# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:18:39 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: methyl 4-thio-alpha-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
 MA3  MA3  'methyl 4-thio-alpha-D-glucopyranoside'  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 GRAND
;

data_comp_MA3
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
 MA3  C1   C  CH1   0   0.260  -2.6535  43.1947  18.9106
 MA3  C2   C  CH1   0   0.011  -3.0632  41.7757  18.5271
 MA3  C3   C  CH1   0   0.049  -4.5738  41.6860  18.3410
 MA3  C4   C  CH1   0  -0.456  -5.2650  42.2208  19.5969
 MA3  C5   C  CH1   0   0.051  -4.7604  43.6239  19.9360
 MA3  C6   C  CH2   0  -0.184  -5.3218  44.1882  21.2232
 MA3  O1   O  O2    0  -0.489  -2.8736  44.0269  17.8230
 MA3  O2   O  OH1   0  -0.663  -2.3537  41.4082  17.3752
 MA3  O3   O  OH1   0  -0.664  -4.8771  40.3353  18.1037
 MA3  S4   S  S2    0  -0.234  -7.0680  42.2179  19.2870
 MA3  O5   O  O2    0  -0.500  -3.3450  43.6030  20.0578
 MA3  O6   O  OH1   0  -0.665  -5.0734  43.3011  22.2864
 MA3  H1   H  HCH1  0   0.235  -1.5932  43.2109  19.2008
 MA3  H2   H  HCH1  0   0.223  -2.7953  41.1334  19.3800
 MA3  H3   H  HCH1  0   0.219  -4.8647  42.3100  17.4822
 MA3  H4   H  HCH1  0   0.298  -5.0681  41.5359  20.4242
 MA3  H5   H  HCH1  0   0.233  -5.0680  44.3084  19.1339
 MA3  H61  H  HCH2  0   0.217  -4.8625  45.1710  21.3936
 MA3  H62  H  HCH2  0   0.208  -6.3933  44.3623  21.0742
 MA3  H71  H  HCH3  0   0.236  -2.4268  45.8188  16.9942
 MA3  H72  H  HCH3  0   0.216  -2.8470  45.9210  18.7103
 MA3  H73  H  HCH3  0   0.212  -1.2648  45.2848  18.2213
 MA3  HO2  H  HOH1  0   0.451  -2.5318  40.4791  17.1980
 MA3  HO3  H  HOH1  0   0.447  -5.8290  40.2573  17.9688
 MA3  HS4  H  HSH1  0   0.237  -7.4645  41.8736  20.5159
 MA3  HO6  H  HOH1  0   0.457  -5.5172  43.6388  23.0693
 MA3  C7   C  CH3   0  -0.406  -2.3275  45.3219  17.9575

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
 MA3  C1  C2   single  1.526  0.020  1.526
 MA3  C1  O1   single  1.387  0.020  1.387
 MA3  C1  O5   single  1.400  0.020  1.400
 MA3  C1  H1   single  0.970  0.020  1.090
 MA3  C2  C3   single  1.525  0.020  1.525
 MA3  C2  O2   single  1.402  0.020  1.402
 MA3  C2  H2   single  0.970  0.020  1.090
 MA3  C3  C4   single  1.530  0.020  1.530
 MA3  C3  O3   single  1.405  0.020  1.405
 MA3  C3  H3   single  0.970  0.020  1.090
 MA3  C4  C5   single  1.529  0.020  1.529
 MA3  C4  S4   single  1.829  0.020  1.829
 MA3  C4  H4   single  0.970  0.020  1.090
 MA3  C5  C6   single  1.513  0.020  1.513
 MA3  C5  O5   single  1.421  0.020  1.421
 MA3  C5  H5   single  0.970  0.020  1.090
 MA3  C6  O6   single  1.407  0.020  1.407
 MA3  C6  H61  single  0.970  0.020  1.090
 MA3  C6  H62  single  0.970  0.020  1.090
 MA3  C7  O1   single  1.412  0.020  1.412
 MA3  C7  H71  single  0.970  0.020  1.090
 MA3  C7  H72  single  0.970  0.020  1.090
 MA3  C7  H73  single  0.970  0.020  1.090
 MA3  O2  HO2  single  0.850  0.020  0.980
 MA3  O3  HO3  single  0.850  0.020  0.980
 MA3  S4  HS4  single  1.200  0.020  1.300
 MA3  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
 MA3  H1   C1  O5   104.82  3.000
 MA3  H1   C1  O1   110.56  3.000
 MA3  O5   C1  O1   112.90  3.000
 MA3  H1   C1  C2   109.81  3.000
 MA3  O5   C1  C2   110.15  3.000
 MA3  O1   C1  C2   108.56  3.000
 MA3  H2   C2  O2   111.13  3.000
 MA3  H2   C2  C3   107.54  3.000
 MA3  O2   C2  C3   112.69  3.000
 MA3  H2   C2  C1   106.41  3.000
 MA3  O2   C2  C1   108.33  3.000
 MA3  C3   C2  C1   110.57  3.000
 MA3  H3   C3  O3   110.88  3.000
 MA3  H3   C3  C4   108.84  3.000
 MA3  O3   C3  C4   112.16  3.000
 MA3  H3   C3  C2   108.89  3.000
 MA3  O3   C3  C2   106.93  3.000
 MA3  C4   C3  C2   109.08  3.000
 MA3  H4   C4  S4   107.77  3.000
 MA3  H4   C4  C5   110.36  3.000
 MA3  S4   C4  C5   111.36  3.000
 MA3  H4   C4  C3   108.74  3.000
 MA3  S4   C4  C3   107.79  3.000
 MA3  C5   C4  C3   110.71  3.000
 MA3  H5   C5  O5   110.53  3.000
 MA3  H5   C5  C6   106.55  3.000
 MA3  O5   C5  C6   107.59  3.000
 MA3  H5   C5  C4   108.51  3.000
 MA3  O5   C5  C4   109.53  3.000
 MA3  C6   C5  C4   114.10  3.000
 MA3  H62  C6  H61  106.72  3.000
 MA3  H62  C6  O6   112.06  3.000
 MA3  H61  C6  O6   111.91  3.000
 MA3  H62  C6  C5   107.84  3.000
 MA3  H61  C6  C5   108.09  3.000
 MA3  O6   C6  C5   110.01  3.000
 MA3  C7   O1  C1   114.47  3.000
 MA3  HO2  O2  C2   108.10  3.000
 MA3  HO3  O3  C3   108.33  3.000
 MA3  HS4  S4  C4    97.88  3.000
 MA3  C5   O5  C1   115.21  3.000
 MA3  HO6  O6  C6   108.21  3.000
 MA3  H73  C7  H72  108.28  3.000
 MA3  H73  C7  H71  108.49  3.000
 MA3  H72  C7  H71  108.41  3.000
 MA3  H73  C7  O1   111.53  3.000
 MA3  H72  C7  O1   112.61  3.000
 MA3  H71  C7  O1   107.41  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
 MA3  Var_01  H71  C7  O1  C1  171.28  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
 MA3  chir_01  C1  C2  O1  O5  negativ
 MA3  chir_02  C2  O2  C1  C3  negativ
 MA3  chir_03  C3  O3  C2  C4  positiv
 MA3  chir_04  C4  S4  C5  C3  positiv
 MA3  chir_05  C5  O5  C4  C6  negativ

