Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : 8ND

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 116


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C1 S N N 0 0.498 3.966 0.926
2 C1 C C2 N N N 0 0.31 4.687 -0.411
3 C3 C C3 N N N 0 -0.867 3.736 1.577
4 C10 C C4 N N N 0 2.49 2.672 0.735
5 C11 C C5 N N N 0 3.234 1.381 0.509
6 C12 C C6 N N N 0 4.74 1.638 0.601
7 C13 C C7 N N N 0 5.496 0.328 0.371
8 C14 C C8 N N N 0 7.001 0.584 0.464
9 C15 C C9 N N N 0 7.757 -0.726 0.234
10 C16 C C10 N N N 0 9.263 -0.469 0.327
11 C17 C C11 N N N 0 10.018 -1.78 0.097
12 C18 C C12 N N N 0 11.524 -1.523 0.19
13 C19 C C13 N N N 0 12.28 -2.833 -0.04
14 C20 C C14 N N N 0 13.785 -2.576 0.052
15 C21 C C15 N N N 0 14.541 -3.887 -0.177
16 C22 C C16 N N N 0 16.046 -3.63 -0.085
17 C23 C C17 N N N 0 16.802 -4.94 -0.314
18 C24 C C18 N N N 0 18.308 -4.684 -0.222
19 C25 C C19 N N N 0 19.064 -5.994 -0.451
20 C30 C C20 N N N 0 -2.941 2.661 1.104
21 C31 C C21 N N N 0 -3.847 1.823 0.24
22 C32 C C22 N N N 0 -5.201 1.656 0.933
23 C33 C C23 N N N 0 -6.122 0.805 0.055
24 C34 C C24 N N N 0 -7.476 0.638 0.748
25 C35 C C25 N N N 0 -8.396 -0.212 -0.13
26 C36 C C26 N N N 0 -9.75 -0.38 0.563
27 C37 C C27 N N N 0 -10.67 -1.23 -0.315
28 C38 C C28 N N N 0 -12.024 -1.398 0.378
29 C39 C C29 N N N 0 -12.945 -2.248 -0.5
30 C40 C C30 N N N 0 -14.298 -2.415 0.193
31 C41 C C31 N N N 0 -15.219 -3.266 -0.685
32 C42 C C32 N N N 0 -16.573 -3.433 0.008
33 C43 C C33 N N N 0 -17.493 -4.284 -0.869
34 C44 C C34 N N N 0 -18.847 -4.451 -0.176
35 C45 C C35 N N N 0 -19.767 -5.301 -1.054
36 O4 O O1 N N N 0 3.101 3.692 0.948
37 O5 O O2 N N N 0 -3.301 2.999 2.207
38 O2 O O3 N N N 0 1.148 2.688 0.699
39 O3 O O4 N N N 0 -1.733 3.03 0.649
40 O3P O O5 N N N 0 1.589 5.003 -0.965
41 H1 H H1 N N N 0 1.116 4.577 1.584
42 H2 H H2 N N N 0 -0.234 4.04 -1.099
43 H3 H H3 N N N 0 -0.254 5.605 -0.252
44 H4 H H4 N N N 0 -0.742 3.141 2.482
45 H5 H H5 N N N 0 -1.314 4.696 1.833
46 H6 H H6 N N N 0 2.942 0.656 1.268
47 H7 H H7 N N N 0 2.992 0.99 -0.48
48 H8 H H8 N N N 0 5.032 2.364 -0.158
49 H9 H H9 N N N 0 4.982 2.029 1.589
50 H10 H H10 N N N 0 5.204 -0.398 1.131
51 H11 H H11 N N N 0 5.254 -0.063 -0.617
52 H12 H H12 N N N 0 7.293 1.31 -0.295
53 H13 H H13 N N N 0 7.243 0.975 1.452
54 H14 H H14 N N N 0 7.465 -1.452 0.993
55 H15 H H15 N N N 0 7.515 -1.117 -0.754
56 H16 H H16 N N N 0 9.555 0.256 -0.433
57 H17 H H17 N N N 0 9.505 -0.079 1.315
58 H18 H H18 N N N 0 9.726 -2.505 0.856
59 H19 H H19 N N N 0 9.776 -2.17 -0.891
60 H20 H H20 N N N 0 11.816 -0.797 -0.57
61 H21 H H21 N N N 0 11.766 -1.132 1.178
62 H22 H H22 N N N 0 11.988 -3.559 0.719
63 H23 H H23 N N N 0 12.038 -3.224 -1.028
64 H24 H H24 N N N 0 14.077 -1.851 -0.707
65 H25 H H25 N N N 0 14.027 -2.186 1.041
66 H26 H H26 N N N 0 14.249 -4.612 0.582
67 H27 H H27 N N N 0 14.299 -4.278 -1.166
68 H28 H H28 N N N 0 16.338 -2.905 -0.844
69 H29 H H29 N N N 0 16.288 -3.239 0.904
70 H30 H H30 N N N 0 16.51 -5.666 0.445
71 H31 H H31 N N N 0 16.56 -5.331 -1.303
72 H35 H H35 N N N 0 20.136 -5.811 -0.386
73 H32 H H32 N N N 0 18.6 -3.958 -0.981
74 H33 H H33 N N N 0 18.55 -4.293 0.766
75 H34 H H34 N N N 0 18.822 -6.385 -1.44
76 H36 H H36 N N N 0 18.772 -6.72 0.308
77 H37 H H37 N N N 0 -3.99 2.316 -0.722
78 H38 H H38 N N N 0 -3.396 0.843 0.082
79 H39 H H39 N N N 0 -5.059 1.163 1.894
80 H40 H H40 N N N 0 -5.652 2.635 1.09
81 H41 H H41 N N N 0 -6.264 1.298 -0.907
82 H42 H H42 N N N 0 -5.67 -0.174 -0.103
83 H43 H H43 N N N 0 -7.333 0.145 1.709
84 H44 H H44 N N N 0 -7.927 1.618 0.905
85 H45 H H45 N N N 0 -8.538 0.281 -1.092
86 H46 H H46 N N N 0 -7.945 -1.192 -0.287
87 H47 H H47 N N N 0 -9.607 -0.873 1.524
88 H48 H H48 N N N 0 -10.201 0.6 0.72
89 H49 H H49 N N N 0 -10.813 -0.737 -1.276
90 H50 H H50 N N N 0 -10.219 -2.21 -0.472
91 H51 H H51 N N N 0 -11.882 -1.891 1.339
92 H52 H H52 N N N 0 -12.475 -0.418 0.535
93 H53 H H53 N N N 0 -13.087 -1.755 -1.461
94 H54 H H54 N N N 0 -12.493 -3.228 -0.657
95 H55 H H55 N N N 0 -14.156 -2.908 1.155
96 H56 H H56 N N N 0 -14.75 -1.436 0.351
97 H57 H H57 N N N 0 -15.361 -2.773 -1.646
98 H58 H H58 N N N 0 -14.768 -4.245 -0.842
99 H59 H H59 N N N 0 -16.43 -3.926 0.97
100 H60 H H60 N N N 0 -17.024 -2.454 0.166
101 H61 H H61 N N N 0 -17.636 -3.79 -1.831
102 H62 H H62 N N N 0 -17.042 -5.263 -1.027
103 H63 H H63 N N N 0 -18.704 -4.944 0.785
104 H64 H H64 N N N 0 -19.298 -3.471 -0.019
105 H65 H H65 N N N 0 -19.91 -4.808 -2.016
106 H66 H H66 N N N 0 -19.316 -6.281 -1.212
107 H67 H H67 N N N 0 -20.732 -5.42 -0.561
108 C4 C C36 N N N 0 1.527 5.778 -2.164
109 C5 C C37 N N N 0 2.936 5.952 -2.733
110 N1 N N1 N N N 0 3.462 4.645 -3.148
111 H68 H H68 N N N 0 0.901 5.267 -2.896
112 H69 H H69 N N N 0 1.101 6.757 -1.942
113 H70 H H70 N N N 0 2.901 6.62 -3.593
114 H71 H H71 N N N 0 3.586 6.379 -1.968
115 H72 H H72 N N N 0 4.418 4.722 -3.46
116 H73 H H73 N N N 0 3.378 3.969 -2.404