Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : YKL

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 123


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -11.247 -1.973 1.075
2 C3 C C2 N Y N 0 -9.426 -0.446 1.148
3 C6 C C3 N N N 0 -9.442 2.502 3.238
4 C7 C C4 N Y N 0 -8.032 1.266 1.587
5 C8 C C5 N Y N 0 -8.159 0.109 0.843
6 C15 C C6 N N N 0 -3.605 1.588 -1.582
7 C17 C C7 N Y N 0 -2.312 2.317 -1.604
8 C18 C C8 N Y N 0 -2.213 3.627 -2.123
9 C19 C C9 N Y N 0 -0.977 4.165 -2.339
10 C23 C C10 S N N 0 2.931 3.399 -0.705
11 C24 C C11 N N N 0 3.412 2.412 -1.759
12 C27 C C12 N Y N 0 5.374 3.625 -0.085
13 C31 C C13 N Y N 0 4.778 5.735 1.595
14 C32 C C14 N Y N 0 3.774 5.088 0.907
15 C33 C C15 N Y N 0 4.065 4.03 0.05
16 C34 C C16 N N N 0 1.876 2.763 0.187
17 C36 C C17 N N N 0 0.685 0.737 0.54
18 C37 C C18 S N N 0 1.643 -0.342 1.002
19 C39 C C19 N N N 0 3.001 0.203 1.495
20 C40 C C20 N N N 0 3.976 -0.929 1.104
21 O41 O O1 N N N 0 3.403 -1.614 -0.012
22 O2 O O2 N N N 0 -9.944 -1.59 0.629
23 N4 N N1 N Y N 0 -10.006 0.333 2.024
24 N5 N N2 N Y N 0 -9.155 1.407 2.308
25 C9 C C21 N N N 0 -7.164 -0.442 -0.093
26 O10 O O3 N N N 0 -7.399 -1.475 -0.69
27 N11 N N3 N N N 0 -5.994 0.198 -0.286
28 S12 S S1 S N N 0 -4.833 -0.479 -1.24
29 O13 O O4 N N N 0 -5.265 -0.474 -2.593
30 N14 N N4 N N N 0 -3.567 0.324 -1.152
31 O16 O O5 N N N 0 -4.637 2.109 -1.979
32 C20 C C22 N Y N 0 0.174 3.477 -1.936
33 O21 O O6 N N N 0 1.345 3.969 -2.385
34 C22 C C23 N N N 0 2.232 4.567 -1.451
35 C25 C C24 N N N 0 4.589 1.58 -1.264
36 C26 C C25 N N N 0 5.782 2.489 -0.984
37 C28 C C26 N Y N 0 6.383 4.275 0.613
38 C29 C C27 N Y N 0 6.095 5.336 1.452
39 CL30 CL CL1 N N N 0 7.366 6.151 2.307
40 N35 N N5 N N N 0 1.168 1.651 -0.516
41 C42 C C28 R N N 0 1.994 -1.337 -0.117
42 C44 C C29 S N N 0 1.254 -2.656 -0.041
43 C45 C C30 N N N 0 2.049 -3.618 0.853
44 N46 N N6 N N N 0 3.39 -3.818 0.287
45 C47 C C31 N N N 0 3.354 -4.778 -0.825
46 C48 C C32 N N N 0 4.752 -4.894 -1.438
47 N49 N N7 N N N 0 5.705 -5.327 -0.406
48 C50 C C33 N N N 0 7.046 -5.507 -0.981
49 C51 C C34 N N N 0 8.001 -6.003 0.107
50 O52 O O7 N N N 0 8.001 -5.072 1.193
51 C53 C C35 N N N 0 6.712 -4.877 1.78
52 C54 C C36 S N N 0 5.738 -4.372 0.711
53 C56 C C37 N N N 0 4.339 -4.253 1.321
54 O57 O O8 N N N 0 1.219 -3.22 -1.36
55 C58 C C38 N N N 0 0.615 -2.374 -2.339
56 C59 C C39 N N N 0 -0.147 -2.576 0.483
57 F60 F F1 N N N 0 -0.437 -1.807 1.554
58 C61 C C40 N N N 0 -1.101 -3.277 -0.093
59 C62 C C41 N N N 0 -2.492 -3.327 0.471
60 C63 C C42 S N N 0 -3.194 -1.984 0.324
61 C65 C C43 N N N 0 -3.646 -1.497 1.704
62 C66 C C44 N N N 0 -4.42 -2.125 -0.587
63 C67 C C45 N Y N 0 0.074 2.243 -1.15
64 C68 C C46 N Y N 0 -1.195 1.674 -1.073
65 H1 H H1 N N N 0 -11.231 -2.123 2.154
66 H2 H H2 N N N 0 -11.961 -1.189 0.827
67 H3 H H3 N N N 0 -11.54 -2.901 0.583
68 H4 H H4 N N N 0 -9.937 3.312 2.703
69 H5 H H5 N N N 0 -10.093 2.141 4.035
70 H6 H H6 N N N 0 -8.509 2.867 3.668
71 H7 H H7 N N N 0 -7.183 1.934 1.59
72 H8 H H8 N N N 0 -3.097 4.19 -2.37
73 H9 H H9 N N N 0 -0.891 5.142 -2.794
74 H10 H H10 N N N 0 2.598 1.745 -2.046
75 H11 H H11 N N N 0 3.723 2.968 -2.649
76 H12 H H12 N N N 0 4.534 6.563 2.247
77 H13 H H13 N N N 0 2.749 5.404 1.038
78 H14 H H14 N N N 0 2.297 2.418 1.114
79 H15 H H15 N N N 0 1.115 3.521 0.417
80 H16 H H16 N N N 0 -0.179 0.187 0.178
81 H17 H H17 N N N 0 0.385 1.34 1.395
82 H18 H H18 N N N 0 1.195 -0.884 1.857
83 H19 H H19 N N N 0 3.281 1.121 0.992
84 H20 H H20 N N N 0 2.994 0.339 2.579
85 H21 H H21 N N N 0 4.939 -0.505 0.828
86 H22 H H22 N N N 0 4.093 -1.618 1.938
87 H23 H H23 N N N 0 -5.835 1.057 0.135
88 H26 H H26 N N N 0 1.685 5.178 -0.739
89 H27 H H27 N N N 0 2.986 5.16 -1.962
90 H28 H H28 N N N 0 4.323 1.043 -0.358
91 H29 H H29 N N N 0 4.869 0.859 -2.039
92 H30 H H30 N N N 0 6.165 2.884 -1.923
93 H31 H H31 N N N 0 6.562 1.902 -0.495
94 H32 H H32 N N N 0 7.403 3.945 0.499
95 H33 H H33 N N N 0 1.801 -0.85 -1.078
96 H34 H H34 N N N 0 2.137 -3.196 1.854
97 H35 H H35 N N N 0 1.531 -4.576 0.908
98 H37 H H37 N N N 0 3.038 -5.753 -0.454
99 H38 H H38 N N N 0 2.652 -4.431 -1.583
100 H39 H H39 N N N 0 4.734 -5.625 -2.246
101 H40 H H40 N N N 0 5.057 -3.924 -1.831
102 H42 H H42 N N N 0 7.001 -6.239 -1.787
103 H43 H H43 N N N 0 7.404 -4.555 -1.374
104 H44 H H44 N N N 0 7.672 -6.979 0.464
105 H45 H H45 N N N 0 9.008 -6.086 -0.302
106 H46 H H46 N N N 0 6.349 -5.821 2.185
107 H50 H H50 N N N 0 4.03 -5.221 1.714
108 H47 H H47 N N N 0 6.785 -4.141 2.581
109 H48 H H48 N N N 0 6.067 -3.398 0.349
110 H49 H H49 N N N 0 4.356 -3.521 2.129
111 H51 H H51 N N N 0 -0.36 -2.043 -1.981
112 H52 H H52 N N N 0 1.252 -1.506 -2.513
113 H53 H H53 N N N 0 0.491 -2.926 -3.271
114 H54 H H54 N N N 0 -0.868 -3.87 -0.968
115 H55 H H55 N N N 0 -3.065 -4.087 -0.059
116 H56 H H56 N N N 0 -2.442 -3.593 1.526
117 H57 H H57 N N N 0 -2.504 -1.261 -0.104
118 H58 H H58 N N N 0 -2.777 -1.386 2.352
119 H59 H H59 N N N 0 -4.149 -0.535 1.602
120 H60 H H60 N N N 0 -4.333 -2.223 2.138
121 H61 H H61 N N N 0 -5.261 -2.515 -0.016
122 H62 H H62 N N N 0 -4.19 -2.802 -1.412
123 H63 H H63 N N N 0 -1.377 0.705 -0.634