Chemical Components in the PDB

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PDBeChem : Chemical Bonds

 Molecule : AKM    

Bonds between two atoms of the molecule

Total Number of Bonds: 67


Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O4A C4 O C sing 1.4386292 N N
2 C6 C5 C C sing 1.5292289 N N
3 O3P P2 O P doub 1.4796922 N N
4 C5 O5 C O sing 1.4167731 N N
5 C5 C4 C C sing 1.5200592 N N
6 O5 C1 O C sing 1.4236692 N N
7 C4 O4B C O sing 1.4395322 N N
8 C4 C3 C C sing 1.5233191 N N
9 O1 P2 O P sing 1.6101134 N N
10 O1 C1 O C sing 1.4335159 N N
11 N3 C3 N C sing 1.4814523 N N
12 P2 O4P P O sing 1.6099739 N N
13 P2 OPP P O sing 1.6101534 N N
14 C2 C1 C C sing 1.5287842 N N
15 C2 C3 C C sing 1.5259017 N N
16 C3 C3M C C sing 1.5306956 N N
17 O3' C3' O C sing 1.429112 N N
18 OPP P O P sing 1.6095431 N N
19 C3' C4' C C sing 1.5497341 N N
20 C3' C2' C C sing 1.5482548 N N
21 P O1P P O doub 1.480583 N N
22 P O2P P O sing 1.610101 N N
23 P O5' P O sing 1.6103108 N N
24 C4' C5' C C sing 1.5303735 N N
25 C4' O4' C O sing 1.4440295 N N
26 C5' O5' C O sing 1.4288282 N N
27 C2' C1' C C sing 1.5407923 N N
28 O4' C1' O C sing 1.4369923 N N
29 C1' N11 C N sing 1.4647423 N N
30 O21 C21 O C doub 1.216668 N N
31 N11 C21 N C sing 1.3451725 N N
32 N11 C61 N C sing 1.3685021 N N
33 C21 N31 C N sing 1.3455694 N N
34 C61 C51 C C doub 1.3504944 N N
35 N31 C41 N C sing 1.348891 N N
36 C51 C41 C C sing 1.415935 N N
37 C51 C5A C C sing 1.5069495 N N
38 C41 O41 C O doub 1.2172333 N N
39 O2P H1 O H sing 0.9672492 N N
40 C1 H2 C H sing 1.0870975 N N
41 C2 H3 C H sing 1.0916464 N N
42 C2 H4 C H sing 1.09285 N N
43 C3M H5 C H sing 1.0899105 N N
44 C3M H6 C H sing 1.0899092 N N
45 C3M H7 C H sing 1.0899894 N N
46 N3 H8 N H sing 1.0092205 N N
47 N3 H9 N H sing 1.0093929 N N
48 O4A H11 O H sing 0.96712613 N N
49 O4B H12 O H sing 0.96718353 N N
50 C5 H13 C H sing 1.111026 N N
51 C6 H14 C H sing 1.0899807 N N
52 C6 H15 C H sing 1.0897678 N N
53 C6 H16 C H sing 1.0908726 N N
54 O4P H17 O H sing 0.9661025 N N
55 C5' H18 C H sing 1.0900624 N N
56 C5' H19 C H sing 1.0900629 N N
57 C4' H20 C H sing 1.0897459 N N
58 C3' H21 C H sing 1.0901271 N N
59 O3' H22 O H sing 0.96670264 N N
60 C2' H23 C H sing 1.0900326 N N
61 C2' H24 C H sing 1.090006 N N
62 C1' H25 C H sing 1.0904572 N N
63 N31 H26 N H sing 0.97031695 N N
64 C5A H27 C H sing 1.0907763 N N
65 C5A H28 C H sing 1.0903623 N N
66 C5A H29 C H sing 1.0897899 N N
67 C61 H30 C H sing 1.0795448 N N