  114.25  3.000
 TM7  C4  C3  S   123.42  3.000
 TM7  C2  C3  S   122.33  3.000
 TM7  H3  C4  C5  118.60  3.000
 TM7  H3  C4  C3  119.00  3.000
 TM7  C5  C4  C3  122.40  3.000
 TM7  C6  C5  C4  125.80  3.000
 TM7  C4  C5  O1  120.43  3.000
 TM7  C6  C5  O1  113.77  3.000
 TM7  H6  C6  H5  108.51  3.000
 TM7  H6  C6  H4  107.69  3.000
 TM7  H5  C6  H4  108.53  3.000
 TM7  H6  C6  C5  110.85  3.000
 TM7  H5  C6  C5  110.28  3.000
 TM7  H4  C6  C5  110.88  3.000
 TM7  H1  O2  C2  110.96  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
 TM7  Var_01  C3  C2  C1  O1   0.20  30.0  1
 TM7  Var_02  C3  C4  C5  O1   0.04  30.0  1
 TM7  Var_03  C4  C5  O1  C1  -0.04  30.0  1
 TM7  Var_04  C4  C3  C2  C1  -0.18  30.0  1
 TM7  Var_05  C5  C4  C3  C2   0.07  30.0  1
 TM7  Var_06  H4  C6  C5  O1  58.79  30.0  3

