# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 01:23:16 2022
#   Inital geometry file: a 173 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{R},6~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-4,5-bis(oxidanyl)-3-(sulfoamino)-6-(sulfooxymethyl)oxan-2-yl]oxy-6-(4-methyl-2-oxidanylidene-chromen-7-yl)oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=O)Oc2cc(O[C@@H]3O[C@@H]([C@@H](O[C@H]4O[C@H](CO[S](O)(=O)=O)[C@@H](O)[C@H](O)[C@H]4N[S](O)(=O)=O)[C@H](O)[C@H]3O)C(O)=O)ccc12
#
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
 QG2  QG2  '(2~{S},3~{S},4~{R},5~{R},6~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-4,5-bis(oxidanyl)-3-(sulfoamino)-6-(sulfooxymethyl)oxan-2-yl]oxy-6-(4-methyl-2-oxidanylidene-chromen-7-yl)oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid'  ligand  68  44  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QG2
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
 QG2  C1    C  CH1    0   0.191  -19.5118  15.4728  57.9970
 QG2  C2    C  CH1    0   0.013  -18.6332  15.6951  56.7528
 QG2  C3    C  CH1    0   0.043  -18.2197  17.1570  56.5930
 QG2  C4    C  CH1    0  -0.060  -19.2514  18.0625  57.2687
 QG2  C5    C  CH1    0  -0.054  -19.2501  17.7461  58.7703
 QG2  C6    C  C      0   0.408  -20.4156  18.4451  59.5112
 QG2  O7    O  OH1    0  -0.668  -17.4552  14.9290  56.8310
 QG2  O8    O  OH1    0  -0.708  -18.0400  17.4071  55.2272
 QG2  O9    O  O2     0  -0.508  -18.8881  19.4280  57.1753
 QG2  O10   O  O2     0  -0.495  -19.2590  16.3410  59.0335
 QG2  O11   O  OC    -1  -0.608  -20.1079  19.4451  60.1894
 QG2  O12   O  O2     0  -0.495  -20.8554  15.5519  57.5498
 QG2  C13   C  CH1    0   0.279  -19.3409  20.1501  56.0742
 QG2  C14   C  CH1    0  -0.132  -18.6338  21.5095  56.0715
 QG2  C15   C  CH1    0  -0.003  -19.1166  22.3331  57.2629
 QG2  C16   C  CH1    0   0.025  -20.6343  22.4743  57.1935
 QG2  C17   C  CH1    0  -0.043  -21.2816  21.0925  57.1324
 QG2  C18   C  CH2    0  -0.165  -22.7690  21.2012  56.8688
 QG2  O19   O  O2     0  -0.499  -20.7281  20.3358  56.0701
 QG2  N20   N  NC1    0  -0.782  -17.1867  21.4040  56.1337
 QG2  O21   O  OH1    0  -0.670  -18.5013  23.6050  57.2077
 QG2  O22   O  OH1    0  -0.668  -21.1430  23.1349  58.3269
 QG2  O23   O  OC2    0  -0.614  -23.3256  19.8969  56.9068
 QG2  S24   S  S      0   1.529  -16.3574  20.8247  54.7739
 QG2  S25   S  S      0   1.573  -24.9010  19.7404  56.4615
 QG2  O26   O  OS     0  -0.729  -25.1034  18.3101  56.6786
 QG2  O27   O  OS     0  -0.743  -24.9564  20.1602  55.0593
 QG2  O28   O  OS    -1  -0.743  -25.6581  20.6121  57.3633
 QG2  O29   O  OS     0  -0.755  -16.2315  19.3632  54.9889
 QG2  O30   O  OS     0  -0.737  -15.0623  21.5068  54.8504
 QG2  O31   O  OS    -1  -0.732  -17.1557  21.1384  53.5801
 QG2  C32   C  CR6    0   0.454  -21.8601  15.0858  58.3026
 QG2  C33   C  CR16   0  -0.345  -23.1462  15.2928  57.7804
 QG2  C34   C  CR16   0  -0.315  -24.2464  14.7992  58.4345
 QG2  C35   C  CR66   0  -0.067  -24.1199  14.0814  59.6325
 QG2  C36   C  CR66   0   0.406  -22.8317  13.9011  60.1347
 QG2  C37   C  CR16   0  -0.467  -21.7024  14.3945  59.4964
 QG2  C38   C  CR6    0   0.269  -25.2260  13.5264  60.3712
 QG2  C39   C  CR16   0  -0.557  -24.9696  12.8583  61.5188
 QG2  C40   C  CR6    0   0.543  -23.6311  12.6838  62.0246
 QG2  O41   O  O      0  -0.470  -22.6223  13.2264  61.2884
 QG2  C42   C  CH3    0  -0.747  -26.6201  13.6933  59.8666
 QG2  O43   O  O      0  -0.435  -23.3220  12.1034  63.0368
 QG2  O44   O  O      0  -0.580  -21.5455  17.9549  59.3477
 QG2  H1    H  HCH1   0   0.257  -19.3184  14.4671  58.3881
 QG2  H2    H  HCH1   0   0.230  -19.2281  15.4112  55.8757
 QG2  H3    H  HCH1   0   0.205  -17.2751  17.2950  57.1432
 QG2  H4    H  HCH1   0   0.233  -20.2477  17.9021  56.8417
 QG2  H5    H  HCH1   0   0.214  -18.2994  18.1151  59.1720
 QG2  HO7   H  HOH1   0   0.453  -17.6742  14.0058  56.6685
 QG2  HO8   H  HOH1   0   0.463  -17.4047  18.1456  55.1207
 QG2  H13   H  HCH1   0   0.229  -19.1468  19.6203  55.1387
 QG2  H14   H  HCH1   0   0.247  -18.9619  22.0184  55.1540
 QG2  H15   H  HCH1   0   0.231  -18.8520  21.8160  58.1941
 QG2  H16   H  HCH1   0   0.211  -20.8847  23.0223  56.2713
 QG2  H17   H  HCH1   0   0.252  -21.1154  20.5961  58.0953
 QG2  H181  H  HCH2   0   0.214  -22.9298  21.6694  55.8909
 QG2  H18   H  HCH2   0   0.228  -23.2228  21.8391  57.6306
 QG2  HN20  H  HNC1   0   0.381  -16.7961  22.3091  56.3745
 QG2  HO21  H  HOH1   0   0.461  -18.2777  23.8845  58.0995
 QG2  HO22  H  HOH1   0   0.452  -20.8857  24.0608  58.2805
 QG2  H33   H  HCR6   0   0.267  -23.2601  15.8494  56.8598
 QG2  H34   H  HCR6   0   0.269  -25.2278  14.9714  58.0130
 QG2  H37   H  HCR6   0   0.296  -20.7379  14.2294  59.9560
 QG2  H39   H  HCR6   0   0.275  -25.7685  12.4258  62.1056
 QG2  H42   H  HCH3   0   0.267  -27.3385  13.2174  60.5301
 QG2  H421  H  HCH3   0   0.264  -26.8787  14.7501  59.7815
 QG2  H422  H  HCH3   0   0.263  -26.7293  13.2570  58.8723

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
 QG2  O27  S25   deloc     1.465  0.020  1.465
 QG2  O8   C3    single    1.400  0.020  1.400
 QG2  O29  S24   deloc     1.483  0.020  1.483
 QG2  O26  S25   deloc     1.461  0.020  1.461
 QG2  S25  O28   deloc     1.465  0.020  1.465
 QG2  S25  O23   single    1.645  0.020  1.645
 QG2  O19  C13   single    1.400  0.020  1.400
 QG2  O19  C17   single    1.417  0.020  1.417
 QG2  O7   C2    single    1.407  0.020  1.407
 QG2  C13  C14   single    1.532  0.020  1.532
 QG2  C13  O9    single    1.392  0.020  1.392
 QG2  C3   C2    single    1.528  0.020  1.528
 QG2  C3   C4    single    1.530  0.020  1.530
 QG2  C2   C1    single    1.539  0.020  1.539
 QG2  C18  O23   single    1.419  0.020  1.419
 QG2  C18  C17   single    1.514  0.020  1.514
 QG2  C14  N20   single    1.452  0.020  1.452
 QG2  C14  C15   single    1.527  0.020  1.527
 QG2  S24  O30   deloc     1.466  0.020  1.466
 QG2  S24  N20   single    1.695  0.020  1.695
 QG2  S24  O31   deloc     1.470  0.020  1.470
 QG2  C17  C16   single    1.527  0.020  1.527
 QG2  O9   C4    single    1.416  0.020  1.416
 QG2  C4   C5    single    1.535  0.020  1.535
 QG2  C16  C15   single    1.526  0.020  1.526
 QG2  C16  O22   single    1.407  0.020  1.407
 QG2  O12  C1    single    1.418  0.020  1.418
 QG2  O12  C32   single    1.339  0.020  1.339
 QG2  C15  O21   single    1.414  0.020  1.414
 QG2  C1   O10   single    1.376  0.020  1.376
 QG2  C33  C32   aromatic  1.403  0.020  1.403
 QG2  C33  C34   aromatic  1.372  0.020  1.372
 QG2  C32  C37   aromatic  1.389  0.020  1.389
 QG2  C5   O10   single    1.430  0.020  1.430
 QG2  C5   C6    single    1.548  0.020  1.548
 QG2  C34  C35   aromatic  1.402  0.020  1.402
 QG2  C6   O44   deloc     1.242  0.020  1.242
 QG2  C6   O11   deloc     1.247  0.020  1.247
 QG2  C37  C36   aromatic  1.388  0.020  1.388
 QG2  C35  C36   aromatic  1.394  0.020  1.394
 QG2  C35  C38   single    1.441  0.020  1.441
 QG2  C36  O41   single    1.353  0.020  1.353
 QG2  C42  C38   single    1.492  0.020  1.492
 QG2  C38  C39   double    1.352  0.020  1.352
 QG2  O41  C40   single    1.362  0.020  1.362
 QG2  C39  C40   single    1.442  0.020  1.442
 QG2  C40  O43   double    1.207  0.020  1.207
 QG2  C1   H1    single    0.970  0.020  1.090
 QG2  C2   H2    single    0.970  0.020  1.090
 QG2  C3   H3    single    0.970  0.020  1.090
 QG2  C4   H4    single    0.970  0.020  1.090
 QG2  C5   H5    single    0.970  0.020  1.090
 QG2  O7   HO7   single    0.850  0.020  0.980
 QG2  O8   HO8   single    0.850  0.020  0.980
 QG2  C13  H13   single    0.970  0.020  1.090
 QG2  C14  H14   single    0.970  0.020  1.090
 QG2  C15  H15   single    0.970  0.020  1.090
 QG2  C16  H16   single    0.970  0.020  1.090
 QG2  C17  H17   single    0.970  0.020  1.090
 QG2  C18  H181  single    0.970  0.020  1.090
 QG2  C18  H18   single    0.970  0.020  1.090
 QG2  N20  HN20  single    0.890  0.020  1.040
 QG2  O21  HO21  single    0.850  0.020  0.980
 QG2  O22  HO22  single    0.850  0.020  0.980
 QG2  C33  H33   single    0.930  0.020  1.080
 QG2  C34  H34   single    0.930  0.020  1.080
 QG2  C37  H37   single    0.930  0.020  1.080
 QG2  C39  H39   single    0.930  0.020  1.080
 QG2  C42  H42   single    0.970  0.020  1.090
 QG2  C42  H421  single    0.970  0.020  1.090
 QG2  C42  H422  single    0.970  0.020  1.090

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
 QG2  H1    C1   O12   109.32  3.000
 QG2  H1    C1   O10   106.13  3.000
 QG2  O12   C1   O10   112.12  3.000
 QG2  H1    C1   C2    108.67  3.000
 QG2  O10   C1   C2    114.39  3.000
 QG2  O12   C1   C2    106.13  3.000
 QG2  H2    C2   O7    110.94  3.000
 QG2  H2    C2   C3    108.10  3.000
 QG2  O7    C2   C3    107.47  3.000
 QG2  H2    C2   C1    107.41  3.000
 QG2  C3    C2   C1    112.16  3.000
 QG2  O7    C2   C1    110.75  3.000
 QG2  H3    C3   O8    110.78  3.000
 QG2  H3    C3   C4    106.47  3.000
 QG2  O8    C3   C4    114.31  3.000
 QG2  H3    C3   C2    107.44  3.000
 QG2  C4    C3   C2    109.73  3.000
 QG2  O8    C3   C2    107.92  3.000
 QG2  H4    C4   O9    110.41  3.000
 QG2  H4    C4   C5    110.60  3.000
 QG2  O9    C4   C5    105.26  3.000
 QG2  H4    C4   C3    110.76  3.000
 QG2  C5    C4   C3    108.03  3.000
 QG2  O9    C4   C3    111.63  3.000
 QG2  H5    C5   O10   105.60  3.000
 QG2  H5    C5   C6    109.01  3.000
 QG2  O10   C5   C6    110.55  3.000
 QG2  H5    C5   C4    106.85  3.000
 QG2  C6    C5   C4    112.00  3.000
 QG2  O10   C5   C4    112.51  3.000
 QG2  O44   C6   O11   127.76  3.000
 QG2  O11   C6   C5    115.89  3.000
 QG2  O44   C6   C5    116.34  3.000
 QG2  HO7   O7   C2    108.80  3.000
 QG2  HO8   O8   C3    108.89  3.000
 QG2  C13   O9   C4    117.96  3.000
 QG2  C5    O10  C1    118.87  3.000
 QG2  C32   O12  C1    120.93  3.000
 QG2  H13   C13  O19   103.76  3.000
 QG2  H13   C13  C14   110.29  3.000
 QG2  O19   C13  C14   109.85  3.000
 QG2  H13   C13  O9    111.59  3.000
 QG2  C14   C13  O9    108.14  3.000
 QG2  O19   C13  O9    113.17  3.000
 QG2  H14   C14  N20   111.52  3.000
 QG2  H14   C14  C15   107.89  3.000
 QG2  N20   C14  C15   108.72  3.000
 QG2  H14   C14  C13   105.93  3.000
 QG2  C15   C14  C13   109.35  3.000
 QG2  N20   C14  C13   113.28  3.000
 QG2  H15   C15  O21   110.61  3.000
 QG2  H15   C15  C16   108.78  3.000
 QG2  O21   C15  C16   110.35  3.000
 QG2  H15   C15  C14   109.37  3.000
 QG2  O21   C15  C14   108.49  3.000
 QG2  C16   C15  C14   109.21  3.000
 QG2  H16   C16  O22   111.01  3.000
 QG2  H16   C16  C17   108.68  3.000
 QG2  O22   C16  C17   107.68  3.000
 QG2  H16   C16  C15   108.07  3.000
 QG2  O22   C16  C15   111.50  3.000
 QG2  C17   C16  C15   109.86  3.000
 QG2  H17   C17  O19   110.95  3.000
 QG2  H17   C17  C18   109.53  3.000
 QG2  O19   C17  C18   106.95  3.000
 QG2  H17   C17  C16   108.08  3.000
 QG2  C18   C17  C16   111.00  3.000
 QG2  O19   C17  C16   110.34  3.000
 QG2  H18   C18  H181  108.17  3.000
 QG2  H18   C18  O23   110.81  3.000
 QG2  H181  C18  O23   111.04  3.000
 QG2  H18   C18  C17   109.18  3.000
 QG2  H181  C18  C17   109.27  3.000
 QG2  O23   C18  C17   108.34  3.000
 QG2  C17   O19  C13   117.12  3.000
 QG2  HN20  N20  S24   107.87  3.000
 QG2  HN20  N20  C14   109.20  3.000
 QG2  S24   N20  C14   118.56  3.000
 QG2  HO21  O21  C15   109.07  3.000
 QG2  HO22  O22  C16   108.44  3.000
 QG2  S25   O23  C18   117.14  3.000
 QG2  O31   S24  O30   115.01  3.000
 QG2  O31   S24  O29   111.98  3.000
 QG2  O30   S24  O29   112.10  3.000
 QG2  O31   S24  N20   108.24  3.000
 QG2  O30   S24  N20   103.38  3.000
 QG2  O29   S24  N20   105.20  3.000
 QG2  O28   S25  O27   113.53  3.000
 QG2  O28   S25  O26   114.80  3.000
 QG2  O27   S25  O26   114.68  3.000
 QG2  O28   S25  O23   105.77  3.000
 QG2  O26   S25  O23   100.70  3.000
 QG2  O27   S25  O23   105.56  3.000
 QG2  C37   C32  C33   119.83  3.000
 QG2  C37   C32  O12   124.85  3.000
 QG2  C33   C32  O12   115.28  3.000
 QG2  H33   C33  C34   120.42  3.000
 QG2  H33   C33  C32   119.27  3.000
 QG2  C34   C33  C32   120.30  3.000
 QG2  H34   C34  C35   119.75  3.000
 QG2  H34   C34  C33   118.98  3.000
 QG2  C35   C34  C33   121.27  3.000
 QG2  C38   C35  C36   118.33  3.000
 QG2  C38   C35  C34   124.46  3.000
 QG2  C36   C35  C34   117.21  3.000
 QG2  O41   C36  C37   116.33  3.000
 QG2  O41   C36  C35   120.98  3.000
 QG2  C37   C36  C35   122.69  3.000
 QG2  H37   C37  C36   118.43  3.000
 QG2  H37   C37  C32   122.88  3.000
 QG2  C36   C37  C32   118.68  3.000
 QG2  C42   C38  C39   121.29  3.000
 QG2  C39   C38  C35   118.67  3.000
 QG2  C42   C38  C35   120.04  3.000
 QG2  H39   C39  C40   116.56  3.000
 QG2  H39   C39  C38   121.19  3.000
 QG2  C40   C39  C38   122.25  3.000
 QG2  O43   C40  O41   117.09  3.000
 QG2  O43   C40  C39   126.17  3.000
 QG2  O41   C40  C39   116.74  3.000
 QG2  C40   O41  C36   123.04  3.000
 QG2  H422  C42  H421  107.00  3.000
 QG2  H422  C42  H42   108.35  3.000
 QG2  H421  C42  H42   108.35  3.000
 QG2  H422  C42  C38   110.91  3.000
 QG2  H421  C42  C38   110.87  3.000
 QG2  H42   C42  C38   111.22  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
 QG2  CONST_01  C35   C34  C33  C32     0.00   0.0  0
 QG2  CONST_02  C35   C36  C37  C32     0.00   0.0  0
 QG2  CONST_03  C36   C37  C32  C33     0.00   0.0  0
 QG2  CONST_04  C36   C35  C34  C33     0.00   0.0  0
 QG2  CONST_05  C37   C32  C33  C34     0.00   0.0  0
 QG2  CONST_06  C37   C36  C35  C34     0.00   0.0  0
 QG2  CONST_07  C34   C33  C32  O12   180.00   0.0  0
 QG2  CONST_08  C36   C37  C32  O12   180.00   0.0  0
 QG2  CONST_09  H34   C34  C33  C32   180.00   0.0  0
 QG2  CONST_10  H37   C37  C32  C33   180.00   0.0  0
 QG2  CONST_11  H33   C33  C34  C35   180.00   0.0  0
 QG2  Var_01    C39   C38  C35  C34  -179.72  30.0  1
 QG2  Var_02    C40   C39  C38  C35    -0.02  30.0  1
 QG2  Var_03    C39   C40  O41  C36    -0.03  30.0  1
 QG2  Var_04    O41   C40  C39  C38    -0.04  30.0  1
 QG2  Var_05    C33   C32  O12  C1    176.53  30.0  2
 QG2  Var_06    H42   C42  C38  C35   179.78  30.0  3
 QG2  Var_07    O29   S24  N20  C14   -92.51  30.0  3
 QG2  Var_08    O27   S25  O23  C18    62.44  30.0  3
 QG2  Var_09    H181  C18  O23  S25   -52.53  30.0  1

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
 QG2  chir_01  C1   C2   O12  O10  positiv
 QG2  chir_02  C2   O7   C1   C3   negativ
 QG2  chir_03  C3   O8   C2   C4   positiv
 QG2  chir_04  C4   O9   C5   C3   positiv
 QG2  chir_05  C5   O10  C4   C6   negativ
 QG2  chir_06  C13  O19  O9   C14  positiv
 QG2  chir_07  C14  N20  C15  C13  positiv
 QG2  chir_08  C15  O21  C14  C16  positiv
 QG2  chir_09  C16  O22  C15  C17  negativ
 QG2  chir_10  C17  O19  C16  C18  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 QG2  plan-1  C5   0.020
 QG2  plan-1  C6   0.020
 QG2  plan-1  O11  0.020
 QG2  plan-1  O44  0.020
 QG2  plan-2  O12  0.020
 QG2  plan-2  C32  0.020
 QG2  plan-2  C33  0.020
 QG2  plan-2  C34  0.020
 QG2  plan-2  C35  0.020
 QG2  plan-2  C36  0.020
 QG2  plan-2  C37  0.020
 QG2  plan-2  C38  0.020
 QG2  plan-2  O41  0.020
 QG2  plan-2  H33  0.020
 QG2  plan-2  H34  0.020
 QG2  plan-2  H37  0.020
 QG2  plan-3  C39  0.020
 QG2  plan-3  C40  0.020
 QG2  plan-3  O41  0.020
 QG2  plan-3  O43  0.020

