# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 16:43:23 2020
#   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  59  36  .  2021-08-11  2021-08-11  
;
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  -0.677   0.1260   3.7139   0.8839
 HU7  C4   C   CR16   0  -0.426  -4.5420  -2.4822   0.7234
 HU7  N2   N   N      0  -0.516  -5.5791  -1.2439  -1.0323
 HU7  C7   C   CR6    0   0.491  -4.7129  -0.2758  -0.8532
 HU7  C6   C   CR6    0  -0.156  -3.7122  -0.2864   0.1289
 HU7  C9   C   CR6    0   0.175  -2.7618   0.8253   0.3140
 HU7  C13  C   CR16   0  -0.242  -2.3071   3.1478   0.9520
 HU7  C20  C   CH1    0   0.014   6.5506   0.1223  -1.1508
 HU7  C21  C   CH1    0   0.033   6.7587  -0.8434   0.0046
 HU7  C18  C   CH1    0   0.287   4.1616   0.2287  -0.4805
 HU7  C16  C   CR5    0  -0.220   0.9429   1.7465   0.2402
 HU7  C19  C   CH1    0  -0.041   5.3842   1.0600  -0.8563
 HU7  C3   C   CR6    0   0.534  -5.5225  -2.3456  -0.2748
 HU7  C5   C   CR16   0  -0.168  -3.6529  -1.4382   0.9015
 HU7  C10  C   CR16   0  -0.441  -1.4067   0.6032   0.1183
 HU7  C11  C   CR56   0   0.133  -0.4854   1.6285   0.3351
 HU7  C12  C   CR56   0   0.341  -0.9586   2.8878   0.7426
 HU7  C14  C   CR6    0  -0.131  -3.1822   2.1040   0.7370
 HU7  CL1  CL  CL     0  -0.131  -4.8643   2.3824   1.0546
 HU7  C15  C   CR15   0   0.010   1.2552   3.0419   0.5894
 HU7  C17  C   C      0   0.540   1.8670   0.7025  -0.1482
 HU7  O2   O   O      0  -0.445   1.5456  -0.4144  -0.4753
 HU7  O3   O   O2     0  -0.503   3.1444   1.1242  -0.1091
 HU7  C22  C   CH1    0  -0.162   5.4234  -1.5319   0.3460
 HU7  O4   O   O2     0  -0.481   4.4300  -0.5713   0.6245
 HU7  C23  C   C      0   0.440   5.5686  -2.4928   1.5415
 HU7  O5   O   O      0  -0.557   4.7035  -2.4855   2.4179
 HU7  O6   O   OC    -1  -0.615   6.5885  -3.2306   1.4891
 HU7  O7   O   OH1    0  -0.702   7.7294  -1.7881  -0.3513
 HU7  O9   O   OH1    0  -0.667   5.1495   1.8269  -2.0116
 HU7  H1   H   HNR5   0   0.426   0.0939   4.6805   1.1673
 HU7  H2   H   HCR6   0   0.265  -4.4816  -3.3563   1.3536
 HU7  H3   H   HCR6   0   0.289  -2.6544   4.1175   1.2817
 HU7  H4   H   HCH1   0   0.206   6.2908  -0.4745  -2.0410
 HU7  H5   H   HCH1   0   0.196   7.0713  -0.2603   0.8886
 HU7  H6   H   HCH3   0   0.226  -5.7602   0.0310  -3.3258
 HU7  H7   H   HCH3   0   0.225  -6.7885   0.8566  -2.1455
 HU7  H8   H   HCH3   0   0.241  -5.6604   1.7963  -3.1446
 HU7  H9   H   HCH1   0   0.214   3.8424  -0.3765  -1.3429
 HU7  H10  H   HCH1   0   0.231   5.6484   1.6953   0.0016
 HU7  H11  H   HCH3   0   0.243  -5.5892  -5.0075   0.3779
 HU7  H12  H   HCH3   0   0.231  -6.8082  -4.1917   1.3667
 HU7  H13  H   HCH3   0   0.257  -7.2865  -5.1413  -0.0418
 HU7  H14  H   HCH3   0   0.224  -8.3302  -2.4253  -0.9328
 HU7  H15  H   HCH3   0   0.252  -7.2230  -2.5070  -2.3023
 HU7  H16  H   HCH3   0   0.238  -8.0070  -3.9747  -1.7201
 HU7  H17  H   HCR6   0   0.257  -2.9011  -1.5131   1.6781
 HU7  H18  H   HCR6   0   0.252  -1.0770  -0.3725  -0.2105
 HU7  H19  H   HCR5   0   0.306   2.2141   3.5307   0.6486
 HU7  H20  H   HCH1   0   0.231   5.1246  -2.1379  -0.5276
 HU7  H22  H   HOH1   0   0.439   7.5653  -2.5257   0.2822
 HU7  H24  H   HOH1   0   0.459   4.6483   2.6112  -1.7695
 HU7  N1   N   NT     0  -0.481  -6.4422  -3.3124  -0.5317
 HU7  C8   C   CH3    0  -0.410  -5.8043   0.8573  -2.6156
 HU7  O1   O   O2     0  -0.461  -4.7619   0.7885  -1.6559
 HU7  O8   O   OH1    0  -0.670   7.7426   0.8364  -1.3600
 HU7  C1   C   CH3    0  -0.534  -6.5321  -4.4593   0.3417
 HU7  C2   C   CH3    0  -0.518  -7.5565  -3.0337  -1.4123
 HU7  H23  H   HOH1   0   0.450   7.6146   1.4197  -2.1154

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  deloc     1.231  0.020  1.231
 HU7  O6   C23  deloc     1.260  0.020  1.260
 HU7  C23  C22  single    1.541  0.020  1.541
 HU7  C8   O1   single    1.419  0.020  1.419
 HU7  C22  O4   single    1.410  0.020  1.410
 HU7  C22  C21  single    1.541  0.020  1.541
 HU7  O4   C18  single    1.390  0.020  1.390
 HU7  O1   C7   single    1.334  0.020  1.334
 HU7  O7   C21  single    1.400  0.020  1.400
 HU7  C21  C20  single    1.520  0.020  1.520
 HU7  C18  O3   single    1.405  0.020  1.405
 HU7  C18  C19  single    1.525  0.020  1.525
 HU7  C7   N2   aromatic  1.311  0.020  1.311
 HU7  C7   C6   aromatic  1.402  0.020  1.402
 HU7  O3   C17  single    1.346  0.020  1.346
 HU7  C2   N1   single    1.447  0.020  1.447
 HU7  N2   C3   aromatic  1.338  0.020  1.338
 HU7  C17  O2   double    1.207  0.020  1.207
 HU7  C17  C16  single    1.447  0.020  1.447
 HU7  C15  N3   aromatic  1.347  0.020  1.347
 HU7  C15  C16  aromatic  1.378  0.020  1.378
 HU7  N3   C12  aromatic  1.371  0.020  1.371
 HU7  C16  C11  aromatic  1.436  0.020  1.436
 HU7  C12  C11  aromatic  1.406  0.020  1.406
 HU7  C12  C13  aromatic  1.389  0.020  1.389
 HU7  C11  C10  aromatic  1.395  0.020  1.395
 HU7  C20  C19  single    1.525  0.020  1.525
 HU7  C20  O8   single    1.405  0.020  1.405
 HU7  C13  C14  aromatic  1.379  0.020  1.379
 HU7  C10  C9   aromatic  1.387  0.020  1.387
 HU7  C14  C9   aromatic  1.411  0.020  1.411
 HU7  C14  CL1  single    1.734  0.020  1.734
 HU7  C9   C6   single    1.474  0.020  1.474
 HU7  C19  O9   single    1.406  0.020  1.406
 HU7  C6   C5   aromatic  1.388  0.020  1.388
 HU7  C3   N1   single    1.359  0.020  1.359
 HU7  C3   C4   aromatic  1.406  0.020  1.406
 HU7  N1   C1   single    1.444  0.020  1.444
 HU7  C5   C4   aromatic  1.383  0.020  1.383
 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  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  124.53  3.000
 HU7  H1   N3   C12  125.58  3.000
 HU7  C15  N3   C12  109.89  3.000
 HU7  H2   C4   C5   120.02  3.000
 HU7  H2   C4   C3   122.16  3.000
 HU7  C5   C4   C3   117.81  3.000
 HU7  C3   N2   C7   120.17  3.000
 HU7  O1   C7   C6   116.98  3.000
 HU7  C6   C7   N2   124.16  3.000
 HU7  O1   C7   N2   118.86  3.000
 HU7  C5   C6   C9   121.89  3.000
 HU7  C5   C6   C7   115.25  3.000
 HU7  C9   C6   C7   122.84  3.000
 HU7  C14  C9   C10  118.59  3.000
 HU7  C14  C9   C6   121.93  3.000
 HU7  C10  C9   C6   119.43  3.000
 HU7  H3   C13  C14  121.50  3.000
 HU7  H3   C13  C12  121.70  3.000
 HU7  C14  C13  C12  116.80  3.000
 HU7  H4   C20  O8   110.77  3.000
 HU7  H4   C20  C19  107.96  3.000
 HU7  O8   C20  C19  111.41  3.000
 HU7  H4   C20  C21  107.58  3.000
 HU7  O8   C20  C21  108.66  3.000
 HU7  C19  C20  C21  110.40  3.000
 HU7  H5   C21  O7   111.31  3.000
 HU7  H5   C21  C22  107.69  3.000
 HU7  O7   C21  C22  110.83  3.000
 HU7  H5   C21  C20  108.17  3.000
 HU7  O7   C21  C20  109.29  3.000
 HU7  C22  C21  C20  109.49  3.000
 HU7  H9   C18  O4   111.24  3.000
 HU7  H9   C18  O3   110.33  3.000
 HU7  O4   C18  O3   107.24  3.000
 HU7  H9   C18  C19  109.82  3.000
 HU7  O3   C18  C19  107.34  3.000
 HU7  O4   C18  C19  110.77  3.000
 HU7  C17  C16  C15  126.99  3.000
 HU7  C15  C16  C11  106.61  3.000
 HU7  C17  C16  C11  126.40  3.000
 HU7  H10  C19  O9   111.47  3.000
 HU7  H10  C19  C18  108.37  3.000
 HU7  O9   C19  C18  111.45  3.000
 HU7  H10  C19  C20  108.78  3.000
 HU7  O9   C19  C20  107.72  3.000
 HU7  C18  C19  C20  108.99  3.000
 HU7  N1   C3   N2   116.75  3.000
 HU7  N1   C3   C4   122.49  3.000
 HU7  N2   C3   C4   120.76  3.000
 HU7  H17  C5   C6   119.07  3.000
 HU7  H17  C5   C4   119.10  3.000
 HU7  C6   C5   C4   121.82  3.000
 HU7  H18  C10  C11  120.61  3.000
 HU7  H18  C10  C9   119.03  3.000
 HU7  C11  C10  C9   120.36  3.000
 HU7  C12  C11  C10  118.75  3.000
 HU7  C10  C11  C16  134.96  3.000
 HU7  C12  C11  C16  106.28  3.000
 HU7  C11  C12  C13  122.56  3.000
 HU7  C13  C12  N3   129.78  3.000
 HU7  C11  C12  N3   107.66  3.000
 HU7  CL1  C14  C13  117.74  3.000
 HU7  CL1  C14  C9   119.30  3.000
 HU7  C13  C14  C9   122.93  3.000
 HU7  H19  C15  C16  129.94  3.000
 HU7  H19  C15  N3   120.51  3.000
 HU7  C16  C15  N3   109.55  3.000
 HU7  O3   C17  O2   123.40  3.000
 HU7  O2   C17  C16  124.75  3.000
 HU7  O3   C17  C16  111.85  3.000
 HU7  C17  O3   C18  118.67  3.000
 HU7  H20  C22  C23  107.28  3.000
 HU7  H20  C22  O4   109.85  3.000
 HU7  C23  C22  O4   109.77  3.000
 HU7  H20  C22  C21  107.72  3.000
 HU7  O4   C22  C21  110.49  3.000
 HU7  C23  C22  C21  111.65  3.000
 HU7  C22  O4   C18  111.79  3.000
 HU7  O6   C23  O5   126.99  3.000
 HU7  O6   C23  C22  114.16  3.000
 HU7  O5   C23  C22  118.84  3.000
 HU7  H22  O7   C21  103.06  3.000
 HU7  H24  O9   C19  108.96  3.000
 HU7  C3   N1   C2   119.94  3.000
 HU7  C3   N1   C1   119.52  3.000
 HU7  C2   N1   C1   118.22  3.000
 HU7  H8   C8   H7   109.25  3.000
 HU7  H8   C8   H6   109.40  3.000
 HU7  H7   C8   H6   108.46  3.000
 HU7  H8   C8   O1   105.89  3.000
 HU7  H7   C8   O1   111.81  3.000
 HU7  H6   C8   O1   111.97  3.000
 HU7  C8   O1   C7   118.21  3.000
 HU7  H23  O8   C20  108.17  3.000
 HU7  H13  C1   H12  107.98  3.000
 HU7  H13  C1   H11  107.23  3.000
 HU7  H12  C1   H11  108.04  3.000
 HU7  H13  C1   N1   109.15  3.000
 HU7  H12  C1   N1   112.82  3.000
 HU7  H11  C1   N1   111.42  3.000
 HU7  H16  C2   H15  108.34  3.000
 HU7  H16  C2   H14  108.17  3.000
 HU7  H15  C2   H14  107.83  3.000
 HU7  H16  C2   N1   108.93  3.000
 HU7  H15  C2   N1   110.82  3.000
 HU7  H14  C2   N1   112.62  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  Var_01    C16  C17  O3   C18  -179.01  30.0  3
 HU7  Var_02    O3   C17  C16  C11  -178.61  30.0  2
 HU7  Var_03    H6   C8   O1   C7    -61.41  30.0  3
 HU7  Var_04    H14  C2   N1   C3    -76.13  30.0  3
 HU7  Var_05    H11  C1   N1   C3    -59.30  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  H2   0.020
 HU7  plan-1  H17  0.020
 HU7  plan-1  N1   0.020
 HU7  plan-1  O1   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  C3   0.020
 HU7  plan-3  N1   0.020
 HU7  plan-3  C1   0.020
 HU7  plan-3  C2   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-5  C16  0.020
 HU7  plan-5  C17  0.020
 HU7  plan-5  O2   0.020
 HU7  plan-5  O3   0.020

