# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jul  6 13:02:28 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: 5'-deoxy-5'-[({6-[(beta-D-talopyranosyloxy)methyl]pyridin-2-yl}carbonyl)amino]uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](OCc2cccc(n2)C(=O)NC[C@H]3O[C@H]([C@H](O)[C@@H]3O)N4C=CC(=O)NC4=O)[C@@H](O)[C@@H](O)[C@H]1O
#
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
 WS2  WS2  5'-deoxy-5'-[({6-[(beta-D-talopyranosyloxy)methyl]pyridin-2-yl}carbonyl)amino]uridine  ligand  66  38  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WS2
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
 WS2  O4   O  O     0  -0.459  -2.6563  -3.9838   1.9084
 WS2  C4   C  CR6   0   0.572  -2.9891  -3.0527   1.2007
 WS2  N3   N  NR16  0  -0.735  -3.4417  -3.2726  -0.0910
 WS2  C2   C  CR6   0   0.740  -3.8535  -2.3483  -1.0144
 WS2  O2   O  O     0  -0.473  -4.2272  -2.6685  -2.1224
 WS2  C5   C  CR16  0  -0.509  -2.9682  -1.6577   1.5702
 WS2  C6   C  CR16  0   0.104  -3.3697  -0.7346   0.6846
 WS2  N1   N  NR6   0  -0.566  -3.8093  -1.0382  -0.5740
 WS2  C1'  C  CR15  0   0.201  -4.2113   0.0294  -1.4765
 WS2  O4'  O  O     0  -0.498  -3.2003   0.9981  -1.5228
 WS2  C2'  C  CR15  0  -0.049  -5.4765   0.7690  -1.0432
 WS2  O2'  O  OH1   0  -0.652  -6.6034   0.0774  -1.4887
 WS2  C3'  C  CR15  0  -0.021  -5.2557   2.1367  -1.6999
 WS2  O3'  O  OH1   0  -0.666  -5.5206   2.0791  -3.0756
 WS2  C4'  C  CR15  0  -0.042  -3.7579   2.3187  -1.4970
 WS2  C5'  C  CH2   0  -0.283  -3.4413   3.0102  -0.1804
 WS2  N11  N  NH1   0  -0.661  -2.0366   2.9018   0.1220
 WS2  C12  C  C     0   0.540  -1.4260   3.6713   1.0284
 WS2  O13  O  O     0  -0.482  -1.9684   4.5842   1.6350
 WS2  C14  C  CR6   0   0.118   0.0189   3.3261   1.2561
 WS2  C15  C  CR16  0  -0.304   0.7836   4.0785   2.1332
 WS2  C16  C  CR16  0  -0.139   2.1093   3.7116   2.3092
 WS2  C17  C  CR16  0  -0.330   2.6141   2.6242   1.6161
 WS2  C18  C  CR6   0   0.199   1.7656   1.9319   0.7555
 WS2  N19  N  N     0  -0.463   0.5007   2.2864   0.5868
 WS2  C20  C  CH2   0  -0.187   2.1992   0.7160  -0.0121
 WS2  O1'  O  O2    0  -0.505   3.6021   0.7131  -0.1359
 WS2  H1   H  HNR6  0   0.428  -3.4795  -4.2354  -0.4034
 WS2  H2   H  HCR6  0   0.297  -2.6255  -1.3668   2.5507
 WS2  H3   H  HCR6  0   0.322  -3.3517   0.3144   0.9439
 WS2  H4   H  HCR5  0   0.280  -4.3614  -0.4286  -2.4555
 WS2  H5   H  HCR5  0   0.255  -5.4879   0.8903   0.0476
 WS2  H6   H  HOH1  0   0.471  -7.3670   0.3632  -0.9768
 WS2  H7   H  HCR5  0   0.258  -5.8335   2.9276  -1.2041
 WS2  H8   H  HOH1  0   0.451  -6.3577   1.6157  -3.1981
 WS2  H9   H  HCR5  0   0.276  -3.3109   2.8870  -2.3170
 WS2  H10  H  HCH2  0   0.277  -3.7217   4.0607  -0.2728
 WS2  H11  H  HCH2  0   0.244  -4.0450   2.5970   0.6366
 WS2  H12  H  HNH1  0   0.404  -1.4944   2.1429  -0.2673
 WS2  H13  H  HCR6  0   0.275   0.3589   4.9219   2.6582
 WS2  H14  H  HCR6  0   0.280   2.7449   4.2678   2.9850
 WS2  H15  H  HCR6  0   0.276   3.6426   2.3202   1.7457
 WS2  H16  H  HCH2  0   0.250   1.8410  -0.1765   0.5144
 WS2  H17  H  HCH2  0   0.243   1.7182   0.7240  -0.9970
 WS2  C11  C  CH1   0   0.314   4.1445  -0.4596  -0.6246
 WS2  C22  C  CH1   0  -0.057   5.5776  -0.1774  -1.0734
 WS2  C33  C  CH1   0   0.005   6.1984  -1.5071  -1.5044
 WS2  C44  C  CH1   0   0.018   6.0520  -2.5984  -0.4440
 WS2  C55  C  CH1   0  -0.018   4.5881  -2.6760  -0.0213
 WS2  O66  O  O2    0  -0.490   4.1151  -1.4141   0.3990
 WS2  H18  H  HCH1  0   0.187   3.5687  -0.8280  -1.4947
 WS2  H19  H  HCH1  0   0.235   5.5255   0.4756  -1.9591
 WS2  H21  H  HCH1  0   0.226   5.6228  -1.8415  -2.3810
 WS2  H23  H  HCH1  0   0.222   6.3059  -3.5587  -0.9208
 WS2  H25  H  HCH1  0   0.223   4.0201  -3.0174  -0.9029
 WS2  C77  C  CH2   0  -0.156   4.3607  -3.6725   1.0945
 WS2  O70  O  OH1   0  -0.670   2.9735  -3.8383   1.2734
 WS2  H26  H  HCH2  0   0.202   4.8478  -4.6139   0.8081
 WS2  H27  H  HCH2  0   0.207   4.8492  -3.3221   2.0107
 WS2  H28  H  HOH1  0   0.456   2.8400  -4.4470   2.0053
 WS2  O71  O  OH1   0  -0.670   6.8554  -2.3749   0.6846
 WS2  O72  O  OH1   0  -0.669   7.5660  -1.4012  -1.8081
 WS2  O73  O  OH1   0  -0.660   6.3458   0.4092  -0.0593
 WS2  H20  H  HOH1  0   0.449   7.6779  -1.9693   0.3904
 WS2  H22  H  HOH1  0   0.459   7.7066  -0.6478  -2.3910
 WS2  H24  H  HOH1  0   0.452   6.0188   1.3026   0.0856

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
 WS2  O2'  C2'  single    1.395  0.020  1.395
 WS2  O3'  C3'  single    1.402  0.020  1.402
 WS2  C2'  C3'  single    1.533  0.020  1.533
 WS2  C2'  C1'  single    1.528  0.020  1.528
 WS2  C4'  C3'  single    1.522  0.020  1.522
 WS2  C4'  C5'  single    1.520  0.020  1.520
 WS2  C4'  O4'  single    1.434  0.020  1.434
 WS2  C5'  N11  single    1.441  0.020  1.441
 WS2  O13  C12  double    1.223  0.020  1.223
 WS2  O4'  C1'  single    1.401  0.020  1.401
 WS2  C1'  N1   single    1.455  0.020  1.455
 WS2  O2   C2   double    1.212  0.020  1.212
 WS2  C12  N11  single    1.337  0.020  1.337
 WS2  C12  C14  single    1.503  0.020  1.503
 WS2  O1'  C20  single    1.408  0.020  1.408
 WS2  N1   C2   single    1.383  0.020  1.383
 WS2  N1   C6   single    1.367  0.020  1.367
 WS2  C2   N3   single    1.370  0.020  1.370
 WS2  N19  C14  aromatic  1.327  0.020  1.327
 WS2  N19  C18  aromatic  1.324  0.020  1.324
 WS2  C14  C15  aromatic  1.386  0.020  1.386
 WS2  C6   C5   double    1.341  0.020  1.341
 WS2  C20  C18  single    1.502  0.020  1.502
 WS2  N3   C4   single    1.386  0.020  1.386
 WS2  C18  C17  aromatic  1.393  0.020  1.393
 WS2  C15  C16  aromatic  1.387  0.020  1.387
 WS2  C5   C4   single    1.443  0.020  1.443
 WS2  C4   O4   double    1.216  0.020  1.216
 WS2  C17  C16  aromatic  1.385  0.020  1.385
 WS2  N3   H1   single    0.860  0.020  1.020
 WS2  C5   H2   single    0.930  0.020  1.080
 WS2  C6   H3   single    0.930  0.020  1.080
 WS2  C1'  H4   single    0.970  0.020  1.090
 WS2  C2'  H5   single    0.970  0.020  1.090
 WS2  O2'  H6   single    0.850  0.020  0.980
 WS2  C3'  H7   single    0.970  0.020  1.090
 WS2  O3'  H8   single    0.850  0.020  0.980
 WS2  C4'  H9   single    0.970  0.020  1.090
 WS2  C5'  H10  single    0.970  0.020  1.090
 WS2  C5'  H11  single    0.970  0.020  1.090
 WS2  N11  H12  single    0.860  0.020  1.020
 WS2  C15  H13  single    0.930  0.020  1.080
 WS2  C16  H14  single    0.930  0.020  1.080
 WS2  C17  H15  single    0.930  0.020  1.080
 WS2  C20  H16  single    0.970  0.020  1.090
 WS2  C20  H17  single    0.970  0.020  1.090
 WS2  O1'  C11  single    1.381  0.020  1.381
 WS2  C11  C22  single    1.528  0.020  1.528
 WS2  C22  C33  single    1.529  0.020  1.529
 WS2  C33  C44  single    1.529  0.020  1.529
 WS2  C44  C55  single    1.526  0.020  1.526
 WS2  C55  O66  single    1.412  0.020  1.412
 WS2  O66  C11  single    1.400  0.020  1.400
 WS2  C11  H18  single    0.970  0.020  1.090
 WS2  C22  H19  single    0.970  0.020  1.090
 WS2  C33  H21  single    0.970  0.020  1.090
 WS2  C44  H23  single    0.970  0.020  1.090
 WS2  C55  H25  single    0.970  0.020  1.090
 WS2  C55  C77  single    1.513  0.020  1.513
 WS2  C77  O70  single    1.408  0.020  1.408
 WS2  C77  H26  single    0.970  0.020  1.090
 WS2  C77  H27  single    0.970  0.020  1.090
 WS2  O70  H28  single    0.850  0.020  0.980
 WS2  C44  O71  single    1.403  0.020  1.403
 WS2  C33  O72  single    1.405  0.020  1.405
 WS2  C22  O73  single    1.401  0.020  1.401
 WS2  O71  H20  single    0.850  0.020  0.980
 WS2  O72  H22  single    0.850  0.020  0.980
 WS2  O73  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
 WS2  C5   C4   N3   113.37  3.000
 WS2  C5   C4   O4   125.96  3.000
 WS2  N3   C4   O4   120.68  3.000
 WS2  H1   N3   C2   114.98  3.000
 WS2  H1   N3   C4   116.77  3.000
 WS2  C2   N3   C4   128.26  3.000
 WS2  N1   C2   O2   123.45  3.000
 WS2  N1   C2   N3   114.51  3.000
 WS2  O2   C2   N3   122.04  3.000
 WS2  H2   C5   C6   120.65  3.000
 WS2  H2   C5   C4   119.87  3.000
 WS2  C6   C5   C4   119.48  3.000
 WS2  H3   C6   N1   116.21  3.000
 WS2  H3   C6   C5   120.32  3.000
 WS2  N1   C6   C5   123.46  3.000
 WS2  C1'  N1   C6   119.80  3.000
 WS2  C6   N1   C2   120.92  3.000
 WS2  C1'  N1   C2   119.27  3.000
 WS2  H4   C1'  C2'  110.10  3.000
 WS2  H4   C1'  O4'  111.09  3.000
 WS2  C2'  C1'  O4'  105.79  3.000
 WS2  H4   C1'  N1   106.66  3.000
 WS2  O4'  C1'  N1   109.18  3.000
 WS2  C2'  C1'  N1   114.09  3.000
 WS2  C4'  O4'  C1'  110.83  3.000
 WS2  H5   C2'  C3'  109.18  3.000
 WS2  H5   C2'  O2'  111.33  3.000
 WS2  C3'  C2'  O2'  114.95  3.000
 WS2  H5   C2'  C1'  110.11  3.000
 WS2  C3'  C2'  C1'  101.02  3.000
 WS2  O2'  C2'  C1'  109.77  3.000
 WS2  H6   O2'  C2'  108.89  3.000
 WS2  H7   C3'  C4'  111.81  3.000
 WS2  H7   C3'  O3'  111.92  3.000
 WS2  C4'  C3'  O3'  108.76  3.000
 WS2  H7   C3'  C2'  111.93  3.000
 WS2  C4'  C3'  C2'  101.02  3.000
 WS2  O3'  C3'  C2'  110.88  3.000
 WS2  H8   O3'  C3'  107.96  3.000
 WS2  H9   C4'  C5'  109.14  3.000
 WS2  H9   C4'  C3'  111.37  3.000
 WS2  C5'  C4'  C3'  112.00  3.000
 WS2  H9   C4'  O4'  107.83  3.000
 WS2  C5'  C4'  O4'  110.70  3.000
 WS2  C3'  C4'  O4'  105.67  3.000
 WS2  H11  C5'  H10  106.52  3.000
 WS2  H11  C5'  N11  110.61  3.000
 WS2  H10  C5'  N11  109.92  3.000
 WS2  H11  C5'  C4'  111.04  3.000
 WS2  H10  C5'  C4'  108.12  3.000
 WS2  N11  C5'  C4'  110.52  3.000
 WS2  H12  N11  C12  116.64  3.000
 WS2  H12  N11  C5'  119.91  3.000
 WS2  C12  N11  C5'  122.98  3.000
 WS2  C14  C12  O13  121.51  3.000
 WS2  C14  C12  N11  114.19  3.000
 WS2  O13  C12  N11  124.30  3.000
 WS2  N19  C14  C15  122.97  3.000
 WS2  C15  C14  C12  120.12  3.000
 WS2  N19  C14  C12  116.91  3.000
 WS2  H13  C15  C16  121.38  3.000
 WS2  H13  C15  C14  120.96  3.000
 WS2  C16  C15  C14  117.66  3.000
 WS2  H14  C16  C17  120.15  3.000
 WS2  H14  C16  C15  120.33  3.000
 WS2  C17  C16  C15  119.52  3.000
 WS2  H15  C17  C18  120.95  3.000
 WS2  H15  C17  C16  120.52  3.000
 WS2  C18  C17  C16  118.53  3.000
 WS2  C20  C18  N19  115.30  3.000
 WS2  C20  C18  C17  122.85  3.000
 WS2  N19  C18  C17  121.83  3.000
 WS2  C18  N19  C14  119.49  3.000
 WS2  H17  C20  H16  107.10  3.000
 WS2  H17  C20  O1'  110.99  3.000
 WS2  H16  C20  O1'  111.46  3.000
 WS2  H17  C20  C18  109.07  3.000
 WS2  H16  C20  C18  108.62  3.000
 WS2  O1'  C20  C18  109.52  3.000
 WS2  C11  O1'  C20  115.09  3.000
 WS2  H18  C11  O66  109.70  3.000
 WS2  H18  C11  C22  108.58  3.000
 WS2  O66  C11  C22  111.12  3.000
 WS2  H18  C11  O1'  110.88  3.000
 WS2  O66  C11  O1'  108.17  3.000
 WS2  C22  C11  O1'  108.38  3.000
 WS2  O73  C22  H19  111.08  3.000
 WS2  O73  C22  C33  110.21  3.000
 WS2  H19  C22  C33  107.94  3.000
 WS2  O73  C22  C11  112.27  3.000
 WS2  H19  C22  C11  107.53  3.000
 WS2  C33  C22  C11  107.63  3.000
 WS2  O72  C33  H21  111.09  3.000
 WS2  O72  C33  C44  107.28  3.000
 WS2  H21  C33  C44  106.59  3.000
 WS2  O72  C33  C22  112.98  3.000
 WS2  H21  C33  C22  106.04  3.000
 WS2  C44  C33  C22  112.72  3.000
 WS2  O71  C44  H23  110.79  3.000
 WS2  O71  C44  C55  109.55  3.000
 WS2  H23  C44  C55  107.26  3.000
 WS2  O71  C44  C33  112.91  3.000
 WS2  H23  C44  C33  107.45  3.000
 WS2  C55  C44  C33  108.69  3.000
 WS2  C77  C55  H25  107.95  3.000
 WS2  C77  C55  O66  108.59  3.000
 WS2  H25  C55  O66  110.00  3.000
 WS2  C77  C55  C44  112.46  3.000
 WS2  H25  C55  C44  106.76  3.000
 WS2  O66  C55  C44  111.01  3.000
 WS2  C55  O66  C11  112.63  3.000
 WS2  H27  C77  H26  107.13  3.000
 WS2  H27  C77  O70  111.75  3.000
 WS2  H26  C77  O70  111.66  3.000
 WS2  H27  C77  C55  109.81  3.000
 WS2  H26  C77  C55  107.80  3.000
 WS2  O70  C77  C55  108.61  3.000
 WS2  H28  O70  C77  107.94  3.000
 WS2  H20  O71  C44  108.08  3.000
 WS2  H22  O72  C33  109.39  3.000
 WS2  H24  O73  C22  108.15  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
 WS2  CONST_01  C17  C18  N19  C14    0.00   0.0  0
 WS2  CONST_02  C17  C16  C15  C14    0.00   0.0  0
 WS2  CONST_03  C18  N19  C14  C15    0.00   0.0  0
 WS2  CONST_04  C18  C17  C16  C15    0.00   0.0  0
 WS2  CONST_05  N19  C14  C15  C16    0.00   0.0  0
 WS2  CONST_06  N19  C18  C17  C16    0.00   0.0  0
 WS2  CONST_07  N1   C2   N3   C4     0.00   0.0  0
 WS2  CONST_08  C1'  N1   C2   N3   180.00   0.0  0
 WS2  CONST_09  C6   N1   C2   N3     0.00   0.0  0
 WS2  CONST_10  C5   C4   N3   C2     0.00   0.0  0
 WS2  CONST_11  C18  N19  C14  C12  180.00   0.0  0
 WS2  CONST_12  C16  C15  C14  C12  180.00   0.0  0
 WS2  CONST_13  C20  C18  N19  C14  180.00   0.0  0
 WS2  CONST_14  C20  C18  C17  C16  180.00   0.0  0
 WS2  CONST_15  C2   N3   C4   O4   180.00   0.0  0
 WS2  CONST_16  O2   C2   N3   C4   180.00   0.0  0
 WS2  CONST_17  C1'  N1   C2   O2     0.00   0.0  0
 WS2  CONST_18  C6   N1   C2   O2   180.00   0.0  0
 WS2  CONST_19  H14  C16  C15  C14  180.00   0.0  0
 WS2  CONST_20  H15  C17  C16  C15  180.00   0.0  0
 WS2  CONST_21  H13  C15  C16  C17  180.00   0.0  0
 WS2  CONST_22  H1   N3   C4   C5   180.00   0.0  0
 WS2  CONST_23  C14  C12  N11  C5'  180.00   0.0  0
 WS2  CONST_24  H12  N11  C12  C14    0.00   0.0  0
 WS2  CONST_25  O13  C12  N11  C5'    0.00   0.0  0
 WS2  Var_01    N19  C14  C12  N11   -2.56  30.0  2
 WS2  Var_02    O1'  C20  C18  C17  -22.28  30.0  1
 WS2  Var_03    C12  N11  C5'  C4'  163.52  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
 WS2  chir_01  C1'  C2'  O4'  N1   negativ
 WS2  chir_02  C2'  O2'  C1'  C3'  negativ
 WS2  chir_03  C3'  O3'  C2'  C4'  negativ
 WS2  chir_04  C4'  O4'  C3'  C5'  negativ
 WS2  chir_05  C11  O1'  C22  O66  negativ
 WS2  chir_06  C22  O73  C11  C33  positiv
 WS2  chir_07  C33  O72  C22  C44  positiv
 WS2  chir_08  C44  O71  C33  C55  positiv
 WS2  chir_09  C55  O66  C44  C77  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
 WS2  plan-1  O4   0.020
 WS2  plan-1  C4   0.020
 WS2  plan-1  N3   0.020
 WS2  plan-1  C2   0.020
 WS2  plan-1  O2   0.020
 WS2  plan-1  C5   0.020
 WS2  plan-1  C6   0.020
 WS2  plan-1  N1   0.020
 WS2  plan-1  C1'  0.020
 WS2  plan-1  H1   0.020
 WS2  plan-1  H2   0.020
 WS2  plan-1  H3   0.020
 WS2  plan-2  C12  0.020
 WS2  plan-2  C14  0.020
 WS2  plan-2  C15  0.020
 WS2  plan-2  C16  0.020
 WS2  plan-2  C17  0.020
 WS2  plan-2  C18  0.020
 WS2  plan-2  N19  0.020
 WS2  plan-2  C20  0.020
 WS2  plan-2  H13  0.020
 WS2  plan-2  H14  0.020
 WS2  plan-2  H15  0.020
 WS2  plan-3  C5'  0.020
 WS2  plan-3  N11  0.020
 WS2  plan-3  C12  0.020
 WS2  plan-3  O13  0.020
 WS2  plan-3  C14  0.020
 WS2  plan-3  H12  0.020

