Chemical Components in the PDB

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PDBeChem : Chemical Bonds

 Molecule : Y3U    

Bonds between two atoms of the molecule

Total Number of Bonds: 60


Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C3U N3 C N sing 1.47 N N
2 O2 C2 O C doub 1.22 N N
3 N3 C2 N C sing 1.35 N N
4 N3 C4 N C sing 1.35 N N
5 C2 N1 C N sing 1.35 N N
6 O4 C4 O C doub 1.22 N N
7 C4 C5 C C sing 1.42 N N
8 N1 C1' N C sing 1.46 N N
9 N1 C6 N C sing 1.37 N N
10 C1' O4' C O sing 1.44 N N
11 C1' C2' C C sing 1.54 N N
12 O4' C4' O C sing 1.44 N N
13 C5 C6 C C doub 1.35 N N
14 O3' C3' O C sing 1.43 N N
15 C4' C3' C C sing 1.55 N N
16 C4' C5' C C sing 1.53 N N
17 O2' C2' O C sing 1.43 N N
18 C2' C3' C C sing 1.55 N N
19 C5' O5' C O sing 1.43 N N
20 O5' SBI O S sing 1.52 N N
21 CE1 CD1 C C doub 1.38 N Y
22 CE1 CZ C C sing 1.39 N Y
23 CD1 CG C C sing 1.38 N Y
24 SBI NAT S N sing 1.66 N N
25 SBI OAE S O doub 1.42 N N
26 SBI OAD S O doub 1.42 N N
27 NAT C N C sing 1.35 N N
28 OH CZ O C sing 1.36 N N
29 CZ CE2 C C doub 1.39 N Y
30 CG CB C C sing 1.51 N N
31 CG CD2 C C doub 1.38 N Y
32 CB CA C C sing 1.53 N N
33 CA C C C sing 1.51 N N
34 CA N C N sing 1.47 N N
35 C O C O doub 1.21 N N
36 CE2 CD2 C C sing 1.38 N Y
37 C3U H1 C H sing 1.09 N N
38 C3U H2 C H sing 1.09 N N
39 C3U H3 C H sing 1.09 N N
40 C5 H4 C H sing 1.08 N N
41 C6 H5 C H sing 1.08 N N
42 C1' H6 C H sing 1.09 N N
43 C4' H7 C H sing 1.09 N N
44 C5' H8 C H sing 1.09 N N
45 C5' H9 C H sing 1.09 N N
46 NAT H10 N H sing 0.97 N N
47 CA H11 C H sing 1.09 N N
48 N H12 N H sing 1.01 N N
49 N H13 N H sing 1.01 N N
50 CB H15 C H sing 1.09 N N
51 CB H16 C H sing 1.09 N N
52 CD1 H17 C H sing 1.08 N N
53 CE1 H18 C H sing 1.08 N N
54 OH H19 O H sing 0.97 N N
55 CE2 H20 C H sing 1.08 N N
56 CD2 H21 C H sing 1.08 N N
57 C3' H22 C H sing 1.09 N N
58 O3' H23 O H sing 0.97 N N
59 C2' H24 C H sing 1.09 N N
60 O2' H25 O H sing 0.97 N N