Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

PDBeChem : Chemical Bonds

 Molecule : 5J9    

Bonds between two atoms of the molecule

Total Number of Bonds: 55


Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O5' C5' O C sing 1.43 N N
2 C5' C4' C C sing 1.53 N N
3 N4T C4T N C sing 1.37 N N
4 N3T C4T N C doub 1.33 N N
5 N3T C2T N C sing 1.33 N N
6 O2T C2T O C doub 1.22 N N
7 C4T C5T C C sing 1.41 N N
8 C2T N1T C N sing 1.35 N N
9 C4' C3' C C sing 1.54 N N
10 C4' O4' C O sing 1.44 N N
11 C3' N10 C N sing 1.47 N N
12 C3' C2' C C sing 1.54 N N
13 O4' C1' O C sing 1.44 N N
14 C5T C6T C C doub 1.35 N N
15 C14 N10 C N sing 1.35 N Y
16 C14 C13 C C doub 1.35 N Y
17 N10 N11 N N sing 1.29 N Y
18 N1T C6T N C sing 1.36 N N
19 N1T C15 N C sing 1.46 N N
20 C2' C1' C C sing 1.54 N N
21 C2' O2' C O sing 1.43 N N
22 C13 C15 C C sing 1.51 N N
23 C13 N12 C N sing 1.34 N Y
24 N11 N12 N N doub 1.29 N Y
25 C1' N9 C N sing 1.47 N N
26 N9 C8 N C sing 1.36 N Y
27 N9 C4 N C sing 1.37 N Y
28 C8 N7 C N doub 1.3 N Y
29 N3 C4 N C doub 1.33 N Y
30 N3 C2 N C sing 1.32 N Y
31 C4 C5 C C sing 1.4 N Y
32 C2 N1 C N doub 1.32 N Y
33 N7 C5 N C sing 1.35 N Y
34 C5 C6 C C doub 1.41 N Y
35 N1 C6 N C sing 1.33 N Y
36 C6 N6 C N sing 1.38 N N
37 C14 H1 C H sing 1.08 N N
38 C8 H2 C H sing 1.08 N N
39 N4T H3 N H sing 0.97 N N
40 N4T H4 N H sing 0.97 N N
41 C5T H5 C H sing 1.08 N N
42 C6T H6 C H sing 1.08 N N
43 C15 H7 C H sing 1.09 N N
44 C15 H8 C H sing 1.09 N N
45 C3' H9 C H sing 1.09 N N
46 C2' H10 C H sing 1.09 N N
47 O2' H11 O H sing 0.97 N N
48 C4' H12 C H sing 1.09 N N
49 C5' H13 C H sing 1.09 N N
50 C5' H14 C H sing 1.09 N N
51 O5' H15 O H sing 0.97 N N
52 C1' H16 C H sing 1.09 N N
53 C2 H17 C H sing 1.08 N N
54 N6 H18 N H sing 0.97 N N
55 N6 H19 N H sing 0.97 N N