Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

PDBeChem : Chemical Bonds

 Molecule : 5HM    

Bonds between two atoms of the molecule

Total Number of Bonds: 40


Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N4 C4 N C sing 1.38 N N
2 C4 N3 C N doub 1.33 N N
3 C4 C5 C C sing 1.41 N N
4 N3 C2 N C sing 1.33 N N
5 CM5 OM5 C O sing 1.43 N N
6 CM5 C5 C C sing 1.51 N N
7 C5 C6 C C doub 1.35 N N
8 C2 O2 C O doub 1.22 N N
9 C2 N1 C N sing 1.35 N N
10 C6 N1 C N sing 1.36 N N
11 N1 C1' N C sing 1.47 N N
12 OP1 P O P doub 1.48 N N
13 C1' O4' C O sing 1.44 N N
14 C1' C2' C C sing 1.54 N N
15 OP2 P O P sing 1.61 N N
16 O4' C4' O C sing 1.44 N N
17 C2' O2' C O sing 1.43 N N
18 C2' C3' C C sing 1.55 N N
19 P O5' P O sing 1.61 N N
20 P OP3 P O sing 1.61 N N
21 O5' C5' O C sing 1.43 N N
22 C5' C4' C C sing 1.53 N N
23 C4' C3' C C sing 1.54 N N
24 C3' O3' C O sing 1.43 N N
25 OP3 H1 O H sing 0.97 N N
26 OP2 H2 O H sing 0.97 N N
27 C5' H3 C H sing 1.09 N N
28 C5' H4 C H sing 1.09 N N
29 C4' H5 C H sing 1.09 N N
30 C3' H6 C H sing 1.09 N N
31 O3' HO3' O H sing 0.97 N N
32 C2' H8 C H sing 1.09 N N
33 O2' H9 O H sing 0.97 N N
34 C1' H10 C H sing 1.09 N N
35 C6 H11 C H sing 1.08 N N
36 CM5 H12 C H sing 1.09 N N
37 CM5 H13 C H sing 1.09 N N
38 OM5 H14 O H sing 0.97 N N
39 N4 H15 N H sing 0.97 N N
40 N4 H16 N H sing 0.97 N N