# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jul  8 09:45:27 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 4-thio-beta-D-glucopyranosyl-(1->4)-4-thio-beta-D-glucopyranosyl-(1->4)-1,4-dithio-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](S[C@H]2[C@H](O)[C@@H](O)[C@@H](O[C@@H]2CO)S[C@H]3[C@H](O)[C@@H](O)[C@H](S)O[C@@H]3CO)[C@H](O)[C@@H](O)[C@@H]1S
#
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
 DP5  DP5  4-thio-beta-D-glucopyranosyl-(1->4)-4-thio-beta-D-glucopyranosyl-(1->4)-1,4-dithio-beta-D-glucopyranose  saccharide  66  34  .  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_DP5
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
 DP5  C1A   C  CH1   0  -0.146  -0.5429   0.1170  -4.0908
 DP5  C2A   C  CH1   0   0.025  -1.6217   0.2409  -5.1667
 DP5  C3A   C  CH1   0   0.078  -1.1046  -0.4013  -6.4537
 DP5  C4A   C  CH1   0  -0.443   0.2443   0.1938  -6.8422
 DP5  C5A   C  CH1   0   0.026   1.2178   0.0916  -5.6649
 DP5  C6A   C  CH2   0  -0.148   2.5400   0.7864  -5.9222
 DP5  O2A   O  OH1   0  -0.659  -2.7933  -0.4380  -4.8067
 DP5  O3A   O  OH1   0  -0.660  -1.9950  -0.2001  -7.5178
 DP5  S4A   S  S2    0  -0.223   0.9604  -0.6914  -8.2713
 DP5  O5A   O  O2    0  -0.479   0.6435   0.7238  -4.5330
 DP5  O6A   O  OH1   0  -0.661   3.3517   0.6176  -4.7872
 DP5  C1B   C  CH1   0  -0.149   0.4599  -0.2126   1.4463
 DP5  C2B   C  CH1   0   0.036   1.4858  -0.4368   0.3335
 DP5  C3B   C  CH1   0   0.082   1.0104   0.2804  -0.9260
 DP5  C4B   C  CH1   0  -0.467  -0.4392  -0.1002  -1.2587
 DP5  C5B   C  CH1   0   0.028  -1.3562   0.0437  -0.0394
 DP5  C6B   C  CH2   0  -0.144  -2.7399  -0.5325  -0.2707
 DP5  O2B   O  OH1   0  -0.656   2.7358   0.0886   0.6787
 DP5  O3B   O  OH1   0  -0.672   1.8938  -0.0664  -1.9529
 DP5  S4B   S  S2    0   0.021  -1.0858   0.9671  -2.5930
 DP5  O5B   O  O2    0  -0.478  -0.7988  -0.6813   1.0430
 DP5  O6B   O  OH1   0  -0.662  -3.4933  -0.3443   0.9012
 DP5  C1C   C  CH1   0  -0.154  -0.3264   0.1152   7.0162
 DP5  C2C   C  CH1   0   0.036  -1.3476   0.4842   5.9388
 DP5  C3C   C  CH1   0   0.083  -0.9942  -0.2552   4.6533
 DP5  C4C   C  CH1   0  -0.468   0.4819  -0.0443   4.2906
 DP5  C5C   C  CH1   0   0.029   1.3977  -0.3331   5.4874
 DP5  C6C   C  CH2   0  -0.147   2.8428   0.0458   5.2262
 DP5  O2C   O  OH1   0  -0.658  -2.6436   0.1032   6.3052
 DP5  O3C   O  OH1   0  -0.673  -1.8575   0.2139   3.6583
 DP5  S4C   S  S2    0   0.015   0.9587  -1.1456   2.9113
 DP5  O5C   O  O2    0  -0.462   0.9678   0.4357   6.5936
 DP5  O6C   O  OH1   0  -0.667   3.5934  -0.2438   6.3791
 DP5  H1A   H  HCH1  0   0.273  -0.3855  -0.9432  -3.8470
 DP5  H2A   H  HCH1  0   0.234  -1.8079   1.3089  -5.3558
 DP5  H3A   H  HCH1  0   0.222  -0.9567  -1.4745  -6.2564
 DP5  H4A   H  HCH1  0   0.293   0.1182   1.2476  -7.1092
 DP5  H5A   H  HCH1  0   0.239   1.4004  -0.9718  -5.4432
 DP5  H6A1  H  HCH2  0   0.210   2.3478   1.8455  -6.1400
 DP5  H6A2  H  HCH2  0   0.213   3.0020   0.3553  -6.8173
 DP5  HO2A  H  HOH1  0   0.454  -3.2093   0.0308  -4.0749
 DP5  HO3A  H  HOH1  0   0.458  -2.8008  -0.6951  -7.3391
 DP5  HS4A  H  HSH1  0   0.239  -0.0389  -0.4507  -9.1247
 DP5  HO6A  H  HOH1  0   0.461   4.1628   1.1158  -4.9222
 DP5  H1B   H  HCH1  0   0.273   0.4286   0.8539   1.7094
 DP5  H2B   H  HCH1  0   0.232   1.5367  -1.5171   0.1252
 DP5  H3B   H  HCH1  0   0.220   1.0339   1.3619  -0.7193
 DP5  H4B   H  HCH1  0   0.302  -0.4741  -1.1365  -1.6103
 DP5  H5B   H  HCH1  0   0.242  -1.4421   1.1076   0.2334
 DP5  H6B1  H  HCH2  0   0.213  -3.1947  -0.0308  -1.1304
 DP5  H6B2  H  HCH2  0   0.207  -2.6388  -1.5944  -0.5326
 DP5  HO2B  H  HOH1  0   0.450   3.0628  -0.3910   1.4485
 DP5  HO3B  H  HOH1  0   0.459   1.7444   0.4863  -2.7314
 DP5  HO6B  H  HOH1  0   0.461  -4.3563  -0.7479   0.7718
 DP5  H1C   H  HCH1  0   0.271  -0.4180  -0.9526   7.2550
 DP5  H2C   H  HCH1  0   0.227  -1.2732   1.5677   5.7526
 DP5  H3C   H  HCH1  0   0.218  -1.1391  -1.3305   4.8427
 DP5  H4C   H  HCH1  0   0.300   0.6373   0.9895   3.9649
 DP5  H5C   H  HCH1  0   0.234   1.3428  -1.4052   5.7375
 DP5  H6C1  H  HCH2  0   0.214   3.2027  -0.5157   4.3590
 DP5  H6C2  H  HCH2  0   0.202   2.8867   1.1116   4.9608
 DP5  HO2C  H  HOH1  0   0.448  -2.8687   0.5491   7.1305
 DP5  HO3C  H  HOH1  0   0.459  -1.8037  -0.3446   2.8718
 DP5  HO6C  H  HOH1  0   0.459   4.5213  -0.1049   6.1703
 DP5  S1C   S  S2    0  -0.216  -0.6861   1.0599   8.5231
 DP5  HS1C  H  HSH1  0   0.245  -0.3919   0.1032   9.4083

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
 DP5  C1A  C2A   single  1.529  0.020  1.529
 DP5  C1A  O5A   single  1.404  0.020  1.404
 DP5  C1A  S4B   single  1.806  0.020  1.806
 DP5  C1A  H1A   single  0.970  0.020  1.090
 DP5  C2A  C3A   single  1.528  0.020  1.528
 DP5  C2A  O2A   single  1.401  0.020  1.401
 DP5  C2A  H2A   single  0.970  0.020  1.090
 DP5  C3A  C4A   single  1.525  0.020  1.525
 DP5  C3A  O3A   single  1.402  0.020  1.402
 DP5  C3A  H3A   single  0.970  0.020  1.090
 DP5  C4A  C5A   single  1.531  0.020  1.531
 DP5  C4A  S4A   single  1.827  0.020  1.827
 DP5  C4A  H4A   single  0.970  0.020  1.090
 DP5  C5A  C6A   single  1.516  0.020  1.516
 DP5  C5A  O5A   single  1.418  0.020  1.418
 DP5  C5A  H5A   single  0.970  0.020  1.090
 DP5  C6A  O6A   single  1.406  0.020  1.406
 DP5  C6A  H6A1  single  0.970  0.020  1.090
 DP5  C6A  H6A2  single  0.970  0.020  1.090
 DP5  O2A  HO2A  single  0.850  0.020  0.980
 DP5  O3A  HO3A  single  0.850  0.020  0.980
 DP5  S4A  HS4A  single  1.200  0.020  1.300
 DP5  O6A  HO6A  single  0.850  0.020  0.980
 DP5  C1B  C2B   single  1.530  0.020  1.530
 DP5  C1B  O5B   single  1.402  0.020  1.402
 DP5  C1B  S4C   single  1.807  0.020  1.807
 DP5  C1B  H1B   single  0.970  0.020  1.090
 DP5  C2B  C3B   single  1.525  0.020  1.525
 DP5  C2B  O2B   single  1.399  0.020  1.399
 DP5  C2B  H2B   single  0.970  0.020  1.090
 DP5  C3B  C4B   single  1.535  0.020  1.535
 DP5  C3B  O3B   single  1.398  0.020  1.398
 DP5  C3B  H3B   single  0.970  0.020  1.090
 DP5  C4B  C5B   single  1.532  0.020  1.532
 DP5  C4B  S4B   single  1.827  0.020  1.827
 DP5  C4B  H4B   single  0.970  0.020  1.090
 DP5  C5B  C6B   single  1.517  0.020  1.517
 DP5  C5B  O5B   single  1.417  0.020  1.417
 DP5  C5B  H5B   single  0.970  0.020  1.090
 DP5  C6B  O6B   single  1.406  0.020  1.406
 DP5  C6B  H6B1  single  0.970  0.020  1.090
 DP5  C6B  H6B2  single  0.970  0.020  1.090
 DP5  O2B  HO2B  single  0.850  0.020  0.980
 DP5  O3B  HO3B  single  0.850  0.020  0.980
 DP5  O6B  HO6B  single  0.850  0.020  0.980
 DP5  C1C  C2C   single  1.530  0.020  1.530
 DP5  C1C  S1C   single  1.815  0.020  1.815
 DP5  C1C  O5C   single  1.399  0.020  1.399
 DP5  C1C  H1C   single  0.970  0.020  1.090
 DP5  C2C  C3C   single  1.525  0.020  1.525
 DP5  C2C  O2C   single  1.400  0.020  1.400
 DP5  C2C  H2C   single  0.970  0.020  1.090
 DP5  C3C  C4C   single  1.535  0.020  1.535
 DP5  C3C  O3C   single  1.398  0.020  1.398
 DP5  C3C  H3C   single  0.970  0.020  1.090
 DP5  C4C  C5C   single  1.534  0.020  1.534
 DP5  C4C  S4C   single  1.828  0.020  1.828
 DP5  C4C  H4C   single  0.970  0.020  1.090
 DP5  C5C  C6C   single  1.517  0.020  1.517
 DP5  C5C  O5C   single  1.414  0.020  1.414
 DP5  C5C  H5C   single  0.970  0.020  1.090
 DP5  C6C  O6C   single  1.406  0.020  1.406
 DP5  C6C  H6C1  single  0.970  0.020  1.090
 DP5  C6C  H6C2  single  0.970  0.020  1.090
 DP5  S1C  HS1C  single  1.200  0.020  1.300
 DP5  O2C  HO2C  single  0.850  0.020  0.980
 DP5  O3C  HO3C  single  0.850  0.020  0.980
 DP5  O6C  HO6C  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
 DP5  H1A   C1A  S4B   108.25  3.000
 DP5  H1A   C1A  O5A   111.45  3.000
 DP5  S4B   C1A  O5A   108.16  3.000
 DP5  H1A   C1A  C2A   109.60  3.000
 DP5  S4B   C1A  C2A   109.48  3.000
 DP5  O5A   C1A  C2A   109.86  3.000
 DP5  H2A   C2A  O2A   111.89  3.000
 DP5  H2A   C2A  C3A   108.68  3.000
 DP5  O2A   C2A  C3A   107.20  3.000
 DP5  H2A   C2A  C1A   108.61  3.000
 DP5  O2A   C2A  C1A   111.71  3.000
 DP5  C3A   C2A  C1A   108.65  3.000
 DP5  H3A   C3A  O3A   111.17  3.000
 DP5  H3A   C3A  C4A   107.89  3.000
 DP5  O3A   C3A  C4A   108.21  3.000
 DP5  H3A   C3A  C2A   107.70  3.000
 DP5  O3A   C3A  C2A   111.35  3.000
 DP5  C4A   C3A  C2A   110.48  3.000
 DP5  H4A   C4A  S4A   108.72  3.000
 DP5  H4A   C4A  C5A   108.97  3.000
 DP5  S4A   C4A  C5A   108.66  3.000
 DP5  H4A   C4A  C3A   109.63  3.000
 DP5  S4A   C4A  C3A   110.91  3.000
 DP5  C5A   C4A  C3A   109.91  3.000
 DP5  H5A   C5A  O5A   109.69  3.000
 DP5  H5A   C5A  C6A   109.39  3.000
 DP5  O5A   C5A  C6A   106.52  3.000
 DP5  H5A   C5A  C4A   108.94  3.000
 DP5  O5A   C5A  C4A   109.06  3.000
 DP5  C6A   C5A  C4A   113.17  3.000
 DP5  H6A2  C6A  H6A1  106.93  3.000
 DP5  H6A2  C6A  O6A   111.65  3.000
 DP5  H6A1  C6A  O6A   112.16  3.000
 DP5  H6A2  C6A  C5A   109.03  3.000
 DP5  H6A1  C6A  C5A   108.84  3.000
 DP5  O6A   C6A  C5A   108.16  3.000
 DP5  HO2A  O2A  C2A   108.69  3.000
 DP5  HO3A  O3A  C3A   108.48  3.000
 DP5  HS4A  S4A  C4A    96.84  3.000
 DP5  C5A   O5A  C1A   113.63  3.000
 DP5  HO6A  O6A  C6A   108.15  3.000
 DP5  H1B   C1B  S4C   108.35  3.000
 DP5  H1B   C1B  O5B   111.57  3.000
 DP5  S4C   C1B  O5B   107.96  3.000
 DP5  H1B   C1B  C2B   109.60  3.000
 DP5  S4C   C1B  C2B   109.20  3.000
 DP5  O5B   C1B  C2B   110.10  3.000
 DP5  H2B   C2B  O2B   111.95  3.000
 DP5  H2B   C2B  C3B   108.63  3.000
 DP5  O2B   C2B  C3B   107.79  3.000
 DP5  H2B   C2B  C1B   108.20  3.000
 DP5  O2B   C2B  C1B   111.38  3.000
 DP5  C3B   C2B  C1B   108.82  3.000
 DP5  H3B   C3B  O3B   111.59  3.000
 DP5  H3B   C3B  C4B   107.72  3.000
 DP5  O3B   C3B  C4B   112.08  3.000
 DP5  H3B   C3B  C2B   107.46  3.000
 DP5  O3B   C3B  C2B   107.03  3.000
 DP5  C4B   C3B  C2B   110.90  3.000
 DP5  H4B   C4B  S4B   107.89  3.000
 DP5  H4B   C4B  C5B   108.98  3.000
 DP5  S4B   C4B  C5B   108.33  3.000
 DP5  H4B   C4B  C3B   109.53  3.000
 DP5  S4B   C4B  C3B   110.34  3.000
 DP5  C5B   C4B  C3B   111.67  3.000
 DP5  H5B   C5B  O5B   109.60  3.000
 DP5  H5B   C5B  C6B   109.48  3.000
 DP5  O5B   C5B  C6B   106.32  3.000
 DP5  H5B   C5B  C4B   109.54  3.000
 DP5  O5B   C5B  C4B   108.93  3.000
 DP5  C6B   C5B  C4B   112.89  3.000
 DP5  H6B2  C6B  H6B1  107.10  3.000
 DP5  H6B2  C6B  O6B   112.18  3.000
 DP5  H6B1  C6B  O6B   111.77  3.000
 DP5  H6B2  C6B  C5B   108.64  3.000
 DP5  H6B1  C6B  C5B   108.95  3.000
 DP5  O6B   C6B  C5B   108.12  3.000
 DP5  HO2B  O2B  C2B   108.25  3.000
 DP5  HO3B  O3B  C3B   110.62  3.000
 DP5  C4B   S4B  C1A   102.97  3.000
 DP5  C5B   O5B  C1B   113.69  3.000
 DP5  HO6B  O6B  C6B   108.22  3.000
 DP5  H1C   C1C  O5C   111.45  3.000
 DP5  H1C   C1C  S1C   108.01  3.000
 DP5  O5C   C1C  S1C   108.36  3.000
 DP5  H1C   C1C  C2C   109.40  3.000
 DP5  O5C   C1C  C2C   110.47  3.000
 DP5  S1C   C1C  C2C   109.09  3.000
 DP5  H2C   C2C  O2C   111.99  3.000
 DP5  H2C   C2C  C3C   108.59  3.000
 DP5  O2C   C2C  C3C   107.66  3.000
 DP5  H2C   C2C  C1C   108.13  3.000
 DP5  O2C   C2C  C1C   111.60  3.000
 DP5  C3C   C2C  C1C   108.79  3.000
 DP5  H3C   C3C  O3C   111.64  3.000
 DP5  H3C   C3C  C4C   107.54  3.000
 DP5  O3C   C3C  C4C   112.31  3.000
 DP5  H3C   C3C  C2C   107.34  3.000
 DP5  O3C   C3C  C2C   107.11  3.000
 DP5  C4C   C3C  C2C   110.83  3.000
 DP5  H4C   C4C  S4C   107.89  3.000
 DP5  H4C   C4C  C5C   108.97  3.000
 DP5  S4C   C4C  C5C   108.63  3.000
 DP5  H4C   C4C  C3C   109.67  3.000
 DP5  S4C   C4C  C3C   110.27  3.000
 DP5  C5C   C4C  C3C   111.34  3.000
 DP5  H5C   C5C  O5C   109.65  3.000
 DP5  H5C   C5C  C6C   109.24  3.000
 DP5  O5C   C5C  C6C   106.78  3.000
 DP5  H5C   C5C  C4C   109.28  3.000
 DP5  O5C   C5C  C4C   109.05  3.000
 DP5  C6C   C5C  C4C   112.79  3.000
 DP5  H6C2  C6C  H6C1  107.05  3.000
 DP5  H6C2  C6C  O6C   112.10  3.000
 DP5  H6C1  C6C  O6C   111.64  3.000
 DP5  H6C2  C6C  C5C   108.78  3.000
 DP5  H6C1  C6C  C5C   108.77  3.000
 DP5  O6C   C6C  C5C   108.42  3.000
 DP5  HO2C  O2C  C2C   108.31  3.000
 DP5  HO3C  O3C  C3C   110.54  3.000
 DP5  C4C   S4C  C1B   103.21  3.000
 DP5  C5C   O5C  C1C   113.15  3.000
 DP5  HO6C  O6C  C6C   107.91  3.000
 DP5  HS1C  S1C  C1C    97.68  3.000

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
 DP5  chir_01  C1A  C2A  O5A  S4B  negativ
 DP5  chir_02  C2A  O2A  C1A  C3A  negativ
 DP5  chir_03  C3A  O3A  C2A  C4A  positiv
 DP5  chir_04  C4A  S4A  C5A  C3A  positiv
 DP5  chir_05  C5A  O5A  C4A  C6A  negativ
 DP5  chir_06  C1B  S4C  O5B  C2B  positiv
 DP5  chir_07  C2B  O2B  C1B  C3B  negativ
 DP5  chir_08  C3B  O3B  C2B  C4B  positiv
 DP5  chir_09  C4B  S4B  C5B  C3B  positiv
 DP5  chir_10  C5B  O5B  C4B  C6B  negativ
 DP5  chir_11  C1C  C2C  S1C  O5C  positiv
 DP5  chir_12  C2C  O2C  C1C  C3C  negativ
 DP5  chir_13  C3C  O3C  C2C  C4C  positiv
 DP5  chir_14  C4C  S4C  C5C  C3C  positiv
 DP5  chir_15  C5C  O5C  C4C  C6C  negativ

