Chemical Components in the PDB

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PDBeChem : Chemical Bonds

 Molecule : YE2    

Bonds between two atoms of the molecule

Total Number of Bonds: 104


Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAB CAC C C doub 1.35 E N
2 CAB SAA C S sing 1.76 N N
3 CAB OAD C O sing 1.35 N N
4 CAC CAF C C sing 1.47 N N
5 CAE CAF C C doub 1.4 N Y
6 CAE CAJ C C sing 1.39 N Y
7 CAF CAG C C sing 1.4 N Y
8 CAG CAH C C doub 1.38 N Y
9 CAH CAI C C sing 1.39 N Y
10 CAH OAK C O sing 1.36 N N
11 CAI CAJ C C doub 1.39 N Y
12 CAJ OAL C O sing 1.36 N N
13 SAA C2P S C sing 1.81 N N
14 P1A O5' P O sing 1.61 N N
15 P1A O1A P O doub 1.48 N N
16 P1A O2A P O sing 1.61 N N
17 P1A O3A P O sing 1.61 N N
18 P2A O3A P O sing 1.61 N N
19 P2A O4A P O doub 1.48 N N
20 P2A O5A P O sing 1.61 N N
21 P2A O6A P O sing 1.61 N N
22 P3' O3' P O sing 1.61 N N
23 P3' O7A P O doub 1.48 N N
24 P3' O8A P O sing 1.61 N N
25 P3' O9A P O sing 1.61 N N
26 C2P C3P C C sing 1.53 N N
27 C3P N4P C N sing 1.47 N N
28 N4P C5P N C sing 1.35 N N
29 C5P O5P C O doub 1.21 N N
30 C5P C6P C C sing 1.51 N N
31 C6P C7P C C sing 1.53 N N
32 C7P N8P C N sing 1.47 N N
33 N8P C9P N C sing 1.35 N N
34 C9P O9P C O doub 1.21 N N
35 C9P C10 C C sing 1.51 N N
36 C5' O5' C O sing 1.43 N N
37 C5' C4' C C sing 1.53 N N
38 C4' O4' C O sing 1.44 N N
39 C4' C3' C C sing 1.54 N N
40 O4' C1' O C sing 1.44 N N
41 C3' O3' C O sing 1.43 N N
42 C3' C2' C C sing 1.55 N N
43 C2' O2' C O sing 1.43 N N
44 C2' C1' C C sing 1.55 N N
45 C1' N9A C N sing 1.47 N N
46 N1A C2A N C doub 1.32 N Y
47 N1A C6A N C sing 1.33 N Y
48 C2A N3A C N sing 1.32 N Y
49 N3A C4A N C doub 1.33 N Y
50 C4A C5A C C sing 1.4 N Y
51 C4A N9A C N sing 1.37 N Y
52 C5A C6A C C doub 1.4 N Y
53 C5A N7A C N sing 1.35 N Y
54 C6A N6A C N sing 1.38 N N
55 O6A C12 O C sing 1.43 N N
56 N7A C8A N C doub 1.3 N Y
57 C8A N9A C N sing 1.36 N Y
58 C10 O10 C O sing 1.43 N N
59 C10 C11 C C sing 1.53 N N
60 C11 C12 C C sing 1.53 N N
61 C11 C13 C C sing 1.53 N N
62 C11 C14 C C sing 1.53 N N
63 CAC H1 C H sing 1.08 N N
64 CAE H2 C H sing 1.08 N N
65 CAG H3 C H sing 1.08 N N
66 CAI H4 C H sing 1.08 N N
67 OAK H5 O H sing 0.97 N N
68 OAL H6 O H sing 0.97 N N
69 C2P H7 C H sing 1.09 N N
70 C2P H8 C H sing 1.09 N N
71 C3P H9 C H sing 1.09 N N
72 C3P H10 C H sing 1.09 N N
73 N4P H11 N H sing 0.97 N N
74 C6P H12 C H sing 1.09 N N
75 C6P H13 C H sing 1.09 N N
76 C7P H14 C H sing 1.09 N N
77 C7P H15 C H sing 1.09 N N
78 N8P H16 N H sing 0.97 N N
79 C5' H17 C H sing 1.09 N N
80 C5' H18 C H sing 1.09 N N
81 C4' H19 C H sing 1.09 N N
82 C3' H20 C H sing 1.09 N N
83 C2' H21 C H sing 1.09 N N
84 O2' H22 O H sing 0.97 N N
85 C1' H23 C H sing 1.09 N N
86 C2A H24 C H sing 1.08 N N
87 O2A H25 O H sing 0.97 N N
88 O5A H26 O H sing 0.97 N N
89 N6A H27 N H sing 0.97 N N
90 N6A H28 N H sing 0.97 N N
91 C8A H29 C H sing 1.08 N N
92 O8A H30 O H sing 0.97 N N
93 O9A H31 O H sing 0.97 N N
94 C10 H32 C H sing 1.09 N N
95 O10 H33 O H sing 0.97 N N
96 C12 H34 C H sing 1.09 N N
97 C12 H35 C H sing 1.09 N N
98 C13 H36 C H sing 1.09 N N
99 C13 H37 C H sing 1.09 N N
100 C13 H38 C H sing 1.09 N N
101 C14 H39 C H sing 1.09 N N
102 C14 H40 C H sing 1.09 N N
103 C14 H41 C H sing 1.09 N N
104 OAD H42 O H sing 0.97 N N