# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 27 10:25:52 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (2S)-4-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)-2-[(3-methylbutanoyl)amino]butanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CC(=O)N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
#
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
 SXZ  SXZ  '(2S)-4-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)-2-[(3-methylbutanoyl)amino]butanoic acid (non-preferred name)'  ligand  59  32  .  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_SXZ
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
 SXZ  O    O  O     -1  -0.594  -6.0515   2.6779  -1.0321
 SXZ  C    C  C      0   0.427  -5.6301   2.9096   0.1170
 SXZ  OXT  O  OC     0  -0.604  -5.8031   3.9393   0.7923
 SXZ  CA   C  CH1    0  -0.217  -4.7541   1.8157   0.7813
 SXZ  N    N  NH1    0  -0.619  -4.8523   0.5877   0.0279
 SXZ  CB   C  CH2    0  -0.412  -3.3120   2.3316   0.8821
 SXZ  CG   C  CH2    0  -0.553  -2.3538   1.3151   1.4808
 SXZ  SD   S  S2     0  -0.018  -0.7067   2.0654   1.6651
 SXZ  C5'  C  CH2    0  -0.605   0.2721   0.5933   2.0659
 SXZ  C4'  C  CH1    0   0.067   0.5730  -0.2764   0.8675
 SXZ  O4'  O  O2     0  -0.492   1.3616   0.4396  -0.0804
 SXZ  C1'  C  CH1    0   0.176   2.3409  -0.3803  -0.6420
 SXZ  C2'  C  CH1    0  -0.045   2.0611  -1.8042  -0.1620
 SXZ  O2'  O  OH1    0  -0.663   1.1580  -2.3832  -1.0625
 SXZ  C3'  C  CH1    0  -0.029   1.3911  -1.5255   1.1881
 SXZ  O3'  O  OH1    0  -0.655   0.5469  -2.5503   1.6274
 SXZ  N9   N  NR5    0  -0.536   3.6555   0.0810  -0.2074
 SXZ  C8   C  CR15   0   0.102   3.9698   0.9859   0.7690
 SXZ  N7   N  N      0  -0.451   5.2499   1.1869   0.8930
 SXZ  C5   C  CR56   0  -0.002   5.8157   0.3755  -0.0538
 SXZ  C6   C  CR6    0   0.458   7.1473   0.1324  -0.4398
 SXZ  N6   N  NH2    0  -0.816   8.1875   0.7305   0.1413
 SXZ  N1   N  N      0  -0.474   7.3623  -0.7367  -1.4339
 SXZ  C2   C  CR16   0   0.040   6.3226  -1.3313  -2.0137
 SXZ  N3   N  N      0  -0.458   5.0372  -1.1875  -1.7420
 SXZ  C4   C  CR56   0   0.485   4.8404  -0.3188  -0.7514
 SXZ  C1   C  C      0   0.535  -4.9493  -0.6373   0.5620
 SXZ  O2   O  O      0  -0.516  -4.8244  -0.8666   1.7617
 SXZ  C3   C  CH2    0  -0.541  -5.2326  -1.7544  -0.4192
 SXZ  C7   C  CH1    0  -0.237  -6.5466  -2.4777  -0.1059
 SXZ  C9   C  CH3    0  -0.656  -7.7365  -1.5268  -0.1907
 SXZ  C10  C  CH3    0  -0.652  -6.7265  -3.6615  -1.0492
 SXZ  H2   H  HCH1   0   0.239  -5.1265   1.6309   1.7923
 SXZ  H3   H  HNH1   0   0.382  -5.1147   0.7190  -0.9385
 SXZ  H4   H  HCH2   0   0.230  -2.9564   2.6175  -0.1127
 SXZ  H5   H  HCH2   0   0.237  -3.3234   3.2381   1.4905
 SXZ  H6   H  HCH2   0   0.262  -2.7019   0.9710   2.4555
 SXZ  H7   H  HCH2   0   0.258  -2.2736   0.4487   0.8238
 SXZ  H8   H  HCH2   0   0.280   1.1952   0.9450   2.5317
 SXZ  H9   H  HCH2   0   0.287  -0.2580   0.0033   2.8169
 SXZ  H10  H  HCH1   0   0.246  -0.3665  -0.5860   0.3935
 SXZ  H11  H  HCH1   0   0.284   2.3196  -0.3138  -1.7334
 SXZ  H12  H  HCH1   0   0.261   2.9794  -2.3959  -0.0674
 SXZ  H13  H  HOH1   0   0.453   0.6380  -3.0381  -0.5804
 SXZ  H14  H  HCH1   0   0.244   2.1619  -1.2905   1.9343
 SXZ  H15  H  HOH1   0   0.469   1.0702  -3.2059   2.0997
 SXZ  H16  H  HCR5   0   0.294   3.2149   1.4846   1.3555
 SXZ  H17  H  HNH2   0   0.411   8.0592   1.3825   0.8946
 SXZ  H18  H  HNH2   0   0.403   9.1243   0.5334  -0.1657
 SXZ  H19  H  HCR6   0   0.252   6.5681  -2.0226  -2.8133
 SXZ  H20  H  HCH2   0   0.236  -5.2576  -1.3833  -1.4478
 SXZ  H21  H  HCH2   0   0.258  -4.4043  -2.4666  -0.3605
 SXZ  H22  H  HCH1   0   0.225  -6.4835  -2.8632   0.9165
 SXZ  H23  H  HCH3   0   0.229  -8.6724  -2.0545  -0.0018
 SXZ  H24  H  HCH3   0   0.230  -7.6680  -0.7159   0.5361
 SXZ  H25  H  HCH3   0   0.215  -7.8055  -1.0765  -1.1839
 SXZ  H26  H  HCH3   0   0.226  -5.8864  -4.3545  -0.9816
 SXZ  H27  H  HCH3   0   0.228  -7.6362  -4.2164  -0.8150
 SXZ  H28  H  HCH3   0   0.215  -6.7995  -3.3274  -2.0869

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
 SXZ  C9   C7   single    1.526  0.020  1.526
 SXZ  C10  C7   single    1.524  0.020  1.524
 SXZ  C7   C3   single    1.532  0.020  1.532
 SXZ  C3   C1   single    1.514  0.020  1.514
 SXZ  C1   O2   double    1.228  0.020  1.228
 SXZ  C1   N    single    1.340  0.020  1.340
 SXZ  N    CA   single    1.444  0.020  1.444
 SXZ  O    C    deloc     1.246  0.020  1.246
 SXZ  CA   C    single    1.551  0.020  1.551
 SXZ  CA   CB   single    1.535  0.020  1.535
 SXZ  C    OXT  deloc     1.243  0.020  1.243
 SXZ  CG   CB   single    1.520  0.020  1.520
 SXZ  CG   SD   single    1.819  0.020  1.819
 SXZ  SD   C5'  single    1.813  0.020  1.813
 SXZ  C5'  C4'  single    1.511  0.020  1.511
 SXZ  O4'  C4'  single    1.426  0.020  1.426
 SXZ  O4'  C1'  single    1.395  0.020  1.395
 SXZ  C4'  C3'  single    1.527  0.020  1.527
 SXZ  C8   N7   aromatic  1.302  0.020  1.302
 SXZ  C8   N9   aromatic  1.368  0.020  1.368
 SXZ  N7   C5   aromatic  1.369  0.020  1.369
 SXZ  N9   C1'  single    1.459  0.020  1.459
 SXZ  N9   C4   aromatic  1.364  0.020  1.364
 SXZ  C3'  C2'  single    1.533  0.020  1.533
 SXZ  C3'  O3'  single    1.399  0.020  1.399
 SXZ  C1'  C2'  single    1.528  0.020  1.528
 SXZ  C5   C4   aromatic  1.386  0.020  1.386
 SXZ  C5   C6   aromatic  1.408  0.020  1.408
 SXZ  N6   C6   single    1.333  0.020  1.333
 SXZ  C2'  O2'  single    1.401  0.020  1.401
 SXZ  C4   N3   aromatic  1.332  0.020  1.332
 SXZ  C6   N1   aromatic  1.338  0.020  1.338
 SXZ  N3   C2   aromatic  1.322  0.020  1.322
 SXZ  N1   C2   aromatic  1.331  0.020  1.331
 SXZ  CA   H2   single    0.970  0.020  1.090
 SXZ  N    H3   single    0.860  0.020  1.020
 SXZ  CB   H4   single    0.970  0.020  1.090
 SXZ  CB   H5   single    0.970  0.020  1.090
 SXZ  CG   H6   single    0.970  0.020  1.090
 SXZ  CG   H7   single    0.970  0.020  1.090
 SXZ  C5'  H8   single    0.970  0.020  1.090
 SXZ  C5'  H9   single    0.970  0.020  1.090
 SXZ  C4'  H10  single    0.970  0.020  1.090
 SXZ  C1'  H11  single    0.970  0.020  1.090
 SXZ  C2'  H12  single    0.970  0.020  1.090
 SXZ  O2'  H13  single    0.850  0.020  0.980
 SXZ  C3'  H14  single    0.970  0.020  1.090
 SXZ  O3'  H15  single    0.850  0.020  0.980
 SXZ  C8   H16  single    0.930  0.020  1.080
 SXZ  N6   H17  single    0.860  0.020  1.020
 SXZ  N6   H18  single    0.860  0.020  1.020
 SXZ  C2   H19  single    0.930  0.020  1.080
 SXZ  C3   H20  single    0.970  0.020  1.090
 SXZ  C3   H21  single    0.970  0.020  1.090
 SXZ  C7   H22  single    0.970  0.020  1.090
 SXZ  C9   H23  single    0.970  0.020  1.090
 SXZ  C9   H24  single    0.970  0.020  1.090
 SXZ  C9   H25  single    0.970  0.020  1.090
 SXZ  C10  H26  single    0.970  0.020  1.090
 SXZ  C10  H27  single    0.970  0.020  1.090
 SXZ  C10  H28  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
 SXZ  CA   C    OXT  115.47  3.000
 SXZ  OXT  C    O    127.44  3.000
 SXZ  CA   C    O    117.06  3.000
 SXZ  H2   CA   CB   108.43  3.000
 SXZ  H2   CA   N    108.40  3.000
 SXZ  CB   CA   N    112.58  3.000
 SXZ  H2   CA   C    108.85  3.000
 SXZ  CB   CA   C    108.77  3.000
 SXZ  N    CA   C    109.75  3.000
 SXZ  H3   N    C1   118.79  3.000
 SXZ  H3   N    CA   113.97  3.000
 SXZ  C1   N    CA   125.06  3.000
 SXZ  H5   CB   H4   107.04  3.000
 SXZ  H5   CB   CG   110.02  3.000
 SXZ  H4   CB   CG   109.14  3.000
 SXZ  H5   CB   CA   107.81  3.000
 SXZ  H4   CB   CA   109.47  3.000
 SXZ  CG   CB   CA   113.17  3.000
 SXZ  H7   CG   H6   108.14  3.000
 SXZ  H7   CG   SD   108.80  3.000
 SXZ  H6   CG   SD   109.18  3.000
 SXZ  H7   CG   CB   109.91  3.000
 SXZ  H6   CG   CB   111.21  3.000
 SXZ  SD   CG   CB   109.56  3.000
 SXZ  C5'  SD   CG   100.15  3.000
 SXZ  H9   C5'  H8   106.91  3.000
 SXZ  H9   C5'  C4'  109.33  3.000
 SXZ  H8   C5'  C4'  110.81  3.000
 SXZ  H9   C5'  SD   109.19  3.000
 SXZ  H8   C5'  SD   106.81  3.000
 SXZ  C4'  C5'  SD   113.56  3.000
 SXZ  H10  C4'  C3'  108.58  3.000
 SXZ  H10  C4'  O4'  109.16  3.000
 SXZ  C3'  C4'  O4'  104.72  3.000
 SXZ  H10  C4'  C5'  109.55  3.000
 SXZ  C3'  C4'  C5'  114.27  3.000
 SXZ  O4'  C4'  C5'  110.39  3.000
 SXZ  C1'  O4'  C4'  111.14  3.000
 SXZ  H11  C1'  N9   107.19  3.000
 SXZ  H11  C1'  C2'  111.50  3.000
 SXZ  N9   C1'  C2'  111.46  3.000
 SXZ  H11  C1'  O4'  110.63  3.000
 SXZ  C2'  C1'  O4'  107.01  3.000
 SXZ  N9   C1'  O4'  109.06  3.000
 SXZ  H12  C2'  C3'  112.84  3.000
 SXZ  H12  C2'  O2'  111.86  3.000
 SXZ  C3'  C2'  O2'  111.08  3.000
 SXZ  H12  C2'  C1'  112.11  3.000
 SXZ  O2'  C2'  C1'  107.53  3.000
 SXZ  C3'  C2'  C1'  100.79  3.000
 SXZ  H13  O2'  C2'  107.86  3.000
 SXZ  H14  C3'  O3'  111.53  3.000
 SXZ  H14  C3'  C2'  109.31  3.000
 SXZ  O3'  C3'  C2'  114.03  3.000
 SXZ  H14  C3'  C4'  110.09  3.000
 SXZ  O3'  C3'  C4'  109.99  3.000
 SXZ  C2'  C3'  C4'  101.42  3.000
 SXZ  H15  O3'  C3'  108.97  3.000
 SXZ  C4   N9   C8   106.20  3.000
 SXZ  C4   N9   C1'  124.83  3.000
 SXZ  C8   N9   C1'  128.95  3.000
 SXZ  H16  C8   N7   124.42  3.000
 SXZ  H16  C8   N9   122.23  3.000
 SXZ  N7   C8   N9   113.33  3.000
 SXZ  C5   N7   C8   104.42  3.000
 SXZ  C4   C5   C6   116.19  3.000
 SXZ  C6   C5   N7   133.07  3.000
 SXZ  C4   C5   N7   110.74  3.000
 SXZ  N1   C6   N6   119.33  3.000
 SXZ  N1   C6   C5   117.91  3.000
 SXZ  N6   C6   C5   122.76  3.000
 SXZ  H18  N6   H17  118.38  3.000
 SXZ  H18  N6   C6   120.40  3.000
 SXZ  H17  N6   C6   121.22  3.000
 SXZ  C2   N1   C6   119.24  3.000
 SXZ  H19  C2   N3   116.16  3.000
 SXZ  H19  C2   N1   115.40  3.000
 SXZ  N3   C2   N1   128.44  3.000
 SXZ  C4   N3   C2   111.56  3.000
 SXZ  N3   C4   C5   126.66  3.000
 SXZ  N3   C4   N9   128.03  3.000
 SXZ  C5   C4   N9   105.30  3.000
 SXZ  C3   C1   O2   120.98  3.000
 SXZ  O2   C1   N    123.56  3.000
 SXZ  C3   C1   N    115.46  3.000
 SXZ  H21  C3   H20  106.78  3.000
 SXZ  H21  C3   C7   109.33  3.000
 SXZ  H20  C3   C7   109.44  3.000
 SXZ  H21  C3   C1   107.70  3.000
 SXZ  H20  C3   C1   111.32  3.000
 SXZ  C7   C3   C1   112.11  3.000
 SXZ  H22  C7   C10  108.14  3.000
 SXZ  H22  C7   C9   108.45  3.000
 SXZ  C10  C7   C9   110.95  3.000
 SXZ  H22  C7   C3   107.93  3.000
 SXZ  C10  C7   C3   109.96  3.000
 SXZ  C9   C7   C3   111.30  3.000
 SXZ  H25  C9   H24  107.65  3.000
 SXZ  H25  C9   H23  107.61  3.000
 SXZ  H24  C9   H23  107.34  3.000
 SXZ  H25  C9   C7   110.89  3.000
 SXZ  H24  C9   C7   112.17  3.000
 SXZ  H23  C9   C7   110.98  3.000
 SXZ  H28  C10  H27  107.69  3.000
 SXZ  H28  C10  H26  107.73  3.000
 SXZ  H27  C10  H26  107.80  3.000
 SXZ  H28  C10  C7   110.98  3.000
 SXZ  H27  C10  C7   111.14  3.000
 SXZ  H26  C10  C7   111.34  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
 SXZ  CONST_01  C5   N7   C8  N9      0.00   0.0  0
 SXZ  CONST_02  N7   C5   C4  N9      0.00   0.0  0
 SXZ  CONST_03  C6   C5   C4  N9    180.00   0.0  0
 SXZ  CONST_04  C2   N3   C4  N9    180.00   0.0  0
 SXZ  CONST_05  C4   C5   N7  C8      0.00   0.0  0
 SXZ  CONST_06  C6   C5   N7  C8    180.00   0.0  0
 SXZ  CONST_07  C5   C4   N9  C8      0.00   0.0  0
 SXZ  CONST_08  N3   C4   N9  C8    180.00   0.0  0
 SXZ  CONST_09  C4   N9   C8  N7      0.00   0.0  0
 SXZ  CONST_10  N3   C4   C5  N7    180.00   0.0  0
 SXZ  CONST_11  N1   C6   C5  N7    180.00   0.0  0
 SXZ  CONST_12  C2   N3   C4  C5      0.00   0.0  0
 SXZ  CONST_13  C2   N1   C6  C5      0.00   0.0  0
 SXZ  CONST_14  N3   C4   C5  C6      0.00   0.0  0
 SXZ  CONST_15  N3   C2   N1  C6      0.00   0.0  0
 SXZ  CONST_16  C4   C5   C6  N1      0.00   0.0  0
 SXZ  CONST_17  C4   N3   C2  N1      0.00   0.0  0
 SXZ  CONST_18  N7   C8   N9  C1'   180.00   0.0  0
 SXZ  CONST_19  C5   C4   N9  C1'   180.00   0.0  0
 SXZ  CONST_20  N3   C4   N9  C1'     0.00   0.0  0
 SXZ  CONST_21  N6   C6   C5  N7      0.00   0.0  0
 SXZ  CONST_22  C4   C5   C6  N6    180.00   0.0  0
 SXZ  CONST_23  C2   N1   C6  N6    180.00   0.0  0
 SXZ  CONST_24  H16  C8   N9  C1'     0.00   0.0  0
 SXZ  CONST_25  H19  C2   N1  C6    180.00   0.0  0
 SXZ  CONST_26  H17  N6   C6  C5      0.00   0.0  0
 SXZ  CONST_27  H18  N6   C6  C5    180.00   0.0  0
 SXZ  CONST_28  C3   C1   N   CA    180.00   0.0  0
 SXZ  CONST_29  O2   C1   N   CA      0.00   0.0  0
 SXZ  CONST_30  H3   N    C1  O2    180.00   0.0  0
 SXZ  Var_01    C4'  C5'  SD  CG     76.68  30.0  3
 SXZ  Var_02    SD   CG   CB  CA   -175.96  30.0  1
 SXZ  Var_03    C7   C3   C1  N    -119.61  30.0  1
 SXZ  Var_04    C9   C7   C3  C1     61.28  30.0  3
 SXZ  Var_05    H23  C9   C7  C3    177.98  30.0  3
 SXZ  Var_06    H26  C10  C7  C3     57.37  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
 SXZ  chir_01  CA   N    C    CB   positiv
 SXZ  chir_02  C4'  O4'  C5'  C3'  positiv
 SXZ  chir_03  C1'  O4'  N9   C2'  negativ
 SXZ  chir_04  C2'  O2'  C1'  C3'  negativ
 SXZ  chir_05  C3'  O3'  C2'  C4'  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
 SXZ  plan-1  C1'  0.020
 SXZ  plan-1  N9   0.020
 SXZ  plan-1  C8   0.020
 SXZ  plan-1  N7   0.020
 SXZ  plan-1  C5   0.020
 SXZ  plan-1  C6   0.020
 SXZ  plan-1  N6   0.020
 SXZ  plan-1  N1   0.020
 SXZ  plan-1  C2   0.020
 SXZ  plan-1  N3   0.020
 SXZ  plan-1  C4   0.020
 SXZ  plan-1  H16  0.020
 SXZ  plan-1  H19  0.020
 SXZ  plan-2  C6   0.020
 SXZ  plan-2  N6   0.020
 SXZ  plan-2  H17  0.020
 SXZ  plan-2  H18  0.020
 SXZ  plan-3  CA   0.020
 SXZ  plan-3  N    0.020
 SXZ  plan-3  C1   0.020
 SXZ  plan-3  O2   0.020
 SXZ  plan-3  C3   0.020
 SXZ  plan-3  H3   0.020
 SXZ  plan-4  O    0.020
 SXZ  plan-4  C    0.020
 SXZ  plan-4  OXT  0.020
 SXZ  plan-4  CA   0.020

