Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : VDA

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 80


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O2 O O2 N N N 0 6.511 1.467 0.718
2 C1 C C1 R N N 0 5.293 -1.082 0.352
3 C2 C C2 N N N 0 6.49 -0.628 -0.485
4 C3 C C3 R N N 0 6.5 0.897 -0.592
5 C4 C C4 N N N 0 5.247 1.363 -1.342
6 C5 C C5 N N N 0 4.031 0.795 -0.645
7 C6 C C6 N N N 0 3.02 1.581 -0.291
8 C7 C C7 N N N 0 1.791 0.993 0.266
9 C8 C C8 N N N 0 0.743 1.768 0.525
10 C9 C C9 N N N 0 0.742 3.271 0.271
11 C10 C C10 N N N 0 3.995 -0.69 -0.362
12 C11 C C11 N N N 0 -0.475 3.687 -0.552
13 C12 C C12 N N N 0 -1.78 3.086 0.001
14 C13 C C13 S N N 0 -1.613 1.595 0.024
15 C14 C C14 S N N 0 -0.544 1.235 1.087
16 C15 C C15 N N N 0 -0.741 -0.283 1.082
17 C16 C C16 N N N 0 -2.246 -0.419 0.87
18 C17 C C17 N N N 0 -2.73 0.665 0.301
19 C18 C C18 N N N 0 -1.029 1.184 -1.329
20 C20 C C20 S N N 0 -4.181 0.911 -0.027
21 C21 C C21 N N N 0 -4.731 2.01 0.885
22 S22 S S22 N N N 0 -5.126 -0.616 0.228
23 C23 C C23 N N N 0 -6.785 -0.172 -0.355
24 C25 C C25 N N N 0 -7.718 -1.375 -0.204
25 O3 O O3 N N N 0 -7.875 -1.685 1.182
26 C26 C C26 N N N 0 -9.083 -1.041 -0.809
27 C27 C C27 N N N 0 -7.118 -2.58 -0.931
28 C30 C C30 N N N 0 8.764 -1.326 -0.78
29 O1 O O1 N N N 0 5.337 -2.5 0.518
30 O4 O O4 N N N 0 7.699 -1.069 0.137
31 C31 C C31 N N N 0 10.001 -1.789 -0.007
32 O5 O O5 N N N 0 9.729 -3.045 0.619
33 C29 C C29 N N N 0 -9.65 0.208 -0.131
34 C28 C C28 N N N 0 -8.052 -3.783 -0.782
35 HO2 H HO2 N N N 0 6.517 2.434 0.726
36 H1 H H1 N N N 0 5.33 -0.6 1.329
37 H2 H H2 N N N 0 6.419 -1.061 -1.483
38 H3 H H3 N N N 0 7.389 1.218 -1.135
39 H4 H H4 N N N 0 5.199 2.452 -1.333
40 H4A H H4A N N N 0 5.281 1.003 -2.371
41 H6 H H6 N N N 0 3.1 2.651 -0.411
42 H7 H H7 N N N 0 1.741 -0.067 0.463
43 H9 H H9 N N N 0 0.724 3.795 1.227
44 H9A H H9A N N N 0 1.649 3.543 -0.268
45 H10 H H10 N N N 0 3.913 -1.24 -1.299
46 H10A H H10A N N N 0 3.142 -0.92 0.277
47 H11 H H11 N N N 0 -0.554 4.774 -0.542
48 H11A H H11A N N N 0 -0.338 3.353 -1.58
49 H12 H H12 N N N 0 -1.959 3.454 1.011
50 H12A H H12A N N N 0 -2.615 3.355 -0.646
51 H14 H H14 N N N 0 -0.77 1.679 2.056
52 H15 H H15 N N N 0 -0.191 -0.742 0.261
53 H15A H H15A N N N 0 -0.444 -0.714 2.038
54 H16 H H16 N N N 0 -2.833 -1.28 1.154
55 H18 H H18 N N N 0 -0.061 1.666 -1.469
56 H18A H H18A N N N 0 -0.903 0.102 -1.357
57 H18B H H18B N N N 0 -1.706 1.492 -2.126
58 H20 H H20 N N N 0 -4.27 1.224 -1.067
59 H21 H H21 N N N 0 -4.642 1.696 1.926
60 H21A H H21A N N N 0 -4.163 2.927 0.732
61 H21B H H21B N N N 0 -5.78 2.187 0.648
62 H23 H H23 N N N 0 -7.167 0.661 0.236
63 H23A H H23A N N N 0 -6.735 0.12 -1.404
64 HO3 H HO3 N N N 0 -8.251 -0.964 1.706
65 H30 H H30 N N N 0 8.461 -2.105 -1.48
66 H26 H H26 N N N 0 -8.97 -0.855 -1.878
67 H26A H H26A N N N 0 -9.763 -1.879 -0.656
68 H27 H H27 N N N 0 -6.997 -2.343 -1.988
69 H27A H H27A N N N 0 -6.146 -2.818 -0.499
70 HO1 H HO1 N N N 0 4.606 -2.858 1.04
71 H30A H H30A N N N 0 8.999 -0.415 -1.329
72 H31 H H31 N N N 0 10.839 -1.9 -0.696
73 H31A H H31A N N N 0 10.252 -1.05 0.754
74 HO5 H HO5 N N N 0 10.472 -3.399 1.128
75 H29 H H29 N N N 0 -9.677 0.054 0.948
76 H29A H H29A N N N 0 -9.017 1.065 -0.36
77 H29B H H29B N N N 0 -10.66 0.393 -0.498
78 H28 H H28 N N N 0 -8.246 -3.962 0.276
79 H28A H H28A N N N 0 -8.992 -3.578 -1.294
80 H28B H H28B N N N 0 -7.583 -4.663 -1.22