Chemical Components in the PDB

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PDBeChem : Chemical Bonds

 Molecule : 8JD    

Bonds between two atoms of the molecule

Total Number of Bonds: 87


Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1M CP C C sing 1.53 N N
2 CP S1 C S sing 1.81 N N
3 S1 C2 S C sing 1.81 N N
4 C2 C3 C C sing 1.53 N N
5 O5 C5 O C doub 1.21 N N
6 C3 N4 C N sing 1.47 N N
7 C5 N4 C N sing 1.35 N N
8 C5 C6 C C sing 1.51 N N
9 C6 C7 C C sing 1.53 N N
10 C7 N8 C N sing 1.46 N N
11 C14 C11 C C sing 1.53 N N
12 N6A C6A N C sing 1.38 N N
13 N8 C9 N C sing 1.35 N N
14 O10 C10 O C sing 1.43 N N
15 C6A N1A C N doub 1.33 N Y
16 C6A C5A C C sing 1.41 N Y
17 C9 C10 C C sing 1.51 N N
18 C9 O9 C O doub 1.21 N N
19 C11 C10 C C sing 1.53 N N
20 C11 C12 C C sing 1.53 N N
21 C11 C13 C C sing 1.53 N N
22 N1A C2A N C sing 1.32 N Y
23 C12 O6A C O sing 1.43 N N
24 N7A C5A N C sing 1.35 N Y
25 N7A C8A N C doub 1.3 N Y
26 C5A C4A C C doub 1.41 N Y
27 C2A N3A C N doub 1.32 N Y
28 C8A N9A C N sing 1.36 N Y
29 O6A P2A O P sing 1.61 N N
30 C4A N3A C N sing 1.33 N Y
31 C4A N9A C N sing 1.37 N Y
32 O4A P2A O P doub 1.48 N N
33 O2A P1A O P doub 1.48 N N
34 O3A P2A O P sing 1.61 N N
35 O3A P1A O P sing 1.61 N N
36 N9A C1X N C sing 1.47 N N
37 P2A O5A P O sing 1.61 N N
38 P1A O1A P O sing 1.61 N N
39 P1A O5X P O sing 1.61 N N
40 C1X O4X C O sing 1.44 N N
41 C1X C2X C C sing 1.54 N N
42 O5X C5X O C sing 1.43 N N
43 O4X C4X O C sing 1.44 N N
44 C2X O2X C O sing 1.43 N N
45 C2X C3X C C sing 1.55 N N
46 C5X C4X C C sing 1.53 N N
47 C4X C3X C C sing 1.55 N N
48 C3X O3X C O sing 1.43 N N
49 N6A H1 N H sing 0.97 N N
50 N6A H2 N H sing 0.97 N N
51 C2A H3 C H sing 1.08 N N
52 C8A H4 C H sing 1.08 N N
53 C1M H5 C H sing 1.09 N N
54 C1M H6 C H sing 1.09 N N
55 C1M H7 C H sing 1.09 N N
56 CP H8 C H sing 1.09 N N
57 CP H9 C H sing 1.09 N N
58 O3X H10 O H sing 0.97 N N
59 N4 H11 N H sing 0.97 N N
60 C6 H12 C H sing 1.09 N N
61 C6 H13 C H sing 1.09 N N
62 C7 H14 C H sing 1.09 N N
63 C7 H15 C H sing 1.09 N N
64 N8 H16 N H sing 0.97 N N
65 C13 H17 C H sing 1.09 N N
66 C13 H18 C H sing 1.09 N N
67 C13 H19 C H sing 1.09 N N
68 C14 H20 C H sing 1.09 N N
69 C14 H21 C H sing 1.09 N N
70 C14 H22 C H sing 1.09 N N
71 C12 H23 C H sing 1.09 N N
72 C12 H24 C H sing 1.09 N N
73 O1A H25 O H sing 0.97 N N
74 C4X H26 C H sing 1.09 N N
75 C1X H27 C H sing 1.09 N N
76 C2X H28 C H sing 1.09 N N
77 O2X H29 O H sing 0.97 N N
78 C3X H30 C H sing 1.09 N N
79 C5X H31 C H sing 1.09 N N
80 C5X H32 C H sing 1.09 N N
81 O5A H33 O H sing 0.97 N N
82 C10 H34 C H sing 1.09 N N
83 O10 H35 O H sing 0.97 N N
84 C3 H36 C H sing 1.09 N N
85 C3 H37 C H sing 1.09 N N
86 C2 H38 C H sing 1.09 N N
87 C2 H39 C H sing 1.09 N N