Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

PDBeChem : Atoms of Molecule

 Molecule : 5YM

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 62


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C13 C C1 N N N 0 -0.742 -1.259 0.549
2 C12 C C2 N N N 0 0.166 -2.428 0.159
3 C11 C C3 N N N 0 1.599 -2.132 0.607
4 C10 C C4 N N N 0 2.493 -3.283 0.223
5 C14 C C5 N N N 0 -2.174 -1.555 0.101
6 C15 C C6 N N N 0 -3.082 -0.387 0.491
7 C21 C C7 N N N 0 -9.185 0.807 -0.198
8 C16 C C8 N N N 0 -4.515 -0.682 0.043
9 C17 C C9 N N N 0 -5.423 0.486 0.434
10 C18 C C10 N N N 0 -6.834 0.195 -0.008
11 C22 C C11 N N N 0 -10.092 1.975 0.193
12 C01 C C12 N N N 0 11.23 3.295 0.405
13 C02 C C13 N N N 0 9.783 3.136 -0.065
14 C03 C C14 N N N 0 9.318 1.701 0.191
15 C04 C C15 N N N 0 7.871 1.542 -0.28
16 C05 C C16 N N N 0 7.407 0.106 -0.024
17 C06 C C17 N N N 0 5.959 -0.053 -0.494
18 C07 C C18 N N N 0 5.495 -1.488 -0.239
19 C08 C C19 N N N 0 4.048 -1.647 -0.709
20 C09 C C20 N N N 0 3.59 -3.06 -0.457
21 N20 N N1 N N N 0 -7.813 1.089 0.231
22 O19 O O1 N N N 0 -7.089 -0.845 -0.578
23 O23 O O2 N N N 0 -9.703 3.143 -0.532
24 H1 H H1 N N N 0 -0.719 -1.128 1.631
25 H2 H H2 N N N 0 -0.39 -0.348 0.065
26 H3 H H3 N N N 0 -0.186 -3.338 0.643
27 H4 H H4 N N N 0 0.144 -2.559 -0.923
28 H5 H H5 N N N 0 1.95 -1.221 0.123
29 H6 H H6 N N N 0 1.621 -2.0 1.689
30 H7 H H7 N N N 0 2.229 -4.29 0.508
31 H8 H H8 N N N 0 -2.197 -1.687 -0.981
32 H9 H H9 N N N 0 -2.526 -2.466 0.586
33 H10 H H10 N N N 0 -3.06 -0.255 1.573
34 H11 H H11 N N N 0 -2.731 0.524 0.007
35 H12 H H12 N N N 0 -9.536 -0.104 0.287
36 H13 H H13 N N N 0 -9.207 0.675 -1.28
37 H14 H H14 N N N 0 -4.537 -0.814 -1.038
38 H15 H H15 N N N 0 -4.867 -1.593 0.528
39 H16 H H16 N N N 0 -5.4 0.618 1.515
40 H17 H H17 N N N 0 -5.071 1.397 -0.051
41 H18 H H18 N N N 0 -11.127 1.727 -0.046
42 H19 H H19 N N N 0 -10.002 2.164 1.262
43 H20 H H20 N N N 0 11.869 2.603 -0.144
44 H21 H H21 N N N 0 11.561 4.317 0.223
45 H22 H H22 N N N 0 11.292 3.077 1.472
46 H23 H H23 N N N 0 9.144 3.828 0.485
47 H24 H H24 N N N 0 9.721 3.353 -1.131
48 H25 H H25 N N N 0 9.957 1.009 -0.359
49 H26 H H26 N N N 0 9.38 1.483 1.257
50 H27 H H27 N N N 0 7.233 2.233 0.27
51 H28 H H28 N N N 0 7.81 1.759 -1.346
52 H29 H H29 N N N 0 8.045 -0.585 -0.573
53 H30 H H30 N N N 0 7.468 -0.111 1.042
54 H31 H H31 N N N 0 5.321 0.639 0.055
55 H32 H H32 N N N 0 5.898 0.165 -1.561
56 H33 H H33 N N N 0 6.133 -2.18 -0.788
57 H34 H H34 N N N 0 5.556 -1.705 0.827
58 H35 H H35 N N N 0 3.409 -0.955 -0.16
59 H36 H H36 N N N 0 3.986 -1.429 -1.775
60 H37 H H37 N N N 0 4.167 -3.891 -0.838
61 H38 H H38 N N N 0 -7.609 1.921 0.688
62 H39 H H39 N N N 0 -10.237 3.925 -0.334