# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 18:18:53 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: 2,6-dideoxy-4-S-methyl-4-thio-beta-D-ribo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CS[C@@H]1[C@@H](C)O[C@@H](O)C[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
 TMR  TMR  2,6-dideoxy-4-S-methyl-4-thio-beta-D-ribo-hexopyranose  D-saccharide  25  11  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TMR
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
 TMR  C1   C  CH1   0   0.293  -5.5664   2.3290  4.4612
 TMR  C2   C  CH2   0  -0.502  -4.1746   1.8639  4.8435
 TMR  C3   C  CH1   0   0.023  -4.1046   0.3444  4.8941
 TMR  C4   C  CH1   0  -0.404  -5.2471  -0.2073  5.7561
 TMR  C5   C  CH1   0   0.081  -6.5996   0.3953  5.3602
 TMR  C6   C  CH3   0  -0.680  -7.7194   0.0086  6.3043
 TMR  O1   O  OH1   0  -0.656  -5.6119   3.7087  4.5323
 TMR  O3   O  OH1   0  -0.665  -4.1802  -0.1366  3.5680
 TMR  O5   O  O2    0  -0.498  -6.5091   1.8087  5.3739
 TMR  S4   S  S2    0  -0.039  -5.2699  -2.0263  5.6044
 TMR  H1   H  HCH1  0   0.181  -5.8195   1.9722  3.4490
 TMR  H2   H  HCH2  0   0.243  -3.9252   2.2656  5.8296
 TMR  H22  H  HCH2  0   0.251  -3.4332   2.2427  4.1364
 TMR  H3   H  HCH1  0   0.237  -3.1552   0.0484  5.3567
 TMR  H4   H  HCH1  0   0.281  -5.0375   0.0334  6.8033
 TMR  H5   H  HCH1  0   0.206  -6.8489   0.0486  4.3456
 TMR  H61  H  HCH3  0   0.241  -8.6561   0.4773  6.0017
 TMR  H62  H  HCH3  0   0.226  -7.4957   0.3168  7.3270
 TMR  H63  H  HCH3  0   0.234  -7.8714  -1.0696  6.2983
 TMR  H71  H  HCH3  0   0.274  -5.2915  -3.6264  7.3505
 TMR  H72  H  HCH3  0   0.266  -4.4509  -2.1632  7.8816
 TMR  H73  H  HCH3  0   0.265  -6.2289  -2.2047  7.8268
 TMR  HO1  H  HOH1  0   0.456  -6.4139   4.0236  4.1013
 TMR  HO3  H  HOH1  0   0.451  -3.9098  -1.0611  3.5652
 TMR  C7   C  CH3   0  -0.763  -5.3157  -2.5382  7.3377

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
 TMR  C1  C2   single  1.516  0.020  1.516
 TMR  C1  O1   single  1.382  0.020  1.382
 TMR  C1  O5   single  1.412  0.020  1.412
 TMR  C1  H1   single  0.970  0.020  1.090
 TMR  C2  C3   single  1.522  0.020  1.522
 TMR  C2  H2   single  0.970  0.020  1.090
 TMR  C2  H22  single  0.970  0.020  1.090
 TMR  C3  C4   single  1.534  0.020  1.534
 TMR  C3  O3   single  1.413  0.020  1.413
 TMR  C3  H3   single  0.970  0.020  1.090
 TMR  C4  C5   single  1.533  0.020  1.533
 TMR  C4  S4   single  1.825  0.020  1.825
 TMR  C4  H4   single  0.970  0.020  1.090
 TMR  C5  C6   single  1.515  0.020  1.515
 TMR  C5  O5   single  1.416  0.020  1.416
 TMR  C5  H5   single  0.970  0.020  1.090
 TMR  C6  H61  single  0.970  0.020  1.090
 TMR  C6  H62  single  0.970  0.020  1.090
 TMR  C6  H63  single  0.970  0.020  1.090
 TMR  C7  S4   single  1.808  0.020  1.808
 TMR  C7  H71  single  0.970  0.020  1.090
 TMR  C7  H72  single  0.970  0.020  1.090
 TMR  C7  H73  single  0.970  0.020  1.090
 TMR  O1  HO1  single  0.850  0.020  0.980
 TMR  O3  HO3  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
 TMR  H1   C1  O5   108.72  3.000
 TMR  H1   C1  O1   111.26  3.000
 TMR  O5   C1  O1   108.22  3.000
 TMR  H1   C1  C2   110.06  3.000
 TMR  O5   C1  C2   109.69  3.000
 TMR  O1   C1  C2   108.87  3.000
 TMR  H22  C2  H2   107.55  3.000
 TMR  H22  C2  C3   109.66  3.000
 TMR  H2   C2  C3   109.05  3.000
 TMR  H22  C2  C1   110.69  3.000
 TMR  H2   C2  C1   108.90  3.000
 TMR  C3   C2  C1   110.90  3.000
 TMR  H3   C3  O3   110.51  3.000
 TMR  H3   C3  C4   108.10  3.000
 TMR  O3   C3  C4   111.42  3.000
 TMR  H3   C3  C2   108.86  3.000
 TMR  O3   C3  C2   107.84  3.000
 TMR  C4   C3  C2   110.09  3.000
 TMR  H4   C4  S4   107.51  3.000
 TMR  H4   C4  C5   109.25  3.000
 TMR  S4   C4  C5   111.06  3.000
 TMR  H4   C4  C3   108.41  3.000
 TMR  S4   C4  C3   108.72  3.000
 TMR  C5   C4  C3   111.76  3.000
 TMR  H5   C5  O5   109.74  3.000
 TMR  H5   C5  C6   109.06  3.000
 TMR  O5   C5  C6   107.22  3.000
 TMR  H5   C5  C4   108.31  3.000
 TMR  O5   C5  C4   109.48  3.000
 TMR  C6   C5  C4   113.01  3.000
 TMR  H63  C6  H62  108.27  3.000
 TMR  H63  C6  H61  107.72  3.000
 TMR  H62  C6  H61  108.35  3.000
 TMR  H63  C6  C5   110.64  3.000
 TMR  H62  C6  C5   111.12  3.000
 TMR  H61  C6  C5   110.63  3.000
 TMR  HO1  O1  C1   109.31  3.000
 TMR  HO3  O3  C3   108.33  3.000
 TMR  C5   O5  C1   113.84  3.000
 TMR  C7   S4  C4   101.70  3.000
 TMR  H73  C7  H72  109.67  3.000
 TMR  H73  C7  H71  108.65  3.000
 TMR  H72  C7  H71  108.72  3.000
 TMR  H73  C7  S4   111.43  3.000
 TMR  H72  C7  S4   111.19  3.000
 TMR  H71  C7  S4   107.09  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
 TMR  Var_01  H71  C7  S4  C4  -177.79  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
 TMR  chir_01  C1  C2  O1  O5  positiv
 TMR  chir_02  C3  O3  C4  C2  positiv
 TMR  chir_03  C4  S4  C5  C3  positiv
 TMR  chir_04  C5  O5  C4  C6  negativ

