# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:09:06 2021
#   Inital geometry file: a 53 line input string
#   Ligand name: 2-(2-ethoxyethoxy)ethanethiol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOCCOCCS
#
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
 S5Y  S5Y  2-(2-ethoxyethoxy)ethanethiol  ligand  23  9  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_S5Y
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
 S5Y  C1   C  CH2   0  -0.141  17.7685  -28.6828  11.7520
 S5Y  C2   C  CH2   0  -0.165  17.7976  -26.3575  12.0468
 S5Y  C3   C  CH2   0  -0.180  16.9204  -25.1548  12.2797
 S5Y  C4   C  CH2   0  -0.165  15.3324  -23.7659  11.1727
 S5Y  C5   C  CH2   0  -0.554  13.8787  -24.0324  11.5213
 S5Y  S    S  S2    0  -0.267  13.6912  -24.5756  13.2544
 S5Y  O1   O  O2    0  -0.488  16.1237  -24.9288  11.1399
 S5Y  O    O  O2    0  -0.485  17.0070  -27.5122  11.9383
 S5Y  C    C  CH3   0  -0.689  16.8374  -29.8709  11.6644
 S5Y  H1   H  HCH2  0   0.196  18.4749  -28.8173  12.5836
 S5Y  H2   H  HCH2  0   0.196  18.3730  -28.6084  10.8370
 S5Y  H3   H  HCH2  0   0.204  18.4977  -26.4348  12.8908
 S5Y  H4   H  HCH2  0   0.202  18.4076  -26.2094  11.1434
 S5Y  H5   H  HCH2  0   0.211  17.5719  -24.2938  12.4802
 S5Y  H6   H  HCH2  0   0.209  16.3120  -25.3142  13.1787
 S5Y  H7   H  HCH2  0   0.217  15.7516  -23.0119  11.8502
 S5Y  H8   H  HCH2  0   0.248  15.3452  -23.3320  10.1686
 S5Y  H9   H  HCH2  0   0.270  13.3176  -23.1090  11.3788
 S5Y  H10  H  HCH2  0   0.269  13.4652  -24.7881  10.8534
 S5Y  H11  H  HSH1  0   0.226  12.3545  -24.5573  13.2933
 S5Y  H12  H  HCH3  0   0.230  17.4146  -30.7858  11.5319
 S5Y  H13  H  HCH3  0   0.228  16.2462  -29.9782  12.5747
 S5Y  H14  H  HCH3  0   0.228  16.1554  -29.7800  10.8185

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
 S5Y  C4  O1   single  1.407  0.020  1.407
 S5Y  C4  C5   single  1.518  0.020  1.518
 S5Y  C   C1   single  1.512  0.020  1.512
 S5Y  O1  C3   single  1.409  0.020  1.409
 S5Y  C5  S    single  1.826  0.020  1.826
 S5Y  C1  O    single  1.409  0.020  1.409
 S5Y  O   C2   single  1.404  0.020  1.404
 S5Y  C3  C2   single  1.507  0.020  1.507
 S5Y  C1  H1   single  0.970  0.020  1.090
 S5Y  C1  H2   single  0.970  0.020  1.090
 S5Y  C2  H3   single  0.970  0.020  1.090
 S5Y  C2  H4   single  0.970  0.020  1.090
 S5Y  C3  H5   single  0.970  0.020  1.090
 S5Y  C3  H6   single  0.970  0.020  1.090
 S5Y  C4  H7   single  0.970  0.020  1.090
 S5Y  C4  H8   single  0.970  0.020  1.090
 S5Y  C5  H9   single  0.970  0.020  1.090
 S5Y  C5  H10  single  0.970  0.020  1.090
 S5Y  S   H11  single  1.200  0.020  1.300
 S5Y  C   H12  single  0.970  0.020  1.090
 S5Y  C   H13  single  0.970  0.020  1.090
 S5Y  C   H14  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
 S5Y  H2   C1  H1   106.54  3.000
 S5Y  H2   C1  C    110.10  3.000
 S5Y  H1   C1  C    110.08  3.000
 S5Y  H2   C1  O    110.55  3.000
 S5Y  H1   C1  O    110.42  3.000
 S5Y  C    C1  O    109.13  3.000
 S5Y  H4   C2  H3   106.67  3.000
 S5Y  H4   C2  O    111.08  3.000
 S5Y  H3   C2  O    111.12  3.000
 S5Y  H4   C2  C3   110.01  3.000
 S5Y  H3   C2  C3   107.95  3.000
 S5Y  O    C2  C3   109.92  3.000
 S5Y  H6   C3  H5   107.06  3.000
 S5Y  H6   C3  O1   111.88  3.000
 S5Y  H5   C3  O1   110.94  3.000
 S5Y  H6   C3  C2   109.48  3.000
 S5Y  H5   C3  C2   107.98  3.000
 S5Y  O1   C3  C2   109.40  3.000
 S5Y  H8   C4  H7   106.85  3.000
 S5Y  H8   C4  O1   107.45  3.000
 S5Y  H7   C4  O1   111.57  3.000
 S5Y  H8   C4  C5   106.95  3.000
 S5Y  H7   C4  C5   110.17  3.000
 S5Y  O1   C4  C5   113.50  3.000
 S5Y  H10  C5  H9   108.18  3.000
 S5Y  H10  C5  S    109.66  3.000
 S5Y  H9   C5  S    108.86  3.000
 S5Y  H10  C5  C4   110.13  3.000
 S5Y  H9   C5  C4   108.31  3.000
 S5Y  S    C5  C4   111.62  3.000
 S5Y  H11  S   C5    97.25  3.000
 S5Y  C4   O1  C3   115.58  3.000
 S5Y  C2   O   C1   112.91  3.000
 S5Y  H14  C   H13  108.46  3.000
 S5Y  H14  C   H12  107.88  3.000
 S5Y  H13  C   H12  107.82  3.000
 S5Y  H14  C   C1   111.38  3.000
 S5Y  H13  C   C1   111.27  3.000
 S5Y  H12  C   C1   109.91  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
 S5Y  Var_01  C3   C2  O   C1  -178.52  30.0  3
 S5Y  Var_02  C    C1  O   C2   179.27  30.0  1
 S5Y  Var_03  C5   C4  O1  C3  -100.83  30.0  1
 S5Y  Var_04  O1   C4  C5  S     68.47  30.0  1
 S5Y  Var_05  O    C2  C3  O1   -65.88  30.0  3
 S5Y  Var_06  H5   C3  O1  C4   -55.85  30.0  3
 S5Y  Var_07  H12  C   C1  O   -179.34  30.0  3

