# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 15:48:06 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 5'-deoxy-5'-({[2-(2-hydroxyphenyl)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)CCc4ccccc4O)[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
 SVS  SVS  5'-deoxy-5'-({[2-(2-hydroxyphenyl)ethyl]sulfonyl}amino)adenosine  ligand  53  31  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SVS
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
 SVS  S     S  S     0   1.365  -2.5836  -1.8277  -1.3484
 SVS  N1    N  N     0  -0.474   5.7141   2.4654  -0.7424
 SVS  C2    C  CR16  0   0.048   5.9610   1.1670  -0.5927
 SVS  N3    N  N     0  -0.457   5.1147   0.2000  -0.2822
 SVS  C4    C  CR56  0   0.495   3.8790   0.6634  -0.1161
 SVS  C5    C  CR56  0  -0.011   3.4683   1.9804  -0.2399
 SVS  C6    C  CR6   0   0.462   4.4657   2.9160  -0.5722
 SVS  N6    N  NH2   0  -0.816   4.2162   4.2172  -0.7165
 SVS  N7    N  N     0  -0.445   2.1216   2.0951  -0.0056
 SVS  C8    C  CR15  0   0.117   1.7349   0.8839   0.2558
 SVS  N9    N  NR5   0  -0.541   2.7503  -0.0349   0.2098
 SVS  C1'   C  CH1   0   0.214   2.6618  -1.4561   0.4155
 SVS  C14   C  CR6   0   0.323  -4.5340   2.5239  -0.2990
 SVS  O14   O  OH1   0  -0.627  -3.9748   2.6034  -1.5239
 SVS  C15   C  CR16  0  -0.373  -4.8340   3.6548   0.4553
 SVS  C16   C  CR16  0  -0.256  -5.4040   3.5232   1.7133
 SVS  C17   C  CR16  0  -0.270  -5.6793   2.2647   2.2274
 SVS  C18   C  CR16  0  -0.295  -5.3785   1.1430   1.4661
 SVS  C19   C  CR6   0   0.026  -4.8101   1.2467   0.2018
 SVS  O1P   O  OS    0  -0.668  -2.7557  -1.5895  -2.7731
 SVS  C2'   C  CH1   0  -0.054   2.1409  -1.8563   1.7954
 SVS  O2'   O  OH1   0  -0.652   3.1899  -1.8575   2.7137
 SVS  C21   C  CH2   0  -0.509  -4.4795   0.0135  -0.5926
 SVS  C22   C  CH2   0  -0.619  -2.9929  -0.3216  -0.4694
 SVS  O2P   O  OS    0  -0.672  -3.2988  -2.9289  -0.7184
 SVS  C3'   C  CH1   0  -0.022   1.5336  -3.2295   1.4960
 SVS  O3'   O  OH1   0  -0.665   2.5311  -4.2063   1.3687
 SVS  C4'   C  CH1   0  -0.023   0.9203  -2.9800   0.1253
 SVS  O4'   O  O2    0  -0.496   1.7646  -2.0132  -0.5089
 SVS  C5'   C  CH2   0  -0.303  -0.5005  -2.4499   0.2239
 SVS  N5'   N  NC1   0  -0.736  -0.9766  -2.0967  -1.1056
 SVS  HN6   H  HNH2  0   0.405   4.9518   4.8473  -0.9863
 SVS  HN6A  H  HNH2  0   0.412   3.2835   4.5815  -0.6318
 SVS  H8    H  HCR5  0   0.282   0.7185   0.6019   0.4880
 SVS  H1'   H  HCH1  0   0.268   3.6742  -1.8447   0.2665
 SVS  HO14  H  HOH1  0   0.476  -3.8512   3.5245  -1.7794
 SVS  H15   H  HCR6  0   0.269  -4.6214   4.6409   0.0578
 SVS  H16   H  HCR6  0   0.259  -5.6310   4.4119   2.2878
 SVS  H17   H  HCR6  0   0.252  -6.1267   2.1547   3.2062
 SVS  H18   H  HCR6  0   0.252  -5.5939   0.1560   1.8586
 SVS  H2'   H  HCH1  0   0.251   1.3349  -1.1771   2.1024
 SVS  HO2'  H  HOH1  0   0.471   2.8256  -1.8225   3.6042
 SVS  H21   H  HCH2  0   0.273  -5.0703  -0.8221  -0.2148
 SVS  H22   H  HCH2  0   0.305  -2.7149  -0.4730   0.5754
 SVS  H3'   H  HCH1  0   0.259   0.7742  -3.5110   2.2372
 SVS  HO3'  H  HOH1  0   0.452   3.1180  -4.1359   2.1308
 SVS  H4'   H  HCH1  0   0.279   0.9179  -3.8873  -0.4842
 SVS  H5'   H  HCH2  0   0.288  -1.1310  -3.2425   0.6251
 SVS  H5'A  H  HCH2  0   0.241  -0.5522  -1.6060   0.9232
 SVS  HN5'  H  HNC1  0   0.412  -0.3931  -1.4324  -1.6038
 SVS  H211  H  HCH2  0   0.272  -4.7431   0.1447  -1.6430
 SVS  H221  H  HCH2  0   0.303  -2.3646   0.4662  -0.8877
 SVS  H2    H  HCR6  0   0.253   6.9922   0.8681  -0.7461

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
 SVS  S    O2P   double    1.456  0.020  1.456
 SVS  N1   C6    aromatic  1.338  0.020  1.338
 SVS  C2   N1    aromatic  1.330  0.020  1.330
 SVS  C2   H2    single    0.930  0.020  1.080
 SVS  N3   C2    aromatic  1.322  0.020  1.322
 SVS  N3   C4    aromatic  1.330  0.020  1.330
 SVS  C4   C5    aromatic  1.385  0.020  1.385
 SVS  C5   C6    aromatic  1.407  0.020  1.407
 SVS  C5   N7    aromatic  1.372  0.020  1.372
 SVS  C6   N6    single    1.333  0.020  1.333
 SVS  N6   HN6   single    0.860  0.020  1.020
 SVS  N6   HN6A  single    0.860  0.020  1.020
 SVS  C8   N7    aromatic  1.298  0.020  1.298
 SVS  C8   H8    single    0.930  0.020  1.080
 SVS  N9   C4    aromatic  1.367  0.020  1.367
 SVS  N9   C8    aromatic  1.370  0.020  1.370
 SVS  C1'  N9    single    1.439  0.020  1.439
 SVS  C1'  O4'   single    1.404  0.020  1.404
 SVS  C1'  H1'   single    0.970  0.020  1.090
 SVS  C14  C19   aromatic  1.399  0.020  1.399
 SVS  O14  C14   single    1.349  0.020  1.349
 SVS  O14  HO14  single    0.850  0.020  0.980
 SVS  C15  C14   aromatic  1.392  0.020  1.392
 SVS  C15  C16   aromatic  1.387  0.020  1.387
 SVS  C15  H15   single    0.930  0.020  1.080
 SVS  C16  C17   aromatic  1.387  0.020  1.387
 SVS  C16  H16   single    0.930  0.020  1.080
 SVS  C17  C18   aromatic  1.389  0.020  1.389
 SVS  C17  H17   single    0.930  0.020  1.080
 SVS  C18  H18   single    0.930  0.020  1.080
 SVS  C19  C18   aromatic  1.390  0.020  1.390
 SVS  C19  C21   single    1.504  0.020  1.504
 SVS  O1P  S     double    1.455  0.020  1.455
 SVS  C2'  C1'   single    1.528  0.020  1.528
 SVS  C2'  H2'   single    0.970  0.020  1.090
 SVS  O2'  C2'   single    1.394  0.020  1.394
 SVS  O2'  HO2'  single    0.850  0.020  0.980
 SVS  C21  H21   single    0.970  0.020  1.090
 SVS  C22  S     single    1.791  0.020  1.791
 SVS  C22  C21   single    1.529  0.020  1.529
 SVS  C22  H22   single    0.970  0.020  1.090
 SVS  C3'  C2'   single    1.531  0.020  1.531
 SVS  C3'  C4'   single    1.522  0.020  1.522
 SVS  C3'  H3'   single    0.970  0.020  1.090
 SVS  O3'  C3'   single    1.402  0.020  1.402
 SVS  O3'  HO3'  single    0.850  0.020  0.980
 SVS  C4'  C5'   single    1.520  0.020  1.520
 SVS  C4'  O4'   single    1.432  0.020  1.432
 SVS  C4'  H4'   single    0.970  0.020  1.090
 SVS  C5'  N5'   single    1.456  0.020  1.456
 SVS  C5'  H5'   single    0.970  0.020  1.090
 SVS  C5'  H5'A  single    0.970  0.020  1.090
 SVS  N5'  S     single    1.647  0.020  1.647
 SVS  N5'  HN5'  single    0.890  0.020  1.040
 SVS  C21  H211  single    0.970  0.020  1.090
 SVS  C22  H221  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
 SVS  N5'   S    O2P  106.97  3.000
 SVS  N5'   S    C22  106.73  3.000
 SVS  O2P   S    C22  108.14  3.000
 SVS  N5'   S    O1P  106.65  3.000
 SVS  C22   S    O1P  108.41  3.000
 SVS  O2P   S    O1P  119.30  3.000
 SVS  C6    N1   C2   119.18  3.000
 SVS  H2    C2   N3   116.12  3.000
 SVS  N3    C2   N1   128.43  3.000
 SVS  H2    C2   N1   115.44  3.000
 SVS  C4    N3   C2   111.67  3.000
 SVS  N9    C4   C5   105.20  3.000
 SVS  N9    C4   N3   128.24  3.000
 SVS  C5    C4   N3   126.55  3.000
 SVS  N7    C5   C6   132.88  3.000
 SVS  N7    C5   C4   110.82  3.000
 SVS  C6    C5   C4   116.30  3.000
 SVS  N6    C6   C5   122.81  3.000
 SVS  N6    C6   N1   119.32  3.000
 SVS  C5    C6   N1   117.86  3.000
 SVS  HN6A  N6   HN6  118.33  3.000
 SVS  HN6A  N6   C6   121.24  3.000
 SVS  HN6   N6   C6   120.26  3.000
 SVS  C8    N7   C5   104.41  3.000
 SVS  H8    C8   N9   121.98  3.000
 SVS  N9    C8   N7   113.47  3.000
 SVS  H8    C8   N7   124.56  3.000
 SVS  C1'   N9   C8   127.74  3.000
 SVS  C1'   N9   C4   126.13  3.000
 SVS  C8    N9   C4   106.11  3.000
 SVS  H1'   C1'  O4'  111.14  3.000
 SVS  H1'   C1'  C2'  110.19  3.000
 SVS  O4'   C1'  C2'  105.84  3.000
 SVS  C2'   C1'  N9   114.13  3.000
 SVS  H1'   C1'  N9   105.92  3.000
 SVS  O4'   C1'  N9   109.70  3.000
 SVS  C19   C14  C15  120.33  3.000
 SVS  C15   C14  O14  122.24  3.000
 SVS  C19   C14  O14  117.43  3.000
 SVS  HO14  O14  C14  110.50  3.000
 SVS  H15   C15  C16  119.95  3.000
 SVS  H15   C15  C14  119.86  3.000
 SVS  C16   C15  C14  120.19  3.000
 SVS  H16   C16  C17  120.44  3.000
 SVS  H16   C16  C15  119.32  3.000
 SVS  C17   C16  C15  120.25  3.000
 SVS  H17   C17  C18  120.23  3.000
 SVS  H17   C17  C16  120.64  3.000
 SVS  C18   C17  C16  119.12  3.000
 SVS  H18   C18  C19  118.60  3.000
 SVS  C19   C18  C17  121.80  3.000
 SVS  H18   C18  C17  119.61  3.000
 SVS  C21   C19  C18  120.61  3.000
 SVS  C21   C19  C14  121.06  3.000
 SVS  C18   C19  C14  118.32  3.000
 SVS  H2'   C2'  C3'  108.56  3.000
 SVS  C3'   C2'  O2'  115.25  3.000
 SVS  H2'   C2'  O2'  111.64  3.000
 SVS  C3'   C2'  C1'  101.16  3.000
 SVS  O2'   C2'  C1'  109.79  3.000
 SVS  H2'   C2'  C1'  109.92  3.000
 SVS  HO2'  O2'  C2'  108.93  3.000
 SVS  H211  C21  H21  107.14  3.000
 SVS  H211  C21  C22  109.81  3.000
 SVS  H21   C21  C22  109.32  3.000
 SVS  H211  C21  C19  110.91  3.000
 SVS  C22   C21  C19  110.54  3.000
 SVS  H21   C21  C19  109.03  3.000
 SVS  H221  C22  H22  108.69  3.000
 SVS  H221  C22  C21  111.77  3.000
 SVS  H22   C22  C21  110.80  3.000
 SVS  H221  C22  S    106.70  3.000
 SVS  H22   C22  S    107.15  3.000
 SVS  C21   C22  S    111.53  3.000
 SVS  H3'   C3'  C4'  111.79  3.000
 SVS  H3'   C3'  O3'  112.02  3.000
 SVS  C4'   C3'  O3'  108.61  3.000
 SVS  O3'   C3'  C2'  111.13  3.000
 SVS  H3'   C3'  C2'  111.86  3.000
 SVS  C4'   C3'  C2'  100.88  3.000
 SVS  HO3'  O3'  C3'  108.08  3.000
 SVS  H4'   C4'  C5'  108.89  3.000
 SVS  H4'   C4'  O4'  108.35  3.000
 SVS  C5'   C4'  O4'  110.16  3.000
 SVS  H4'   C4'  C3'  111.52  3.000
 SVS  O4'   C4'  C3'  105.78  3.000
 SVS  C5'   C4'  C3'  112.05  3.000
 SVS  C4'   O4'  C1'  110.68  3.000
 SVS  H5'A  C5'  H5'  107.32  3.000
 SVS  H5'A  C5'  N5'  112.34  3.000
 SVS  H5'   C5'  N5'  108.88  3.000
 SVS  H5'A  C5'  C4'  110.71  3.000
 SVS  H5'   C5'  C4'  108.14  3.000
 SVS  N5'   C5'  C4'  109.34  3.000
 SVS  HN5'  N5'  C5'  114.78  3.000
 SVS  HN5'  N5'  S    112.44  3.000
 SVS  C5'   N5'  S    119.55  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
 SVS  CONST_01  C4    C5   C6   N1      0.00   0.0  0
 SVS  CONST_02  N7    C5   C6   N1    180.00   0.0  0
 SVS  CONST_03  C4    N3   C2   N1      0.00   0.0  0
 SVS  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 SVS  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 SVS  CONST_06  N9    C4   N3   C2    180.00   0.0  0
 SVS  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 SVS  CONST_08  C6    C5   C4   N3      0.00   0.0  0
 SVS  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 SVS  CONST_10  C8    N9   C4   N3    180.00   0.0  0
 SVS  CONST_11  C8    N7   C5   C4      0.00   0.0  0
 SVS  CONST_12  N7    C8   N9   C4      0.00   0.0  0
 SVS  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 SVS  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 SVS  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 SVS  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 SVS  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 SVS  CONST_18  C17   C18  C19  C14     0.00   0.0  0
 SVS  CONST_19  C17   C16  C15  C14     0.00   0.0  0
 SVS  CONST_20  C18   C19  C14  C15     0.00   0.0  0
 SVS  CONST_21  C18   C17  C16  C15     0.00   0.0  0
 SVS  CONST_22  C19   C14  C15  C16     0.00   0.0  0
 SVS  CONST_23  C19   C18  C17  C16     0.00   0.0  0
 SVS  CONST_24  C1'   N9   C4   N3      0.00   0.0  0
 SVS  CONST_25  C1'   N9   C4   C5    180.00   0.0  0
 SVS  CONST_26  C1'   N9   C8   N7    180.00   0.0  0
 SVS  CONST_27  N6    C6   N1   C2    180.00   0.0  0
 SVS  CONST_28  N6    C6   C5   C4    180.00   0.0  0
 SVS  CONST_29  N7    C5   C6   N6      0.00   0.0  0
 SVS  CONST_30  C18   C19  C14  O14   180.00   0.0  0
 SVS  CONST_31  C16   C15  C14  O14   180.00   0.0  0
 SVS  CONST_32  C21   C19  C14  C15   180.00   0.0  0
 SVS  CONST_33  C21   C19  C18  C17   180.00   0.0  0
 SVS  CONST_34  H2    C2   N3   C4    180.00   0.0  0
 SVS  CONST_35  H8    C8   N9   C4    180.00   0.0  0
 SVS  CONST_36  H18   C18  C19  C14   180.00   0.0  0
 SVS  CONST_37  H16   C16  C15  C14   180.00   0.0  0
 SVS  CONST_38  H17   C17  C16  C15   180.00   0.0  0
 SVS  CONST_39  H15   C15  C16  C17   180.00   0.0  0
 SVS  CONST_40  HN6   N6   C6   N1      0.00   0.0  0
 SVS  CONST_41  HN6A  N6   C6   N1    180.00   0.0  0
 SVS  Var_01    C22   C21  C19  C14    79.65  30.0  2
 SVS  Var_02    C19   C21  C22  S     177.52  30.0  3
 SVS  Var_03    C4'   C5'  N5'  S     165.91  30.0  2
 SVS  Var_04    C21   C22  S    O1P    66.94  30.0  1
 SVS  Var_05    C5'   N5'  S    O1P  -176.22  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
 SVS  chir_01  C1'  N9   O4'  C2'  positiv
 SVS  chir_02  C2'  O2'  C1'  C3'  negativ
 SVS  chir_03  C3'  O3'  C4'  C2'  positiv
 SVS  chir_04  C4'  O4'  C3'  C5'  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
 SVS  plan-1  C14   0.020
 SVS  plan-1  O14   0.020
 SVS  plan-1  C15   0.020
 SVS  plan-1  C16   0.020
 SVS  plan-1  C17   0.020
 SVS  plan-1  C18   0.020
 SVS  plan-1  C19   0.020
 SVS  plan-1  C21   0.020
 SVS  plan-1  H15   0.020
 SVS  plan-1  H16   0.020
 SVS  plan-1  H17   0.020
 SVS  plan-1  H18   0.020
 SVS  plan-2  N1    0.020
 SVS  plan-2  C2    0.020
 SVS  plan-2  N3    0.020
 SVS  plan-2  C4    0.020
 SVS  plan-2  C5    0.020
 SVS  plan-2  C6    0.020
 SVS  plan-2  N6    0.020
 SVS  plan-2  N7    0.020
 SVS  plan-2  C8    0.020
 SVS  plan-2  N9    0.020
 SVS  plan-2  C1'   0.020
 SVS  plan-2  H8    0.020
 SVS  plan-2  H2    0.020
 SVS  plan-3  C6    0.020
 SVS  plan-3  N6    0.020
 SVS  plan-3  HN6   0.020
 SVS  plan-3  HN6A  0.020

