# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 12:56:15 2021
#   Inital geometry file: a 145 line input string
#   Ligand name: 1-O-{6-chloro-5-[6-(dimethylamino)-2-methoxypyridin-3-yl]-1H-indole-3-carbonyl}-beta-D-glucopyranuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1nc(ccc1c2cc3c([nH]cc3C(=O)O[C@@H]4O[C@@H]([C@@H](O)[C@H](O)[C@H]4O)C(O)=O)cc2Cl)N(C)C
#
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
 HU7  HU7  '1-O-{6-chloro-5-[6-(dimethylamino)-2-methoxypyridin-3-yl]-1H-indole-3-carbonyl}-beta-D-glucopyranuronic acid'  ligand  60  36  .  2021-08-11  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HU7
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
 HU7  N3   N   NR15  0  -0.678  43.1046  -78.0752  -39.7817
 HU7  C4   C   CR16  0  -0.424  49.3124  -82.4838  -38.0498
 HU7  N2   N   N     0  -0.516  48.9467  -83.1382  -40.3149
 HU7  C7   C   CR6   0   0.484  47.9665  -82.2688  -40.4000
 HU7  C6   C   CR6   0  -0.155  47.5583  -81.4382  -39.3500
 HU7  C9   C   CR6   0   0.170  46.4279  -80.4974  -39.4836
 HU7  C13  C   CR16  0  -0.241  45.5920  -78.1950  -39.5867
 HU7  C20  C   CH1   0  -0.034  37.3701  -83.1167  -39.7178
 HU7  C21  C   CH1   0   0.009  37.3943  -83.5480  -41.1835
 HU7  C18  C   CH1   0   0.290  39.7145  -82.3869  -39.9920
 HU7  C16  C   CR5   0  -0.222  42.6317  -80.2495  -39.7966
 HU7  C19  C   CH1   0  -0.003  38.3413  -81.9606  -39.4928
 HU7  C1   C   CH3   0  -0.533  51.3251  -84.4851  -37.9381
 HU7  C2   C   CH3   0  -0.513  50.8148  -85.0539  -40.3058
 HU7  C3   C   CR6   0   0.533  49.6352  -83.2636  -39.1755
 HU7  C5   C   CR16  0  -0.156  48.2758  -81.5787  -38.1688
 HU7  O1   O   O2    0  -0.466  47.3088  -82.1571  -41.5583
 HU7  C10  C   CR16  0  -0.426  45.1328  -80.9837  -39.5870
 HU7  C11  C   CR56  0   0.131  44.0569  -80.1032  -39.6884
 HU7  C12  C   CR56  0   0.343  44.3105  -78.7198  -39.6819
 HU7  C14  C   CR6   0  -0.139  46.6277  -79.1025  -39.4933
 HU7  CL1  CL  CL    0  -0.131  48.2440  -78.4761  -39.4060
 HU7  C15  C   CR15  0   0.014  42.1072  -78.9767  -39.8489
 HU7  C17  C   C     0   0.542  41.8964  -81.4932  -39.8463
 HU7  O2   O   O     0  -0.444  42.3933  -82.5930  -39.8240
 HU7  O3   O   O2    0  -0.493  40.5664  -81.2829  -39.9166
 HU7  C22  C   CH1   0  -0.066  38.8421  -83.8759  -41.5665
 HU7  O4   O   O2    0  -0.489  39.6568  -82.7535  -41.3418
 HU7  C23  C   C     0   0.514  38.9275  -84.1908  -43.0468
 HU7  O5   O   O     0  -0.427  38.9891  -83.3433  -43.8975
 HU7  O6   O   OH1   0  -0.579  38.8990  -85.4901  -43.2802
 HU7  O7   O   OH1   0  -0.665  36.6199  -84.6932  -41.4185
 HU7  O9   O   OH1   0  -0.666  38.4664  -81.6338  -38.1370
 HU7  H1   H   HNR5  0   0.427  42.9740  -77.0760  -39.8010
 HU7  H2   H   HCR6  0   0.264  49.8414  -82.5766  -37.1136
 HU7  H3   H   HCR6  0   0.289  45.7715  -77.1285  -39.5911
 HU7  H4   H   HCH1  0   0.234  37.6961  -83.9683  -39.1022
 HU7  H5   H   HCH1  0   0.238  37.0602  -82.7043  -41.8047
 HU7  H6   H   HCH3  0   0.241  47.0275  -82.7594  -43.4540
 HU7  H7   H   HCH3  0   0.225  48.7239  -82.8432  -42.9332
 HU7  H8   H   HCH3  0   0.226  47.5693  -84.0618  -42.3727
 HU7  H9   H   HCH1  0   0.229  40.0914  -83.2193  -39.3807
 HU7  H10  H   HCH1  0   0.229  38.0074  -81.0975  -40.0904
 HU7  H11  H   HCH3  0   0.231  50.6743  -84.9922  -37.2184
 HU7  H12  H   HCH3  0   0.257  52.1651  -85.1408  -38.1502
 HU7  H13  H   HCH3  0   0.243  51.7246  -83.5899  -37.4601
 HU7  H14  H   HCH3  0   0.238  51.7624  -85.5778  -40.2045
 HU7  H15  H   HCH3  0   0.224  50.0179  -85.8004  -40.3774
 HU7  H16  H   HCH3  0   0.246  50.8323  -84.4981  -41.2407
 HU7  H17  H   HCR6  0   0.255  48.0085  -80.9707  -37.3128
 HU7  H18  H   HCR6  0   0.249  44.9715  -82.0526  -39.5750
 HU7  H19  H   HCR5  0   0.308  41.0817  -78.6550  -39.9327
 HU7  H20  H   HCH1  0   0.271  39.1874  -84.7398  -40.9806
 HU7  H21  H   HOH1  0   0.488  38.9034  -85.6602  -44.2351
 HU7  H22  H   HOH1  0   0.462  35.6921  -84.4397  -41.4394
 HU7  H24  H   HOH1  0   0.457  37.5890  -81.4276  -37.7971
 HU7  N1   N   NT    0  -0.481  50.6506  -84.1659  -39.1748
 HU7  O8   O   OH1   0  -0.670  36.0879  -82.6823  -39.3291
 HU7  C8   C   CH3   0  -0.410  47.6896  -83.0082  -42.6282
 HU7  H23  H   HOH1  0   0.464  35.5970  -83.4285  -38.9737

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
 HU7  O5   C23  double    1.202  0.020  1.202
 HU7  O6   C23  single    1.320  0.020  1.320
 HU7  C23  C22  single    1.516  0.020  1.516
 HU7  C8   O1   single    1.419  0.020  1.419
 HU7  C22  O4   single    1.405  0.020  1.405
 HU7  C22  C21  single    1.533  0.020  1.533
 HU7  O4   C18  single    1.400  0.020  1.400
 HU7  O1   C7   single    1.337  0.020  1.337
 HU7  O7   C21  single    1.402  0.020  1.402
 HU7  C21  C20  single    1.528  0.020  1.528
 HU7  C18  O3   single    1.397  0.020  1.397
 HU7  C18  C19  single    1.522  0.020  1.522
 HU7  C7   N2   aromatic  1.313  0.020  1.313
 HU7  C7   C6   aromatic  1.400  0.020  1.400
 HU7  O3   C17  single    1.348  0.020  1.348
 HU7  C2   N1   single    1.447  0.020  1.447
 HU7  N2   C3   aromatic  1.337  0.020  1.337
 HU7  C17  O2   double    1.207  0.020  1.207
 HU7  C17  C16  single    1.446  0.020  1.446
 HU7  C15  N3   aromatic  1.346  0.020  1.346
 HU7  C15  C16  aromatic  1.378  0.020  1.378
 HU7  N3   C12  aromatic  1.371  0.020  1.371
 HU7  C16  C11  aromatic  1.437  0.020  1.437
 HU7  C12  C11  aromatic  1.406  0.020  1.406
 HU7  C12  C13  aromatic  1.388  0.020  1.388
 HU7  C11  C10  aromatic  1.394  0.020  1.394
 HU7  C20  C19  single    1.527  0.020  1.527
 HU7  C20  O8   single    1.408  0.020  1.408
 HU7  C13  C14  aromatic  1.380  0.020  1.380
 HU7  C10  C9   aromatic  1.387  0.020  1.387
 HU7  C14  C9   aromatic  1.409  0.020  1.409
 HU7  C14  CL1  single    1.736  0.020  1.736
 HU7  C9   C6   single    1.477  0.020  1.477
 HU7  C19  O9   single    1.400  0.020  1.400
 HU7  C6   C5   aromatic  1.389  0.020  1.389
 HU7  C3   N1   single    1.358  0.020  1.358
 HU7  C3   C4   aromatic  1.407  0.020  1.407
 HU7  N1   C1   single    1.444  0.020  1.444
 HU7  C5   C4   aromatic  1.381  0.020  1.381
 HU7  N3   H1   single    0.860  0.020  1.020
 HU7  C4   H2   single    0.930  0.020  1.080
 HU7  C13  H3   single    0.930  0.020  1.080
 HU7  C20  H4   single    0.970  0.020  1.090
 HU7  C21  H5   single    0.970  0.020  1.090
 HU7  C8   H6   single    0.970  0.020  1.090
 HU7  C8   H7   single    0.970  0.020  1.090
 HU7  C8   H8   single    0.970  0.020  1.090
 HU7  C18  H9   single    0.970  0.020  1.090
 HU7  C19  H10  single    0.970  0.020  1.090
 HU7  C1   H11  single    0.970  0.020  1.090
 HU7  C1   H12  single    0.970  0.020  1.090
 HU7  C1   H13  single    0.970  0.020  1.090
 HU7  C2   H14  single    0.970  0.020  1.090
 HU7  C2   H15  single    0.970  0.020  1.090
 HU7  C2   H16  single    0.970  0.020  1.090
 HU7  C5   H17  single    0.930  0.020  1.080
 HU7  C10  H18  single    0.930  0.020  1.080
 HU7  C15  H19  single    0.930  0.020  1.080
 HU7  C22  H20  single    0.970  0.020  1.090
 HU7  O6   H21  single    0.850  0.020  0.980
 HU7  O7   H22  single    0.850  0.020  0.980
 HU7  O8   H23  single    0.850  0.020  0.980
 HU7  O9   H24  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
 HU7  H1   N3   C15  124.54  3.000
 HU7  H1   N3   C12  125.55  3.000
 HU7  C15  N3   C12  109.91  3.000
 HU7  H2   C4   C5   119.93  3.000
 HU7  H2   C4   C3   122.27  3.000
 HU7  C5   C4   C3   117.80  3.000
 HU7  C3   N2   C7   120.11  3.000
 HU7  O1   C7   C6   117.19  3.000
 HU7  C6   C7   N2   124.20  3.000
 HU7  O1   C7   N2   118.61  3.000
 HU7  C5   C6   C9   122.46  3.000
 HU7  C5   C6   C7   115.29  3.000
 HU7  C9   C6   C7   122.24  3.000
 HU7  C14  C9   C10  118.62  3.000
 HU7  C14  C9   C6   121.52  3.000
 HU7  C10  C9   C6   119.86  3.000
 HU7  H3   C13  C14  121.61  3.000
 HU7  H3   C13  C12  121.72  3.000
 HU7  C14  C13  C12  116.67  3.000
 HU7  H4   C20  O8   110.73  3.000
 HU7  H4   C20  C19  108.37  3.000
 HU7  O8   C20  C19  107.75  3.000
 HU7  H4   C20  C21  108.27  3.000
 HU7  O8   C20  C21  111.48  3.000
 HU7  C19  C20  C21  110.19  3.000
 HU7  H5   C21  O7   111.36  3.000
 HU7  H5   C21  C22  108.05  3.000
 HU7  O7   C21  C22  107.75  3.000
 HU7  H5   C21  C20  108.69  3.000
 HU7  O7   C21  C20  112.49  3.000
 HU7  C22  C21  C20  108.36  3.000
 HU7  H9   C18  O4   110.61  3.000
 HU7  H9   C18  O3   111.07  3.000
 HU7  O4   C18  O3   106.51  3.000
 HU7  H9   C18  C19  109.81  3.000
 HU7  O3   C18  C19  108.14  3.000
 HU7  O4   C18  C19  110.64  3.000
 HU7  C17  C16  C15  126.86  3.000
 HU7  C15  C16  C11  106.64  3.000
 HU7  C17  C16  C11  126.49  3.000
 HU7  H10  C19  O9   111.68  3.000
 HU7  H10  C19  C18  108.36  3.000
 HU7  O9   C19  C18  107.60  3.000
 HU7  H10  C19  C20  108.69  3.000
 HU7  O9   C19  C20  112.11  3.000
 HU7  C18  C19  C20  108.27  3.000
 HU7  H13  C1   H12  107.32  3.000
 HU7  H13  C1   H11  108.05  3.000
 HU7  H12  C1   H11  107.96  3.000
 HU7  H13  C1   N1   111.40  3.000
 HU7  H12  C1   N1   109.10  3.000
 HU7  H11  C1   N1   112.81  3.000
 HU7  H16  C2   H15  107.70  3.000
 HU7  H16  C2   H14  108.20  3.000
 HU7  H15  C2   H14  108.18  3.000
 HU7  H16  C2   N1   111.10  3.000
 HU7  H15  C2   N1   112.77  3.000
 HU7  H14  C2   N1   108.76  3.000
 HU7  N1   C3   N2   116.59  3.000
 HU7  N1   C3   C4   122.63  3.000
 HU7  N2   C3   C4   120.78  3.000
 HU7  H17  C5   C6   119.18  3.000
 HU7  H17  C5   C4   119.00  3.000
 HU7  C6   C5   C4   121.81  3.000
 HU7  C8   O1   C7   118.11  3.000
 HU7  H18  C10  C11  120.67  3.000
 HU7  H18  C10  C9   119.02  3.000
 HU7  C11  C10  C9   120.30  3.000
 HU7  C12  C11  C10  118.80  3.000
 HU7  C10  C11  C16  134.97  3.000
 HU7  C12  C11  C16  106.22  3.000
 HU7  C11  C12  C13  122.60  3.000
 HU7  C13  C12  N3   129.74  3.000
 HU7  C11  C12  N3   107.67  3.000
 HU7  CL1  C14  C13  117.70  3.000
 HU7  CL1  C14  C9   119.27  3.000
 HU7  C13  C14  C9   123.02  3.000
 HU7  H19  C15  C16  129.85  3.000
 HU7  H19  C15  N3   120.59  3.000
 HU7  C16  C15  N3   109.56  3.000
 HU7  O3   C17  O2   123.31  3.000
 HU7  O2   C17  C16  125.02  3.000
 HU7  O3   C17  C16  111.67  3.000
 HU7  C17  O3   C18  118.77  3.000
 HU7  H20  C22  C23  109.85  3.000
 HU7  H20  C22  O4   111.12  3.000
 HU7  C23  C22  O4   106.82  3.000
 HU7  H20  C22  C21  109.36  3.000
 HU7  O4   C22  C21  109.68  3.000
 HU7  C23  C22  C21  109.97  3.000
 HU7  C22  O4   C18  112.78  3.000
 HU7  O6   C23  O5   124.72  3.000
 HU7  O6   C23  C22  112.07  3.000
 HU7  O5   C23  C22  123.19  3.000
 HU7  H21  O6   C23  110.28  3.000
 HU7  H22  O7   C21  108.72  3.000
 HU7  H24  O9   C19  108.07  3.000
 HU7  C3   N1   C2   119.47  3.000
 HU7  C3   N1   C1   119.76  3.000
 HU7  C2   N1   C1   118.72  3.000
 HU7  H23  O8   C20  109.12  3.000
 HU7  H8   C8   H7   108.43  3.000
 HU7  H8   C8   H6   109.37  3.000
 HU7  H7   C8   H6   109.29  3.000
 HU7  H8   C8   O1   111.91  3.000
 HU7  H7   C8   O1   111.99  3.000
 HU7  H6   C8   O1   105.78  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
 HU7  CONST_01  C11  C16  C15  N3     0.00   0.0  0
 HU7  CONST_02  C16  C11  C12  N3     0.00   0.0  0
 HU7  CONST_03  C10  C11  C12  N3   180.00   0.0  0
 HU7  CONST_04  C14  C13  C12  N3   180.00   0.0  0
 HU7  CONST_05  C7   N2   C3   C4     0.00   0.0  0
 HU7  CONST_06  C7   C6   C5   C4     0.00   0.0  0
 HU7  CONST_07  C9   C6   C5   C4   180.00   0.0  0
 HU7  CONST_08  C9   C6   C7   N2   180.00   0.0  0
 HU7  CONST_09  C5   C6   C7   N2     0.00   0.0  0
 HU7  CONST_10  C5   C4   C3   N2     0.00   0.0  0
 HU7  CONST_13  C3   N2   C7   C6     0.00   0.0  0
 HU7  CONST_14  C11  C10  C9   C6   180.00   0.0  0
 HU7  CONST_15  C13  C14  C9   C6   180.00   0.0  0
 HU7  CONST_16  C3   C4   C5   C6     0.00   0.0  0
 HU7  CONST_17  C16  C11  C10  C9   180.00   0.0  0
 HU7  CONST_18  C12  C11  C10  C9     0.00   0.0  0
 HU7  CONST_19  C12  C13  C14  C9     0.00   0.0  0
 HU7  CONST_20  C15  N3   C12  C13  180.00   0.0  0
 HU7  CONST_21  C16  C11  C12  C13  180.00   0.0  0
 HU7  CONST_22  C10  C11  C12  C13    0.00   0.0  0
 HU7  CONST_23  C10  C9   C14  C13    0.00   0.0  0
 HU7  CONST_24  C12  N3   C15  C16    0.00   0.0  0
 HU7  CONST_27  C15  C16  C11  C10  180.00   0.0  0
 HU7  CONST_28  C15  N3   C12  C11    0.00   0.0  0
 HU7  CONST_29  C14  C13  C12  C11    0.00   0.0  0
 HU7  CONST_30  C14  C9   C10  C11    0.00   0.0  0
 HU7  CONST_31  C15  C16  C11  C12    0.00   0.0  0
 HU7  CONST_32  C17  C16  C15  N3   180.00   0.0  0
 HU7  CONST_33  N1   C3   N2   C7   180.00   0.0  0
 HU7  CONST_34  CL1  C14  C9   C6     0.00   0.0  0
 HU7  CONST_35  O1   C7   C6   C9     0.00   0.0  0
 HU7  CONST_36  C5   C4   C3   N1   180.00   0.0  0
 HU7  CONST_37  O1   C7   N2   C3   180.00   0.0  0
 HU7  CONST_38  O1   C7   C6   C5   180.00   0.0  0
 HU7  CONST_39  C17  C16  C11  C10    0.00   0.0  0
 HU7  CONST_40  CL1  C14  C9   C10  180.00   0.0  0
 HU7  CONST_41  C17  C16  C11  C12  180.00   0.0  0
 HU7  CONST_42  CL1  C14  C13  C12  180.00   0.0  0
 HU7  CONST_43  H3   C13  C12  N3     0.00   0.0  0
 HU7  CONST_44  H2   C4   C3   N2   180.00   0.0  0
 HU7  CONST_45  H17  C5   C6   C7   180.00   0.0  0
 HU7  CONST_46  H18  C10  C9   C6     0.00   0.0  0
 HU7  CONST_47  H1   N3   C12  C13    0.00   0.0  0
 HU7  CONST_48  H19  C15  C16  C11  180.00   0.0  0
 HU7  CONST_49  C2   N1   C3   C4   180.00   0.0  0
 HU7  CONST_50  C1   N1   C3   C4     0.00   0.0  0
 HU7  CONST_51  C2   N1   C3   N2     0.00   0.0  0
 HU7  CONST_52  C1   N1   C3   N2   180.00   0.0  0
 HU7  CONST_53  H21  O6   C23  C22  180.00   0.0  0
 HU7  Var_01    C16  C17  O3   C18  179.05  30.0  3
 HU7  Var_02    O3   C17  C16  C11  178.52  30.0  2
 HU7  Var_03    H6   C8   O1   C7   179.35  30.0  3
 HU7  Var_04    H14  C2   N1   C3   170.55  30.0  3
 HU7  Var_05    H11  C1   N1   C3    65.75  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
 HU7  chir_01  C20  C21  C19  O8   negativ
 HU7  chir_02  C21  O7   C20  C22  negativ
 HU7  chir_03  C18  O3   O4   C19  positiv
 HU7  chir_04  C19  O9   C18  C20  negativ
 HU7  chir_05  C22  O4   C21  C23  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
 HU7  plan-1  C4   0.020
 HU7  plan-1  N2   0.020
 HU7  plan-1  C7   0.020
 HU7  plan-1  C6   0.020
 HU7  plan-1  C9   0.020
 HU7  plan-1  C3   0.020
 HU7  plan-1  C5   0.020
 HU7  plan-1  O1   0.020
 HU7  plan-1  H2   0.020
 HU7  plan-1  H17  0.020
 HU7  plan-1  N1   0.020
 HU7  plan-2  N3   0.020
 HU7  plan-2  C6   0.020
 HU7  plan-2  C9   0.020
 HU7  plan-2  C13  0.020
 HU7  plan-2  C16  0.020
 HU7  plan-2  C10  0.020
 HU7  plan-2  C11  0.020
 HU7  plan-2  C12  0.020
 HU7  plan-2  C14  0.020
 HU7  plan-2  CL1  0.020
 HU7  plan-2  C15  0.020
 HU7  plan-2  C17  0.020
 HU7  plan-2  H1   0.020
 HU7  plan-2  H3   0.020
 HU7  plan-2  H18  0.020
 HU7  plan-2  H19  0.020
 HU7  plan-3  C1   0.020
 HU7  plan-3  C2   0.020
 HU7  plan-3  C3   0.020
 HU7  plan-3  N1   0.020
 HU7  plan-4  C22  0.020
 HU7  plan-4  C23  0.020
 HU7  plan-4  O5   0.020
 HU7  plan-4  O6   0.020
 HU7  plan-4  H21  0.020
 HU7  plan-5  C16  0.020
 HU7  plan-5  C17  0.020
 HU7  plan-5  O2   0.020
 HU7  plan-5  O3   0.020

