# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 09:26:03 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: methyl 4-thio-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](CO)[C@@H](S)[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
 GTM  GTM  'methyl 4-thio-beta-D-glucopyranoside'  D-saccharide  27  13  .  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_GTM
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
 GTM  C1    C  CH1   0   0.298   0.0367  -0.2056   1.5012
 GTM  C2    C  CH1   0  -0.024  -1.3162   0.2824   0.9954
 GTM  C3    C  CH1   0   0.068  -1.4856  -0.1386  -0.4623
 GTM  C4    C  CH1   0  -0.440  -0.2921   0.3214  -1.2922
 GTM  C5    C  CH1   0   0.029   1.0140  -0.1447  -0.6364
 GTM  C6    C  CH2   0  -0.151   2.2443   0.3878  -1.3436
 GTM  O1    O  O2    0  -0.495   0.2147   0.2459   2.7887
 GTM  O2    O  OH1   0  -0.669  -2.3802  -0.2830   1.7185
 GTM  O3    O  OH1   0  -0.662  -2.6473   0.4148  -1.0248
 GTM  S4    S  S2    0  -0.233  -0.3739  -0.3587  -2.9865
 GTM  O5    O  O2    0  -0.489   1.0562   0.3223   0.6925
 GTM  O6    O  OH1   0  -0.665   3.3853  -0.1431  -0.7180
 GTM  H1    H  HCH1  0   0.185   0.0713  -1.3119   1.4624
 GTM  H2    H  HCH1  0   0.224  -1.3270   1.3817   1.0503
 GTM  H3    H  HCH1  0   0.219  -1.5199  -1.2388  -0.4972
 GTM  H4    H  HCH1  0   0.287  -0.2888   1.4145  -1.3482
 GTM  H5    H  HCH1  0   0.228   1.0428  -1.2467  -0.6539
 GTM  H6C1  H  HCH2  0   0.212   2.1959   0.1042  -2.4009
 GTM  H6C2  H  HCH2  0   0.202   2.2252   1.4859  -1.3086
 GTM  H7C1  H  HCH3  0   0.240   1.2083  -0.0547   4.5288
 GTM  H7C2  H  HCH3  0   0.213   1.2543  -1.4416   3.4264
 GTM  H7C3  H  HCH3  0   0.222   2.2629  -0.0165   3.1068
 GTM  HB    H  HOH1  0   0.458  -2.3897   0.1015   2.6007
 GTM  HA    H  HOH1  0   0.457  -3.4117   0.0371  -0.5782
 GTM  HS4   H  HSH1  0   0.237  -1.6203   0.0370  -3.2621
 GTM  H6    H  HOH1  0   0.458   4.1527   0.1136  -1.2368
 GTM  C7    C  CH3   0  -0.409   1.2937  -0.3491   3.4845

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
 GTM  C1  C2    single  1.525  0.020  1.525
 GTM  C1  O1    single  1.376  0.020  1.376
 GTM  C1  O5    single  1.404  0.020  1.404
 GTM  C1  H1    single  0.970  0.020  1.090
 GTM  C2  C3    single  1.527  0.020  1.527
 GTM  C2  O2    single  1.405  0.020  1.405
 GTM  C2  H2    single  0.970  0.020  1.090
 GTM  C3  C4    single  1.525  0.020  1.525
 GTM  C3  O3    single  1.404  0.020  1.404
 GTM  C3  H3    single  0.970  0.020  1.090
 GTM  C4  C5    single  1.534  0.020  1.534
 GTM  C4  S4    single  1.827  0.020  1.827
 GTM  C4  H4    single  0.970  0.020  1.090
 GTM  C5  C6    single  1.516  0.020  1.516
 GTM  C5  O5    single  1.409  0.020  1.409
 GTM  C5  H5    single  0.970  0.020  1.090
 GTM  C6  O6    single  1.405  0.020  1.405
 GTM  C6  H6C1  single  0.970  0.020  1.090
 GTM  C6  H6C2  single  0.970  0.020  1.090
 GTM  C7  O1    single  1.415  0.020  1.415
 GTM  C7  H7C1  single  0.970  0.020  1.090
 GTM  C7  H7C2  single  0.970  0.020  1.090
 GTM  C7  H7C3  single  0.970  0.020  1.090
 GTM  O2  HB    single  0.850  0.020  0.980
 GTM  O3  HA    single  0.850  0.020  0.980
 GTM  S4  HS4   single  1.200  0.020  1.300
 GTM  O6  H6    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
 GTM  H1    C1  O5    109.43  3.000
 GTM  H1    C1  O1    110.89  3.000
 GTM  O5    C1  O1    108.76  3.000
 GTM  H1    C1  C2    109.62  3.000
 GTM  O5    C1  C2    109.44  3.000
 GTM  O1    C1  C2    108.68  3.000
 GTM  H2    C2  O2    111.64  3.000
 GTM  H2    C2  C3    108.78  3.000
 GTM  O2    C2  C3    107.24  3.000
 GTM  H2    C2  C1    108.17  3.000
 GTM  O2    C2  C1    111.87  3.000
 GTM  C3    C2  C1    109.09  3.000
 GTM  H3    C3  O3    110.81  3.000
 GTM  H3    C3  C4    107.97  3.000
 GTM  O3    C3  C4    108.10  3.000
 GTM  H3    C3  C2    108.00  3.000
 GTM  O3    C3  C2    111.44  3.000
 GTM  C4    C3  C2    110.47  3.000
 GTM  H4    C4  S4    108.93  3.000
 GTM  H4    C4  C5    108.82  3.000
 GTM  S4    C4  C5    108.75  3.000
 GTM  H4    C4  C3    109.36  3.000
 GTM  S4    C4  C3    110.94  3.000
 GTM  C5    C4  C3    110.01  3.000
 GTM  H5    C5  O5    110.20  3.000
 GTM  H5    C5  C6    108.82  3.000
 GTM  O5    C5  C6    107.41  3.000
 GTM  H5    C5  C4    108.61  3.000
 GTM  O5    C5  C4    109.15  3.000
 GTM  C6    C5  C4    112.64  3.000
 GTM  H6C2  C6  H6C1  106.77  3.000
 GTM  H6C2  C6  O6    112.17  3.000
 GTM  H6C1  C6  O6    111.57  3.000
 GTM  H6C2  C6  C5    108.79  3.000
 GTM  H6C1  C6  C5    108.87  3.000
 GTM  O6    C6  C5    108.58  3.000
 GTM  C7    O1  C1    114.88  3.000
 GTM  HB    O2  C2    108.57  3.000
 GTM  HA    O3  C3    108.45  3.000
 GTM  HS4   S4  C4     97.05  3.000
 GTM  C5    O5  C1    113.38  3.000
 GTM  H6    O6  C6    107.88  3.000
 GTM  H7C3  C7  H7C2  108.52  3.000
 GTM  H7C3  C7  H7C1  108.61  3.000
 GTM  H7C2  C7  H7C1  108.54  3.000
 GTM  H7C3  C7  O1    112.25  3.000
 GTM  H7C2  C7  O1    111.47  3.000
 GTM  H7C1  C7  O1    107.35  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
 GTM  Var_01  H7C1  C7  O1  C1  -169.35  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
 GTM  chir_01  C1  C2  O1  O5  positiv
 GTM  chir_02  C2  O2  C1  C3  negativ
 GTM  chir_03  C3  O3  C2  C4  positiv
 GTM  chir_04  C4  S4  C5  C3  positiv
 GTM  chir_05  C5  O5  C4  C6  negativ

