Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

PDBeChem : Chemical Bonds

 Molecule : Z5A    

Bonds between two atoms of the molecule

Total Number of Bonds: 85


Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1T C2T N C sing 1.41 N N
2 N1T C6T N C sing 1.39 N N
3 N1T C1' N C sing 1.43 N N
4 C2T O2T C O doub 1.23 N N
5 C2T N3T C N sing 1.4 N N
6 N3T C4T N C sing 1.39 N N
7 N3T H3T N H sing 1.02 N N
8 C4T O4T C O doub 1.23 N N
9 C4T C5T C C sing 1.49 N N
10 C5T C6T C C doub 1.34 N N
11 C5T C7T C C sing 1.5 N N
12 C6T H6T C H sing 1.09 N N
13 C7T H7T1 C H sing 1.09 N N
14 C7T H7T2 C H sing 1.09 N N
15 C7T H7T3 C H sing 1.09 N N
16 C5' O5' C O sing 1.42 N N
17 C5' C4' C C sing 1.52 N N
18 C5' H5'1 C H sing 1.09 N N
19 C5' H5'2 C H sing 1.09 N N
20 O5' PA O P sing 1.64 N N
21 C4' O4' C O sing 1.44 N N
22 C4' C3' C C sing 1.52 N N
23 C4' H4' C H sing 1.1 N N
24 O4' C1' O C sing 1.43 N N
25 C3' C2' C C sing 1.51 N N
26 C3' NA3 C N sing 1.47 N N
27 C3' H3' C H sing 1.09 N N
28 C2' C1' C C sing 1.52 N N
29 C2' H2'1 C H sing 1.1 N N
30 C2' H2'2 C H sing 1.09 N N
31 C1' H1' C H sing 1.09 N N
32 NA3 N3B N N doub 1.24 N N
33 N3B N3C N N doub 1.14 N N
34 PA O1P P O doub 1.51 N N
35 PA O2P P O sing 1.51 N N
36 PA OPA P O sing 1.63 N N
37 OPA PB O P sing 1.63 N N
38 PB O3P P O doub 1.51 N N
39 PB O4P P O sing 1.51 N N
40 PB OPB P O sing 1.63 N N
41 OPB PC O P sing 1.63 N N
42 PC O5P P O doub 1.51 N N
43 PC O6P P O sing 1.51 N N
44 PC OPC P O sing 1.63 N N
45 OPC PD O P sing 1.63 N N
46 PD O7P P O doub 1.51 N N
47 PD O8P P O sing 1.51 N N
48 PD OPD P O sing 1.63 N N
49 OPD PE O P sing 1.63 N N
50 PE O9P P O doub 1.51 N N
51 PE OAP P O sing 1.51 N N
52 PE O5B P O sing 1.63 N N
53 O5B C5B O C sing 1.42 N N
54 C5B C4B C C sing 1.52 N N
55 C5B H5A1 C H sing 1.09 N N
56 C5B H5A2 C H sing 1.09 N N
57 C4B O4B C O sing 1.44 N N
58 C4B C3B C C sing 1.52 N N
59 C4B H4B C H sing 1.1 N N
60 O4B C1B O C sing 1.44 N N
61 C3B O3' C O sing 1.41 N N
62 C3B C2B C C sing 1.52 N N
63 C3B H3B C H sing 1.1 N N
64 O3' HO'3 O H sing 0.97 N N
65 C2B O2' C O sing 1.43 N N
66 C2B C1B C C sing 1.53 N N
67 C2B H2' C H sing 1.09 N N
68 O2' HO'2 O H sing 0.97 N N
69 C1B N9A C N sing 1.46 N N
70 C1B H1B C H sing 1.09 N N
71 N9A C8A N C sing 1.37 N Y
72 N9A C4A N C sing 1.37 N Y
73 C8A N7A C N doub 1.32 N Y
74 C8A H8A C H sing 1.08 N N
75 N7A C5A N C sing 1.37 N Y
76 C5A C6A C C sing 1.39 N Y
77 C5A C4A C C doub 1.39 N Y
78 C6A N6A C N sing 1.41 N N
79 C6A N1A C N doub 1.35 N Y
80 N6A H6A1 N H sing 1.0 N N
81 N6A H6A2 N H sing 1.0 N N
82 N1A C2A N C sing 1.36 N Y
83 C2A N3A C N doub 1.35 N Y
84 C2A H2A C H sing 1.09 N N
85 N3A C4A N C sing 1.34 N Y