# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:27:43 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: 4-S-methyl-4-thio-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CS[C@@H]1[C@@H](CO)O[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
 MA2  MA2  4-S-methyl-4-thio-alpha-D-glucopyranose  D-saccharide  27  13  .  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_MA2
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
 MA2  C1   C  CH1   0   0.229   -7.7392  41.7521  20.7929
 MA2  C2   C  CH1   0   0.018   -8.6501  40.5277  20.7950
 MA2  C3   C  CH1   0   0.055   -9.9522  40.8349  20.0640
 MA2  C4   C  CH1   0  -0.463  -10.5900  42.0762  20.6872
 MA2  C5   C  CH1   0   0.043   -9.6028  43.2444  20.6992
 MA2  C6   C  CH2   0  -0.175  -10.1224  44.4844  21.3950
 MA2  O1   O  OH1   0  -0.659   -7.3219  41.9953  19.4898
 MA2  O2   O  OH1   0  -0.665   -7.9499  39.4518  20.2297
 MA2  O3   O  OH1   0  -0.667  -10.7759  39.7029  20.1834
 MA2  S4   S  S2    0  -0.022  -12.1845  42.4686  19.9002
 MA2  O5   O  O2    0  -0.499   -8.4092  42.8454  21.3612
 MA2  O6   O  OH1   0  -0.665  -10.5429  44.1625  22.6974
 MA2  H1   H  HCH1  0   0.236   -6.8851  41.5741  21.4570
 MA2  H2   H  HCH1  0   0.219   -8.9006  40.3278  21.8483
 MA2  H3   H  HCH1  0   0.214   -9.7243  41.0406  19.0080
 MA2  H4   H  HCH1  0   0.294  -10.8717  41.8382  21.7179
 MA2  H5   H  HCH1  0   0.232   -9.3744  43.5372  19.6666
 MA2  H61  H  HCH2  0   0.215   -9.3218  45.2359  21.3961
 MA2  H62  H  HCH2  0   0.207  -10.9389  44.8914  20.7880
 MA2  H71  H  HCH3  0   0.283  -12.6240  43.1055  17.6708
 MA2  H72  H  HCH3  0   0.267  -11.1903  43.9587  18.2482
 MA2  H73  H  HCH3  0   0.270  -11.0793  42.2575  17.7388
 MA2  HO1  H  HOH1  0   0.460   -6.5943  42.6266  19.5056
 MA2  HO2  H  HOH1  0   0.451   -8.4858  38.6595  20.3345
 MA2  HO3  H  HOH1  0   0.444  -11.6299  39.9212  19.7895
 MA2  HO6  H  HOH1  0   0.456  -10.9354  44.9473  23.0898
 MA2  C7   C  CH3   0  -0.779  -11.7010  42.9981  18.2381

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
 MA2  C1  C2   single  1.526  0.020  1.526
 MA2  C1  O1   single  1.390  0.020  1.390
 MA2  C1  O5   single  1.402  0.020  1.402
 MA2  C1  H1   single  0.970  0.020  1.090
 MA2  C2  C3   single  1.525  0.020  1.525
 MA2  C2  O2   single  1.403  0.020  1.403
 MA2  C2  H2   single  0.970  0.020  1.090
 MA2  C3  C4   single  1.528  0.020  1.528
 MA2  C3  O3   single  1.405  0.020  1.405
 MA2  C3  H3   single  0.970  0.020  1.090
 MA2  C4  C5   single  1.529  0.020  1.529
 MA2  C4  S4   single  1.821  0.020  1.821
 MA2  C4  H4   single  0.970  0.020  1.090
 MA2  C5  C6   single  1.514  0.020  1.514
 MA2  C5  O5   single  1.422  0.020  1.422
 MA2  C5  H5   single  0.970  0.020  1.090
 MA2  C6  O6   single  1.406  0.020  1.406
 MA2  C6  H61  single  0.970  0.020  1.090
 MA2  C6  H62  single  0.970  0.020  1.090
 MA2  C7  S4   single  1.810  0.020  1.810
 MA2  C7  H71  single  0.970  0.020  1.090
 MA2  C7  H72  single  0.970  0.020  1.090
 MA2  C7  H73  single  0.970  0.020  1.090
 MA2  O1  HO1  single  0.850  0.020  0.980
 MA2  O2  HO2  single  0.850  0.020  0.980
 MA2  O3  HO3  single  0.850  0.020  0.980
 MA2  O6  HO6  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
 MA2  H1   C1  O5   104.67  3.000
 MA2  H1   C1  O1   111.25  3.000
 MA2  O5   C1  O1   112.77  3.000
 MA2  H1   C1  C2   109.50  3.000
 MA2  O5   C1  C2   109.86  3.000
 MA2  O1   C1  C2   108.72  3.000
 MA2  H2   C2  O2   111.09  3.000
 MA2  H2   C2  C3   107.52  3.000
 MA2  O2   C2  C3   112.81  3.000
 MA2  H2   C2  C1   106.43  3.000
 MA2  O2   C2  C1   108.48  3.000
 MA2  C3   C2  C1   110.33  3.000
 MA2  H3   C3  O3   110.72  3.000
 MA2  H3   C3  C4   109.04  3.000
 MA2  O3   C3  C4   112.03  3.000
 MA2  H3   C3  C2   108.73  3.000
 MA2  O3   C3  C2   107.31  3.000
 MA2  C4   C3  C2   108.94  3.000
 MA2  H4   C4  S4   103.21  3.000
 MA2  H4   C4  C5   108.95  3.000
 MA2  S4   C4  C5   113.83  3.000
 MA2  H4   C4  C3   108.34  3.000
 MA2  S4   C4  C3   111.36  3.000
 MA2  C5   C4  C3   110.74  3.000
 MA2  H5   C5  O5   109.77  3.000
 MA2  H5   C5  C6   106.58  3.000
 MA2  O5   C5  C6   107.70  3.000
 MA2  H5   C5  C4   109.31  3.000
 MA2  O5   C5  C4   109.34  3.000
 MA2  C6   C5  C4   114.06  3.000
 MA2  H62  C6  H61  106.83  3.000
 MA2  H62  C6  O6   112.04  3.000
 MA2  H61  C6  O6   111.95  3.000
 MA2  H62  C6  C5   107.78  3.000
 MA2  H61  C6  C5   108.11  3.000
 MA2  O6   C6  C5   109.93  3.000
 MA2  HO1  O1  C1   109.03  3.000
 MA2  HO2  O2  C2   108.04  3.000
 MA2  HO3  O3  C3   107.55  3.000
 MA2  C7   S4  C4   103.06  3.000
 MA2  C5   O5  C1   115.53  3.000
 MA2  HO6  O6  C6   108.26  3.000
 MA2  H73  C7  H72  109.69  3.000
 MA2  H73  C7  H71  108.21  3.000
 MA2  H72  C7  H71  108.41  3.000
 MA2  H73  C7  S4   112.01  3.000
 MA2  H72  C7  S4   112.03  3.000
 MA2  H71  C7  S4   106.31  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
 MA2  Var_01  H71  C7  S4  C4  171.80  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
 MA2  chir_01  C1  C2  O1  O5  negativ
 MA2  chir_02  C2  O2  C1  C3  negativ
 MA2  chir_03  C3  O3  C2  C4  positiv
 MA2  chir_04  C4  S4  C5  C3  positiv
 MA2  chir_05  C5  O5  C4  C6  negativ

