Chemical Components in the PDB

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PDBeChem : Chemical Bonds

 Molecule : OI3    

Bonds between two atoms of the molecule

Total Number of Bonds: 61


Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C4' C5' C C sing 1.53 N N
2 C4' C3' C C sing 1.54 N N
3 C4' O4' C O sing 1.44 N N
4 C1' C2' C C sing 1.55 N N
5 C1' N9 C N sing 1.47 N N
6 C1' O4' C O sing 1.44 N N
7 C5 C6 C C doub 1.41 N Y
8 C5 C4 C C sing 1.41 N Y
9 C5 N7 C N sing 1.35 N Y
10 C6 N6 C N sing 1.38 N N
11 C6 N1 C N sing 1.33 N Y
12 C2' C3' C C sing 1.55 N N
13 C2' F1 C F sing 1.4 N N
14 C3D C4D C C sing 1.54 N N
15 C3D C2D C C sing 1.55 N N
16 C3D O3D C O sing 1.43 N N
17 C4D C5D C C sing 1.53 N N
18 C5D O5D C O sing 1.43 N N
19 C5' O5' C O sing 1.43 N N
20 C8 N9 C N sing 1.36 N Y
21 C8 N7 C N doub 1.3 N Y
22 C2 N1 C N doub 1.32 N Y
23 C2 N3 C N sing 1.32 N Y
24 C4 N9 C N sing 1.37 N Y
25 C4 N3 C N doub 1.33 N Y
26 C3' O3' C O sing 1.43 N N
27 C1D C2D C C sing 1.55 N N
28 C1D O4D C O sing 1.44 N N
29 C1D O1D C O sing 1.43 N N
30 C2D O2D C O sing 1.43 N N
31 O5D PB O P sing 1.61 N N
32 O1B PB O P doub 1.48 N N
33 O2B PB O P sing 1.61 N N
34 O3A PB O P sing 1.61 N N
35 O3A PA O P sing 1.61 N N
36 O1A PA O P doub 1.48 N N
37 O2A PA O P sing 1.61 N N
38 O5' PA O P sing 1.61 N N
39 C4' H'4 C H sing 1.09 N N
40 C1' H'1 C H sing 1.09 N N
41 C2' H'2 C H sing 1.09 N N
42 C3D HR'3 C H sing 1.09 N N
43 C4D HR'4 C H sing 1.09 N N
44 C5D H5R1 C H sing 1.09 N N
45 C5D H5R2 C H sing 1.09 N N
46 C5' H5'1 C H sing 1.09 N N
47 C5' H5'2 C H sing 1.09 N N
48 C8 H8 C H sing 1.08 N N
49 C2 H2 C H sing 1.08 N N
50 C3' H'3 C H sing 1.09 N N
51 C2D HR'2 C H sing 1.09 N N
52 N6 H61 N H sing 0.97 N N
53 N6 H62 N H sing 0.97 N N
54 O3D HOR3 O H sing 0.97 N N
55 O2B HOB2 O H sing 0.97 N N
56 O2A HOA2 O H sing 0.97 N N
57 O3' HO'3 O H sing 0.97 N N
58 O1D HOR1 O H sing 0.97 N N
59 O2D HOR2 O H sing 0.97 N N
60 C4D O4D C O sing 1.44 N N
61 C1D HR'1 C H sing 1.09 N N