Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : YLP

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 66


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C N N N 0 2.835 3.188 0.301
2 N N N N N N 0 5.227 3.601 0.18
3 O O O N N N 0 2.816 3.952 1.236
4 N1 N N1 N Y N 0 -6.618 -4.633 -0.174
5 C2 C C2 N Y N 0 -6.929 -3.645 -0.993
6 N3 N N3 N Y N 0 -6.257 -2.514 -1.023
7 C4 C C4 N Y N 0 -5.22 -2.321 -0.214
8 C5 C C5 N Y N 0 -4.849 -3.342 0.676
9 C6 C C6 N Y N 0 -5.598 -4.531 0.671
10 N6 N N6 N N N 0 -5.28 -5.572 1.526
11 N7 N N7 N Y N 0 -3.778 -2.894 1.374
12 C8 C C8 N Y N 0 -3.475 -1.692 0.978
13 N9 N N9 N Y N 0 -4.336 -1.293 -0.001
14 CA C CA S N N 0 4.152 2.692 -0.24
15 CB C CB N N N 0 4.43 1.288 0.302
16 C1' C C1' R N N 0 -4.319 -0.005 -0.698
17 C2' C C2' R N N 0 -5.297 0.992 -0.026
18 O2' O O2' N N N 0 -6.619 0.839 -0.546
19 C3' C C3' S N N 0 -4.698 2.36 -0.434
20 O3' O O3' N N N 0 -5.386 2.889 -1.569
21 C4' C C4' R N N 0 -3.234 2.038 -0.793
22 O4' O O4' N N N 0 -3.033 0.635 -0.554
23 C5' C C5' N N N 0 -2.29 2.856 0.091
24 O5' O O5' N N N 0 -0.94 2.64 -0.326
25 OAD O OAD N N N 0 9.344 -2.758 -1.171
26 OAF O OAF N N N 0 0.244 4.937 0.155
27 OAI O OAI N N N 0 0.296 3.054 1.835
28 CAM C CAM N N N 0 5.98 -0.668 0.199
29 CAN C CAN N N N 0 5.702 0.735 -0.343
30 CAO C CAO N N N 0 7.253 -1.222 -0.445
31 NAW N NAW N N N 0 7.519 -2.565 0.074
32 OAY O OAY N N N 0 1.684 2.776 -0.254
33 CBA C CBA N N N 0 8.596 -3.253 -0.355
34 CBF C CBF N N N 0 10.142 -5.188 -0.466
35 CBK C CBK N N N 0 8.869 -4.635 0.179
36 PBN P PBN N N N 0 0.321 3.346 0.384
37 HN H HN N N N 0 5.101 4.519 -0.219
38 HNA H HNA N N N 0 5.288 3.649 1.186
39 H2 H H2 N N N 0 -7.766 -3.77 -1.664
40 HN6 H HN6 N N N 0 -5.804 -6.388 1.513
41 HN6A H HN6A N N N 0 -4.532 -5.485 2.139
42 H8 H H8 N N N 0 -2.662 -1.097 1.368
43 HA H HA N N N 0 4.108 2.659 -1.329
44 HB H HB N N N 0 4.562 1.336 1.383
45 HBA H HBA N N N 0 3.59 0.635 0.067
46 H1' H H1' N N N 0 -4.569 -0.137 -1.751
47 H2' H H2' N N N 0 -5.291 0.872 1.058
48 HO2' H HO2' N N N 0 -7.267 1.441 -0.156
49 H3' H H3' N N N 0 -4.743 3.06 0.4
50 HO3' H HO3' N N N 0 -6.326 3.055 -1.416
51 H4' H H4' N N N 0 -3.051 2.265 -1.843
52 H5' H H5' N N N 0 -2.533 3.915 0.0
53 H5'A H H5'A N N N 0 -2.403 2.545 1.129
54 HAM H HAM N N N 0 6.112 -0.621 1.281
55 HAMA H HAMA N N N 0 5.14 -1.322 -0.036
56 HAN H HAN N N N 0 5.57 0.688 -1.424
57 HANA H HANA N N N 0 6.542 1.388 -0.107
58 HAO H HAO N N N 0 7.121 -1.269 -1.526
59 HAOA H HAOA N N N 0 8.093 -0.568 -0.21
60 HNAW H HNAW N N N 0 6.92 -2.96 0.726
61 HBF H HBF N N N 0 10.01 -5.236 -1.547
62 HBFA H HBFA N N N 0 10.982 -4.535 -0.231
63 HBFB H HBFB N N N 0 10.34 -6.188 -0.08
64 HBK H HBK N N N 0 9.001 -4.587 1.26
65 HBKA H HBKA N N N 0 8.029 -5.288 -0.057
66 HAF H HAF N N N 0 0.256 5.202 -0.775