# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 11:48:18 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 5'-deoxy-5'-({[2-(2,3-dihydroxyphenyl)ethyl]sulfonyl}amino)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CN[S](=O)(=O)CCc4cccc(O)c4O)[C@@H](O)[C@H]3O
#
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
 1HZ  1HZ  5'-deoxy-5'-({[2-(2,3-dihydroxyphenyl)ethyl]sulfonyl}amino)adenosine  ligand  54  32  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1HZ
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
 1HZ  O1P  O  OS    0  -0.670   2.9553  -3.2254   0.7183
 1HZ  S    S  S     0   1.367   2.3056  -2.0768   1.3335
 1HZ  O2P  O  OS    0  -0.666   2.5034  -1.8190   2.7513
 1HZ  C22  C  CH2   0  -0.613   2.7957  -0.6142   0.4223
 1HZ  C21  C  CH2   0  -0.545   4.3012  -0.3706   0.5281
 1HZ  C19  C  CR6   0   0.035   4.6909   0.8396  -0.2764
 1HZ  C18  C  CR16  0  -0.337   5.2453   0.6920  -1.5462
 1HZ  C17  C  CR16  0  -0.249   5.5570   1.8024  -2.3137
 1HZ  C16  C  CR16  0  -0.359   5.3252   3.0801  -1.8237
 1HZ  C15  C  CR6   0   0.312   4.7850   3.2469  -0.5562
 1HZ  O15  O  OH1   0  -0.633   4.5746   4.4941  -0.0900
 1HZ  C14  C  CR6   0   0.197   4.4652   2.1223   0.2134
 1HZ  O14  O  OH1   0  -0.647   3.8957   2.3718   1.4256
 1HZ  N5'  N  NC1   0  -0.736   0.6856  -2.2566   1.1077
 1HZ  C5'  C  CH2   0  -0.303   0.1746  -2.5986  -0.2116
 1HZ  C4'  C  CH1   0  -0.022  -1.2706  -3.0540  -0.0876
 1HZ  O4'  O  O2    0  -0.497  -2.0507  -2.0439   0.5606
 1HZ  C1'  C  CH1   0   0.214  -2.9367  -1.4426  -0.3464
 1HZ  C2'  C  CH1   0  -0.054  -2.4639  -1.8687  -1.7364
 1HZ  O2'  O  OH1   0  -0.652  -3.5312  -1.8190  -2.6322
 1HZ  C3'  C  CH1   0  -0.022  -1.9213  -3.2712  -1.4463
 1HZ  O3'  O  OH1   0  -0.665  -2.9660  -4.1941  -1.2965
 1HZ  N9   N  NR5   0  -0.541  -2.9477  -0.0190  -0.1388
 1HZ  C8   C  CR15  0   0.119  -1.8816   0.8404  -0.1795
 1HZ  N7   N  N     0  -0.445  -2.2003   2.0719   0.0794
 1HZ  C5   C  CR56  0  -0.011  -3.5525   2.0340   0.3063
 1HZ  C6   C  CR6   0   0.462  -4.4966   3.0250   0.6332
 1HZ  N6   N  NH2   0  -0.816  -4.1730   4.3087   0.7865
 1HZ  N1   N  N     0  -0.474  -5.7695   2.6463   0.7971
 1HZ  C2   C  CR16  0   0.047  -6.0888   1.3638   0.6477
 1HZ  N3   N  N     0  -0.457  -5.2974   0.3499   0.3420
 1HZ  C4   C  CR56  0   0.495  -4.0366   0.7422   0.1812
 1HZ  H1   H  HCH2  0   0.310   2.5026  -0.7656  -0.6183
 1HZ  H2   H  HCH2  0   0.302   2.2188   0.2184   0.8280
 1HZ  H3   H  HCH2  0   0.270   4.5901  -0.2689   1.5773
 1HZ  H4   H  HCH2  0   0.289   4.8387  -1.2390   0.1468
 1HZ  H5   H  HCR6  0   0.252   5.4285  -0.3038  -1.9300
 1HZ  H6   H  HCR6  0   0.255   5.9864   1.6769  -3.2988
 1HZ  H7   H  HCR6  0   0.264   5.5698   3.9540  -2.4146
 1HZ  H8   H  HOH1  0   0.471   4.2457   4.4538   0.8167
 1HZ  H9   H  HOH1  0   0.480   4.2080   1.7511   2.0940
 1HZ  H10  H  HNC1  0   0.414   0.1438  -1.5588   1.6074
 1HZ  H11  H  HCH2  0   0.240   0.2592  -1.7652  -0.9202
 1HZ  H12  H  HCH2  0   0.289   0.7590  -3.4257  -0.6129
 1HZ  H13  H  HCH1  0   0.279  -1.3043  -3.9596   0.5234
 1HZ  H14  H  HCH1  0   0.269  -3.9644  -1.7808  -0.1794
 1HZ  H15  H  HCH1  0   0.251  -1.6334  -1.2289  -2.0627
 1HZ  H16  H  HOH1  0   0.471  -3.1847  -1.7959  -3.5300
 1HZ  H17  H  HCH1  0   0.259  -1.1927  -3.5943  -2.2012
 1HZ  H18  H  HOH1  0   0.452  -3.5644  -4.0951  -2.0462
 1HZ  H19  H  HCR5  0   0.281  -0.8810   0.5017  -0.4044
 1HZ  H20  H  HNH2  0   0.412  -3.2294   4.6287   0.6561
 1HZ  H21  H  HNH2  0   0.405  -4.8807   4.9866   1.0114
 1HZ  H22  H  HCR6  0   0.253  -7.1361   1.1241   0.7962

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
 1HZ  O3'  C3'  single    1.402  0.020  1.402
 1HZ  N5'  C5'  single    1.456  0.020  1.456
 1HZ  N5'  S    single    1.646  0.020  1.646
 1HZ  O2'  C2'  single    1.394  0.020  1.394
 1HZ  C5'  C4'  single    1.520  0.020  1.520
 1HZ  C3'  C4'  single    1.522  0.020  1.522
 1HZ  C3'  C2'  single    1.531  0.020  1.531
 1HZ  C4'  O4'  single    1.431  0.020  1.431
 1HZ  O1P  S    double    1.456  0.020  1.456
 1HZ  C2'  C1'  single    1.529  0.020  1.529
 1HZ  S    C22  single    1.792  0.020  1.792
 1HZ  S    O2P  double    1.454  0.020  1.454
 1HZ  C22  C21  single    1.529  0.020  1.529
 1HZ  O4'  C1'  single    1.403  0.020  1.403
 1HZ  C1'  N9   single    1.439  0.020  1.439
 1HZ  O14  C14  single    1.362  0.020  1.362
 1HZ  C21  C19  single    1.505  0.020  1.505
 1HZ  N9   C8   aromatic  1.370  0.020  1.370
 1HZ  N9   C4   aromatic  1.367  0.020  1.367
 1HZ  C14  C19  aromatic  1.392  0.020  1.392
 1HZ  C14  C15  aromatic  1.400  0.020  1.400
 1HZ  C8   N7   aromatic  1.298  0.020  1.298
 1HZ  C19  C18  aromatic  1.393  0.020  1.393
 1HZ  N3   C4   aromatic  1.330  0.020  1.330
 1HZ  N3   C2   aromatic  1.322  0.020  1.322
 1HZ  O15  C15  single    1.348  0.020  1.348
 1HZ  C4   C5   aromatic  1.385  0.020  1.385
 1HZ  C15  C16  aromatic  1.388  0.020  1.388
 1HZ  C18  C17  aromatic  1.385  0.020  1.385
 1HZ  N7   C5   aromatic  1.372  0.020  1.372
 1HZ  C2   N1   aromatic  1.330  0.020  1.330
 1HZ  C5   C6   aromatic  1.407  0.020  1.407
 1HZ  C16  C17  aromatic  1.388  0.020  1.388
 1HZ  N1   C6   aromatic  1.338  0.020  1.338
 1HZ  C6   N6   single    1.333  0.020  1.333
 1HZ  C22  H1   single    0.970  0.020  1.090
 1HZ  C22  H2   single    0.970  0.020  1.090
 1HZ  C21  H3   single    0.970  0.020  1.090
 1HZ  C21  H4   single    0.970  0.020  1.090
 1HZ  C18  H5   single    0.930  0.020  1.080
 1HZ  C17  H6   single    0.930  0.020  1.080
 1HZ  C16  H7   single    0.930  0.020  1.080
 1HZ  O15  H8   single    0.850  0.020  0.980
 1HZ  O14  H9   single    0.850  0.020  0.980
 1HZ  N5'  H10  single    0.890  0.020  1.040
 1HZ  C5'  H11  single    0.970  0.020  1.090
 1HZ  C5'  H12  single    0.970  0.020  1.090
 1HZ  C4'  H13  single    0.970  0.020  1.090
 1HZ  C1'  H14  single    0.970  0.020  1.090
 1HZ  C2'  H15  single    0.970  0.020  1.090
 1HZ  O2'  H16  single    0.850  0.020  0.980
 1HZ  C3'  H17  single    0.970  0.020  1.090
 1HZ  O3'  H18  single    0.850  0.020  0.980
 1HZ  C8   H19  single    0.930  0.020  1.080
 1HZ  N6   H20  single    0.860  0.020  1.020
 1HZ  N6   H21  single    0.860  0.020  1.020
 1HZ  C2   H22  single    0.930  0.020  1.080

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
 1HZ  N5'  S    C22  106.78  3.000
 1HZ  C22  S    O2P  108.29  3.000
 1HZ  N5'  S    O2P  106.68  3.000
 1HZ  O2P  S    O1P  119.41  3.000
 1HZ  C22  S    O1P  107.88  3.000
 1HZ  N5'  S    O1P  107.17  3.000
 1HZ  H2   C22  H1   108.56  3.000
 1HZ  H2   C22  C21  111.92  3.000
 1HZ  H1   C22  C21  110.64  3.000
 1HZ  H2   C22  S    106.81  3.000
 1HZ  H1   C22  S    107.35  3.000
 1HZ  C21  C22  S    111.36  3.000
 1HZ  H4   C21  H3   106.23  3.000
 1HZ  H4   C21  C19  109.03  3.000
 1HZ  H3   C21  C19  111.71  3.000
 1HZ  H4   C21  C22  109.54  3.000
 1HZ  H3   C21  C22  109.97  3.000
 1HZ  C19  C21  C22  110.26  3.000
 1HZ  C14  C19  C18  118.88  3.000
 1HZ  C18  C19  C21  120.34  3.000
 1HZ  C14  C19  C21  120.75  3.000
 1HZ  H5   C18  C17  120.18  3.000
 1HZ  H5   C18  C19  119.19  3.000
 1HZ  C17  C18  C19  120.63  3.000
 1HZ  H6   C17  C16  119.64  3.000
 1HZ  H6   C17  C18  120.05  3.000
 1HZ  C16  C17  C18  120.31  3.000
 1HZ  H7   C16  C15  119.29  3.000
 1HZ  H7   C16  C17  120.83  3.000
 1HZ  C15  C16  C17  119.87  3.000
 1HZ  C14  C15  O15  121.17  3.000
 1HZ  O15  C15  C16  119.19  3.000
 1HZ  C14  C15  C16  119.64  3.000
 1HZ  H8   O15  C15  109.84  3.000
 1HZ  O14  C14  C15  115.96  3.000
 1HZ  C15  C14  C19  120.66  3.000
 1HZ  O14  C14  C19  123.35  3.000
 1HZ  H9   O14  C14  111.32  3.000
 1HZ  H10  N5'  C5'  114.86  3.000
 1HZ  H10  N5'  S    112.51  3.000
 1HZ  C5'  N5'  S    119.71  3.000
 1HZ  H12  C5'  H11  107.30  3.000
 1HZ  H12  C5'  C4'  108.22  3.000
 1HZ  H11  C5'  C4'  110.70  3.000
 1HZ  H12  C5'  N5'  108.90  3.000
 1HZ  H11  C5'  N5'  112.32  3.000
 1HZ  C4'  C5'  N5'  109.28  3.000
 1HZ  H13  C4'  C3'  111.57  3.000
 1HZ  H13  C4'  O4'  108.34  3.000
 1HZ  C3'  C4'  O4'  105.78  3.000
 1HZ  H13  C4'  C5'  108.85  3.000
 1HZ  O4'  C4'  C5'  110.10  3.000
 1HZ  C3'  C4'  C5'  112.11  3.000
 1HZ  C1'  O4'  C4'  110.72  3.000
 1HZ  H14  C1'  N9   106.05  3.000
 1HZ  H14  C1'  C2'  110.05  3.000
 1HZ  N9   C1'  C2'  114.17  3.000
 1HZ  H14  C1'  O4'  111.20  3.000
 1HZ  N9   C1'  O4'  109.61  3.000
 1HZ  C2'  C1'  O4'  105.84  3.000
 1HZ  H15  C2'  C3'  108.78  3.000
 1HZ  H15  C2'  O2'  111.54  3.000
 1HZ  C3'  C2'  O2'  115.19  3.000
 1HZ  H15  C2'  C1'  109.98  3.000
 1HZ  C3'  C2'  C1'  101.11  3.000
 1HZ  O2'  C2'  C1'  109.72  3.000
 1HZ  H16  O2'  C2'  108.94  3.000
 1HZ  H17  C3'  O3'  111.98  3.000
 1HZ  H17  C3'  C2'  111.99  3.000
 1HZ  O3'  C3'  C2'  111.05  3.000
 1HZ  H17  C3'  C4'  111.84  3.000
 1HZ  C2'  C3'  C4'  100.95  3.000
 1HZ  O3'  C3'  C4'  108.49  3.000
 1HZ  H18  O3'  C3'  108.16  3.000
 1HZ  C4   N9   C8   106.12  3.000
 1HZ  C4   N9   C1'  126.23  3.000
 1HZ  C8   N9   C1'  127.62  3.000
 1HZ  H19  C8   N7   124.51  3.000
 1HZ  H19  C8   N9   122.03  3.000
 1HZ  N7   C8   N9   113.46  3.000
 1HZ  C5   N7   C8   104.41  3.000
 1HZ  C4   C5   C6   116.31  3.000
 1HZ  C6   C5   N7   132.87  3.000
 1HZ  C4   C5   N7   110.82  3.000
 1HZ  N1   C6   N6   119.31  3.000
 1HZ  N6   C6   C5   122.83  3.000
 1HZ  N1   C6   C5   117.86  3.000
 1HZ  H21  N6   H20  118.38  3.000
 1HZ  H21  N6   C6   120.29  3.000
 1HZ  H20  N6   C6   121.32  3.000
 1HZ  C2   N1   C6   119.18  3.000
 1HZ  H22  C2   N3   116.12  3.000
 1HZ  H22  C2   N1   115.43  3.000
 1HZ  N3   C2   N1   128.45  3.000
 1HZ  C4   N3   C2   111.66  3.000
 1HZ  N3   C4   C5   126.55  3.000
 1HZ  C5   C4   N9   105.19  3.000
 1HZ  N3   C4   N9   128.26  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
 1HZ  CONST_01  C16  C15  C14  C19    0.00   0.0  0
 1HZ  CONST_02  C16  C17  C18  C19    0.00   0.0  0
 1HZ  CONST_03  C15  C14  C19  C18    0.00   0.0  0
 1HZ  CONST_04  C15  C16  C17  C18    0.00   0.0  0
 1HZ  CONST_05  C14  C19  C18  C17    0.00   0.0  0
 1HZ  CONST_06  C14  C15  C16  C17    0.00   0.0  0
 1HZ  CONST_07  C5   N7   C8   N9     0.00   0.0  0
 1HZ  CONST_08  C2   N3   C4   N9   180.00   0.0  0
 1HZ  CONST_09  N7   C5   C4   N9     0.00   0.0  0
 1HZ  CONST_10  C6   C5   C4   N9   180.00   0.0  0
 1HZ  CONST_11  N3   C4   N9   C8   180.00   0.0  0
 1HZ  CONST_12  C5   C4   N9   C8     0.00   0.0  0
 1HZ  CONST_13  C4   C5   N7   C8     0.00   0.0  0
 1HZ  CONST_14  C6   C5   N7   C8   180.00   0.0  0
 1HZ  CONST_15  C4   N9   C8   N7     0.00   0.0  0
 1HZ  CONST_16  N3   C4   C5   N7   180.00   0.0  0
 1HZ  CONST_17  N1   C6   C5   N7   180.00   0.0  0
 1HZ  CONST_18  C2   N3   C4   C5     0.00   0.0  0
 1HZ  CONST_19  C2   N1   C6   C5     0.00   0.0  0
 1HZ  CONST_20  N3   C4   C5   C6     0.00   0.0  0
 1HZ  CONST_21  N3   C2   N1   C6     0.00   0.0  0
 1HZ  CONST_22  C4   N3   C2   N1     0.00   0.0  0
 1HZ  CONST_23  C4   C5   C6   N1     0.00   0.0  0
 1HZ  CONST_24  N7   C8   N9   C1'  180.00   0.0  0
 1HZ  CONST_25  N3   C4   N9   C1'    0.00   0.0  0
 1HZ  CONST_26  C5   C4   N9   C1'  180.00   0.0  0
 1HZ  CONST_27  C15  C14  C19  C21  180.00   0.0  0
 1HZ  CONST_28  C17  C18  C19  C21  180.00   0.0  0
 1HZ  CONST_29  O15  C15  C14  C19  180.00   0.0  0
 1HZ  CONST_30  O14  C14  C19  C18  180.00   0.0  0
 1HZ  CONST_31  O15  C15  C16  C17  180.00   0.0  0
 1HZ  CONST_32  O14  C14  C15  C16  180.00   0.0  0
 1HZ  CONST_33  N6   C6   C5   N7     0.00   0.0  0
 1HZ  CONST_34  C4   C5   C6   N6   180.00   0.0  0
 1HZ  CONST_35  C2   N1   C6   N6   180.00   0.0  0
 1HZ  CONST_36  H6   C17  C18  C19  180.00   0.0  0
 1HZ  CONST_37  H7   C16  C17  C18  180.00   0.0  0
 1HZ  CONST_38  H5   C18  C17  C16  180.00   0.0  0
 1HZ  CONST_39  H19  C8   N9   C1'    0.00   0.0  0
 1HZ  CONST_40  H22  C2   N1   C6   180.00   0.0  0
 1HZ  CONST_41  H20  N6   C6   C5     0.00   0.0  0
 1HZ  CONST_42  H21  N6   C6   C5   180.00   0.0  0
 1HZ  Var_01    C14  C19  C21  C22   78.15  30.0  2
 1HZ  Var_02    C4'  C5'  N5'  S    165.51  30.0  3
 1HZ  Var_03    C19  C21  C22  S    178.42  30.0  3
 1HZ  Var_04    C5'  N5'  S    O1P  -47.74  30.0  1
 1HZ  Var_05    C21  C22  S    O1P  -63.44  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
 1HZ  chir_01  C4'  C5'  C3'  O4'  positiv
 1HZ  chir_02  C1'  O4'  N9   C2'  negativ
 1HZ  chir_03  C2'  O2'  C1'  C3'  negativ
 1HZ  chir_04  C3'  O3'  C4'  C2'  positiv

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
 1HZ  plan-1  C21  0.020
 1HZ  plan-1  C19  0.020
 1HZ  plan-1  C18  0.020
 1HZ  plan-1  C17  0.020
 1HZ  plan-1  C16  0.020
 1HZ  plan-1  C15  0.020
 1HZ  plan-1  O15  0.020
 1HZ  plan-1  C14  0.020
 1HZ  plan-1  O14  0.020
 1HZ  plan-1  H5   0.020
 1HZ  plan-1  H6   0.020
 1HZ  plan-1  H7   0.020
 1HZ  plan-2  C1'  0.020
 1HZ  plan-2  N9   0.020
 1HZ  plan-2  C8   0.020
 1HZ  plan-2  N7   0.020
 1HZ  plan-2  C5   0.020
 1HZ  plan-2  C6   0.020
 1HZ  plan-2  N6   0.020
 1HZ  plan-2  N1   0.020
 1HZ  plan-2  C2   0.020
 1HZ  plan-2  N3   0.020
 1HZ  plan-2  C4   0.020
 1HZ  plan-2  H19  0.020
 1HZ  plan-2  H22  0.020
 1HZ  plan-3  C6   0.020
 1HZ  plan-3  N6   0.020
 1HZ  plan-3  H20  0.020
 1HZ  plan-3  H21  0.020

