# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon May 18 22:52:19 2020
#   Inital geometry file: a 163 line input string
#   Ligand name: undecyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[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
 0SA  0SA  'undecyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside'  ligand  78  34  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0SA
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
 0SA  CL   C  CH3   0  -0.663  14.6781   1.7822  -1.0143
 0SA  CK   C  CH2   0  -0.418  13.6249   0.9451  -0.3016
 0SA  CJ   C  CH2   0  -0.406  12.2027   1.3046  -0.7155
 0SA  CI   C  CH2   0  -0.411  11.1419   0.4564  -0.0257
 0SA  CH   C  CH2   0  -0.412   9.7193   0.8115  -0.4415
 0SA  CG   C  CH2   0  -0.412   8.6664  -0.0783   0.2073
 0SA  CF   C  CH2   0  -0.413   7.2414   0.2707  -0.2048
 0SA  CD   C  CH2   0  -0.414   6.2015  -0.6786   0.3776
 0SA  CC   C  CH2   0  -0.411   4.7757  -0.3252  -0.0273
 0SA  CB   C  CH2   0  -0.424   3.7491  -1.3316   0.4812
 0SA  CA   C  CH2   0  -0.550   2.3368  -0.9371   0.0793
 0SA  S1'  S  S2    0  -0.010   1.1554  -2.2168   0.6090
 0SA  C1'  C  CH1   0  -0.137  -0.4034  -1.4590   0.1079
 0SA  C2'  C  CH1   0   0.021  -1.4030  -2.5492  -0.2802
 0SA  O2'  O  OH1   0  -0.662  -0.9777  -3.2728  -1.4036
 0SA  C3'  C  CH1   0   0.018  -2.7218  -1.8810  -0.6461
 0SA  O3'  O  OH1   0  -0.668  -3.7408  -2.8265  -0.8767
 0SA  O5'  O  O2    0  -0.469  -0.9052  -0.6955   1.1693
 0SA  C5'  C  CH1   0  -0.004  -2.0681   0.0358   0.8266
 0SA  C6'  C  CH2   0  -0.190  -2.4168   0.9073   2.0131
 0SA  O6'  O  OH1   0  -0.669  -1.3587   1.8114   2.2337
 0SA  C4'  C  CH1   0   0.017  -3.1935  -0.9409   0.4573
 0SA  O1   O  O2    0  -0.517  -4.3128  -0.2518  -0.0526
 0SA  C1   C  CH1   0   0.219  -5.4998  -0.1809   0.6859
 0SA  O5   O  O2    0  -0.496  -5.7137   1.0990   1.1910
 0SA  C5   C  CH1   0  -0.015  -5.8256   2.1311   0.2207
 0SA  C6   C  CH2   0  -0.160  -6.0204   3.4289   0.9755
 0SA  O6   O  OH1   0  -0.663  -4.8648   3.6862   1.7378
 0SA  C4   C  CH1   0   0.034  -6.9883   1.8366  -0.7290
 0SA  O4   O  OH1   0  -0.673  -7.0045   2.8431  -1.7116
 0SA  C3   C  CH1   0  -0.011  -6.8191   0.4503  -1.3403
 0SA  O3   O  OH1   0  -0.677  -7.9605   0.1916  -2.1256
 0SA  C2   C  CH1   0  -0.010  -6.6566  -0.5846  -0.2290
 0SA  O2   O  OH1   0  -0.688  -6.5226  -1.8887  -0.7280
 0SA  H1   H  HCH3  0   0.226  15.6873   1.5085  -0.7047
 0SA  H2   H  HCH3  0   0.216  14.6179   1.6517  -2.0966
 0SA  H3   H  HCH3  0   0.216  14.5466   2.8455  -0.8049
 0SA  H4   H  HCH2  0   0.210  13.8011  -0.1158  -0.5041
 0SA  H5   H  HCH2  0   0.210  13.7280   1.0679   0.7811
 0SA  H6   H  HCH2  0   0.206  12.0216   2.3638  -0.5015
 0SA  H7   H  HCH2  0   0.205  12.1041   1.1942  -1.8014
 0SA  H8   H  HCH2  0   0.206  11.3267  -0.6012  -0.2446
 0SA  H9   H  HCH2  0   0.206  11.2395   0.5624   1.0605
 0SA  H10  H  HCH2  0   0.207   9.5192   1.8593  -0.1924
 0SA  H11  H  HCH2  0   0.206   9.6316   0.7368  -1.5312
 0SA  H12  H  HCH2  0   0.206   8.8699  -1.1231  -0.0524
 0SA  H13  H  HCH2  0   0.207   8.7553  -0.0146   1.2975
 0SA  H14  H  HCH2  0   0.208   7.0143   1.2972   0.1024
 0SA  H15  H  HCH2  0   0.207   7.1669   0.2576  -1.2980
 0SA  H16  H  HCH2  0   0.210   6.4264  -1.7003   0.0529
 0SA  H17  H  HCH2  0   0.211   6.2795  -0.6827   1.4702
 0SA  H18  H  HCH2  0   0.217   4.5264   0.6732   0.3465
 0SA  H19  H  HCH2  0   0.215   4.7114  -0.2681  -1.1191
 0SA  H20  H  HCH2  0   0.230   3.9842  -2.3221   0.0799
 0SA  H21  H  HCH2  0   0.232   3.8137  -1.4105   1.5702
 0SA  H22  H  HCH2  0   0.269   2.0573   0.0103   0.5423
 0SA  H23  H  HCH2  0   0.267   2.2632  -0.8233  -1.0035
 0SA  H24  H  HCH1  0   0.258  -0.2012  -0.8271  -0.7704
 0SA  H25  H  HCH1  0   0.229  -1.5614  -3.2052   0.5903
 0SA  H26  H  HOH1  0   0.450  -0.1211  -3.6682  -1.2020
 0SA  H27  H  HCH1  0   0.230  -2.5457  -1.2732  -1.5474
 0SA  H28  H  HOH1  0   0.466  -3.5475  -3.2959  -1.6951
 0SA  H29  H  HCH1  0   0.227  -1.8683   0.6795  -0.0456
 0SA  H30  H  HCH2  0   0.241  -3.3515   1.4313   1.8061
 0SA  H31  H  HCH2  0   0.193  -2.5914   0.2642   2.8880
 0SA  H32  H  HOH1  0   0.455  -1.6810   2.5052   2.8150
 0SA  H33  H  HCH1  0   0.242  -3.4680  -1.5259   1.3472
 0SA  H34  H  HCH1  0   0.255  -5.4567  -0.8474   1.5557
 0SA  H35  H  HCH1  0   0.229  -4.9002   2.2018  -0.3675
 0SA  H36  H  HCH2  0   0.211  -6.2096   4.2260   0.2490
 0SA  H37  H  HCH2  0   0.196  -6.9172   3.3449   1.6055
 0SA  H38  H  HOH1  0   0.456  -4.9795   4.5343   2.1755
 0SA  H39  H  HCH1  0   0.210  -7.9227   1.8402  -0.1440
 0SA  H40  H  HOH1  0   0.455  -7.7322   2.6639  -2.3159
 0SA  H41  H  HCH1  0   0.211  -5.9130   0.4540  -1.9655
 0SA  H42  H  HOH1  0   0.453  -7.8396  -0.6599  -2.5584
 0SA  H43  H  HCH1  0   0.237  -7.5683  -0.5752   0.3794
 0SA  H44  H  HOH1  0   0.447  -5.5953  -2.0587  -0.9586

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
 0SA  CL   CK   single  1.522  0.020  1.522
 0SA  CK   CJ   single  1.524  0.020  1.524
 0SA  CJ   CI   single  1.523  0.020  1.523
 0SA  CI   CH   single  1.524  0.020  1.524
 0SA  CH   CG   single  1.524  0.020  1.524
 0SA  CG   CF   single  1.524  0.020  1.524
 0SA  CF   CD   single  1.524  0.020  1.524
 0SA  CD   CC   single  1.524  0.020  1.524
 0SA  CC   CB   single  1.525  0.020  1.525
 0SA  CA   CB   single  1.520  0.020  1.520
 0SA  CA   S1'  single  1.820  0.020  1.820
 0SA  S1'  C1'  single  1.804  0.020  1.804
 0SA  O2'  C2'  single  1.402  0.020  1.402
 0SA  C1'  C2'  single  1.529  0.020  1.529
 0SA  C1'  O5'  single  1.400  0.020  1.400
 0SA  C2'  C3'  single  1.523  0.020  1.523
 0SA  O5'  C5'  single  1.416  0.020  1.416
 0SA  O6'  C6'  single  1.409  0.020  1.409
 0SA  C5'  C6'  single  1.513  0.020  1.513
 0SA  C5'  C4'  single  1.535  0.020  1.535
 0SA  C3'  O3'  single  1.409  0.020  1.409
 0SA  C3'  C4'  single  1.524  0.020  1.524
 0SA  C4'  O1   single  1.410  0.020  1.410
 0SA  O1   C1   single  1.400  0.020  1.400
 0SA  O6   C6   single  1.408  0.020  1.408
 0SA  C1   O5   single  1.393  0.020  1.393
 0SA  C1   C2   single  1.529  0.020  1.529
 0SA  O5   C5   single  1.421  0.020  1.421
 0SA  C6   C5   single  1.514  0.020  1.514
 0SA  C5   C4   single  1.530  0.020  1.530
 0SA  O2   C2   single  1.403  0.020  1.403
 0SA  C2   C3   single  1.527  0.020  1.527
 0SA  C4   C3   single  1.524  0.020  1.524
 0SA  C4   O4   single  1.407  0.020  1.407
 0SA  C3   O3   single  1.409  0.020  1.409
 0SA  CL   H1   single  0.970  0.020  1.090
 0SA  CL   H2   single  0.970  0.020  1.090
 0SA  CL   H3   single  0.970  0.020  1.090
 0SA  CK   H4   single  0.970  0.020  1.090
 0SA  CK   H5   single  0.970  0.020  1.090
 0SA  CJ   H6   single  0.970  0.020  1.090
 0SA  CJ   H7   single  0.970  0.020  1.090
 0SA  CI   H8   single  0.970  0.020  1.090
 0SA  CI   H9   single  0.970  0.020  1.090
 0SA  CH   H10  single  0.970  0.020  1.090
 0SA  CH   H11  single  0.970  0.020  1.090
 0SA  CG   H12  single  0.970  0.020  1.090
 0SA  CG   H13  single  0.970  0.020  1.090
 0SA  CF   H14  single  0.970  0.020  1.090
 0SA  CF   H15  single  0.970  0.020  1.090
 0SA  CD   H16  single  0.970  0.020  1.090
 0SA  CD   H17  single  0.970  0.020  1.090
 0SA  CC   H18  single  0.970  0.020  1.090
 0SA  CC   H19  single  0.970  0.020  1.090
 0SA  CB   H20  single  0.970  0.020  1.090
 0SA  CB   H21  single  0.970  0.020  1.090
 0SA  CA   H22  single  0.970  0.020  1.090
 0SA  CA   H23  single  0.970  0.020  1.090
 0SA  C1'  H24  single  0.970  0.020  1.090
 0SA  C2'  H25  single  0.970  0.020  1.090
 0SA  O2'  H26  single  0.850  0.020  0.980
 0SA  C3'  H27  single  0.970  0.020  1.090
 0SA  O3'  H28  single  0.850  0.020  0.980
 0SA  C5'  H29  single  0.970  0.020  1.090
 0SA  C6'  H30  single  0.970  0.020  1.090
 0SA  C6'  H31  single  0.970  0.020  1.090
 0SA  O6'  H32  single  0.850  0.020  0.980
 0SA  C4'  H33  single  0.970  0.020  1.090
 0SA  C1   H34  single  0.970  0.020  1.090
 0SA  C5   H35  single  0.970  0.020  1.090
 0SA  C6   H36  single  0.970  0.020  1.090
 0SA  C6   H37  single  0.970  0.020  1.090
 0SA  O6   H38  single  0.850  0.020  0.980
 0SA  C4   H39  single  0.970  0.020  1.090
 0SA  O4   H40  single  0.850  0.020  0.980
 0SA  C3   H41  single  0.970  0.020  1.090
 0SA  O3   H42  single  0.850  0.020  0.980
 0SA  C2   H43  single  0.970  0.020  1.090
 0SA  O2   H44  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
 0SA  H3   CL   H2   107.45  3.000
 0SA  H3   CL   H1   107.55  3.000
 0SA  H2   CL   H1   107.61  3.000
 0SA  H3   CL   CK   111.25  3.000
 0SA  H2   CL   CK   111.11  3.000
 0SA  H1   CL   CK   111.67  3.000
 0SA  H5   CK   H4   106.06  3.000
 0SA  H5   CK   CJ   109.27  3.000
 0SA  H4   CK   CJ   109.19  3.000
 0SA  H5   CK   CL   109.65  3.000
 0SA  H4   CK   CL   109.57  3.000
 0SA  CJ   CK   CL   112.87  3.000
 0SA  H7   CJ   H6   106.02  3.000
 0SA  H7   CJ   CI   109.26  3.000
 0SA  H6   CJ   CI   109.55  3.000
 0SA  H7   CJ   CK   109.22  3.000
 0SA  H6   CJ   CK   109.22  3.000
 0SA  CI   CJ   CK   113.30  3.000
 0SA  H9   CI   H8   106.04  3.000
 0SA  H9   CI   CH   109.33  3.000
 0SA  H8   CI   CH   109.14  3.000
 0SA  H9   CI   CJ   109.45  3.000
 0SA  H8   CI   CJ   109.24  3.000
 0SA  CH   CI   CJ   113.38  3.000
 0SA  H11  CH   H10  106.06  3.000
 0SA  H11  CH   CG   109.17  3.000
 0SA  H10  CH   CG   109.61  3.000
 0SA  H11  CH   CI   109.27  3.000
 0SA  H10  CH   CI   109.35  3.000
 0SA  CG   CH   CI   113.13  3.000
 0SA  H13  CG   H12  106.04  3.000
 0SA  H13  CG   CF   109.36  3.000
 0SA  H12  CG   CF   109.14  3.000
 0SA  H13  CG   CH   109.49  3.000
 0SA  H12  CG   CH   109.13  3.000
 0SA  CF   CG   CH   113.41  3.000
 0SA  H15  CF   H14  106.07  3.000
 0SA  H15  CF   CD   109.12  3.000
 0SA  H14  CF   CD   109.59  3.000
 0SA  H15  CF   CG   109.30  3.000
 0SA  H14  CF   CG   109.43  3.000
 0SA  CD   CF   CG   113.09  3.000
 0SA  H17  CD   H16  106.11  3.000
 0SA  H17  CD   CC   109.42  3.000
 0SA  H16  CD   CC   109.25  3.000
 0SA  H17  CD   CF   109.57  3.000
 0SA  H16  CD   CF   109.13  3.000
 0SA  CC   CD   CF   113.12  3.000
 0SA  H19  CC   H18  106.23  3.000
 0SA  H19  CC   CB   109.10  3.000
 0SA  H18  CC   CB   109.56  3.000
 0SA  H19  CC   CD   109.38  3.000
 0SA  H18  CC   CD   109.51  3.000
 0SA  CB   CC   CD   112.85  3.000
 0SA  H21  CB   H20  106.69  3.000
 0SA  H21  CB   CA   109.68  3.000
 0SA  H20  CB   CA   109.73  3.000
 0SA  H21  CB   CC   109.86  3.000
 0SA  H20  CB   CC   109.30  3.000
 0SA  CA   CB   CC   111.47  3.000
 0SA  H23  CA   H22  108.26  3.000
 0SA  H23  CA   S1'  108.56  3.000
 0SA  H22  CA   S1'  108.70  3.000
 0SA  H23  CA   CB   110.61  3.000
 0SA  H22  CA   CB   110.56  3.000
 0SA  S1'  CA   CB   110.09  3.000
 0SA  C1'  S1'  CA   100.64  3.000
 0SA  H24  C1'  O5'  110.95  3.000
 0SA  H24  C1'  C2'  109.08  3.000
 0SA  O5'  C1'  C2'  110.29  3.000
 0SA  H24  C1'  S1'  107.70  3.000
 0SA  O5'  C1'  S1'  109.15  3.000
 0SA  C2'  C1'  S1'  109.62  3.000
 0SA  H25  C2'  C3'  109.07  3.000
 0SA  H25  C2'  O2'  111.68  3.000
 0SA  C3'  C2'  O2'  107.25  3.000
 0SA  H25  C2'  C1'  108.55  3.000
 0SA  C3'  C2'  C1'  108.31  3.000
 0SA  O2'  C2'  C1'  111.89  3.000
 0SA  H26  O2'  C2'  108.27  3.000
 0SA  H27  C3'  C4'  107.55  3.000
 0SA  H27  C3'  O3'  110.61  3.000
 0SA  C4'  C3'  O3'  107.97  3.000
 0SA  H27  C3'  C2'  107.48  3.000
 0SA  C4'  C3'  C2'  111.39  3.000
 0SA  O3'  C3'  C2'  111.78  3.000
 0SA  H28  O3'  C3'  108.72  3.000
 0SA  C5'  O5'  C1'  113.11  3.000
 0SA  H29  C5'  C4'  108.30  3.000
 0SA  H29  C5'  C6'  109.02  3.000
 0SA  C4'  C5'  C6'  112.72  3.000
 0SA  H29  C5'  O5'  110.13  3.000
 0SA  C4'  C5'  O5'  109.38  3.000
 0SA  C6'  C5'  O5'  107.28  3.000
 0SA  H31  C6'  H30  107.20  3.000
 0SA  H31  C6'  O6'  111.71  3.000
 0SA  H30  C6'  O6'  111.39  3.000
 0SA  H31  C6'  C5'  108.88  3.000
 0SA  H30  C6'  C5'  108.98  3.000
 0SA  O6'  C6'  C5'  108.62  3.000
 0SA  H32  O6'  C6'  107.83  3.000
 0SA  H33  C4'  O1   110.77  3.000
 0SA  H33  C4'  C5'  109.06  3.000
 0SA  O1   C4'  C5'  110.98  3.000
 0SA  H33  C4'  C3'  109.56  3.000
 0SA  O1   C4'  C3'  106.58  3.000
 0SA  C5'  C4'  C3'  109.85  3.000
 0SA  C1   O1   C4'  120.48  3.000
 0SA  H34  C1   C2   110.11  3.000
 0SA  H34  C1   O5   106.08  3.000
 0SA  C2   C1   O5   110.09  3.000
 0SA  H34  C1   O1   110.75  3.000
 0SA  C2   C1   O1   108.21  3.000
 0SA  O5   C1   O1   111.60  3.000
 0SA  C5   O5   C1   115.60  3.000
 0SA  H35  C5   C4   108.67  3.000
 0SA  H35  C5   C6   108.67  3.000
 0SA  C4   C5   C6   112.13  3.000
 0SA  H35  C5   O5   110.24  3.000
 0SA  C4   C5   O5   110.11  3.000
 0SA  C6   C5   O5   107.00  3.000
 0SA  H37  C6   H36  107.15  3.000
 0SA  H37  C6   O6   111.91  3.000
 0SA  H36  C6   O6   111.59  3.000
 0SA  H37  C6   C5   108.98  3.000
 0SA  H36  C6   C5   108.39  3.000
 0SA  O6   C6   C5   108.72  3.000
 0SA  H38  O6   C6   108.05  3.000
 0SA  H39  C4   C3   108.05  3.000
 0SA  H39  C4   O4   111.01  3.000
 0SA  C3   C4   O4   111.83  3.000
 0SA  H39  C4   C5   108.31  3.000
 0SA  O4   C4   C5   107.73  3.000
 0SA  C3   C4   C5   109.86  3.000
 0SA  H40  O4   C4   108.29  3.000
 0SA  H41  C3   C2   109.15  3.000
 0SA  H41  C3   O3   110.53  3.000
 0SA  C2   C3   O3   111.54  3.000
 0SA  H41  C3   C4   108.42  3.000
 0SA  O3   C3   C4   107.49  3.000
 0SA  C2   C3   C4   109.65  3.000
 0SA  H42  O3   C3   108.13  3.000
 0SA  H43  C2   O2   106.55  3.000
 0SA  H43  C2   C3   108.03  3.000
 0SA  O2   C2   C3   112.42  3.000
 0SA  H43  C2   C1   107.15  3.000
 0SA  C3   C2   C1   109.69  3.000
 0SA  O2   C2   C1   112.71  3.000
 0SA  H44  O2   C2   109.79  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
 0SA  Var_01  H22  CA  S1'  C1'    55.48  30.0  1
 0SA  Var_02  CI   CJ  CK   CL    179.01  30.0  3
 0SA  Var_03  CH   CI  CJ   CK   -179.83  30.0  3
 0SA  Var_04  CG   CH  CI   CJ    177.60  30.0  3
 0SA  Var_05  CF   CG  CH   CI   -179.96  30.0  3
 0SA  Var_06  CD   CF  CG   CH    176.33  30.0  3
 0SA  Var_07  CC   CD  CF   CG    179.65  30.0  3
 0SA  Var_08  CB   CC  CD   CF    176.16  30.0  3
 0SA  Var_09  CA   CB  CC   CD    179.07  30.0  3
 0SA  Var_10  S1'  CA  CB   CC    176.30  30.0  2
 0SA  Var_11  H1   CL  CK   CJ   -179.95  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
 0SA  chir_01  C1'  S1'  C2'  O5'  negativ
 0SA  chir_02  C2'  O2'  C1'  C3'  negativ
 0SA  chir_03  C3'  O3'  C2'  C4'  positiv
 0SA  chir_04  C5'  O5'  C6'  C4'  positiv
 0SA  chir_05  C4'  O1   C3'  C5'  negativ
 0SA  chir_06  C1   O1   O5   C2   negativ
 0SA  chir_07  C5   O5   C6   C4   positiv
 0SA  chir_08  C4   O4   C5   C3   positiv
 0SA  chir_09  C3   O3   C4   C2   negativ
 0SA  chir_10  C2   O2   C3   C1   positiv

