Chemical Components in the PDB

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PDBeChem : Chemical Bonds

 Molecule : XQD    

Bonds between two atoms of the molecule

Total Number of Bonds: 160


Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O9A P3B O P doub 1.48 N N
2 O8A P3B O P sing 1.61 N N
3 P3B O7A P O sing 1.61 N N
4 P3B O3C P O sing 1.61 N N
5 O3C C3C O C sing 1.43 N N
6 C4C C3C C C sing 1.54 N N
7 C4C O4C C O sing 1.44 N N
8 C4C C5C C C sing 1.53 N N
9 C3C C2C C C sing 1.55 N N
10 O4C C1A O C sing 1.44 N N
11 C5C O5C C O sing 1.43 N N
12 C1A C2C C C sing 1.54 N N
13 C1A N9A C N sing 1.47 N N
14 C2C O2C C O sing 1.43 N N
15 O5C P1A O P sing 1.61 N N
16 O2A P1A O P doub 1.48 N N
17 N3A C4A N C doub 1.33 N Y
18 N3A C2A N C sing 1.32 N Y
19 N9A C4A N C sing 1.37 N Y
20 N9A C8A N C sing 1.36 N Y
21 P1A O3A P O sing 1.61 N N
22 P1A O1A P O sing 1.61 N N
23 C4A C5A C C sing 1.41 N Y
24 O4E P2A O P doub 1.48 N N
25 C2A N1A C N doub 1.32 N Y
26 O3A P2A O P sing 1.61 N N
27 C8A N7A C N doub 1.3 N Y
28 P2A O5A P O sing 1.61 N N
29 P2A O6A P O sing 1.61 N N
30 C5A N7A C N sing 1.36 N Y
31 C5A C6A C C doub 1.4 N Y
32 N1A C6A N C sing 1.33 N Y
33 CCP O6A C O sing 1.43 N N
34 CCP CBP C C sing 1.53 N N
35 C6A N6A C N sing 1.38 N N
36 CEP CBP C C sing 1.53 N N
37 CBP CDP C C sing 1.53 N N
38 CBP CAP C C sing 1.53 N N
39 OAP CAP O C sing 1.43 N N
40 CAP C9P C C sing 1.51 N N
41 O9P C9P O C doub 1.21 N N
42 C9P N8P C N sing 1.35 N N
43 N8P C7P N C sing 1.46 N N
44 C7P C6P C C sing 1.53 N N
45 C6P C5P C C sing 1.51 N N
46 C5P O5P C O doub 1.21 N N
47 C5P N4P C N sing 1.35 N N
48 N4P C3P N C sing 1.46 N N
49 O7' C7' O C doub 1.21 N N
50 C8' C7' C C sing 1.51 N N
51 C3P C2P C C sing 1.53 N N
52 C7' N2' C N sing 1.35 N N
53 C2P S1P C S sing 1.81 N N
54 N2' C2' N C sing 1.46 N N
55 O4D PA O P doub 1.48 N N
56 C2' C1' C C sing 1.53 N N
57 C2' C3' C C sing 1.53 N N
58 O3' C3' O C sing 1.43 N N
59 O C O C sing 1.43 N N
60 S1P C S C sing 1.81 N N
61 C1' O5' C O sing 1.43 N N
62 C1' O1' C O sing 1.43 N N
63 C3' C4' C C sing 1.53 N N
64 PA O5B P O sing 1.61 N N
65 PA O3B P O sing 1.61 N N
66 PA O6B P O sing 1.61 N N
67 C4' N4A C N sing 1.47 N N
68 C4' C5' C C sing 1.53 N N
69 C N4A C N sing 1.47 N N
70 C CH3 C C sing 1.53 N N
71 O5' C5' O C sing 1.43 N N
72 O3B PB O P sing 1.61 N N
73 O1' PB O P sing 1.61 N N
74 C5' C6' C C sing 1.53 N N
75 O6B C5B O C sing 1.43 N N
76 O1B PB O P doub 1.48 N N
77 PB O2B P O sing 1.61 N N
78 C5B C4B C C sing 1.53 N N
79 C5 C6 C C doub 1.35 N N
80 C5 C4 C C sing 1.42 N N
81 C6 N1 C N sing 1.37 N N
82 C3B C2B C C sing 1.55 N N
83 C3B O2' C O sing 1.43 N N
84 C3B C1B C C sing 1.55 N N
85 C2B C4B C C sing 1.54 N N
86 C2B O4A C O sing 1.43 N N
87 O4 C4 O C doub 1.22 N N
88 C4 N3 C N sing 1.35 N N
89 C4B O4B C O sing 1.44 N N
90 O4B C1B O C sing 1.44 N N
91 N1 C1B N C sing 1.47 N N
92 N1 C2 N C sing 1.35 N N
93 N3 C2 N C sing 1.35 N N
94 C2 O2 C O doub 1.22 N N
95 N3 H1 N H sing 0.97 N N
96 C5 H2 C H sing 1.08 N N
97 C6 H3 C H sing 1.08 N N
98 C6P H4 C H sing 1.09 N N
99 C6P H5 C H sing 1.09 N N
100 C7P H6 C H sing 1.09 N N
101 C7P H7 C H sing 1.09 N N
102 N8P H8 N H sing 0.97 N N
103 CAP H9 C H sing 1.09 N N
104 OAP H10 O H sing 0.97 N N
105 CDP H11 C H sing 1.09 N N
106 CDP H12 C H sing 1.09 N N
107 CDP H13 C H sing 1.09 N N
108 CEP H14 C H sing 1.09 N N
109 CEP H15 C H sing 1.09 N N
110 CEP H16 C H sing 1.09 N N
111 CCP H17 C H sing 1.09 N N
112 CCP H18 C H sing 1.09 N N
113 O5A H19 O H sing 0.97 N N
114 O1A H20 O H sing 0.97 N N
115 C5C H21 C H sing 1.09 N N
116 C5C H22 C H sing 1.09 N N
117 C4C H23 C H sing 1.09 N N
118 C3C H24 C H sing 1.09 N N
119 O8A H25 O H sing 0.97 N N
120 O7A H26 O H sing 0.97 N N
121 C2C H27 C H sing 1.09 N N
122 O2C H28 O H sing 0.97 N N
123 C1A H29 C H sing 1.09 N N
124 C2A H30 C H sing 1.08 N N
125 C8A H31 C H sing 1.08 N N
126 N6A H32 N H sing 0.97 N N
127 N6A H33 N H sing 0.97 N N
128 N4P H34 N H sing 0.97 N N
129 C3P H35 C H sing 1.09 N N
130 C3P H36 C H sing 1.09 N N
131 C2P H37 C H sing 1.09 N N
132 C2P H38 C H sing 1.09 N N
133 O H39 O H sing 0.97 N N
134 CH3 H40 C H sing 1.09 N N
135 CH3 H41 C H sing 1.09 N N
136 CH3 H42 C H sing 1.09 N N
137 N4A H43 N H sing 1.01 N N
138 C4' H45 C H sing 1.09 N N
139 C3' H46 C H sing 1.09 N N
140 O3' H47 O H sing 0.97 N N
141 C5' H48 C H sing 1.09 N N
142 C6' H49 C H sing 1.09 N N
143 C6' H50 C H sing 1.09 N N
144 C6' H51 C H sing 1.09 N N
145 C1' H52 C H sing 1.09 N N
146 C2' H53 C H sing 1.09 N N
147 N2' H54 N H sing 0.97 N N
148 C8' H55 C H sing 1.09 N N
149 C8' H56 C H sing 1.09 N N
150 C8' H57 C H sing 1.09 N N
151 O2B H58 O H sing 0.97 N N
152 O5B H59 O H sing 0.97 N N
153 C5B H60 C H sing 1.09 N N
154 C5B H61 C H sing 1.09 N N
155 C4B H62 C H sing 1.09 N N
156 C2B H63 C H sing 1.09 N N
157 O4A H64 O H sing 0.97 N N
158 C3B H65 C H sing 1.09 N N
159 O2' H66 O H sing 0.97 N N
160 C1B H67 C H sing 1.09 N N