Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : KDM

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 34


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C1 R N N 0 1.449 1.064 -0.746
2 C1 C C10 N N N 0 1.643 1.705 0.604
3 C3 C C2 N N N 0 2.487 -0.045 -0.938
4 C4 C C3 S N N 0 2.27 -1.126 0.125
5 C5 C C4 R N N 0 0.834 -1.649 0.021
6 C6 C C5 R N N 0 -0.14 -0.477 0.176
7 C7 C C6 R N N 0 -1.575 -0.982 0.013
8 C8 C C7 R N N 0 -2.539 0.205 0.044
9 C9 C C9 N N N 0 -3.975 -0.299 -0.119
10 O5 O O4 N N N 0 0.598 -2.606 1.055
11 O1A O O8 N N N 0 1.804 2.9 0.688
12 O1B O O9 N N N 0 1.638 0.949 1.713
13 O4 O O3 N N N 0 3.187 -2.2 -0.092
14 O6 O O5 N N N 0 0.136 0.506 -0.824
15 O7 O O6 N N N 0 -1.701 -1.666 -1.235
16 O8 O O7 N N N 0 -2.414 0.889 1.293
17 O9 O O10 N N N 0 -4.864 0.816 -0.207
18 O2 O O1 N N Y 0 1.609 2.049 -1.769
19 H31 H H21C N N N 0 2.373 -0.482 -1.931
20 H32 H H22C N N N 0 3.489 0.372 -0.836
21 HO2 H H1 N N Y 0 0.983 2.784 -1.709
22 HO1B H H9 N N N 0 1.766 1.405 2.556
23 H4 H H3 N N N 0 2.432 -0.701 1.115
24 H5 H H4 N N N 0 0.687 -2.118 -0.952
25 HO4 H HA N N Y 0 4.117 -1.939 -0.047
26 H6 H H5 N N N 0 -0.02 -0.034 1.165
27 HO5 H HB N N Y 0 1.184 -3.375 1.02
28 H7 H H6 N N N 0 -1.814 -1.666 0.828
29 H8 H H7 N N N 0 -2.3 0.889 -0.77
30 HO7 H HC N N Y 0 -1.502 -1.117 -2.006
31 H91 H H91C N N N 0 -4.049 -0.896 -1.028
32 H92 H H92C N N N 0 -4.244 -0.912 0.742
33 HO8 H HD N N Y 0 -2.612 0.34 2.064
34 HO9 H H10 N N Y 0 -5.794 0.57 -0.311