Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : 5BD

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 54


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 -2.488 -3.141 0.359
2 C2 C C2 N Y N 0 -3.681 -2.48 0.148
3 C3 C C3 N Y N 0 -3.687 -1.156 -0.276
4 C5 C C5 N Y N 0 2.486 -0.484 -0.49
5 C6 C C6 N Y N 0 3.686 -1.156 -0.275
6 C7 C C7 N Y N 0 3.681 -2.481 0.149
7 C8 C C8 N Y N 0 2.487 -3.14 0.363
8 C9 C C9 N N N 0 -5.011 0.813 -0.2
9 C11 C C11 N Y N 0 -1.278 -2.481 0.148
10 C12 C C12 N Y N 0 -1.279 -1.14 -0.28
11 C13 C C13 N N N 0 0.0 -0.434 -0.506
12 C14 C C14 N N N 0 0.0 -3.183 0.374
13 O1 O O1 N N N 0 -4.038 1.441 0.161
14 N1 N N1 N N N 0 -4.898 -0.499 -0.486
15 C4 C C4 N Y N 0 -2.486 -0.484 -0.49
16 O2 O O2 N N N 0 0.0 0.723 -0.876
17 O3 O O3 N N N 0 0.0 -4.341 0.744
18 C15 C C15 N Y N 0 1.278 -2.48 0.15
19 C16 C C16 N Y N 0 1.279 -1.14 -0.281
20 N2 N N2 N N N 0 4.898 -0.499 -0.485
21 C10 C C10 N N N 0 5.011 0.813 -0.2
22 O4 O O4 N N N 0 4.039 1.441 0.161
23 H1 H H1 N N N 0 -2.491 -4.168 0.693
24 H2 H H2 N N N 0 -4.616 -2.995 0.312
25 H5 H H5 N N N 0 2.493 0.545 -0.819
26 H7 H H7 N N N 0 4.616 -2.995 0.313
27 H8 H H8 N N N 0 2.49 -4.169 0.691
28 C17 C C17 N N N 0 -6.346 1.5 -0.329
29 H4 H H4 N N N 0 -2.493 0.545 -0.819
30 HN2 H HN2 N N N 0 5.659 -0.987 -0.837
31 C18 C C18 N N N 0 6.346 1.5 -0.329
32 H81 H H81 N N N 0 -5.66 -0.986 -0.838
33 H9 H H9 N N N 0 -7.066 1.023 0.336
34 N3 N N3 N N N 0 -6.206 2.916 0.037
35 H10 H H10 N N N 0 -6.696 1.424 -1.358
36 H11 H H11 N N N 0 7.066 1.023 0.336
37 C20 C C20 N N N 0 -5.874 3.062 1.461
38 H12 H H12 N N N 0 6.697 1.423 -1.358
39 N4 N N4 N N N 0 6.206 2.916 0.036
40 C19 C C19 N N N 0 -7.421 3.67 -0.3
41 H13 H H13 N N N 0 -4.933 2.552 1.668
42 H14 H H14 N N N 0 -5.775 4.12 1.704
43 H15 H H15 N N N 0 -6.666 2.621 2.066
44 H16 H H16 N N N 0 -8.27 3.251 0.241
45 H17 H H17 N N N 0 -7.29 4.715 -0.019
46 H18 H H18 N N N 0 -7.605 3.602 -1.372
47 C21 C C21 N N N 0 5.874 3.062 1.46
48 C22 C C22 N N N 0 7.421 3.669 -0.301
49 H19 H H19 N N N 0 6.667 2.622 2.065
50 H20 H H20 N N N 0 5.776 4.12 1.703
51 H21 H H21 N N N 0 4.933 2.553 1.668
52 H22 H H22 N N N 0 7.605 3.601 -1.373
53 H23 H H23 N N N 0 7.291 4.714 -0.02
54 H24 H H24 N N N 0 8.27 3.251 0.241