# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun  3 23:33:50 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 2-(trimethylsilyl)ethyl 4-O-beta-D-galactopyranosyl-6-Se-methyl-6-seleno-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[Se]C[C@H]1O[C@@H](OCC[Si](C)(C)C)[C@H](O)[C@@H](O)[C@@H]1O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O
#
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
 LSE  LSE  '2-(trimethylsilyl)ethyl 4-O-beta-D-galactopyranosyl-6-Se-methyl-6-seleno-beta-D-glucopyranoside'  ligand  66  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LSE
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
 LSE  O4   O   OH1   0  -0.669  -1.1182   3.5693  -1.4770
 LSE  C9   C   CH1   0  -0.031  -0.7175   2.5686  -0.5752
 LSE  C10  C   CH1   0   0.007   0.6198   2.0228  -1.0694
 LSE  O3   O   OH1   0  -0.655   1.6218   3.0015  -1.0361
 LSE  C8   C   CH1   0   0.299  -1.7365   1.4374  -0.5029
 LSE  O5   O   O2    0  -0.502  -2.9099   1.9209   0.0247
 LSE  C13  C   CH2   0  -0.152  -4.0566   1.1165  -0.2446
 LSE  C14  C   CH2   0  -0.754  -5.2755   1.7309   0.4039
 LSE  SI   SI  SI    0   1.041  -6.8802   0.7940   0.0136
 LSE  C18  C   CH3   0  -0.982  -6.6733  -1.0214   0.4783
 LSE  C17  C   CH3   0  -0.970  -8.2812   1.5653   1.0076
 LSE  C16  C   CH3   0  -0.980  -7.2469   0.9375  -1.8304
 LSE  O2   O   O2    0  -0.497  -1.2453   0.4296   0.3492
 LSE  C7   C   CH1   0   0.041  -0.0757  -0.1886  -0.1400
 LSE  C11  C   CH2   0  -0.625   0.2305  -1.3526   0.7793
 LSE  SE6  SE  SE    0   0.048  -1.3624  -2.4891   0.9312
 LSE  C12  C   CH3   0  -0.807  -0.4301  -4.1439   1.3849
 LSE  C6   C   CH1   0   0.027   1.0601   0.8439  -0.2088
 LSE  O1   O   O2    0  -0.513   2.1964   0.2485  -0.8043
 LSE  C5   C   CH1   0   0.292   3.2693  -0.0257   0.0211
 LSE  O    O   O2    0  -0.476   4.0143   1.1456   0.1935
 LSE  C4   C   CH1   0  -0.030   4.1248  -1.1022  -0.6464
 LSE  O7   O   OH1   0  -0.666   3.4298  -2.3204  -0.7738
 LSE  C3   C   CH1   0   0.002   5.3502  -1.3615   0.2212
 LSE  O8   O   OH1   0  -0.674   6.2537  -2.2520  -0.3859
 LSE  C2   C   CH1   0  -0.002   6.0947  -0.0570   0.4951
 LSE  O9   O   OH1   0  -0.671   6.6756   0.4645  -0.6744
 LSE  C1   C   CH1   0  -0.018   5.1156   0.9665   1.0595
 LSE  C    C   CH2   0  -0.153   5.7680   2.3121   1.2966
 LSE  O10  O   OH1   0  -0.669   4.8957   3.1112   2.0589
 LSE  H1   H   HOH1  0   0.457  -1.8591   4.0489  -1.0933
 LSE  H2   H   HCH1  0   0.224  -0.5815   2.9722   0.4402
 LSE  H3   H   HCH1  0   0.212   0.4699   1.6471  -2.0961
 LSE  H4   H   HOH1  0   0.450   1.3404   3.7318  -1.5974
 LSE  H5   H   HCH1  0   0.187  -1.8977   1.0186  -1.5147
 LSE  H6   H   HCH2  0   0.208  -4.1878   1.0408  -1.3319
 LSE  H7   H   HCH2  0   0.212  -3.8964   0.1002   0.1320
 LSE  H8   H   HCH2  0   0.244  -5.1450   1.7611   1.4905
 LSE  H9   H   HCH2  0   0.243  -5.3958   2.7670   0.0702
 LSE  H10  H   HCH3  0   0.242  -6.3978  -1.1360   1.5284
 LSE  H11  H   HCH3  0   0.243  -7.5971  -1.5798   0.3161
 LSE  H12  H   HCH3  0   0.239  -5.8955  -1.4995  -0.1202
 LSE  H13  H   HCH3  0   0.241  -8.3739   2.6329   0.7999
 LSE  H14  H   HCH3  0   0.241  -9.2377   1.0989   0.7639
 LSE  H15  H   HCH3  0   0.242  -8.1214   1.4484   2.0811
 LSE  H16  H   HCH3  0   0.240  -6.4330   0.5363  -2.4380
 LSE  H17  H   HCH3  0   0.241  -8.1531   0.3897  -2.0963
 LSE  H18  H   HCH3  0   0.241  -7.3946   1.9788  -2.1235
 LSE  H19  H   HCH1  0   0.232  -0.2476  -0.5743  -1.1581
 LSE  H20  H   HCH2  0   0.270   1.0394  -1.9546   0.3653
 LSE  H21  H   HCH2  0   0.269   0.5334  -1.0033   1.7694
 LSE  H22  H   HCH3  0   0.260   0.2959  -4.4036   0.6151
 LSE  H23  H   HCH3  0   0.263   0.0753  -4.0601   2.3459
 LSE  H24  H   HCH3  0   0.270  -1.1709  -4.9401   1.4495
 LSE  H25  H   HCH1  0   0.245   1.2857   1.2045   0.8037
 LSE  H26  H   HCH1  0   0.187   2.9307  -0.3955   1.0077
 LSE  H27  H   HCH1  0   0.230   4.4509  -0.7260  -1.6256
 LSE  H28  H   HOH1  0   0.461   2.8341  -2.2593  -1.5266
 LSE  H29  H   HCH1  0   0.216   5.0056  -1.7586   1.1894
 LSE  H30  H   HOH1  0   0.456   5.7638  -3.0191  -0.7016
 LSE  H31  H   HCH1  0   0.234   6.8563  -0.2480   1.2659
 LSE  H32  H   HOH1  0   0.452   7.1858  -0.2391  -1.0900
 LSE  H33  H   HCH1  0   0.227   4.7724   0.5774   2.0326
 LSE  H34  H   HCH2  0   0.200   6.7177   2.1381   1.8203
 LSE  H35  H   HCH2  0   0.207   6.0120   2.7782   0.3356
 LSE  H36  H   HOH1  0   0.456   5.2849   3.9869   2.1324

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
 LSE  O8   C3   single  1.406  0.020  1.406
 LSE  C3   C4   single  1.524  0.020  1.524
 LSE  C3   C2   single  1.527  0.020  1.527
 LSE  O7   C4   single  1.408  0.020  1.408
 LSE  O9   C2   single  1.406  0.020  1.406
 LSE  C4   C5   single  1.529  0.020  1.529
 LSE  C2   C1   single  1.525  0.020  1.525
 LSE  C1   O    single  1.412  0.020  1.412
 LSE  C1   C    single  1.514  0.020  1.514
 LSE  C5   O    single  1.399  0.020  1.399
 LSE  C5   O1   single  1.381  0.020  1.381
 LSE  C12  SE6  single  1.953  0.020  1.953
 LSE  O1   C6   single  1.414  0.020  1.414
 LSE  C    O10  single  1.407  0.020  1.407
 LSE  C11  SE6  single  1.963  0.020  1.963
 LSE  C11  C7   single  1.515  0.020  1.515
 LSE  C6   C7   single  1.537  0.020  1.537
 LSE  C6   C10  single  1.525  0.020  1.525
 LSE  C7   O2   single  1.410  0.020  1.410
 LSE  O3   C10  single  1.401  0.020  1.401
 LSE  C10  C9   single  1.527  0.020  1.527
 LSE  O2   C8   single  1.408  0.020  1.408
 LSE  C9   C8   single  1.524  0.020  1.524
 LSE  C9   O4   single  1.405  0.020  1.405
 LSE  C8   O5   single  1.374  0.020  1.374
 LSE  O5   C13  single  1.426  0.020  1.426
 LSE  C13  C14  single  1.511  0.020  1.511
 LSE  C16  SI   single  1.886  0.020  1.886
 LSE  C14  SI   single  1.899  0.020  1.899
 LSE  C17  SI   single  1.883  0.020  1.883
 LSE  SI   C18  single  1.885  0.020  1.885
 LSE  O4   H1   single  0.850  0.020  0.980
 LSE  C9   H2   single  0.970  0.020  1.090
 LSE  C10  H3   single  0.970  0.020  1.090
 LSE  O3   H4   single  0.850  0.020  0.980
 LSE  C8   H5   single  0.970  0.020  1.090
 LSE  C13  H6   single  0.970  0.020  1.090
 LSE  C13  H7   single  0.970  0.020  1.090
 LSE  C14  H8   single  0.970  0.020  1.090
 LSE  C14  H9   single  0.970  0.020  1.090
 LSE  C18  H10  single  0.970  0.020  1.090
 LSE  C18  H11  single  0.970  0.020  1.090
 LSE  C18  H12  single  0.970  0.020  1.090
 LSE  C17  H13  single  0.970  0.020  1.090
 LSE  C17  H14  single  0.970  0.020  1.090
 LSE  C17  H15  single  0.970  0.020  1.090
 LSE  C16  H16  single  0.970  0.020  1.090
 LSE  C16  H17  single  0.970  0.020  1.090
 LSE  C16  H18  single  0.970  0.020  1.090
 LSE  C7   H19  single  0.970  0.020  1.090
 LSE  C11  H20  single  0.970  0.020  1.090
 LSE  C11  H21  single  0.970  0.020  1.090
 LSE  C12  H22  single  0.970  0.020  1.090
 LSE  C12  H23  single  0.970  0.020  1.090
 LSE  C12  H24  single  0.970  0.020  1.090
 LSE  C6   H25  single  0.970  0.020  1.090
 LSE  C5   H26  single  0.970  0.020  1.090
 LSE  C4   H27  single  0.970  0.020  1.090
 LSE  O7   H28  single  0.850  0.020  0.980
 LSE  C3   H29  single  0.970  0.020  1.090
 LSE  O8   H30  single  0.850  0.020  0.980
 LSE  C2   H31  single  0.970  0.020  1.090
 LSE  O9   H32  single  0.850  0.020  0.980
 LSE  C1   H33  single  0.970  0.020  1.090
 LSE  C    H34  single  0.970  0.020  1.090
 LSE  C    H35  single  0.970  0.020  1.090
 LSE  O10  H36  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
 LSE  H1   O4   C9   108.57  3.000
 LSE  H2   C9   C8   108.11  3.000
 LSE  H2   C9   C10  108.75  3.000
 LSE  C8   C9   C10  109.61  3.000
 LSE  H2   C9   O4   111.46  3.000
 LSE  C8   C9   O4   111.61  3.000
 LSE  C10  C9   O4   107.25  3.000
 LSE  H3   C10  C6   107.53  3.000
 LSE  H3   C10  O3   110.92  3.000
 LSE  C6   C10  O3   108.67  3.000
 LSE  H3   C10  C9   107.69  3.000
 LSE  O3   C10  C9   111.65  3.000
 LSE  C6   C10  C9   110.28  3.000
 LSE  H4   O3   C10  107.87  3.000
 LSE  H5   C8   O2   109.46  3.000
 LSE  H5   C8   O5   111.08  3.000
 LSE  O2   C8   O5   108.50  3.000
 LSE  H5   C8   C9   109.56  3.000
 LSE  O5   C8   C9   109.14  3.000
 LSE  O2   C8   C9   109.06  3.000
 LSE  C13  O5   C8   114.55  3.000
 LSE  H7   C13  H6   107.09  3.000
 LSE  H7   C13  C14  110.34  3.000
 LSE  H6   C13  C14  110.90  3.000
 LSE  H7   C13  O5   109.92  3.000
 LSE  H6   C13  O5   108.79  3.000
 LSE  C14  C13  O5   109.77  3.000
 LSE  H9   C14  H8   106.82  3.000
 LSE  H9   C14  SI   108.14  3.000
 LSE  H8   C14  SI   108.57  3.000
 LSE  H9   C14  C13  110.03  3.000
 LSE  H8   C14  C13  109.94  3.000
 LSE  SI   C14  C13  113.13  3.000
 LSE  C16  SI   C17  109.90  3.000
 LSE  C17  SI   C18  110.24  3.000
 LSE  C16  SI   C18  109.61  3.000
 LSE  C18  SI   C14  109.37  3.000
 LSE  C17  SI   C14  108.55  3.000
 LSE  C16  SI   C14  109.14  3.000
 LSE  H12  C18  H11  107.31  3.000
 LSE  H12  C18  H10  107.55  3.000
 LSE  H11  C18  H10  107.63  3.000
 LSE  H12  C18  SI   111.40  3.000
 LSE  H11  C18  SI   111.29  3.000
 LSE  H10  C18  SI   111.46  3.000
 LSE  H15  C17  H14  107.58  3.000
 LSE  H15  C17  H13  107.72  3.000
 LSE  H14  C17  H13  107.52  3.000
 LSE  H15  C17  SI   111.49  3.000
 LSE  H14  C17  SI   111.04  3.000
 LSE  H13  C17  SI   111.30  3.000
 LSE  H18  C16  H17  107.51  3.000
 LSE  H18  C16  H16  107.57  3.000
 LSE  H17  C16  H16  107.39  3.000
 LSE  H18  C16  SI   111.19  3.000
 LSE  H17  C16  SI   111.18  3.000
 LSE  H16  C16  SI   111.79  3.000
 LSE  C7   O2   C8   113.15  3.000
 LSE  H19  C7   C6   108.00  3.000
 LSE  H19  C7   C11  108.86  3.000
 LSE  C6   C7   C11  113.22  3.000
 LSE  H19  C7   O2   110.15  3.000
 LSE  C6   C7   O2   109.51  3.000
 LSE  C11  C7   O2   107.10  3.000
 LSE  H21  C11  H20  108.36  3.000
 LSE  H21  C11  SE6  109.87  3.000
 LSE  H20  C11  SE6  108.17  3.000
 LSE  H21  C11  C7   111.12  3.000
 LSE  H20  C11  C7   110.12  3.000
 LSE  SE6  C11  C7   109.14  3.000
 LSE  C12  SE6  C11   96.96  3.000
 LSE  H24  C12  H23  108.64  3.000
 LSE  H24  C12  H22  108.71  3.000
 LSE  H23  C12  H22  109.42  3.000
 LSE  H24  C12  SE6  107.96  3.000
 LSE  H23  C12  SE6  111.19  3.000
 LSE  H22  C12  SE6  110.85  3.000
 LSE  H25  C6   O1   111.18  3.000
 LSE  H25  C6   C7   109.35  3.000
 LSE  O1   C6   C7   109.26  3.000
 LSE  H25  C6   C10  109.02  3.000
 LSE  C7   C6   C10  109.35  3.000
 LSE  O1   C6   C10  108.65  3.000
 LSE  C5   O1   C6   117.13  3.000
 LSE  H26  C5   C4   108.98  3.000
 LSE  H26  C5   O    109.45  3.000
 LSE  C4   C5   O    110.21  3.000
 LSE  H26  C5   O1   111.19  3.000
 LSE  O    C5   O1   108.73  3.000
 LSE  C4   C5   O1   108.28  3.000
 LSE  C1   O    C5   112.62  3.000
 LSE  H27  C4   C3   109.10  3.000
 LSE  H27  C4   O7   111.23  3.000
 LSE  C3   C4   O7   107.53  3.000
 LSE  H27  C4   C5   108.32  3.000
 LSE  O7   C4   C5   111.87  3.000
 LSE  C3   C4   C5   108.74  3.000
 LSE  H28  O7   C4   108.75  3.000
 LSE  H29  C3   C2   107.63  3.000
 LSE  H29  C3   O8   110.61  3.000
 LSE  C2   C3   O8   107.77  3.000
 LSE  H29  C3   C4   108.07  3.000
 LSE  C2   C3   C4   110.42  3.000
 LSE  O8   C3   C4   112.25  3.000
 LSE  H30  O8   C3   108.60  3.000
 LSE  H31  C2   C1   107.56  3.000
 LSE  H31  C2   O9   111.16  3.000
 LSE  C1   C2   O9   108.92  3.000
 LSE  H31  C2   C3   108.35  3.000
 LSE  C1   C2   C3   109.08  3.000
 LSE  O9   C2   C3   111.66  3.000
 LSE  H32  O9   C2   107.87  3.000
 LSE  H33  C1   C    108.03  3.000
 LSE  H33  C1   C2   106.84  3.000
 LSE  C    C1   C2   112.20  3.000
 LSE  H33  C1   O    110.07  3.000
 LSE  C    C1   O    108.62  3.000
 LSE  C2   C1   O    111.03  3.000
 LSE  H35  C    H34  107.04  3.000
 LSE  H35  C    O10  111.81  3.000
 LSE  H34  C    O10  111.57  3.000
 LSE  H35  C    C1   109.67  3.000
 LSE  H34  C    C1   107.85  3.000
 LSE  O10  C    C1   108.81  3.000
 LSE  H36  O10  C    107.93  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
 LSE  Var_01  C14  C13  O5   C8   178.93  30.0  3
 LSE  Var_02  SI   C14  C13  O5   176.36  30.0  3
 LSE  Var_03  C16  SI   C14  C13  -65.47  30.0  3
 LSE  Var_04  H16  C16  SI   C14   58.68  30.0  3
 LSE  Var_05  H13  C17  SI   C14   56.52  30.0  3
 LSE  Var_06  H10  C18  SI   C14   56.81  30.0  3
 LSE  Var_07  H22  C12  SE6  C11  -57.34  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
 LSE  chir_01  C9   C10  C8   O4   positiv
 LSE  chir_02  C10  O3   C9   C6   positiv
 LSE  chir_03  C8   O5   O2   C9   positiv
 LSE  chir_04  C7   O2   C6   C11  negativ
 LSE  chir_05  C6   O1   C10  C7   negativ
 LSE  chir_06  C5   O1   O    C4   positiv
 LSE  chir_07  C4   O7   C5   C3   negativ
 LSE  chir_08  C3   O8   C4   C2   positiv
 LSE  chir_09  C2   O9   C1   C3   negativ
 LSE  chir_10  C1   O    C2   C    negativ

