Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : ODP

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 O1X O AOP1 N N N 0 -5.632 4.022 -0.99
2 P2B P AP2* N N N 0 -5.315 5.479 -0.816
3 O2X O AOP2 N N N 0 -4.467 6.151 -2.018
4 O3X O AOP3 N N N 0 -6.603 6.447 -0.684
5 O2B O AO2* N N N 0 -4.451 5.836 0.509
6 C2B C AC2* R N N 0 -3.173 5.254 0.661
7 C3B C AC3* R N N 0 -3.21 3.739 0.693
8 O3B O AO3* N N N 0 -4.311 3.306 1.492
9 C1B C AC1* R N N 0 -2.563 5.57 2.018
10 N9A N AN9 N Y N 0 -1.88 6.86 2.078
11 C8A C AC8 N Y N 0 -0.577 7.101 1.727
12 N7A N AN7 N Y N 0 -0.243 8.365 1.89
13 C5A C AC5 N Y N 0 -1.379 8.969 2.368
14 C4A C AC4 N Y N 0 -2.409 8.051 2.492
15 N3A N AN3 N Y N 0 -3.657 8.284 2.925
16 C2A C AC2 N Y N 0 -3.809 9.587 3.246
17 N1A N AN1 N Y N 0 -2.902 10.591 3.178
18 C6A C AC6 N Y N 0 -1.661 10.283 2.731
19 N6A N AN6 N N N 0 -0.675 11.28 2.638
20 O4B O AO4* N N N 0 -1.626 4.511 2.293
21 C4B C AC4* R N N 0 -1.912 3.396 1.416
22 C5B C AC5* N N N 0 -0.734 3.217 0.469
23 O5B O AO5* N N N 0 0.425 2.914 1.226
24 PA P AP R N N 0 1.82 2.676 0.441
25 O1A O AO1 N N N 0 2.311 3.834 -0.378
26 O2A O AO2 N N N 0 2.836 2.177 1.596
27 O3 O O3 N N N 0 1.537 1.327 -0.403
28 PN P NP R N N 0 2.519 0.416 -1.307
29 O1N O NO1 N N N 0 3.689 -0.167 -0.569
30 O2N O NO2 N N N 0 2.922 1.391 -2.534
31 O5D O NO5* N N N 0 1.509 -0.668 -1.959
32 C5D C NC5* N N N 0 0.37 -0.232 -2.679
33 C4D C NC4* R N N 0 -0.392 -1.455 -3.173
34 O4D O NO4* N N N 0 -0.84 -2.204 -2.023
35 C1D C NC1* R N N 0 -2.264 -2.051 -1.879
36 C2D C NC2* R N N 0 -2.679 -0.956 -2.854
37 O2D O NO2* N N N 0 -3.998 -1.119 -3.34
38 C3D C NC3* S N N 0 -1.65 -1.105 -3.956
39 O3D O NO3* N N N 0 -1.996 -2.213 -4.787
40 N1N N NN1 N N N 1 -2.751 -1.701 -0.537
41 C2N C NC2 N N N 0 -2.076 -1.016 0.326
42 C3N C NC3 S N N 0 -2.614 -0.693 1.692
43 C7N C NC7 N N N 0 -1.636 -1.093 2.76
44 N7N N NN7 N N N 0 -0.669 -0.147 3.008
45 O7N O NO7 N N N 0 -1.721 -2.164 3.356
46 C4N C NC4 N N N 0 -4.008 -1.188 1.994
47 O99 O O99 N N N 0 -4.577 -0.963 3.06
48 C5N C NC5 N N N 0 -4.687 -1.978 0.953
49 C6N C NC6 N N N 0 -4.045 -2.173 -0.201
50 HOP2 H 2HOP N N N 0 -4.76 6.007 -2.943
51 HOP3 H 3HOP N N N 0 -7.335 6.354 -1.33
52 H2B H AH2* N N N 0 -2.525 5.602 -0.153
53 H3B H AH3* N N N 0 -3.314 3.278 -0.293
54 HO3A H AHO3 N N N 0 -4.783 4.108 1.765
55 H1B H AH1* N N N 0 -3.311 5.601 2.819
56 H8A H AH8 N N N 0 0.076 6.32 1.362
57 H2A H AH2 N N N 0 -4.792 9.869 3.609
58 H62A H AH62 N N N 0 -0.628 11.851 1.815
59 H61A H AH61 N N N 0 0.027 11.347 3.35
60 H4B H AH4* N N N 0 -2.014 2.503 2.04
61 H51A H AH51 N N N 0 -0.554 4.135 -0.098
62 H1D H NH1* N N N 0 -2.734 -3.009 -2.125
63 H52A H AH52 N N N 0 -0.924 2.396 -0.229
64 HOA2 H 2HOA N N N 0 3.235 2.84 2.198
65 H51N H NH51 N N N 0 -0.264 0.363 -2.02
66 H52N H NH52 N N N 0 0.692 0.377 -3.525
67 H4D H NH4* N N N 0 0.284 -2.098 -3.746
68 H2D H NH2* N N N 0 -2.594 0.041 -2.402
69 HO2N H NHO2 N N N 0 -3.928 -1.393 -4.271
70 H3D H NH3* N N N 0 -1.555 -0.224 -4.596
71 HO3N H NHO3 N N N 0 -1.181 -2.483 -5.237
72 H2N H NH2 N N N 0 -1.061 -0.683 0.055
73 H3N H NH3 N N N 0 -2.662 0.404 1.733
74 H72N H NH72 N N N 0 0.03 -0.34 3.719
75 H71N H NH71 N N N 0 -0.625 0.735 2.51
76 H5N H NH5 N N N 0 -5.679 -2.369 1.141
77 H6N H NH6 N N N 0 -4.551 -2.75 -0.971
78 HO1 H HO1 N N N 0 3.615 2.071 -2.391