Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : PED

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 25


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P N N N 0 -2.567 0.061 -0.043
2 O1P O O1P N N N 0 -2.764 -0.106 -1.5
3 O2P O O2P N N N 0 -2.795 1.604 0.357
4 O3P O O3P N N N 0 -3.623 -0.86 0.75
5 O5' O O5* N N N 0 -1.069 -0.38 0.351
6 C2' C C2* N N N 0 3.844 -0.413 0.375
7 C5' C C5* N N N 0 0.093 0.178 -0.265
8 C4' C C4* R N N 0 1.346 -0.46 0.339
9 O4' O O4* N N N 0 1.377 -1.851 0.013
10 C3' C C3* S N N 0 2.591 0.225 -0.229
11 C1' C C1* N N N 0 5.088 0.185 -0.284
12 H2'1 H 1H2* N N N 0 3.871 -0.217 1.447
13 O3' O O3* N N N 0 2.56 1.616 0.097
14 HOP2 H 2HOP N N N 0 -2.681 1.787 1.299
15 HOP3 H 3HOP N N N 0 -4.548 -0.65 0.562
16 H2'2 H 2H2* N N N 0 3.823 -1.489 0.203
17 H5'1 H 1H5* N N N 0 0.066 -0.018 -1.337
18 H5'2 H 2H5* N N N 0 0.114 1.254 -0.093
19 H4'1 H 1H4* N N N 0 1.328 -0.341 1.422
20 HO'4 H 4HO* N N N 0 1.394 -2.032 -0.936
21 H1'3 H 3H1* N N N 0 5.981 -0.27 0.146
22 H3' H H3* N N N 0 2.609 0.105 -1.312
23 H1'1 H 1H1* N N N 0 5.062 -0.012 -1.356
24 H1'2 H 2H1* N N N 0 5.109 1.261 -0.112
25 H3T H H3T N N N 0 2.543 1.797 1.047