Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : DZ

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 37


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P1 N N N 0 4.648 1.157 0.341
2 OP1 O O1 N N N 0 5.985 0.282 0.147
3 OP2 O O2 N N N 0 4.387 1.938 -0.888
4 O5' O O3 N N N 0 3.403 0.177 0.628
5 C5' C C1 N N N 0 2.913 -0.761 -0.332
6 C4' C C2 R N N 0 1.73 -1.528 0.261
7 O4' O O4 N N N 0 0.623 -0.635 0.468
8 C1' C C3 R N N 0 -0.582 -1.394 0.229
9 C1 C C4 N N N 0 -1.732 -0.475 -0.093
10 C2 C C5 N N N 0 -1.615 0.469 -1.119
11 O2 O O5 N N N 0 -0.575 0.548 -1.755
12 N3 N N1 N N N 0 -2.641 1.29 -1.408
13 C4 C C6 N N N 0 -3.809 1.219 -0.71
14 C5 C C7 N N N 0 -3.96 0.301 0.308
15 C6 C C8 N N N 0 -2.911 -0.563 0.618
16 N N N2 N N N 1 -5.231 0.228 1.062
17 ON1 O O6 N N N -1 -5.324 -0.507 2.029
18 ON2 O O7 N N N 0 -6.183 0.905 0.717
19 N4 N N3 N N N 0 -4.845 2.068 -1.023
20 C2' C C9 N N N 0 -0.221 -2.267 -1.0
21 C3' C C10 S N N 0 1.262 -2.616 -0.725
22 O3' O O8 N N N 0 1.369 -3.911 -0.13
23 OP3 O O9 N N Y 0 4.838 2.161 1.585
24 H1 H H1 N N N 0 6.218 -0.257 0.916
25 H5'' H H2 N N N 0 2.59 -0.23 -1.227
26 H5' H H3 N N N 0 3.706 -1.462 -0.593
27 H4' H H4 N N N 0 2.02 -1.984 1.208
28 H1' H H5 N N N 0 -0.82 -2.018 1.09
29 H3 H H6 N N N 0 -2.549 1.941 -2.121
30 H6 H H7 N N N 0 -3.016 -1.287 1.413
31 H42 H H8 N N N 0 -4.716 2.768 -1.681
32 H41 H H9 N N N 0 -5.704 1.967 -0.584
33 H2'' H H10 N N N 0 -0.833 -3.168 -1.03
34 H2' H H11 N N N 0 -0.322 -1.699 -1.924
35 H3' H H12 N N N 0 1.842 -2.572 -1.647
36 H2 H H13 N N N 0 1.034 -4.628 -0.685
37 H4 H H14 N N N 0 5.572 2.782 1.481