Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : N5M

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 O4 O O4 N N N 0 5.171 -0.195 2.237
2 N5 N N5 N N N 1 5.088 -0.765 1.164
3 O3 O O3 N N N -1 5.992 -1.492 0.79
4 C5 C C5 N N N 0 3.888 -0.581 0.318
5 C4 C C4 N N N 0 3.829 -1.143 -0.973
6 N4 N N4 N N N 0 4.89 -1.871 -1.46
7 N3 N N3 N N N 0 2.744 -0.967 -1.716
8 C2 C C2 N N N 0 1.711 -0.264 -1.255
9 O2 O O2 N N N 0 0.725 -0.116 -1.958
10 C6 C C6 N N N 0 2.827 0.126 0.775
11 N1 N N1 N N N 0 1.737 0.284 -0.027
12 C1' C C1' R N N 0 0.585 1.051 0.453
13 O4' O O4' N N N 0 -0.624 0.269 0.338
14 C2' C C2' R N N 0 0.345 2.283 -0.448
15 O2' O O2' N N N 0 0.912 3.454 0.142
16 C5' C C5' N N N 0 -2.964 0.621 -0.266
17 C3' C C3' S N N 0 -1.194 2.402 -0.519
18 O3' O O3' N N N 0 -1.624 3.651 0.026
19 C4' C C4' R N N 0 -1.702 1.229 0.348
20 O5' O O5' N N N 0 -3.441 -0.433 0.573
21 P P P N N N 0 -4.756 -1.298 0.232
22 OP2 O OP2 N N N 0 -4.623 -1.888 -1.119
23 OP1 O OP1 N N N 0 -4.92 -2.475 1.318
24 OP3 O OP3 N N Y 0 -6.052 -0.343 0.276
25 HN4 H HN4 N N N 0 5.648 -2.066 -0.887
26 HN4A H HN4A N N N 0 4.88 -2.19 -2.376
27 H6 H H6 N N N 0 2.846 0.562 1.763
28 H1' H H1' N N N 0 0.739 1.36 1.487
29 H2' H H2' N N N 0 0.763 2.116 -1.441
30 HO2' H HO2' N N N 0 0.79 4.257 -0.382
31 H3' H H3' N N N 0 -1.538 2.297 -1.548
32 HO3' H HO3' N N Y 0 -1.284 4.424 -0.445
33 H4' H H4' N N N 0 -1.899 1.567 1.366
34 H5' H H5' N N N 0 -3.732 1.389 -0.356
35 H5'A H H5'A N N N 0 -2.732 0.222 -1.254
36 HOP1 H HOP1 N N N 0 -5.694 -3.038 1.174
37 HOP3 H HOP3 N N N 0 -6.202 0.078 1.133