Chemical Components in the PDB

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PDBeChem : Chemical Bonds

 Molecule : 5Y1    

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 O5 C23 O C doub 1.21 N N
2 O4 C22 O C sing 1.43 N N
3 C23 C22 C C sing 1.52 N N
4 C23 N3 C N sing 1.34 N N
5 C22 C10 C C sing 1.52 N N
6 N3 C11 N C doub 1.31 N N
7 O1 C1 O C doub 1.21 N N
8 C10 C1 C C sing 1.48 N N
9 C10 N2 C N doub 1.3 N N
10 C11 N2 C N sing 1.35 N N
11 C11 C12 C C sing 1.48 N N
12 C1 N1 C N sing 1.36 N N
13 C21 C12 C C doub 1.4 N Y
14 C21 C16 C C sing 1.38 N Y
15 C12 C13 C C sing 1.4 N Y
16 C17 O2 C O sing 1.43 N N
17 C17 C18 C C sing 1.53 N N
18 O2 C16 O C sing 1.36 N N
19 C16 C15 C C doub 1.39 N Y
20 C13 C14 C C doub 1.38 N Y
21 N1 C2 N C sing 1.48 N N
22 C18 C19 C C sing 1.53 N N
23 C15 C14 C C sing 1.38 N Y
24 C2 C3 C C sing 1.53 N N
25 C19 C20 C C sing 1.53 N N
26 C20 O3 C O sing 1.43 N N
27 C3 C4 C C sing 1.51 N N
28 C5 C4 C C doub 1.38 N Y
29 C5 C6 C C sing 1.39 N Y
30 C4 C9 C C sing 1.38 N Y
31 O3 C6 O C sing 1.36 N N
32 C6 C7 C C doub 1.39 N Y
33 C9 C8 C C doub 1.38 N Y
34 C7 C8 C C sing 1.38 N Y
35 C3 H1 C H sing 1.09 N N
36 C3 H2 C H sing 1.09 N N
37 C2 H3 C H sing 1.09 N N
38 C2 H4 C H sing 1.09 N N
39 C13 H5 C H sing 1.08 N N
40 C14 H6 C H sing 1.08 N N
41 C15 H7 C H sing 1.08 N N
42 C17 H8 C H sing 1.09 N N
43 C17 H9 C H sing 1.09 N N
44 C18 H10 C H sing 1.09 N N
45 C18 H11 C H sing 1.09 N N
46 C19 H12 C H sing 1.09 N N
47 C19 H13 C H sing 1.09 N N
48 C20 H14 C H sing 1.09 N N
49 C20 H15 C H sing 1.09 N N
50 C21 H16 C H sing 1.08 N N
51 C22 H17 C H sing 1.09 N N
52 C5 H18 C H sing 1.08 N N
53 C7 H19 C H sing 1.08 N N
54 C8 H20 C H sing 1.08 N N
55 C9 H21 C H sing 1.08 N N
56 N1 H22 N H sing 0.97 N N
57 O4 H23 O H sing 0.97 N N