# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 01:37:45 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 5-S-methyl-5-thio-alpha-D-ribofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O
#
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
 SR1  SR1  5-S-methyl-5-thio-alpha-D-ribofuranose  D-saccharide  23  11  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SR1
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
 SR1  CS    C  CH3   0  -0.764   4.2211  -0.1325  -0.3569
 SR1  S     S  S2    0  -0.039   2.7012   0.5445   0.3446
 SR1  C5'   C  CH2   0  -0.567   1.4921  -0.5358  -0.4708
 SR1  C4'   C  CR15  0   0.048   0.1019  -0.2653   0.0600
 SR1  O4'   O  O     0  -0.513  -0.2726   1.0745  -0.2104
 SR1  C1'   C  CR15  0   0.280  -1.6367   1.1550  -0.5951
 SR1  O1'   O  OH1   0  -0.663  -2.3215   2.0737   0.1780
 SR1  C2'   C  CR15  0  -0.099  -2.2185  -0.2466  -0.3874
 SR1  O2'   O  OH1   0  -0.666  -2.6609  -0.4517   0.9260
 SR1  C3'   C  CR15  0   0.025  -0.9800  -1.1069  -0.6179
 SR1  O3'   O  OH1   0  -0.660  -1.0071  -2.3911  -0.0748
 SR1  HS1   H  HCH3  0   0.274   5.0560   0.4239   0.0652
 SR1  HS2   H  HCH3  0   0.261   4.3382  -1.1851  -0.1034
 SR1  HS3   H  HCH3  0   0.261   4.2400  -0.0181  -1.4399
 SR1  H5'1  H  HCH2  0   0.262   1.5283  -0.3778  -1.5518
 SR1  H5'2  H  HCH2  0   0.272   1.7525  -1.5772  -0.2689
 SR1  H4'   H  HCR5  0   0.227   0.0847  -0.4567   1.1421
 SR1  H1'   H  HCR5  0   0.212  -1.6753   1.4325  -1.6558
 SR1  HO'1  H  HOH1  0   0.470  -2.2190   2.9540  -0.1966
 SR1  H2'   H  HCR5  0   0.242  -3.0123  -0.4464  -1.1192
 SR1  HO'2  H  HOH1  0   0.453  -3.3001   0.2360   1.1403
 SR1  H3'   H  HCR5  0   0.226  -0.7834  -1.1282  -1.7002
 SR1  HO'3  H  HOH1  0   0.459  -1.6066  -2.9350  -0.5947

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
 SR1  CS   S     single  1.806  0.020  1.806
 SR1  CS   HS1   single  0.970  0.020  1.090
 SR1  CS   HS2   single  0.970  0.020  1.090
 SR1  CS   HS3   single  0.970  0.020  1.090
 SR1  S    C5'   single  1.815  0.020  1.815
 SR1  C5'  C4'   single  1.512  0.020  1.512
 SR1  C5'  H5'1  single  0.970  0.020  1.090
 SR1  C5'  H5'2  single  0.970  0.020  1.090
 SR1  C4'  O4'   single  1.417  0.020  1.417
 SR1  C4'  C3'   single  1.529  0.020  1.529
 SR1  C4'  H4'   single  0.970  0.020  1.090
 SR1  O4'  C1'   single  1.420  0.020  1.420
 SR1  C1'  O1'   single  1.382  0.020  1.382
 SR1  C1'  C2'   single  1.532  0.020  1.532
 SR1  C1'  H1'   single  0.970  0.020  1.090
 SR1  O1'  HO'1  single  0.850  0.020  0.980
 SR1  C2'  O2'   single  1.401  0.020  1.401
 SR1  C2'  C3'   single  1.526  0.020  1.526
 SR1  C2'  H2'   single  0.970  0.020  1.090
 SR1  O2'  HO'2  single  0.850  0.020  0.980
 SR1  C3'  O3'   single  1.395  0.020  1.395
 SR1  C3'  H3'   single  0.970  0.020  1.090
 SR1  O3'  HO'3  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
 SR1  HS3   CS   HS2   109.34  3.000
 SR1  HS3   CS   HS1   108.58  3.000
 SR1  HS2   CS   HS1   108.74  3.000
 SR1  HS3   CS   S     111.19  3.000
 SR1  HS2   CS   S     111.25  3.000
 SR1  HS1   CS   S     107.66  3.000
 SR1  C5'   S    CS     99.39  3.000
 SR1  H5'2  C5'  H5'1  108.22  3.000
 SR1  H5'2  C5'  C4'   108.95  3.000
 SR1  H5'1  C5'  C4'   110.59  3.000
 SR1  H5'2  C5'  S     109.00  3.000
 SR1  H5'1  C5'  S     109.65  3.000
 SR1  C4'   C5'  S     110.38  3.000
 SR1  H4'   C4'  C3'   109.24  3.000
 SR1  H4'   C4'  O4'   110.39  3.000
 SR1  C3'   C4'  O4'   104.41  3.000
 SR1  H4'   C4'  C5'   109.19  3.000
 SR1  C3'   C4'  C5'   113.35  3.000
 SR1  O4'   C4'  C5'   110.18  3.000
 SR1  C1'   O4'  C4'   111.05  3.000
 SR1  H1'   C1'  C2'   110.44  3.000
 SR1  H1'   C1'  O1'   110.80  3.000
 SR1  C2'   C1'  O1'   110.13  3.000
 SR1  H1'   C1'  O4'   108.06  3.000
 SR1  C2'   C1'  O4'   106.05  3.000
 SR1  O1'   C1'  O4'   111.23  3.000
 SR1  HO'1  O1'  C1'   109.73  3.000
 SR1  H2'   C2'  C3'   112.55  3.000
 SR1  H2'   C2'  O2'   111.72  3.000
 SR1  C3'   C2'  O2'   108.39  3.000
 SR1  H2'   C2'  C1'   110.53  3.000
 SR1  C3'   C2'  C1'   100.79  3.000
 SR1  O2'   C2'  C1'   112.40  3.000
 SR1  HO'2  O2'  C2'   108.28  3.000
 SR1  H3'   C3'  O3'   111.64  3.000
 SR1  H3'   C3'  C2'   107.74  3.000
 SR1  O3'   C3'  C2'   116.40  3.000
 SR1  H3'   C3'  C4'   108.68  3.000
 SR1  O3'   C3'  C4'   110.36  3.000
 SR1  C2'   C3'  C4'   101.36  3.000
 SR1  HO'3  O3'  C3'   108.80  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
 SR1  Var_01  C4'  C5'  S  CS    174.30  30.0  3
 SR1  Var_02  HS1  CS   S  C5'  -179.16  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
 SR1  chir_01  C4'  C5'  O4'  C3'  negativ
 SR1  chir_02  C1'  O1'  O4'  C2'  negativ
 SR1  chir_03  C2'  O2'  C1'  C3'  negativ
 SR1  chir_04  C3'  O3'  C2'  C4'  negativ

