Chemical Components in the PDB

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PDBeChem : Chemical Bonds

 Molecule : 1YJ    

Bonds between two atoms of the molecule

Total Number of Bonds: 57


Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C7 N8 C N sing 1.47 N N
2 C7 C6 C C sing 1.54 N N
3 N8 C8A N C sing 1.39 N N
4 C6 N5 C N sing 1.47 N N
5 C6 C9 C C sing 1.53 N N
6 N10 C9 N C sing 1.47 N N
7 N10 C4' N C sing 1.39 N N
8 C3' C4' C C doub 1.39 N Y
9 C3' C2' C C sing 1.38 N Y
10 C8A C4A C C doub 1.39 N N
11 C8A N1 C N sing 1.34 N N
12 N5 C4A N C sing 1.41 N N
13 C4' C5' C C sing 1.39 N Y
14 C4A C4 C C sing 1.4 N N
15 N1 C2 N C doub 1.32 N N
16 C2' C1' C C doub 1.4 N Y
17 C2 N3 C N sing 1.36 N N
18 C2 N2 C N sing 1.37 N N
19 C4 N3 C N sing 1.35 N N
20 C4 O4 C O doub 1.22 N N
21 C5' C6' C C doub 1.38 N Y
22 C1' C6' C C sing 1.4 N Y
23 C1' C11 C C sing 1.48 N N
24 O11 C11 O C doub 1.22 N N
25 C11 N C N sing 1.35 N N
26 N CA N C sing 1.46 N N
27 CA C C C sing 1.51 N N
28 CA CB C C sing 1.53 N N
29 C OX1 C O doub 1.21 N N
30 C OX2 C O sing 1.34 N N
31 CG CB C C sing 1.53 N N
32 CG CD C C sing 1.51 N N
33 OE1 CD O C doub 1.21 N N
34 CD OE2 C O sing 1.34 N N
35 C7 H3 C H sing 1.09 N N
36 C7 H4 C H sing 1.09 N N
37 C6 H5 C H sing 1.09 N N
38 N5 H6 N H sing 0.97 N N
39 C9 H8 C H sing 1.09 N N
40 C3' H9 C H sing 1.08 N N
41 C2' H10 C H sing 1.08 N N
42 C6' H11 C H sing 1.08 N N
43 C5' H12 C H sing 1.08 N N
44 N H13 N H sing 0.97 N N
45 CA H14 C H sing 1.09 N N
46 OX2 H15 O H sing 0.97 N N
47 CB H16 C H sing 1.09 N N
48 CB H17 C H sing 1.09 N N
49 CG H18 C H sing 1.09 N N
50 CG H19 C H sing 1.09 N N
51 OE2 H20 O H sing 0.97 N N
52 N2 H21 N H sing 0.97 N N
53 N2 H22 N H sing 0.97 N N
54 N3 H23 N H sing 0.97 N N
55 N8 H1 N H sing 0.97 N N
56 C9 H2 C H sing 1.09 N N
57 N10 H7 N H sing 0.97 N N