Chemical Components in the PDB

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PDBeChem : Chemical Bonds

 Molecule : ODP    

Bonds between two atoms of the molecule

Total Number of Bonds: 82


Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1X P2B O P doub 1.5 N N
2 P2B O2X P O sing 1.62 N N
3 P2B O3X P O sing 1.62 N N
4 P2B O2B P O sing 1.62 N N
5 O2X HOP2 O H sing 0.98 N N
6 O3X HOP3 O H sing 0.98 N N
7 O2B C2B O C sing 1.41 N N
8 C2B C3B C C sing 1.52 N N
9 C2B C1B C C sing 1.52 N N
10 C2B H2B C H sing 1.1 N N
11 C3B O3B C O sing 1.43 N N
12 C3B C4B C C sing 1.52 N N
13 C3B H3B C H sing 1.09 N N
14 O3B HO3A O H sing 0.97 N N
15 C1B N9A C N sing 1.46 N N
16 C1B O4B C O sing 1.44 N N
17 C1B H1B C H sing 1.1 N N
18 N9A C8A N C sing 1.37 N Y
19 N9A C4A N C sing 1.37 N Y
20 C8A N7A C N doub 1.32 N Y
21 C8A H8A C H sing 1.08 N N
22 N7A C5A N C sing 1.37 N Y
23 C5A C4A C C doub 1.39 N Y
24 C5A C6A C C sing 1.39 N Y
25 C4A N3A C N sing 1.34 N Y
26 N3A C2A N C doub 1.35 N Y
27 C2A N1A C N sing 1.35 N Y
28 C2A H2A C H sing 1.09 N N
29 N1A C6A N C doub 1.35 N Y
30 C6A N6A C N sing 1.41 N N
31 N6A H62A N H sing 1.0 N N
32 N6A H61A N H sing 1.0 N N
33 O4B C4B O C sing 1.45 N N
34 C4B C5B C C sing 1.52 N N
35 C4B H4B C H sing 1.09 N N
36 C5B O5B C O sing 1.42 N N
37 C5B H51A C H sing 1.09 N N
38 C5B H52A C H sing 1.09 N N
39 O5B PA O P sing 1.62 N N
40 PA O1A P O doub 1.5 N N
41 PA O2A P O sing 1.62 N N
42 PA O3 P O sing 1.62 N N
43 O2A HOA2 O H sing 0.98 N N
44 O3 PN O P sing 1.62 N N
45 PN O1N P O doub 1.5 N N
46 PN O2N P O sing 1.62 N N
47 PN O5D P O sing 1.62 N N
48 O5D C5D O C sing 1.42 N N
49 C5D C4D C C sing 1.52 N N
50 C5D H51N C H sing 1.09 N N
51 C5D H52N C H sing 1.09 N N
52 C4D O4D C O sing 1.44 N N
53 C4D C3D C C sing 1.52 N N
54 C4D H4D C H sing 1.09 N N
55 O4D C1D O C sing 1.44 N N
56 C1D C2D C C sing 1.52 N N
57 C1D N1N C N sing 1.47 N N
58 C1D H1D C H sing 1.1 N N
59 C2D O2D C O sing 1.42 N N
60 C2D C3D C C sing 1.52 N N
61 C2D H2D C H sing 1.1 N N
62 O2D HO2N O H sing 0.97 N N
63 C3D O3D C O sing 1.43 N N
64 C3D H3D C H sing 1.09 N N
65 O3D HO3N O H sing 0.97 N N
66 N1N C2N N C doub 1.29 N N
67 N1N C6N N C sing 1.42 N N
68 C2N C3N C C sing 1.5 N N
69 C2N H2N C H sing 1.1 N N
70 C3N C7N C C sing 1.5 N N
71 C3N C4N C C sing 1.51 N N
72 C3N H3N C H sing 1.1 N N
73 C7N N7N C N sing 1.38 N N
74 C7N O7N C O doub 1.23 N N
75 N7N H72N N H sing 1.02 N N
76 N7N H71N N H sing 1.01 N N
77 C4N O99 C O doub 1.23 N N
78 C4N C5N C C sing 1.47 N N
79 C5N C6N C C doub 1.33 N N
80 C5N H5N C H sing 1.08 N N
81 C6N H6N C H sing 1.09 N N
82 HO1 O2N H O sing 0.98 N N