Chemical Components in the PDB

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PDBeChem : Chemical Bonds

 Molecule : 25L    

Bonds between two atoms of the molecule

Total Number of Bonds: 123


Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C doub 1.3209713 N Y
2 N1 C6 N C sing 1.3286674 N Y
3 C2 N3 C N sing 1.315704 N Y
4 N3 C4 N C doub 1.3297447 N Y
5 C4 C5 C C sing 1.405232 N Y
6 C4 N9 C N sing 1.3714347 N Y
7 C5 C6 C C doub 1.4055159 N Y
8 C5 N7 C N sing 1.3541721 N Y
9 C6 N6 C N sing 1.3846782 N N
10 N7 C8 N C doub 1.3012751 N Y
11 C8 N9 C N sing 1.3630601 N Y
12 N9 C1' N C sing 1.4654753 N N
13 C1' C2' C C sing 1.5498948 N N
14 C1' O4' C O sing 1.4439695 N N
15 C2' O2' C O sing 1.4290903 N N
16 C2' C3' C C sing 1.5476837 N N
17 C3' O3' C O sing 1.4294496 N N
18 C3' C4' C C sing 1.5408325 N N
19 C4' O4' C O sing 1.4375027 N N
20 C4' C5' C C sing 1.530148 N N
21 C5' O5' C O sing 1.4285609 N N
22 O5' PCU O P sing 1.609453 N N
23 NAB CBV N C sing 1.3842723 N N
24 NAC CBW N C sing 1.3832014 N N
25 OAD PCS O P doub 1.4799497 N N
26 OAE PCT O P doub 1.4810216 N N
27 OAF PCU O P doub 1.4800696 N N
28 OAG PCV O P doub 1.4808164 N N
29 OAH PCW O P doub 1.4801973 N N
30 OAK CCF O C sing 1.4281198 N N
31 OAL CCG O C sing 1.4287236 N N
32 OAM PCT O P sing 1.6099683 N N
33 OAN PCS O P sing 1.6094328 N N
34 OAO PCS O P sing 1.6099211 N N
35 OAP PCU O P sing 1.609394 N N
36 OAQ PCV O P sing 1.6095428 N N
37 OAR PCW O P sing 1.6100528 N N
38 CAT NBC C N doub 1.3212494 N Y
39 CAT NBF C N sing 1.316451 N Y
40 CAU NBD C N doub 1.3202826 N Y
41 CAU NBG C N sing 1.3166332 N Y
42 CAW NBI C N doub 1.3009127 N Y
43 CAW NCQ C N sing 1.36304 N Y
44 CAX NBJ C N doub 1.3018022 N Y
45 CAX NCR C N sing 1.3633932 N Y
46 CAY OBK C O sing 1.4280851 N N
47 CAY CCI C C sing 1.5298607 N N
48 CBA OBM C O sing 1.4286476 N N
49 CBA CCJ C C sing 1.5302725 N N
50 NBC CBV N C sing 1.3289846 N Y
51 NBD CBW N C sing 1.3294635 N Y
52 NBF CCB N C doub 1.3282056 N Y
53 NBG CCC N C doub 1.3285666 N Y
54 NBI CBY N C sing 1.354494 N Y
55 NBJ CBZ N C sing 1.3547373 N Y
56 OBK PCT O P sing 1.6102726 N N
57 OBM PCV O P sing 1.6103404 N N
58 OBO CCI O C sing 1.4438397 N N
59 OBO CCN O C sing 1.4432731 N N
60 OBP CCJ O C sing 1.4436759 N N
61 OBP CCO O C sing 1.4444065 N N
62 OBQ CCK O C sing 1.4295202 N N
63 OBQ PCV O P sing 1.6093583 N N
64 OBR CCL O C sing 1.4288335 N N
65 OBR PCU O P sing 1.6099696 N N
66 OBS PCS O P sing 1.6094524 N N
67 OBS PCW O P sing 1.6103767 N N
68 OBT PCT O P sing 1.6100022 N N
69 OBT PCW O P sing 1.6096127 N N
70 CBV CBY C C doub 1.404433 N Y
71 CBW CBZ C C doub 1.4051812 N Y
72 CBY CCB C C sing 1.4058154 N Y
73 CBZ CCC C C sing 1.404602 N Y
74 CCB NCQ C N sing 1.3728143 N Y
75 CCC NCR C N sing 1.3725145 N Y
76 CCF CCI C C sing 1.545286 N N
77 CCF CCK C C sing 1.5448433 N N
78 CCG CCJ C C sing 1.5450528 N N
79 CCG CCL C C sing 1.5448239 N N
80 CCK CCN C C sing 1.5453025 N N
81 CCL CCO C C sing 1.5448252 N N
82 CCN NCQ C N sing 1.4648938 N N
83 CCO NCR C N sing 1.4652576 N N
84 C2 H2 C H sing 1.0803027 N N
85 N6 HN6 N H sing 0.96986496 N N
86 N6 HN6A N H sing 0.969423 N N
87 C8 H8 C H sing 1.0801041 N N
88 C1' H1' C H sing 1.0898794 N N
89 C2' H2' C H sing 1.0899197 N N
90 O2' HO2' O H sing 0.9670414 N N
91 C3' H3' C H sing 1.0909908 N N
92 O3' HO3' O H sing 0.96732205 N N
93 C4' H4' C H sing 1.0902317 N N
94 C5' H5' C H sing 1.0898303 N N
95 C5' H5'A C H sing 1.0895972 N N
96 NAB HNAB N H sing 0.9695571 N N
97 NAB HNAA N H sing 0.9697737 N N
98 NAC HNAC N H sing 0.9704087 N N
99 NAC HNAD N H sing 0.97058797 N N
100 OAK HOAK O H sing 0.9677215 N N
101 OAL HOAL O H sing 0.9669359 N N
102 OAM HOAM O H sing 0.96658266 N N
103 OAN HOAN O H sing 0.9667399 N N
104 OAO HOAO O H sing 0.9669219 N N
105 OAP HOAP O H sing 0.966414 N N
106 OAQ HOAQ O H sing 0.9672735 N N
107 OAR HOAR O H sing 0.9669695 N N
108 CAT HAT C H sing 1.0795064 N N
109 CAU HAU C H sing 1.0806276 N N
110 CAW HAW C H sing 1.0805004 N N
111 CAX HAX C H sing 1.0796263 N N
112 CAY HAY C H sing 1.0901932 N N
113 CAY HAYA C H sing 1.0904889 N N
114 CBA HBA C H sing 1.0891433 N N
115 CBA HBAA C H sing 1.0899715 N N
116 CCF HCF C H sing 1.0901835 N N
117 CCG HCG C H sing 1.0899807 N N
118 CCI HCI C H sing 1.0898743 N N
119 CCJ HCJ C H sing 1.0895963 N N
120 CCK HCK C H sing 1.0896211 N N
121 CCL HCL C H sing 1.0905563 N N
122 CCN HCN C H sing 1.0897532 N N
123 CCO HCO C H sing 1.0901954 N N