# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jul  6 11:59:53 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: 5'-deoxy-5'-[({6-[(alpha-L-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
 WS1  WS1  5'-deoxy-5'-[({6-[(alpha-L-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_WS1
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
 WS1  O4   O  O     0  -0.465  -4.9058  -4.8708   0.7395
 WS1  C4   C  CR6   0   0.566  -4.7724  -3.7384   0.3139
 WS1  N3   N  NR16  0  -0.731  -5.4721  -3.3200  -0.8087
 WS1  C2   C  CR6   0   0.740  -5.4403  -2.0904  -1.4078
 WS1  O2   O  O     0  -0.479  -6.0976  -1.8257  -2.3940
 WS1  C5   C  CR16  0  -0.508  -3.9209  -2.7161   0.8667
 WS1  C6   C  CR16  0   0.091  -3.8743  -1.5023   0.2914
 WS1  N1   N  NR6   0  -0.569  -4.6100  -1.1689  -0.8052
 WS1  C1'  C  CR15  0   0.188  -4.5540   0.1701  -1.4337
 WS1  O4'  O  O     0  -0.498  -3.4490   0.8668  -0.9500
 WS1  C2'  C  CR15  0  -0.042  -5.7898   1.0053  -1.0935
 WS1  O2'  O  OH1   0  -0.663  -6.0079   1.8838  -2.1623
 WS1  C3'  C  CR15  0  -0.030  -5.3062   1.7592   0.1499
 WS1  O3'  O  OH1   0  -0.656  -5.9676   2.9702   0.3759
 WS1  C4'  C  CR15  0   0.030  -3.8422   2.0103  -0.1899
 WS1  C5'  C  CH2   0  -0.319  -2.9535   2.1615   1.0299
 WS1  N11  N  NH1   0  -0.645  -1.5593   2.3059   0.7048
 WS1  C12  C  C     0   0.536  -0.9564   3.4869   0.5281
 WS1  O13  O  O     0  -0.480  -1.5133   4.5706   0.6318
 WS1  C14  C  CR6   0   0.115   0.5075   3.3889   0.1997
 WS1  C15  C  CR16  0  -0.303   1.2641   4.5418   0.0630
 WS1  C16  C  CR16  0  -0.139   2.6121   4.3974  -0.2279
 WS1  C17  C  CR16  0  -0.327   3.1458   3.1281  -0.3737
 WS1  C18  C  CR6   0   0.204   2.3030   2.0301  -0.2210
 WS1  N19  N  N     0  -0.465   1.0172   2.1708   0.0645
 WS1  C20  C  CH2   0  -0.184   2.7716   0.6137  -0.4052
 WS1  O21  O  O2    0  -0.505   4.1680   0.5546  -0.2586
 WS1  H1   H  HNR6  0   0.427  -6.0889  -3.9956  -1.2431
 WS1  H2   H  HCR6  0   0.292  -3.3183  -2.9311   1.7352
 WS1  H3   H  HCR6  0   0.323  -3.2242  -0.7356   0.6813
 WS1  H4   H  HCR5  0   0.289  -4.4580   0.0117  -2.5093
 WS1  H5   H  HCR5  0   0.262  -6.6699   0.3858  -0.8888
 WS1  H6   H  HOH1  0   0.453  -6.4541   2.6667  -1.8166
 WS1  H7   H  HCR5  0   0.244  -5.3738   1.0948   1.0228
 WS1  H8   H  HOH1  0   0.470  -6.7751   2.7976   0.8705
 WS1  H9   H  HCR5  0   0.256  -3.7526   2.9041  -0.8189
 WS1  H10  H  HCH2  0   0.274  -3.2902   3.0349   1.5889
 WS1  H11  H  HCH2  0   0.262  -3.0653   1.2994   1.6906
 WS1  H12  H  HNH1  0   0.407  -0.9962   1.4802   0.5645
 WS1  H13  H  HCR6  0   0.274   0.8170   5.5177   0.1853
 WS1  H14  H  HCR6  0   0.279   3.2430   5.2688  -0.3415
 WS1  H15  H  HCR6  0   0.275   4.1931   2.9957  -0.6026
 WS1  H16  H  HCH2  0   0.243   2.2586  -0.0305   0.3168
 WS1  H17  H  HCH2  0   0.241   2.4688   0.2737  -1.4060
 WS1  C22  C  CH1   0   0.256   4.7783  -0.5380  -0.8769
 WS1  C23  C  CH1   0  -0.048   6.2934  -0.3662  -0.7128
 WS1  C24  C  CH1   0   0.011   6.6846  -0.6366   0.7411
 WS1  C25  C  CH1   0   0.017   6.1208  -1.9574   1.2614
 WS1  C26  C  CH1   0  -0.022   4.6203  -1.9763   1.0025
 WS1  O27  O  O2    0  -0.496   4.3320  -1.7563  -0.3698
 WS1  C28  C  CH2   0  -0.159   3.9705  -3.2800   1.4109
 WS1  O29  O  OH1   0  -0.670   2.5721  -3.1218   1.3398
 WS1  O30  O  OH1   0  -0.672   6.7182  -3.0815   0.6701
 WS1  O31  O  OH1   0  -0.671   8.0777  -0.6764   0.9314
 WS1  O32  O  OH1   0  -0.664   6.9793  -1.2490  -1.5624
 WS1  H18  H  HCH1  0   0.240   4.5175  -0.5601  -1.9450
 WS1  H19  H  HCH1  0   0.240   6.5420   0.6776  -0.9530
 WS1  H20  H  HCH1  0   0.229   6.2277   0.1598   1.3453
 WS1  H21  H  HCH1  0   0.222   6.2618  -1.9698   2.3542
 WS1  H22  H  HCH1  0   0.231   4.1835  -1.1783   1.6200
 WS1  H23  H  HCH2  0   0.205   4.3208  -4.0928   0.7641
 WS1  H24  H  HCH2  0   0.202   4.2994  -3.5131   2.4321
 WS1  H25  H  HOH1  0   0.456   2.1662  -3.9533   1.6002
 WS1  H26  H  HOH1  0   0.448   7.6483  -2.8819   0.5205
 WS1  H27  H  HOH1  0   0.457   8.4830   0.0771   0.4902
 WS1  H28  H  HOH1  0   0.456   6.9667  -0.8814  -2.4511

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
 WS1  O2'  C2'  single    1.401  0.020  1.401
 WS1  O3'  C3'  single    1.398  0.020  1.398
 WS1  C3'  C2'  single    1.532  0.020  1.532
 WS1  C3'  C4'  single    1.524  0.020  1.524
 WS1  C2'  C1'  single    1.530  0.020  1.530
 WS1  C4'  C5'  single    1.517  0.020  1.517
 WS1  C4'  O4'  single    1.428  0.020  1.428
 WS1  C5'  N11  single    1.439  0.020  1.439
 WS1  O13  C12  double    1.223  0.020  1.223
 WS1  O4'  C1'  single    1.393  0.020  1.393
 WS1  C1'  N1   single    1.480  0.020  1.480
 WS1  C12  N11  single    1.338  0.020  1.338
 WS1  C12  C14  single    1.504  0.020  1.504
 WS1  O2   C2   double    1.214  0.020  1.214
 WS1  O21  C20  single    1.405  0.020  1.405
 WS1  N1   C2   single    1.379  0.020  1.379
 WS1  N1   C6   single    1.362  0.020  1.362
 WS1  C2   N3   single    1.368  0.020  1.368
 WS1  N19  C14  aromatic  1.327  0.020  1.327
 WS1  N19  C18  aromatic  1.325  0.020  1.325
 WS1  C14  C15  aromatic  1.386  0.020  1.386
 WS1  C6   C5   double    1.344  0.020  1.344
 WS1  C20  C18  single    1.503  0.020  1.503
 WS1  C18  C17  aromatic  1.393  0.020  1.393
 WS1  N3   C4   single    1.387  0.020  1.387
 WS1  C15  C16  aromatic  1.387  0.020  1.387
 WS1  C5   C4   single    1.441  0.020  1.441
 WS1  C4   O4   double    1.217  0.020  1.217
 WS1  C17  C16  aromatic  1.385  0.020  1.385
 WS1  N3   H1   single    0.860  0.020  1.020
 WS1  C5   H2   single    0.930  0.020  1.080
 WS1  C6   H3   single    0.930  0.020  1.080
 WS1  C1'  H4   single    0.970  0.020  1.090
 WS1  C2'  H5   single    0.970  0.020  1.090
 WS1  O2'  H6   single    0.850  0.020  0.980
 WS1  C3'  H7   single    0.970  0.020  1.090
 WS1  O3'  H8   single    0.850  0.020  0.980
 WS1  C4'  H9   single    0.970  0.020  1.090
 WS1  C5'  H10  single    0.970  0.020  1.090
 WS1  C5'  H11  single    0.970  0.020  1.090
 WS1  N11  H12  single    0.860  0.020  1.020
 WS1  C15  H13  single    0.930  0.020  1.080
 WS1  C16  H14  single    0.930  0.020  1.080
 WS1  C17  H15  single    0.930  0.020  1.080
 WS1  C20  H16  single    0.970  0.020  1.090
 WS1  C20  H17  single    0.970  0.020  1.090
 WS1  O21  C22  single    1.396  0.020  1.396
 WS1  C22  C23  single    1.534  0.020  1.534
 WS1  C23  C24  single    1.530  0.020  1.530
 WS1  C24  C25  single    1.527  0.020  1.527
 WS1  C25  C26  single    1.523  0.020  1.523
 WS1  C26  O27  single    1.419  0.020  1.419
 WS1  O27  C22  single    1.393  0.020  1.393
 WS1  C26  C28  single    1.513  0.020  1.513
 WS1  C28  O29  single    1.409  0.020  1.409
 WS1  C25  O30  single    1.404  0.020  1.404
 WS1  C24  O31  single    1.407  0.020  1.407
 WS1  C23  O32  single    1.404  0.020  1.404
 WS1  C22  H18  single    0.970  0.020  1.090
 WS1  C23  H19  single    0.970  0.020  1.090
 WS1  C24  H20  single    0.970  0.020  1.090
 WS1  C25  H21  single    0.970  0.020  1.090
 WS1  C26  H22  single    0.970  0.020  1.090
 WS1  C28  H23  single    0.970  0.020  1.090
 WS1  C28  H24  single    0.970  0.020  1.090
 WS1  O29  H25  single    0.850  0.020  0.980
 WS1  O30  H26  single    0.850  0.020  0.980
 WS1  O31  H27  single    0.850  0.020  0.980
 WS1  O32  H28  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
 WS1  C5   C4   N3   113.24  3.000
 WS1  C5   C4   O4   126.21  3.000
 WS1  N3   C4   O4   120.55  3.000
 WS1  H1   N3   C2   115.21  3.000
 WS1  H1   N3   C4   116.94  3.000
 WS1  C2   N3   C4   127.85  3.000
 WS1  N1   C2   O2   122.35  3.000
 WS1  N1   C2   N3   115.04  3.000
 WS1  O2   C2   N3   122.61  3.000
 WS1  H2   C5   C6   120.34  3.000
 WS1  H2   C5   C4   119.85  3.000
 WS1  C6   C5   C4   119.81  3.000
 WS1  H3   C6   N1   116.28  3.000
 WS1  H3   C6   C5   120.56  3.000
 WS1  N1   C6   C5   123.16  3.000
 WS1  C1'  N1   C6   122.88  3.000
 WS1  C6   N1   C2   120.90  3.000
 WS1  C1'  N1   C2   116.22  3.000
 WS1  H4   C1'  C2'  111.68  3.000
 WS1  H4   C1'  O4'  110.18  3.000
 WS1  C2'  C1'  O4'  106.89  3.000
 WS1  H4   C1'  N1   106.88  3.000
 WS1  O4'  C1'  N1   109.57  3.000
 WS1  C2'  C1'  N1   111.65  3.000
 WS1  C4'  O4'  C1'  111.52  3.000
 WS1  H5   C2'  C3'  112.34  3.000
 WS1  H5   C2'  O2'  111.85  3.000
 WS1  C3'  C2'  O2'  111.08  3.000
 WS1  H5   C2'  C1'  112.44  3.000
 WS1  C3'  C2'  C1'  101.19  3.000
 WS1  O2'  C2'  C1'  107.37  3.000
 WS1  H6   O2'  C2'  107.91  3.000
 WS1  H7   C3'  C4'  109.63  3.000
 WS1  H7   C3'  O3'  111.47  3.000
 WS1  C4'  C3'  O3'  110.35  3.000
 WS1  H7   C3'  C2'  109.12  3.000
 WS1  C4'  C3'  C2'  101.73  3.000
 WS1  O3'  C3'  C2'  114.07  3.000
 WS1  H8   O3'  C3'  108.94  3.000
 WS1  H9   C4'  C5'  109.41  3.000
 WS1  H9   C4'  C3'  109.92  3.000
 WS1  C5'  C4'  C3'  113.58  3.000
 WS1  H9   C4'  O4'  108.95  3.000
 WS1  C5'  C4'  O4'  110.27  3.000
 WS1  C3'  C4'  O4'  104.55  3.000
 WS1  H11  C5'  H10  106.89  3.000
 WS1  H11  C5'  N11  108.38  3.000
 WS1  H10  C5'  N11  109.55  3.000
 WS1  H11  C5'  C4'  110.36  3.000
 WS1  H10  C5'  C4'  108.13  3.000
 WS1  N11  C5'  C4'  113.33  3.000
 WS1  H12  N11  C12  116.90  3.000
 WS1  H12  N11  C5'  119.33  3.000
 WS1  C12  N11  C5'  123.73  3.000
 WS1  C14  C12  O13  121.31  3.000
 WS1  C14  C12  N11  114.21  3.000
 WS1  O13  C12  N11  124.47  3.000
 WS1  N19  C14  C15  122.95  3.000
 WS1  C15  C14  C12  119.93  3.000
 WS1  N19  C14  C12  117.12  3.000
 WS1  H13  C15  C16  121.34  3.000
 WS1  H13  C15  C14  120.96  3.000
 WS1  C16  C15  C14  117.70  3.000
 WS1  H14  C16  C17  120.17  3.000
 WS1  H14  C16  C15  120.34  3.000
 WS1  C17  C16  C15  119.49  3.000
 WS1  H15  C17  C18  120.89  3.000
 WS1  H15  C17  C16  120.56  3.000
 WS1  C18  C17  C16  118.55  3.000
 WS1  C20  C18  N19  115.41  3.000
 WS1  C20  C18  C17  122.74  3.000
 WS1  N19  C18  C17  121.83  3.000
 WS1  C18  N19  C14  119.48  3.000
 WS1  H17  C20  H16  106.81  3.000
 WS1  H17  C20  O21  110.84  3.000
 WS1  H16  C20  O21  111.83  3.000
 WS1  H17  C20  C18  108.48  3.000
 WS1  H16  C20  C18  109.11  3.000
 WS1  O21  C20  C18  109.67  3.000
 WS1  C22  O21  C20  114.91  3.000
 WS1  H18  C22  O27  105.07  3.000
 WS1  H18  C22  C23  109.90  3.000
 WS1  O27  C22  C23  112.06  3.000
 WS1  H18  C22  O21  110.01  3.000
 WS1  O27  C22  O21  112.53  3.000
 WS1  C23  C22  O21  107.27  3.000
 WS1  H19  C23  O32  110.75  3.000
 WS1  H19  C23  C24  108.51  3.000
 WS1  O32  C23  C24  109.82  3.000
 WS1  H19  C23  C22  107.84  3.000
 WS1  O32  C23  C22  110.33  3.000
 WS1  C24  C23  C22  109.54  3.000
 WS1  H20  C24  O31  110.97  3.000
 WS1  H20  C24  C25  106.61  3.000
 WS1  O31  C24  C25  107.16  3.000
 WS1  H20  C24  C23  106.75  3.000
 WS1  O31  C24  C23  112.76  3.000
 WS1  C25  C24  C23  112.47  3.000
 WS1  H21  C25  O30  110.75  3.000
 WS1  H21  C25  C26  107.13  3.000
 WS1  O30  C25  C26  109.75  3.000
 WS1  H21  C25  C24  107.48  3.000
 WS1  O30  C25  C24  113.07  3.000
 WS1  C26  C25  C24  108.45  3.000
 WS1  H22  C26  C28  107.65  3.000
 WS1  H22  C26  O27  110.48  3.000
 WS1  C28  C26  O27  107.90  3.000
 WS1  H22  C26  C25  106.67  3.000
 WS1  C28  C26  C25  112.83  3.000
 WS1  O27  C26  C25  111.26  3.000
 WS1  C26  O27  C22  114.99  3.000
 WS1  H24  C28  H23  107.20  3.000
 WS1  H24  C28  O29  111.60  3.000
 WS1  H23  C28  O29  111.75  3.000
 WS1  H24  C28  C26  107.78  3.000
 WS1  H23  C28  C26  110.02  3.000
 WS1  O29  C28  C26  108.42  3.000
 WS1  H25  O29  C28  107.96  3.000
 WS1  H26  O30  C25  108.09  3.000
 WS1  H27  O31  C24  109.44  3.000
 WS1  H28  O32  C23  108.20  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
 WS1  CONST_01  C17  C18  N19  C14    0.00   0.0  0
 WS1  CONST_02  C17  C16  C15  C14    0.00   0.0  0
 WS1  CONST_03  C18  N19  C14  C15    0.00   0.0  0
 WS1  CONST_04  C18  C17  C16  C15    0.00   0.0  0
 WS1  CONST_05  N19  C14  C15  C16    0.00   0.0  0
 WS1  CONST_06  N19  C18  C17  C16    0.00   0.0  0
 WS1  CONST_07  N1   C2   N3   C4     0.00   0.0  0
 WS1  CONST_08  C1'  N1   C2   N3   180.00   0.0  0
 WS1  CONST_09  C6   N1   C2   N3     0.00   0.0  0
 WS1  CONST_10  C5   C4   N3   C2     0.00   0.0  0
 WS1  CONST_11  C18  N19  C14  C12  180.00   0.0  0
 WS1  CONST_12  C16  C15  C14  C12  180.00   0.0  0
 WS1  CONST_13  C20  C18  N19  C14  180.00   0.0  0
 WS1  CONST_14  C20  C18  C17  C16  180.00   0.0  0
 WS1  CONST_15  C2   N3   C4   O4   180.00   0.0  0
 WS1  CONST_16  O2   C2   N3   C4   180.00   0.0  0
 WS1  CONST_17  C1'  N1   C2   O2     0.00   0.0  0
 WS1  CONST_18  C6   N1   C2   O2   180.00   0.0  0
 WS1  CONST_19  H14  C16  C15  C14  180.00   0.0  0
 WS1  CONST_20  H15  C17  C16  C15  180.00   0.0  0
 WS1  CONST_21  H13  C15  C16  C17  180.00   0.0  0
 WS1  CONST_22  H1   N3   C4   C5   180.00   0.0  0
 WS1  CONST_23  C14  C12  N11  C5'  180.00   0.0  0
 WS1  CONST_24  H12  N11  C12  C14    0.00   0.0  0
 WS1  CONST_25  O13  C12  N11  C5'    0.00   0.0  0
 WS1  Var_01    N19  C14  C12  N11    2.88  30.0  2
 WS1  Var_02    O21  C20  C18  C17   21.13  30.0  1
 WS1  Var_03    C12  N11  C5'  C4'   91.95  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
 WS1  chir_01  C1'  C2'  O4'  N1   negativ
 WS1  chir_02  C2'  O2'  C1'  C3'  negativ
 WS1  chir_03  C3'  O3'  C2'  C4'  negativ
 WS1  chir_04  C4'  O4'  C3'  C5'  negativ
 WS1  chir_05  C22  O21  C23  O27  negativ
 WS1  chir_06  C23  O32  C22  C24  negativ
 WS1  chir_07  C24  O31  C23  C25  negativ
 WS1  chir_08  C25  O30  C24  C26  negativ
 WS1  chir_09  C26  O27  C25  C28  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
 WS1  plan-1  O4   0.020
 WS1  plan-1  C4   0.020
 WS1  plan-1  N3   0.020
 WS1  plan-1  C2   0.020
 WS1  plan-1  O2   0.020
 WS1  plan-1  C5   0.020
 WS1  plan-1  C6   0.020
 WS1  plan-1  N1   0.020
 WS1  plan-1  C1'  0.020
 WS1  plan-1  H1   0.020
 WS1  plan-1  H2   0.020
 WS1  plan-1  H3   0.020
 WS1  plan-2  C12  0.020
 WS1  plan-2  C14  0.020
 WS1  plan-2  C15  0.020
 WS1  plan-2  C16  0.020
 WS1  plan-2  C17  0.020
 WS1  plan-2  C18  0.020
 WS1  plan-2  N19  0.020
 WS1  plan-2  C20  0.020
 WS1  plan-2  H13  0.020
 WS1  plan-2  H14  0.020
 WS1  plan-2  H15  0.020
 WS1  plan-3  C5'  0.020
 WS1  plan-3  N11  0.020
 WS1  plan-3  C12  0.020
 WS1  plan-3  O13  0.020
 WS1  plan-3  C14  0.020
 WS1  plan-3  H12  0.020

