Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : DM2

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 68


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 -0.791 -0.376 6.114
2 C2 C C2 N Y N 0 0.106 0.151 7.027
3 C3 C C3 N Y N 0 1.331 0.63 6.611
4 C4 C C4 N Y N 0 1.682 0.59 5.264
5 O4 O O4 N N N 0 2.887 1.062 4.859
6 C5 C C5 N Y N 0 0.784 0.066 4.332
7 C6 C C6 N N N 0 1.136 0.0080 2.9
8 O6 O O6 N N N 0 2.284 0.186 2.539
9 C7 C C7 N Y N 0 0.076 -0.262 1.91
10 C8 C C8 N Y N 0 0.293 -0.04 0.553
11 O8 O O8 N N N 0 1.493 0.428 0.131
12 C9 C C9 N Y N 0 -0.721 -0.297 -0.379
13 C10 C C10 S N N 0 -0.413 -0.024 -1.829
14 O10 O O10 N N N 0 0.906 -0.487 -2.124
15 C11 C C11 N N N 0 -1.412 -0.739 -2.736
16 C12 C C12 S N N 0 -2.828 -0.395 -2.259
17 O12 O O12 N N N 0 -3.784 -0.864 -3.212
18 C13 C C13 N N N 0 -2.962 1.096 -2.096
19 O13 O O13 N N N 0 -2.78 1.605 -1.016
20 C14 C C14 N N N 0 -3.323 1.954 -3.282
21 O14 O O14 N N N 0 -3.389 3.323 -2.877
22 C15 C C15 N N N 0 -3.061 -1.082 -0.915
23 C16 C C16 N Y N 0 -1.936 -0.777 0.039
24 C17 C C17 N Y N 0 -2.17 -1.005 1.402
25 O17 O O17 N N N 0 -3.374 -1.478 1.809
26 C18 C C18 N Y N 0 -1.174 -0.751 2.341
27 C19 C C19 N N N 0 -1.41 -0.985 3.778
28 O19 O O19 N N N 0 -2.373 -1.63 4.146
29 C20 C C20 N Y N 0 -0.462 -0.426 4.765
30 C21 C C21 N N N 0 3.562 1.529 6.029
31 C1' C C1* R N N 0 1.598 0.601 -2.737
32 C2' C C2* N N N 0 3.094 0.283 -2.798
33 C3' C C3* S N N 0 3.298 -1.006 -3.599
34 N3' N N3* N N N 0 4.735 -1.242 -3.796
35 C4' C C4* S N N 0 2.607 -0.854 -4.959
36 O4' O O4* N N N 0 3.273 0.154 -5.723
37 C5' C C5* S N N 0 1.148 -0.45 -4.735
38 O5' O O5* N N N 0 1.094 0.801 -4.056
39 C6' C C6* N N N 0 0.441 -0.326 -6.086
40 H1 H H1 N N N 0 -1.747 -0.749 6.45
41 H2 H H2 N N N 0 -0.154 0.188 8.075
42 H3 H H3 N N N 0 2.022 1.038 7.334
43 HO8 H HO8 N N N 0 1.418 1.392 0.091
44 H10 H H10 N N N 0 -0.466 1.048 -2.011
45 H111 H 1H11 N N N 0 -1.256 -1.816 -2.677
46 H112 H 2H11 N N N 0 -1.279 -0.403 -3.764
47 HO12 H 2HO1 N N N 0 -4.658 -0.643 -2.862
48 H141 H 1H14 N N N 0 -2.564 1.84 -4.057
49 H142 H 2H14 N N N 0 -4.291 1.643 -3.674
50 HO14 H 4HO1 N N N 0 -3.622 3.836 -3.663
51 H151 H 1H15 N N N 0 -3.12 -2.16 -1.068
52 H152 H 2H15 N N N 0 -4.0 -0.729 -0.489
53 HO17 H 7HO1 N N N 0 -3.932 -0.707 1.985
54 H211 H 1H21 N N N 0 4.541 1.92 5.752
55 H212 H 2H21 N N N 0 2.975 2.319 6.497
56 H213 H 3H21 N N N 0 3.686 0.704 6.731
57 H1' H H1* N N N 0 1.444 1.506 -2.149
58 H2'1 H 1H2* N N N 0 3.621 1.103 -3.286
59 H2'2 H 2H2* N N N 0 3.48 0.15 -1.787
60 H3' H H3* N N N 0 2.86 -1.846 -3.059
61 HN'1 H 1HN* N N N 0 5.144 -1.323 -2.877
62 HN'2 H 2HN* N N N 0 4.823 -2.147 -4.233
63 H4' H H4* N N N 0 2.645 -1.802 -5.496
64 HO4' H *HO4 N N N 0 2.807 0.217 -6.568
65 H5' H H5* N N N 0 0.65 -1.21 -4.134
66 H6'1 H 1H6* N N N 0 -0.597 -0.038 -5.927
67 H6'2 H 2H6* N N N 0 0.94 0.432 -6.689
68 H6'3 H 3H6* N N N 0 0.478 -1.284 -6.605