Chemical Components in the PDB

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PDBeChem : Chemical Bonds

 Molecule : NDC    

Bonds between two atoms of the molecule

Total Number of Bonds: 91


Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 PA O1A P O doub 1.48 N N
2 PA O2A P O sing 1.61 N N
3 PA O5' P O sing 1.61 N N
4 PA OPP P O sing 1.61 N N
5 O2A HOA2 O H sing 0.97 N N
6 O5' C5' O C sing 1.43 N N
7 C5' C4' C C sing 1.53 N N
8 C5' H5'1 C H sing 1.09 N N
9 C5' H5'2 C H sing 1.09 N N
10 C4' O4' C O sing 1.44 N N
11 C4' C3' C C sing 1.54 N N
12 C4' H4' C H sing 1.09 N N
13 O4' C1' O C sing 1.44 N N
14 C3' O3' C O sing 1.43 N N
15 C3' C2' C C sing 1.55 N N
16 C3' H3' C H sing 1.09 N N
17 O3' HO'3 O H sing 0.97 N N
18 C2' O2' C O sing 1.43 N N
19 C2' C1' C C sing 1.55 N N
20 C2' H2' C H sing 1.09 N N
21 O2' HO'2 O H sing 0.97 N N
22 C1' N9A C N sing 1.46 N N
23 C1' H1' C H sing 1.09 N N
24 N9A C8A N C sing 1.36 N Y
25 N9A C4A N C sing 1.37 N Y
26 C8A N7A C N doub 1.3 N Y
27 C8A H8A C H sing 1.08 N N
28 N7A C5A N C sing 1.35 N Y
29 C5A C6A C C sing 1.41 N Y
30 C5A C4A C C doub 1.4 N Y
31 C6A N6A C N sing 1.38 N N
32 C6A N1A C N doub 1.33 N Y
33 N6A H6A1 N H sing 0.97 N N
34 N6A H6A2 N H sing 0.97 N N
35 N1A C2A N C sing 1.32 N Y
36 C2A N3A C N doub 1.32 N Y
37 C2A H2A C H sing 1.08 N N
38 N3A C4A N C sing 1.33 N Y
39 OPP PN O P sing 1.61 N N
40 PN O1N P O doub 1.54 N N
41 PN O2N P O sing 1.55 N N
42 PN O5B P O sing 1.61 N N
43 O5B C5B O C sing 1.43 N N
44 C5B C4B C C sing 1.53 N N
45 C5B H5A1 C H sing 1.09 N N
46 C5B H5A2 C H sing 1.09 N N
47 C4B O4B C O sing 1.44 N N
48 C4B C3B C C sing 1.54 N N
49 C4B H4B C H sing 1.09 N N
50 O4B C1B O C sing 1.44 N N
51 C3B O3B C O sing 1.43 N N
52 C3B C2B C C sing 1.55 N N
53 C3B H3B C H sing 1.09 N N
54 O3B HOA3 O H sing 0.97 N N
55 C2B O2B C O sing 1.43 N N
56 C2B C1B C C sing 1.55 N N
57 C2B H2B C H sing 1.09 N N
58 O2B HOB2 O H sing 0.97 N N
59 C1B N1N C N sing 1.46 N N
60 C1B H1B C H sing 1.09 N N
61 N1N C2N N C sing 1.32 N Y
62 N1N C6N N C doub 1.32 N Y
63 C2N C3N C C doub 1.39 N Y
64 C2N H2N C H sing 1.08 N N
65 C3N C7N C C sing 1.48 N N
66 C3N C4N C C sing 1.4 N Y
67 C7N O7N C O doub 1.22 N N
68 C7N N7N C N sing 1.35 N N
69 N7N H7N1 N H sing 0.97 N N
70 N7N H7N2 N H sing 0.97 N N
71 C4N C5N C C doub 1.38 N Y
72 C4N CC6 C C sing 1.51 N N
73 C5N C6N C C sing 1.38 N Y
74 C5N H5N C H sing 1.08 N N
75 C6N H6N C H sing 1.08 N N
76 CC1 OC1 C O doub 1.21 N N
77 CC1 CC2 C C sing 1.51 N N
78 CC1 CC6 C C sing 1.51 N N
79 CC2 CC3 C C sing 1.53 N N
80 CC2 HC21 C H sing 1.09 N N
81 CC2 HC22 C H sing 1.09 N N
82 CC3 CC4 C C sing 1.53 N N
83 CC3 HC31 C H sing 1.09 N N
84 CC3 HC32 C H sing 1.09 N N
85 CC4 CC5 C C sing 1.53 N N
86 CC4 HC41 C H sing 1.09 N N
87 CC4 HC42 C H sing 1.09 N N
88 CC5 CC6 C C sing 1.53 N N
89 CC5 HC51 C H sing 1.09 N N
90 CC5 HC52 C H sing 1.09 N N
91 CC6 HC6 C H sing 1.09 N N