# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 09:33:47 2021
#   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  60  32  .  2021-08-23  2022-11-17
;
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     0  -0.425  -32.8915  26.6413   -9.7767
 SXZ  C    C  C     0   0.540  -31.8753  26.0661   -9.4852
 SXZ  OXT  O  OH1   0  -0.602  -31.8025  25.0900   -8.5921
 SXZ  CA   C  CH1   0  -0.162  -30.4986  26.4333  -10.0119
 SXZ  N    N  NH1   0  -0.638  -30.5685  26.9659  -11.3448
 SXZ  CB   C  CH2   0  -0.454  -29.8993  27.4739   -9.0551
 SXZ  CG   C  CH2   0  -0.579  -28.4094  27.6675   -9.2842
 SXZ  SD   S  S2    0  -0.003  -27.6871  29.0607   -8.3806
 SXZ  C5'  C  CH2   0  -0.594  -27.7582  28.5334   -6.6398
 SXZ  C4'  C  CR15  0   0.044  -28.6665  29.4220   -5.8072
 SXZ  O4'  O  O     0  -0.479  -30.0174  29.3100   -6.2551
 SXZ  C1'  C  CR15  0   0.206  -30.8511  28.9565   -5.1816
 SXZ  C2'  C  CR15  0  -0.040  -29.9380  28.2098   -4.2070
 SXZ  O2'  O  OH1   0  -0.653  -30.4104  28.1590   -2.8978
 SXZ  C3'  C  CR15  0  -0.043  -28.6730  29.0584   -4.3183
 SXZ  O3'  O  OH1   0  -0.665  -28.7840  30.2467   -3.5779
 SXZ  N9   N  NR5   0  -0.551  -31.9661  28.1989   -5.6807
 SXZ  C8   C  CR15  0   0.110  -32.0521  26.8526   -5.9092
 SXZ  N7   N  N     0  -0.486  -33.1533  26.4996   -6.5037
 SXZ  C5   C  CR56  0   0.026  -33.8328  27.6748   -6.6998
 SXZ  C6   C  CR6   0   0.466  -35.0560  27.9812   -7.3227
 SXZ  N6   N  NH2   0  -0.813  -35.8473  27.0497   -7.8589
 SXZ  N1   N  N     0  -0.472  -35.4364  29.2626   -7.3505
 SXZ  C2   C  CR16  0   0.044  -34.6475  30.1864   -6.8078
 SXZ  N3   N  N     0  -0.457  -33.4745  30.0222   -6.2207
 SXZ  C4   C  CR56  0   0.495  -33.1134  28.7430   -6.1953
 SXZ  C1   C  C     0   0.555  -30.9953  26.2122  -12.3752
 SXZ  O2   O  O     0  -0.498  -31.2816  25.0315  -12.2264
 SXZ  C3   C  CH2   0  -0.546  -31.0938  26.9048  -13.7133
 SXZ  C7   C  CH1   0  -0.242  -32.5279  26.9074  -14.2544
 SXZ  C9   C  CH3   0  -0.652  -32.5514  27.4345  -15.6841
 SXZ  C10  C  CH3   0  -0.665  -33.4525  27.7258  -13.3592
 SXZ  H1   H  HOH1  0   0.479  -32.6065  25.0923   -8.0401
 SXZ  H2   H  HCH1  0   0.283  -29.8707  25.5375  -10.0032
 SXZ  H3   H  HNH1  0   0.404  -30.4574  27.9589  -11.4747
 SXZ  H4   H  HCH2  0   0.257  -30.4301  28.4218   -9.1685
 SXZ  H5   H  HCH2  0   0.264  -30.0651  27.1471   -8.0283
 SXZ  H6   H  HCH2  0   0.279  -27.8625  26.7541   -9.0437
 SXZ  H7   H  HCH2  0   0.284  -28.1998  27.8974  -10.3308
 SXZ  H8   H  HCH2  0   0.278  -28.0610  27.4850   -6.5916
 SXZ  H9   H  HCH2  0   0.290  -26.7456  28.5962   -6.2386
 SXZ  H10  H  HCR5  0   0.258  -28.3355  30.4602   -5.9163
 SXZ  H11  H  HCR5  0   0.255  -31.2697  29.8429   -4.6931
 SXZ  H12  H  HCR5  0   0.249  -29.7048  27.2110   -4.5993
 SXZ  H13  H  HOH1  0   0.467  -30.9958  27.4032   -2.7945
 SXZ  H14  H  HCR5  0   0.259  -27.7801  28.4890   -4.0332
 SXZ  H15  H  HOH1  0   0.456  -28.8717  30.0202   -2.6457
 SXZ  H16  H  HCR5  0   0.310  -31.2741  26.1668   -5.6118
 SXZ  H17  H  HNH2  0   0.403  -36.6520  27.3315   -8.3928
 SXZ  H18  H  HNH2  0   0.407  -35.5073  26.1138   -7.9950
 SXZ  H19  H  HCR6  0   0.254  -35.0160  31.2051   -6.8627
 SXZ  H20  H  HCH2  0   0.269  -30.4409  26.3673  -14.4066
 SXZ  H21  H  HCH2  0   0.242  -30.7196  27.9309  -13.6558
 SXZ  H22  H  HCH1  0   0.229  -32.8805  25.8715  -14.2684
 SXZ  H23  H  HCH3  0   0.228  -31.9131  26.8421  -16.3418
 SXZ  H24  H  HCH3  0   0.229  -33.5636  27.4082  -16.0907
 SXZ  H25  H  HCH3  0   0.216  -32.2055  28.4700  -15.7282
 SXZ  H26  H  HCH3  0   0.237  -33.4677  27.3581  -12.3322
 SXZ  H27  H  HCH3  0   0.215  -33.1364  28.7715  -13.3321
 SXZ  H28  H  HCH3  0   0.229  -34.4778  27.7015  -13.7313

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    1.524  0.020  1.524
 SXZ  C10  C7   single    1.525  0.020  1.525
 SXZ  C7   C3   single    1.533  0.020  1.533
 SXZ  C3   C1   single    1.510  0.020  1.510
 SXZ  C1   O2   double    1.224  0.020  1.224
 SXZ  C1   N    single    1.346  0.020  1.346
 SXZ  N    CA   single    1.437  0.020  1.437
 SXZ  O    C    double    1.204  0.020  1.204
 SXZ  CA   C    single    1.519  0.020  1.519
 SXZ  CA   CB   single    1.535  0.020  1.535
 SXZ  C    OXT  single    1.325  0.020  1.325
 SXZ  CG   CB   single    1.520  0.020  1.520
 SXZ  CG   SD   single    1.811  0.020  1.811
 SXZ  SD   C5'  single    1.820  0.020  1.820
 SXZ  C5'  C4'  single    1.519  0.020  1.519
 SXZ  O4'  C4'  single    1.428  0.020  1.428
 SXZ  O4'  C1'  single    1.404  0.020  1.404
 SXZ  C4'  C3'  single    1.533  0.020  1.533
 SXZ  C8   N7   aromatic  1.300  0.020  1.300
 SXZ  C8   N9   aromatic  1.368  0.020  1.368
 SXZ  N7   C5   aromatic  1.372  0.020  1.372
 SXZ  N9   C1'  single    1.437  0.020  1.437
 SXZ  N9   C4   aromatic  1.370  0.020  1.370
 SXZ  C3'  C2'  single    1.527  0.020  1.527
 SXZ  C3'  O3'  single    1.405  0.020  1.405
 SXZ  C1'  C2'  single    1.530  0.020  1.530
 SXZ  C5   C4   aromatic  1.383  0.020  1.383
 SXZ  C5   C6   aromatic  1.406  0.020  1.406
 SXZ  N6   C6   single    1.335  0.020  1.335
 SXZ  C2'  O2'  single    1.393  0.020  1.393
 SXZ  C4   N3   aromatic  1.329  0.020  1.329
 SXZ  C6   N1   aromatic  1.337  0.020  1.337
 SXZ  N3   C2   aromatic  1.322  0.020  1.322
 SXZ  N1   C2   aromatic  1.331  0.020  1.331
 SXZ  OXT  H1   single    0.850  0.020  0.980
 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  111.22  3.000
 SXZ  OXT  C    O    124.18  3.000
 SXZ  CA   C    O    124.45  3.000
 SXZ  H1   OXT  C    109.54  3.000
 SXZ  H2   CA   CB   109.02  3.000
 SXZ  H2   CA   N    109.80  3.000
 SXZ  CB   CA   N    110.23  3.000
 SXZ  H2   CA   C    108.63  3.000
 SXZ  CB   CA   C    107.55  3.000
 SXZ  N    CA   C    111.54  3.000
 SXZ  H3   N    C1   119.21  3.000
 SXZ  H3   N    CA   118.65  3.000
 SXZ  C1   N    CA   121.19  3.000
 SXZ  H5   CB   H4   106.50  3.000
 SXZ  H5   CB   CG   109.22  3.000
 SXZ  H4   CB   CG   110.50  3.000
 SXZ  H5   CB   CA   108.93  3.000
 SXZ  H4   CB   CA   109.50  3.000
 SXZ  CG   CB   CA   112.03  3.000
 SXZ  H7   CG   H6   106.93  3.000
 SXZ  H7   CG   SD   103.87  3.000
 SXZ  H6   CG   SD   109.51  3.000
 SXZ  H7   CG   CB   111.07  3.000
 SXZ  H6   CG   CB   110.58  3.000
 SXZ  SD   CG   CB   114.45  3.000
 SXZ  C5'  SD   CG   103.81  3.000
 SXZ  H9   C5'  H8   107.24  3.000
 SXZ  H9   C5'  C4'  108.65  3.000
 SXZ  H8   C5'  C4'  111.81  3.000
 SXZ  H9   C5'  SD   107.38  3.000
 SXZ  H8   C5'  SD   109.33  3.000
 SXZ  C4'  C5'  SD   112.21  3.000
 SXZ  H10  C4'  C3'  108.84  3.000
 SXZ  H10  C4'  O4'  109.21  3.000
 SXZ  C3'  C4'  O4'  106.39  3.000
 SXZ  H10  C4'  C5'  108.62  3.000
 SXZ  C3'  C4'  C5'  113.34  3.000
 SXZ  O4'  C4'  C5'  110.36  3.000
 SXZ  C1'  O4'  C4'  109.98  3.000
 SXZ  H11  C1'  N9   106.56  3.000
 SXZ  H11  C1'  C2'  109.81  3.000
 SXZ  N9   C1'  C2'  115.27  3.000
 SXZ  H11  C1'  O4'  111.35  3.000
 SXZ  C2'  C1'  O4'  104.80  3.000
 SXZ  N9   C1'  O4'  109.13  3.000
 SXZ  H12  C2'  C3'  107.66  3.000
 SXZ  H12  C2'  O2'  112.01  3.000
 SXZ  C3'  C2'  O2'  111.70  3.000
 SXZ  H12  C2'  C1'  110.06  3.000
 SXZ  O2'  C2'  C1'  114.47  3.000
 SXZ  C3'  C2'  C1'  100.17  3.000
 SXZ  H13  O2'  C2'  109.64  3.000
 SXZ  H14  C3'  O3'  111.50  3.000
 SXZ  H14  C3'  C2'  111.53  3.000
 SXZ  O3'  C3'  C2'  111.48  3.000
 SXZ  H14  C3'  C4'  111.85  3.000
 SXZ  O3'  C3'  C4'  108.16  3.000
 SXZ  C2'  C3'  C4'  101.90  3.000
 SXZ  H15  O3'  C3'  108.56  3.000
 SXZ  C4   N9   C8   105.99  3.000
 SXZ  C4   N9   C1'  124.80  3.000
 SXZ  C8   N9   C1'  128.70  3.000
 SXZ  H16  C8   N7   124.34  3.000
 SXZ  H16  C8   N9   122.28  3.000
 SXZ  N7   C8   N9   113.37  3.000
 SXZ  C5   N7   C8   104.62  3.000
 SXZ  C4   C5   C6   116.47  3.000
 SXZ  C6   C5   N7   132.91  3.000
 SXZ  C4   C5   N7   110.60  3.000
 SXZ  N1   C6   N6   119.46  3.000
 SXZ  N1   C6   C5   117.74  3.000
 SXZ  N6   C6   C5   122.79  3.000
 SXZ  H18  N6   H17  117.35  3.000
 SXZ  H18  N6   C6   120.25  3.000
 SXZ  H17  N6   C6   119.48  3.000
 SXZ  C2   N1   C6   119.23  3.000
 SXZ  H19  C2   N3   116.14  3.000
 SXZ  H19  C2   N1   115.47  3.000
 SXZ  N3   C2   N1   128.39  3.000
 SXZ  C4   N3   C2   111.65  3.000
 SXZ  N3   C4   C5   126.50  3.000
 SXZ  N3   C4   N9   128.08  3.000
 SXZ  C5   C4   N9   105.42  3.000
 SXZ  C3   C1   O2   122.34  3.000
 SXZ  O2   C1   N    121.41  3.000
 SXZ  C3   C1   N    116.24  3.000
 SXZ  H21  C3   H20  106.87  3.000
 SXZ  H21  C3   C7   109.70  3.000
 SXZ  H20  C3   C7   109.61  3.000
 SXZ  H21  C3   C1   111.19  3.000
 SXZ  H20  C3   C1   107.30  3.000
 SXZ  C7   C3   C1   112.01  3.000
 SXZ  H22  C7   C10  108.67  3.000
 SXZ  H22  C7   C9   108.09  3.000
 SXZ  C10  C7   C9   110.84  3.000
 SXZ  H22  C7   C3   107.73  3.000
 SXZ  C10  C7   C3   111.15  3.000
 SXZ  C9   C7   C3   110.26  3.000
 SXZ  H25  C9   H24  107.55  3.000
 SXZ  H25  C9   H23  107.76  3.000
 SXZ  H24  C9   H23  107.75  3.000
 SXZ  H25  C9   C7   111.15  3.000
 SXZ  H24  C9   C7   110.82  3.000
 SXZ  H23  C9   C7   111.63  3.000
 SXZ  H28  C10  H27  107.55  3.000
 SXZ  H28  C10  H26  107.49  3.000
 SXZ  H27  C10  H26  107.65  3.000
 SXZ  H28  C10  C7   110.96  3.000
 SXZ  H27  C10  C7   110.65  3.000
 SXZ  H26  C10  C7   112.34  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    180.00   0.0  0
 SXZ  CONST_27  H18  N6   C6  C5      0.00   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   -116.05  30.0  3
 SXZ  Var_02    SD   CG   CB  CA    170.72  30.0  2
 SXZ  Var_03    C7   C3   C1  N    -118.77  30.0  1
 SXZ  Var_04    C9   C7   C3  C1   -171.99  30.0  3
 SXZ  Var_05    H23  C9   C7  C3     57.94  30.0  3
 SXZ  Var_06    H26  C10  C7  C3    -58.00  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
 SXZ  plan-4  H1   0.020

