Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : PDD

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 38


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N N N N 0 0.731 -0.122 1.963
2 N1 N N1 N Y N 0 -3.55 -0.52 -0.45
3 C2 C C2 N Y N 0 -3.594 -0.174 0.821
4 C2A C C2A N N N 0 -4.882 -0.321 1.59
5 C3 C C3 N Y N 0 -2.467 0.323 1.458
6 O3A O O3A N N N 0 -2.517 0.679 2.769
7 C4 C C4 N Y N 0 -1.285 0.453 0.736
8 C4A C C4A N N N 0 -0.037 0.989 1.388
9 C5 C C5 N Y N 0 -1.284 0.082 -0.598
10 C5A C C5A N N N 0 -0.029 0.204 -1.423
11 OP4 O OP4 N N N 0 -0.287 -0.25 -2.753
12 P P P N N N 0 1.089 -0.092 -3.573
13 OP1 O OP1 N N N 0 2.141 -0.912 -2.933
14 OP2 O OP2 N N N 0 0.87 -0.589 -5.089
15 OP3 O OP3 N N N 0 1.539 1.452 -3.575
16 C6 C C6 N Y N 0 -2.446 -0.41 -1.162
17 CA C CA R N N 0 1.927 0.465 2.58
18 CB C CB N N N 0 3.058 0.52 1.55
19 C C C N N N 0 2.356 -0.379 3.752
20 O O O N N N 0 1.729 -1.37 4.043
21 OXT O OXT N N Y 0 3.434 -0.032 4.471
22 H H HN N N N 0 1.051 -0.685 1.189
23 H2A1 H 1H2A N N N 0 -5.462 0.597 1.506
24 H2A2 H 2H2A N N N 0 -5.457 -1.152 1.181
25 H2A3 H 3H2A N N N 0 -4.658 -0.515 2.639
26 HO3 H HO3 N N N 0 -2.77 1.612 2.795
27 H4A1 H 1H4A N N N 0 -0.311 1.688 2.179
28 H4A2 H 2H4A N N N 0 0.569 1.504 0.644
29 H5A1 H 1H5A N N N 0 0.287 1.246 -1.45
30 H5A2 H 2H5A N N N 0 0.758 -0.403 -0.977
31 HOP2 H 2HOP N N N 0 1.716 -0.479 -5.544
32 HOP3 H 3HOP N N N 0 0.827 1.95 -4.0
33 H6 H H6 N N N 0 -2.451 -0.704 -2.201
34 HA H HA N N N 0 1.7 1.474 2.924
35 HB1 H 1HB N N N 0 3.285 -0.488 1.206
36 HB2 H 2HB N N N 0 2.747 1.132 0.703
37 HB3 H 3HB N N N 0 3.945 0.957 2.008
38 HXT H HXT N N Y 0 3.709 -0.574 5.223