Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

PDBeChem : Atoms of Molecule

 Molecule : NDP

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 78


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 PA P AP S N N 0 -1.275 0.043 -0.038
2 O1A O AO1 N N N 0 -1.71 -1.293 -0.5
3 O2A O AO2 N N N 0 -2.565 0.915 0.371
4 O5B O AO5* N N N 0 -0.479 0.787 -1.223
5 C5B C AC5* N N N 0 -1.385 0.901 -2.322
6 C4B C AC4* R N N 0 -0.687 1.603 -3.489
7 O4B O AO4* N N N 0 0.439 0.824 -3.924
8 C3B C AC3* R N N 0 -1.654 1.723 -4.682
9 O3B O AO3* N N N 0 -1.863 3.094 -5.029
10 C2B C AC2* R N N 0 -0.927 0.977 -5.832
11 O2B O AO2* N N N 0 -1.073 1.68 -7.068
12 C1B C AC1* R N N 0 0.546 1.001 -5.353
13 N9A N AN9 N Y N 0 1.304 -0.099 -5.954
14 C8A C AC8 N Y N 0 1.388 -1.374 -5.479
15 N7A N AN7 N Y N 0 2.145 -2.09 -6.259
16 C5A C AC5 N Y N 0 2.594 -1.322 -7.28
17 C6A C AC6 N Y N 0 3.422 -1.544 -8.394
18 N6A N AN6 N N N 0 3.976 -2.791 -8.627
19 N1A N AN1 N Y N 0 3.659 -0.53 -9.219
20 C2A C AC2 N Y N 0 3.134 0.662 -9.005
21 N3A N AN3 N Y N 0 2.354 0.916 -7.976
22 C4A C AC4 N Y N 0 2.056 -0.037 -7.1
23 O3 O O3 N N N 0 -0.309 -0.118 1.238
24 PN P NP S N N 0 -1.165 -0.865 2.378
25 O1N O NO1 N N N 0 -2.352 -0.049 2.718
26 O2N O NO2 N N N 0 -1.64 -2.304 1.835
27 O5D O NO5* N N N 0 -0.255 -1.061 3.692
28 C5D C NC5* N N N 0 -1.066 -1.726 4.661
29 C4D C NC4* R N N 0 -0.257 -1.944 5.941
30 O4D O NO4* N N N 0 0.15 -0.676 6.5
31 C3D C NC3* S N N 0 -1.136 -2.592 7.033
32 O3D O NO3* N N N 0 -0.916 -4.003 7.081
33 C2D C NC2* R N N 0 -0.661 -1.924 8.345
34 O2D O NO2* N N N 0 -0.136 -2.903 9.244
35 C1D C NC1* R N N 0 0.446 -0.949 7.887
36 N1N N NN1 N N N 0 0.394 0.286 8.672
37 C2N C NC2 N N N 0 1.485 0.682 9.394
38 C3N C NC3 N N N 0 1.592 1.952 9.826
39 C7N C NC7 N N N 0 2.727 2.334 10.58
40 O7N O NO7 N N N 0 3.594 1.517 10.831
41 N7N N NN7 N N N 0 2.848 3.602 11.019
42 C4N C NC4 N N N 0 0.528 2.97 9.53
43 C5N C NC5 N N N 0 -0.737 2.307 9.075
44 C6N C NC6 N N N 0 -0.762 1.053 8.683
45 P2B P AP2* N N N 0 -1.639 0.622 -8.141
46 O1X O AOP1 N N N 0 -2.944 0.099 -7.677
47 O2X O AOP2 N N N 0 -1.829 1.351 -9.564
48 O3X O AOP3 N N N 0 -0.597 -0.594 -8.296
49 H51A H AH51 N N N 0 -1.703 -0.093 -2.635
50 HOA2 H 2HOA N N N 0 -2.238 1.777 0.665
51 H52A H AH52 N N N 0 -2.256 1.481 -2.017
52 H4B H AH4* N N N 0 -0.355 2.594 -3.179
53 H3B H AH3* N N N 0 -2.604 1.239 -4.454
54 HO3A H AHO3 N N N 0 -2.317 3.505 -4.281
55 H2B H AH2* N N N 0 -1.29 -0.046 -5.924
56 H1B H AH1* N N N 0 1.011 1.958 -5.588
57 H8A H AH8 N N N 0 0.898 -1.737 -4.588
58 H61A H AH61 N N N 0 4.545 -2.932 -9.399
59 H62A H AH62 N N N 0 3.795 -3.524 -8.018
60 H2A H AH2 N N N 0 3.354 1.459 -9.7
61 H21N H NH21 N N N 0 -0.838 -2.803 1.626
62 H51N H NH51 N N N 0 -1.388 -2.69 4.267
63 H52N H NH52 N N N 0 -1.941 -1.115 4.884
64 H4D H NH4* N N N 0 0.614 -2.566 5.737
65 H3D H NH3* N N N 0 -2.189 -2.377 6.853
66 HO3N H NHO3 N N N 0 -1.489 -4.352 7.777
67 H2D H NH2* N N N 0 -1.48 -1.377 8.813
68 HO2N H NHO2 N N N 0 -0.857 -3.514 9.444
69 H1D H NH1* N N N 0 1.426 -1.417 7.981
70 H2N H NH2 N N N 0 2.266 -0.028 9.619
71 H71N H NH71 N N N 0 3.626 3.864 11.535
72 H72N H NH72 N N N 0 2.159 4.254 10.815
73 H41N H NH41 N N N 0 0.325 3.556 10.426
74 H42N H NH42 N N N 0 0.888 3.634 8.743
75 H5N H NH5 N N N 0 -1.656 2.876 9.075
76 H6N H NH6 N N N 0 -1.695 0.614 8.363
77 HOP2 H 2HOP N N N 0 -2.169 0.684 -10.176
78 HOP3 H 3HOP N N N 0 0.236 -0.211 -8.599