Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : XQD

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 155


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -17.612 2.442 -1.647
2 N3 N N2 N N N 0 -17.911 4.382 -2.924
3 C4 C C1 N N N 0 -17.655 3.696 -4.057
4 C5 C C2 N N N 0 -17.359 2.314 -3.981
5 C6 C C3 N N N 0 -17.342 1.711 -2.773
6 O5P O O1 N N N 0 -0.284 0.609 -1.755
7 C5P C C4 N N N 0 -0.413 0.115 -0.655
8 C6P C C5 N N N 0 0.579 -0.91 -0.168
9 C7P C C6 N N N 0 1.64 -1.145 -1.245
10 N8P N N3 N N N 0 2.604 -2.141 -0.772
11 C9P C C7 N N N 0 3.635 -2.509 -1.559
12 O9P O O2 N N N 0 3.712 -2.086 -2.693
13 CAP C C8 R N N 0 4.691 -3.444 -1.03
14 OAP O O3 N N N 0 4.277 -3.962 0.236
15 CBP C C9 N N N 0 6.009 -2.685 -0.864
16 CDP C C10 N N N 0 6.527 -2.257 -2.239
17 CEP C C11 N N N 0 5.778 -1.446 0.002
18 CCP C C12 N N N 0 7.039 -3.593 -0.191
19 O6A O O4 N N N 0 8.27 -2.884 -0.036
20 P2A P P1 N N N 0 9.579 -3.536 0.638
21 O4E O O5 N N N 0 9.923 -4.791 -0.067
22 O5A O O6 N N N 0 9.283 -3.855 2.188
23 O3A O O7 N N N 0 10.81 -2.504 0.528
24 P1A P P2 N N N 0 12.41 -2.659 0.612
25 O1A O O8 N N N 0 12.849 -2.877 2.145
26 O2A O O9 N N N 0 12.836 -3.825 -0.194
27 O5C O O10 N N N 0 13.109 -1.327 0.038
28 C5C C C13 N N N 0 14.523 -1.195 -0.118
29 C4C C C14 R N N 0 14.848 0.189 -0.684
30 C3C C C15 S N N 0 16.359 0.308 -0.979
31 O3C O O11 N N N 0 16.618 0.08 -2.366
32 P3B P P3 N N N 0 17.569 -1.106 -2.896
33 O9A O O12 N N N 0 18.896 -1.001 -2.251
34 O8A O O13 N N N 0 16.907 -2.528 -2.532
35 O7A O O14 N N N 0 17.737 -0.986 -4.493
36 C2C C C16 R N N 0 16.702 1.766 -0.597
37 O2C O O15 N N N 0 17.183 2.482 -1.737
38 O4C O O16 N N N 0 14.582 1.21 0.303
39 C1A C C17 R N N 0 15.357 2.354 -0.117
40 N9A N N4 N Y N 0 15.572 3.265 1.01
41 C4A C C18 N Y N 0 15.844 4.607 0.929
42 N3A N N5 N Y N 0 15.995 5.476 -0.065
43 N6A N N7 N N N 0 16.391 6.918 3.751
44 C2A C C19 N Y N 0 16.26 6.741 0.183
45 C8A C C20 N Y N 0 15.534 2.935 2.333
46 N7A N N6 N Y N 0 15.77 3.988 3.061
47 C5A C C21 N Y N 0 15.971 5.058 2.254
48 C6A C C22 N Y N 0 16.254 6.417 2.468
49 N1A N N8 N Y N 0 16.389 7.21 1.411
50 N4P N N9 N N N 0 -1.443 0.483 0.132
51 C3P C C23 N N N 0 -2.407 1.479 -0.341
52 C2P C C24 N N N 0 -3.468 1.714 0.736
53 S1P S S1 N N N 0 -4.662 2.947 0.15
54 C C C25 S N N 0 -5.734 3.196 1.592
55 O O O17 N N N 0 -5.102 2.654 2.754
56 CH3 C C26 N N N 0 -5.977 4.692 1.795
57 N4A N N10 N N N 0 -7.017 2.516 1.371
58 C4' C C27 S N N 0 -6.814 1.094 1.064
59 C3' C C28 S N N 0 -7.346 0.24 2.219
60 O3' O O18 N N N 0 -6.596 0.518 3.403
61 C5' C C29 R N N 0 -7.572 0.734 -0.217
62 C6' C C30 N N N 0 -7.006 1.54 -1.388
63 O5' O O19 N N N 0 -7.42 -0.662 -0.482
64 C1' C C31 R N N 0 -7.942 -1.51 0.542
65 C2' C C32 R N N 0 -7.2 -1.24 1.854
66 N2' N N11 N N N 0 -7.773 -2.066 2.919
67 C7' C C33 N N N 0 -7.349 -3.334 3.091
68 C8' C C34 N N N 0 -7.939 -4.184 4.187
69 O7' O O20 N N N 0 -6.493 -3.791 2.363
70 O1' O O21 N N N 0 -9.335 -1.242 0.719
71 PB P P4 N N N 0 -10.487 -2.014 -0.099
72 O2B O O22 N N N 0 -10.365 -1.656 -1.664
73 O1B O O23 N N N 0 -10.331 -3.474 0.087
74 O3B O O24 N N N 0 -11.931 -1.555 0.445
75 PA P P5 N N N 0 -13.408 -2.192 0.373
76 O4D O O25 N N N 0 -13.625 -2.783 -0.967
77 O5B O O26 N N N 0 -13.553 -3.338 1.494
78 O6B O O27 N N N 0 -14.502 -1.041 0.636
79 C5B C C35 N N N 0 -15.909 -1.267 0.535
80 C4B C C36 R N N 0 -16.658 0.03 0.846
81 C2B C C37 S N N 0 -18.177 -0.229 0.845
82 O4A O O28 N N N 0 -18.738 0.081 2.122
83 C3B C C38 R N N 0 -18.726 0.735 -0.236
84 O2' O O29 N N N 0 -19.948 1.339 0.193
85 C1B C C39 R N N 0 -17.593 1.788 -0.336
86 O4B O O30 N N N 0 -16.39 1.006 -0.175
87 C2 C C40 N N N 0 -17.888 3.756 -1.733
88 O2 O O31 N N N 0 -18.12 4.387 -0.72
89 O4 O O32 N N N 0 -17.676 4.261 -5.135
90 H1 H H1 N N N 0 -18.111 5.33 -2.968
91 H2 H H2 N N N 0 -17.148 1.749 -4.877
92 H3 H H3 N N N 0 -17.117 0.658 -2.695
93 H4 H H4 N N N 0 1.058 -0.548 0.742
94 H5 H H5 N N N 0 0.061 -1.846 0.042
95 H6 H H6 N N N 0 1.161 -1.506 -2.155
96 H7 H H7 N N N 0 2.158 -0.209 -1.455
97 H8 H H8 N N N 0 2.501 -2.536 0.108
98 H9 H H9 N N N 0 4.831 -4.267 -1.73
99 H10 H H10 N N N 0 4.133 -3.284 0.911
100 H11 H H11 N N N 0 5.825 -1.556 -2.69
101 H12 H H12 N N N 0 7.499 -1.777 -2.127
102 H13 H H13 N N N 0 6.626 -3.134 -2.878
103 H14 H H14 N N N 0 5.043 -0.798 -0.478
104 H15 H H15 N N N 0 5.408 -1.75 0.982
105 H16 H H16 N N N 0 6.716 -0.905 0.12
106 H17 H H17 N N N 0 6.67 -3.898 0.789
107 H18 H H18 N N N 0 7.204 -4.477 -0.808
108 H19 H H19 N N N 0 9.05 -3.076 2.712
109 H20 H H20 N N N 0 12.601 -2.15 2.733
110 H21 H H21 N N N 0 15.009 -1.315 0.85
111 H22 H H22 N N N 0 14.886 -1.962 -0.803
112 H23 H H23 N N N 0 14.269 0.375 -1.588
113 H24 H H24 N N N 0 16.925 -0.391 -0.363
114 H25 H H25 N N N 0 16.033 -2.666 -2.922
115 H26 H H26 N N N 0 18.299 -1.67 -4.882
116 H27 H H27 N N N 0 17.439 1.787 0.205
117 H28 H H28 N N N 0 17.414 3.403 -1.554
118 H29 H H29 N N N 0 14.856 2.873 -0.934
119 H30 H H30 N N N 0 16.378 7.42 -0.648
120 H31 H H31 N N N 0 15.336 1.946 2.719
121 H32 H H32 N N N 0 16.29 6.33 4.515
122 H33 H H33 N N N 0 16.587 7.859 3.886
123 H34 H H34 N N N 0 -1.546 0.088 1.012
124 H35 H H35 N N N 0 -1.889 2.415 -0.551
125 H36 H H36 N N N 0 -2.887 1.117 -1.251
126 H37 H H37 N N N 0 -3.986 0.778 0.946
127 H38 H H38 N N N 0 -2.989 2.076 1.645
128 H39 H H39 N N N 0 -4.927 1.705 2.699
129 H40 H H40 N N N 0 -6.459 5.106 0.909
130 H41 H H41 N N N 0 -6.622 4.841 2.662
131 H42 H H42 N N N 0 -5.025 5.196 1.959
132 H43 H H43 N N N 0 -7.547 2.971 0.642
133 H45 H H45 N N N 0 -5.751 0.9 0.925
134 H46 H H46 N N N 0 -8.397 0.471 2.39
135 H47 H H47 N N N 0 -6.88 0.011 4.176
136 H48 H H48 N N N 0 -8.629 0.968 -0.092
137 H49 H H49 N N N 0 -5.968 1.253 -1.56
138 H50 H H50 N N N 0 -7.592 1.339 -2.285
139 H51 H H51 N N N 0 -7.054 2.604 -1.154
140 H52 H H52 N N N 0 -7.806 -2.553 0.255
141 H53 H H53 N N N 0 -6.144 -1.483 1.731
142 H54 H H54 N N N 0 -8.457 -1.701 3.501
143 H55 H H55 N N N 0 -8.807 -4.719 3.805
144 H56 H H56 N N N 0 -7.193 -4.9 4.532
145 H57 H H57 N N N 0 -8.241 -3.546 5.018
146 H58 H H58 N N N 0 -10.457 -0.714 -1.861
147 H59 H H59 N N N 0 -13.423 -3.021 2.399
148 H60 H H60 N N N 0 -16.153 -1.594 -0.476
149 H61 H H61 N N N 0 -16.205 -2.038 1.247
150 H62 H H62 N N N 0 -16.346 0.414 1.817
151 H63 H H63 N N N 0 -18.388 -1.264 0.578
152 H64 H H64 N N N 0 -19.693 -0.064 2.178
153 H65 H H65 N N N 0 -18.862 0.217 -1.185
154 H66 H H66 N N N 0 -20.662 0.708 0.357
155 H67 H H67 N N N 0 -17.684 2.526 0.461