Chemical Components in the PDB

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PDBeChem : Chemical Bonds

 Molecule : Y4I    

Bonds between two atoms of the molecule

Total Number of Bonds: 65


Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OP1 P O P sing 1.61 N N
2 SP P S P doub 1.86 N N
3 O5' P O P sing 1.61 N N
4 P N14 P N sing 1.68 N N
5 C5' O5' C O sing 1.43 N N
6 C4' C5' C C sing 1.53 N N
7 C4' O4' C O sing 1.44 N N
8 C3' C4' C C sing 1.55 N N
9 O4' C1' O C sing 1.44 N N
10 O3' C3' O C sing 1.43 N N
11 C2' C3' C C sing 1.55 N N
12 C1' C2' C C sing 1.54 N N
13 N1 C1' N C sing 1.46 N N
14 N1 C2 N C sing 1.35 N N
15 C6 N1 C N sing 1.37 N N
16 O2 C2 O C doub 1.22 N N
17 C2 N3 C N sing 1.35 N N
18 N3 C4 N C sing 1.35 N N
19 O4 C4 O C doub 1.22 N N
20 C4 C5 C C sing 1.42 N N
21 C5M C5 C C sing 1.51 N N
22 C5 C6 C C doub 1.35 N N
23 O11 C12 O C sing 1.43 N N
24 O11 C16 O C sing 1.43 N N
25 C13 C12 C C sing 1.53 N N
26 C12 N17 C N sing 1.46 N N
27 O12 C18 O C doub 1.22 N N
28 N14 C13 N C sing 1.47 N N
29 C20 O13 C O doub 1.22 N N
30 C15 N14 C N sing 1.47 N N
31 C16 C15 C C sing 1.53 N N
32 O15 C23 O C sing 1.43 N N
33 C23 C16 C C sing 1.53 N N
34 N17 C18 N C sing 1.35 N N
35 N17 C22 N C sing 1.37 N N
36 C18 N19 C N sing 1.35 N N
37 N19 C20 N C sing 1.35 N N
38 C21 C20 C C sing 1.42 N N
39 C22 C21 C C doub 1.35 N N
40 N19 H1 N H sing 0.97 N N
41 C21 H2 C H sing 1.08 N N
42 C22 H22 C H sing 1.08 N N
43 C12 H12 C H sing 1.09 N N
44 C13 H131 C H sing 1.09 N N
45 C13 H132 C H sing 1.09 N N
46 C15 H151 C H sing 1.09 N N
47 C15 H152 C H sing 1.09 N N
48 C16 H16 C H sing 1.09 N N
49 C23 H231 C H sing 1.09 N N
50 C23 H232 C H sing 1.09 N N
51 O15 HO15 O H sing 0.97 N N
52 OP1 HOP1 O H sing 0.97 N N
53 C5' H5'2 C H sing 1.09 N N
54 C5' H5'1 C H sing 1.09 N N
55 C4' H4' C H sing 1.09 N N
56 C3' H3' C H sing 1.09 N N
57 O3' HO3' O H sing 0.97 N N
58 C2' H2'2 C H sing 1.09 N N
59 C2' H2'1 C H sing 1.09 N N
60 C1' H1' C H sing 1.09 N N
61 C6 H6 C H sing 1.08 N N
62 C5M H5M3 C H sing 1.09 N N
63 C5M H5M1 C H sing 1.09 N N
64 C5M H5M2 C H sing 1.09 N N
65 N3 H3 N H sing 0.97 N N