Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : MCD

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 97


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C8 C C8 N Y N 0 -2.382 1.392 -8.07
2 N9 N N9 N Y N 0 -2.282 0.128 -8.571
3 C4 C C4 N Y N 0 -3.216 0.006 -9.569
4 C5 C C5 N Y N 0 -3.879 1.243 -9.632
5 N7 N N7 N Y N 0 -3.319 2.044 -8.694
6 N3 N N3 N Y N 0 -3.586 -0.968 -10.393
7 C2 C C2 N Y N 0 -4.553 -0.777 -11.266
8 N1 N N1 N Y N 0 -5.201 0.368 -11.366
9 C6 C C6 N Y N 0 -4.904 1.398 -10.58
10 N6 N N6 N N N 0 -5.588 2.596 -10.694
11 C1' C C1' R N N 0 -1.344 -0.906 -8.13
12 C2' C C2' R N N 0 0.015 -0.763 -8.859
13 O2' O O2' N N N 0 -0.001 -1.45 -10.112
14 C3' C C3' S N N 0 0.991 -1.448 -7.866
15 O3' O O3' N N N 0 1.245 -2.796 -8.265
16 C4' C C4' R N N 0 0.242 -1.408 -6.52
17 O4' O O4' N N N 0 -1.002 -0.723 -6.739
18 C5' C C5' N N N 0 1.076 -0.652 -5.483
19 O5' O O5' N N N 0 0.371 -0.614 -4.241
20 P1 P P1 S N N 0 1.301 0.191 -3.203
21 O11 O O11 N N N 0 1.54 1.559 -3.713
22 O12 O O12 N N N 0 2.709 -0.573 -3.038
23 O6 O O6 N N N 0 0.565 0.272 -1.773
24 P2 P P2 R N N 0 1.546 1.086 -0.79
25 O21 O O21 N N N 0 1.781 2.441 -1.338
26 O22 O O22 N N N 0 2.949 0.307 -0.666
27 O7 O O7 N N N 0 0.868 1.206 0.665
28 CP7 C CP7 R N N 0 2.173 2.864 3.773
29 CPB C CPB N N N 0 1.782 1.934 1.487
30 CPA C CPA N N N 0 1.195 2.085 2.892
31 CP9 C CP9 N N N 0 0.958 0.699 3.497
32 CP8 C CP8 N N N 0 -0.132 2.84 2.812
33 OP3 O OP3 N N N 0 2.485 4.112 3.15
34 CP6 C CP6 N N N 0 1.545 3.118 5.119
35 OP2 O OP2 N N N 0 1.144 4.227 5.402
36 NP2 N NP2 N N N 0 1.429 2.112 6.009
37 CP5 C CP5 N N N 0 0.8 2.354 7.31
38 CP4 C CP4 N N N 0 0.795 1.058 8.122
39 CP3 C CP3 N N N 0 0.148 1.307 9.461
40 OP1 O OP1 N N N 0 -0.266 2.412 9.737
41 NP1 N NP1 N N N 0 0.032 0.301 10.35
42 CP2 C CP2 N N N 0 -0.596 0.543 11.651
43 CP1 C CP1 N N N 0 -0.601 -0.752 12.464
44 P3 P P3 N N N 0 2.834 -2.925 -8.484
45 O31 O O31 N N N 0 3.534 -2.611 -7.218
46 O32 O O32 N N N 0 3.194 -4.428 -8.937
47 O33 O O33 N N N 0 3.304 -1.893 -9.627
48 CPS C CPS N N N 0 -1.258 -0.499 13.823
49 CS1 C CS1 N N N 0 -1.263 -1.776 14.624
50 OS1 O OS1 N N N 0 -0.79 -2.784 14.156
51 OS4 O OS4 N N N 0 -2.335 -4.037 15.465
52 CS2 C CS2 S N N 0 -1.858 -1.795 16.008
53 CS3 C CS3 N N N 0 -0.774 -1.457 17.034
54 CS4 C CS4 N N N 0 -2.414 -3.165 16.297
55 OS5 O OS5 N N N 0 -2.996 -3.417 17.48
56 H8 H H8 N N N 0 -1.773 1.793 -7.273
57 H2 H H2 N N N 0 -4.827 -1.588 -11.924
58 HN61 H 1HN6 N N N 0 -6.294 2.69 -11.352
59 HN62 H 2HN6 N N N 0 -5.362 3.34 -10.115
60 H1' H H1' N N N 0 -1.764 -1.899 -8.294
61 H2' H H2' N N N 0 0.273 0.286 -8.998
62 HO2' H 'HO2 N N N 0 -0.69 -1.036 -10.648
63 H3' H H3' N N N 0 1.924 -0.888 -7.8
64 H4' H H4' N N N 0 0.05 -2.423 -6.172
65 H5'1 H 1H5' N N N 0 1.253 0.365 -5.832
66 H5'2 H 2H5' N N N 0 2.03 -1.16 -5.344
67 H12 H H12 N N N 0 2.509 -1.458 -2.704
68 H22 H H22 N N N 0 2.751 -0.568 -0.306
69 HPB1 H 1HPB N N N 0 1.951 2.921 1.057
70 HPB2 H 2HPB N N N 0 2.728 1.396 1.544
71 HP7 H HP7 N N N 0 3.087 2.285 3.902
72 HP91 H 1HP9 N N N 0 1.916 0.212 3.675
73 HP92 H 2HP9 N N N 0 0.421 0.801 4.44
74 HP93 H 3HP9 N N N 0 0.367 0.098 2.805
75 HP81 H 1HP8 N N N 0 0.036 3.827 2.382
76 HP82 H 2HP8 N N N 0 -0.829 2.285 2.185
77 HP83 H 3HP8 N N N 0 -0.55 2.947 3.813
78 HOP3 H 3HOP N N N 0 1.651 4.593 3.054
79 HNP2 H 2HNP N N N 0 1.761 1.228 5.788
80 HP51 H 1HP5 N N N 0 -0.224 2.694 7.16
81 HP52 H 2HP5 N N N 0 1.361 3.118 7.848
82 HP41 H 1HP4 N N N 0 1.82 0.719 8.272
83 HP42 H 2HP4 N N N 0 0.234 0.294 7.584
84 HNP1 H 1HNP N N N 0 0.364 -0.582 10.129
85 HP21 H 1HP2 N N N 0 -1.621 0.883 11.502
86 HP22 H 2HP2 N N N 0 -0.035 1.307 12.19
87 HP11 H 1HP1 N N N 0 0.423 -1.091 12.614
88 HP12 H 2HP1 N N N 0 -1.162 -1.516 11.926
89 H32 H H32 N N N 0 4.153 -4.462 -9.057
90 H33 H H33 N N N 0 2.826 -2.132 -10.433
91 HPS1 H 1HPS N N N 0 -2.283 -0.16 13.674
92 HPS2 H 2HPS N N N 0 -0.696 0.264 14.361
93 HS2 H HS2 N N N 0 -2.658 -1.057 16.07
94 HS31 H 1HS3 N N N 0 0.026 -2.194 16.972
95 HS32 H 2HS3 N N N 0 -0.372 -0.466 16.824
96 HS33 H 3HS3 N N N 0 -1.204 -1.47 18.035
97 HOS5 H 5HOS N N N 0 -3.353 -4.296 17.666