Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : PPD

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 41


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 3.866 0.664 0.325
2 C2 C C2 N Y N 0 3.811 0.436 -0.971
3 C2A C C2A N N N 0 5.015 0.723 -1.831
4 C3 C C3 N Y N 0 2.654 -0.058 -1.554
5 O3 O O3 N N N 0 2.601 -0.291 -2.892
6 C4 C C4 N Y N 0 1.551 -0.324 -0.748
7 C4A C C4A N N N 0 0.276 -0.868 -1.338
8 C5 C C5 N Y N 0 1.653 -0.07 0.609
9 C6 C C6 N Y N 0 2.838 0.429 1.116
10 C5A C C5A N N N 0 0.485 -0.335 1.524
11 O4P O O4P N N N 0 0.842 0.005 2.865
12 P P P N N N 0 -0.444 -0.3 3.782
13 O1P O O1P N N N 0 -0.792 -1.735 3.68
14 O2P O O2P N N N 0 -0.11 0.063 5.314
15 O3P O O3P N N N 0 -1.687 0.589 3.277
16 N N N N N N 0 -0.593 0.245 -1.737
17 CA C CA S N N 0 -1.811 -0.351 -2.301
18 CB C CB N N N 0 -2.998 0.581 -2.053
19 CG C CG N N N 0 -3.177 0.782 -0.57
20 OD1 O OD1 N N N 0 -2.432 0.235 0.207
21 OD2 O OD2 N N N 0 -4.165 1.568 -0.113
22 C C C N N N 0 -1.632 -0.551 -3.784
23 O O O N N N 0 -2.202 -1.457 -4.344
24 OXT O OXT N N N 0 -0.839 0.276 -4.482
25 H2A1 H 1H2A N N N 0 5.643 -0.165 -1.885
26 H2A2 H 2H2A N N N 0 4.688 0.998 -2.834
27 H2A3 H 3H2A N N N 0 5.584 1.545 -1.397
28 HO3 H HO3 N N N 0 2.282 0.523 -3.305
29 H4A1 H 1H4A N N N 0 0.511 -1.477 -2.212
30 H4A2 H 2H4A N N N 0 -0.234 -1.481 -0.596
31 H6 H H6 N N N 0 2.923 0.628 2.174
32 H5A1 H 1H5A N N N 0 -0.366 0.267 1.21
33 H5A2 H 2H5A N N N 0 0.219 -1.391 1.477
34 HOP2 H 2HOP N N N 0 -0.905 -0.134 5.828
35 HOP3 H 3HOP N N N 0 -1.419 1.515 3.36
36 HN H HN N N N 0 -0.867 0.717 -0.888
37 HA H HA N N N 0 -1.999 -1.313 -1.825
38 HOD H HOD N N N 0 -4.28 1.697 0.837
39 HXT H HXT N N N 0 -0.724 0.147 -5.434
40 HB2 H 2HB N N N 0 -3.902 0.139 -2.471
41 HB1 H 1HB N N N 0 -2.81 1.543 -2.529