Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : DM1

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 67


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 -0.723 -0.349 6.044
2 C2 C C2 N Y N 0 0.243 0.085 6.939
3 C3 C C3 N Y N 0 1.488 0.476 6.492
4 C4 C C4 N Y N 0 1.792 0.441 5.134
5 O4 O O4 N N N 0 3.017 0.827 4.699
6 C5 C C5 N Y N 0 0.826 0.012 4.221
7 C6 C C6 N N N 0 1.126 -0.038 2.777
8 O6 O O6 N N N 0 2.273 0.058 2.382
9 C7 C C7 N Y N 0 0.018 -0.201 1.818
10 C8 C C8 N Y N 0 0.208 0.035 0.459
11 O8 O O8 N N N 0 1.428 0.419 0.007
12 C9 C C9 N Y N 0 -0.851 -0.118 -0.444
13 C10 C C10 S N N 0 -0.569 0.164 -1.897
14 O10 O O10 N N N 0 0.699 -0.393 -2.246
15 C11 C C11 N N N 0 -1.649 -0.447 -2.785
16 C12 C C12 S N N 0 -3.018 -0.005 -2.254
17 O12 O O12 N N N 0 -4.038 -0.375 -3.184
18 C13 C C13 N N N 0 -3.029 1.487 -2.055
19 O13 O O13 N N N 0 -2.773 1.954 -0.971
20 C14 C C14 N N N 0 -3.358 2.399 -3.209
21 C15 C C15 N N N 0 -3.262 -0.705 -0.918
22 C16 C C16 N Y N 0 -2.087 -0.511 0.004
23 C17 C C17 N Y N 0 -2.295 -0.754 1.369
24 O17 O O17 N N N 0 -3.519 -1.14 1.806
25 C18 C C18 N Y N 0 -1.252 -0.601 2.28
26 C19 C C19 N N N 0 -1.461 -0.851 3.718
27 O19 O O19 N N N 0 -2.46 -1.427 4.104
28 C20 C C20 N Y N 0 -0.44 -0.391 4.685
29 C21 C C21 N N N 0 3.763 1.211 5.855
30 C1' C C1* R N N 0 1.456 0.653 -2.858
31 C2' C C2* N N N 0 2.919 0.22 -2.976
32 C3' C C3* S N N 0 2.995 -1.062 -3.812
33 N3' N N3* N N N 0 4.402 -1.404 -4.061
34 C4' C C4* S N N 0 2.276 -0.822 -5.144
35 O4' O O4* N N N 0 2.994 0.148 -5.907
36 C5' C C5* S N N 0 0.861 -0.311 -4.862
37 O5' O O5* N N N 0 0.927 0.923 -4.155
38 C6' C C6* N N N 0 0.124 -0.1 -6.186
39 H1 H H1 N N N 0 -1.694 -0.654 6.405
40 H2 H H2 N N N 0 0.019 0.116 7.995
41 H3 H H3 N N N 0 2.231 0.811 7.2
42 HO8 H HO8 N N N 0 1.428 1.386 -0.008
43 H10 H H10 N N N 0 -0.542 1.242 -2.054
44 H111 H 1H11 N N N 0 -1.577 -1.534 -2.755
45 H112 H 2H11 N N N 0 -1.523 -0.098 -3.81
46 HO12 H 2HO1 N N N 0 -4.88 -0.095 -2.801
47 H151 H 1H15 N N N 0 -3.41 -1.77 -1.093
48 H141 H 1H14 N N N 0 -3.316 3.436 -2.876
49 H142 H 2H14 N N N 0 -2.636 2.245 -4.011
50 H143 H 3H14 N N N 0 -4.36 2.175 -3.574
51 H152 H 2H15 N N N 0 -4.156 -0.289 -0.454
52 HO17 H 7HO1 N N N 0 -4.008 -0.333 2.017
53 H211 H 1H21 N N N 0 4.761 1.531 5.554
54 H212 H 2H21 N N N 0 3.255 2.033 6.36
55 H213 H 3H21 N N N 0 3.843 0.362 6.534
56 H1' H H1* N N N 0 1.392 1.552 -2.246
57 H2'1 H 1H2* N N N 0 3.494 1.008 -3.463
58 H2'2 H 2H2* N N N 0 3.325 0.033 -1.982
59 H3' H H3* N N N 0 2.51 -1.877 -3.275
60 HN'1 H 1HN* N N N 0 4.832 -1.539 -3.159
61 HN'2 H 2HN* N N N 0 4.404 -2.303 -4.521
62 H4' H H4* N N N 0 2.222 -1.757 -5.702
63 HO4' H *HO4 N N N 0 2.509 0.268 -6.735
64 H5' H H5* N N N 0 0.324 -1.045 -4.261
65 H6'1 H 1H6* N N N 0 -0.883 0.263 -5.986
66 H6'2 H 2H6* N N N 0 0.662 0.631 -6.789
67 H6'3 H 3H6* N N N 0 0.068 -1.045 -6.726