Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : CDP

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 40


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O3B O O3B N N N 0 -5.483 2.208 0.404
2 PB P PB N N N 0 -5.253 0.897 -0.502
3 O1B O O1B N N N 0 -6.075 -0.216 0.023
4 O2B O O2B N N N 0 -5.684 1.213 -2.021
5 O3A O O3A N N N 0 -3.698 0.482 -0.461
6 PA P PA R N N 0 -2.78 -0.313 0.596
7 O1A O O1A N N N 0 -3.496 -1.524 1.057
8 O2A O O2A N N N 0 -2.466 0.638 1.856
9 O5' O O5' N N N 0 -1.398 -0.743 -0.11
10 C5' C C5' N N N 0 -0.414 -1.554 0.535
11 C4' C C4' R N N 0 0.768 -1.77 -0.411
12 O4' O O4' N N N 0 1.444 -0.523 -0.642
13 C3' C C3' S N N 0 1.786 -2.731 0.234
14 O3' O O3' N N N 0 1.956 -3.896 -0.575
15 C2' C C2' R N N 0 3.099 -1.912 0.287
16 O2' O O2' N N N 0 4.222 -2.725 -0.06
17 C1' C C1' R N N 0 2.849 -0.826 -0.789
18 N1 N N1 N N N 0 3.663 0.362 -0.523
19 C2 C C2 N N N 0 3.505 1.038 0.63
20 O2 O O2 N N N 0 2.681 0.652 1.443
21 N3 N N3 N N N 0 4.232 2.121 0.898
22 C4 C C4 N N N 0 5.134 2.562 0.031
23 N4 N N4 N N N 0 5.88 3.681 0.319
24 C5 C C5 N N N 0 5.325 1.877 -1.186
25 C6 C C6 N N N 0 4.581 0.774 -1.442
26 H5'1 H H5'1 N N N 0 -0.068 -1.054 1.44
27 H5'2 H H5'2 N N N 0 -0.852 -2.517 0.797
28 H4' H H4' N N N 0 0.415 -2.181 -1.357
29 H3' H H3' N N N 0 1.466 -3.008 1.238
30 HA H HA N N N 0 2.587 -4.536 -0.216
31 H2' H H2' N N N 0 3.237 -1.462 1.27
32 HB H HB N N N 0 4.365 -3.474 0.535
33 H1' H H1' N N N 0 3.054 -1.218 -1.786
34 H4N1 H H4N1 N N N 0 5.747 4.15 1.158
35 H4N2 H H4N2 N N N 0 6.539 4.002 -0.317
36 H5 H H5 N N N 0 6.055 2.224 -1.903
37 H6 H H6 N N N 0 4.712 0.23 -2.365
38 HO1 H HO1 N N N 0 -1.997 1.452 1.628
39 HO2 H HO2 N N N 0 -6.611 1.47 -2.121
40 HO3 H HO3 N N N 0 -4.974 2.979 0.117