0.00
4.906
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1
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4.754
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1
1
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1
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3.729
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1
1
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1
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4.962
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1
1
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1
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5.858
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1
1
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4.080
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1
1
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3.036
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1
1
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1
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2.325
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2.873
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1
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1
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5.117
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1
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1
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1
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1
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1
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1
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2
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1
2
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2
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1
2
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2
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2
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2
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2
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5.071
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2
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1
2
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2
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1
2
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4.526
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2
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1
2
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2
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1
2
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4.425
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2
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1
2
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2
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1
2
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5.375
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2
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1
2
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5.037
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2
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1
2
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2
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1
2
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2
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1
2
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2
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1
2
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2
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1
2
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2
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1
2
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1
2
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2
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1
2
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2
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2
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1
2
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2
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2
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2
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1
2
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4.701
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2
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1
2
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3.411
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2
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2
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2
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1
2
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2
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1
2
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2
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1
2
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1
2
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3.686
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3
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3
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3
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3
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3
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3
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3
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3
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3
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0.046
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3
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3
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0.897
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3
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0.512
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1
3
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3
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1
3
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1.450
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1
3
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2.725
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1
3
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3.615
1.789
0.168
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1
3
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3.146
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1
3
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2.208
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1
3
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1.878
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3
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1
3
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1.671
8.661
3.626
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3
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1
3
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-0.479
8.066
3.158
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3
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0.431
6.852
5.369
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1
3
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1.035
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4.580
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3
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1
3
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-0.684
4.396
4.759
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3
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1
3
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-1.110
4.497
2.496
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3
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1
3
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1.186
-0.586
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3
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1
3
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4.589
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0.436
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3
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1
3
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4.190
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2.164
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3
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1
3
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2.498
4.831
3.263
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3
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1
3
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-2.224
6.038
6.172
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4
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P
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1
4
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1
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-3.306
6.917
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4
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1
4
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-1.115
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4
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1
4
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-2.887
4.711
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4
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4
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4
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4
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4
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1
4
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C
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4
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4
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4
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4
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4
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4
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1
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-3.045
1.520
4.172
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4
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1
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1.340
3.967
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4
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1
4
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-0.591
1.874
4.716
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4
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1
4
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0.595
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4
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1
4
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0.343
0.734
3.183
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4
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1
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C
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1.238
0.074
2.303
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4
ATOM
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1
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1
C
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2.474
0.073
2.320
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4
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1
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1
O
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0.559
-0.640
1.322
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N1
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4
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N1
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1
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1.00
1
N
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-0.805
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1.201
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4
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1
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1.00
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C
0.00
-1.270
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0.187
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N2
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4
ATOM
A
N2
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1
4
1.00
1
N
0.00
-1.652
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2.013
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4
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N3
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1
4
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1
N
0.00
-1.014
0.600
2.974
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4
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1
4
1.00
1
C
0.00
-3.694
5.300
3.779
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4
ATOM
A
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1
4
1.00
1
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-4.815
5.321
5.157
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4
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A
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1
4
1.00
1
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-5.401
3.489
3.783
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4
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1
4
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3.034
6.421
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4
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1
4
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-2.724
2.141
6.234
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4
ATOM
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1
4
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1
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-3.665
0.665
6.075
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4
ATOM
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1
4
1.00
1
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-3.574
0.709
3.670
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4
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1
4
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5.577
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1.817
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-3.728
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-8.707
5.472
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-10.542
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-11.331
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1.954
-10.920
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1.123
-11.750
6.288
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1.732
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5.887
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4.843
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3.271
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4.661
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6.876
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2.965
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3.084
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2.733
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2
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-8.143
3.561
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2
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8.956
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3.128
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1.245
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2
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0.672
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2
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2
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0.522
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6.812
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2
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6.304
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2
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6.260
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-1.086
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2
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-0.236
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2
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-4.999
0.690
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2
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5.491
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1.231
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2
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4.872
-3.233
2.049
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2
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3.559
-3.683
2.044
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2
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2.423
-3.205
2.745
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2
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C
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2.349
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3.540
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2
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O
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1.289
-3.951
2.450
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2
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1.249
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1.590
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2
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0.056
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1.436
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2
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2.300
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0.929
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2
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2
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3.415
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1.204
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2
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6.959
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1.463
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2
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5
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5
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5
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1
5
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6
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1
6
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6
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6
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O
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6
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6
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6
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B
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6
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6
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6
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O
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6
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6
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6
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6
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O
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6
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B
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6
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6
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B
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1
6
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6
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1
6
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N
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6
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B
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1
6
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C
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N7
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6
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B
N7
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1
6
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6
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C5
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1
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1
C
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6
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B
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1
6
1.00
1
C
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N6
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6
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B
N6
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1
6
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N
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6
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B
N1
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1
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N
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C2
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6
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B
C2
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1
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C
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-4.681
4.285
-2.791
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6
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B
N3
DA
1
6
1.00
1
N
0.00
-4.955
5.400
-3.489
B
C4
DA
6
ATOM
B
C4
DA
1
6
1.00
1
C
0.00
-8.460
6.192
-7.997
B
H5'
DA
6
ATOM
B
H5'
DA
1
6
1.00
1
H
0.00
-6.838
5.769
-7.409
B
H5''
DA
6
ATOM
B
H5''
DA
1
6
1.00
1
H
0.00
-9.270
4.264
-6.502
B
H4'
DA
6
ATOM
B
H4'
DA
1
6
1.00
1
H
0.00
-8.581
7.021
-5.674
B
H3'
DA
6
ATOM
B
H3'
DA
1
6
1.00
1
H
0.00
-10.794
6.324
-4.678
B
HO3'
DA
6
ATOM
B
HO3'
DA
1
6
1.00
1
H
0.00
-8.508
6.508
-3.343
B
H2'
DA
6
ATOM
B
H2'
DA
1
6
1.00
1
H
0.00
-9.395
5.005
-3.549
B
H2''
DA
6
ATOM
B
H2''
DA
1
6
1.00
1
H
0.00
-7.232
4.075
-3.470
B
H1'
DA
6
ATOM
B
H1'
DA
1
6
1.00
1
H
0.00
-6.678
7.461
-5.277
B
H8
DA
6
ATOM
B
H8
DA
1
6
1.00
1
H
0.00
-0.999
7.245
-2.822
B
H61
DA
6
ATOM
B
H61
DA
1
6
1.00
1
H
0.00
-2.119
8.195
-3.772
B
H62
DA
6
ATOM
B
H62
DA
1
6
1.00
1
H
0.00
-3.139
3.459
-1.722
B
H2
DA
6
ATOM
B
H2
DA
1
6
1.00
1
H
0.00
3.639
5.955
-4.509
A
C1
OXI
0
HETATM
C
C1
OXI
2
1.00
1
C
0.00
3.380
6.597
-3.524
A
O1
OXI
0
HETATM
C
O1
OXI
2
1.00
1
O
0.00
2.638
5.872
-5.600
A
C3
OXI
0
HETATM
C
C3
OXI
2
1.00
1
C
0.00
2.882
5.124
-6.749
A
C2
OXI
0
HETATM
C
C2
OXI
2
1.00
1
C
0.00
2.092
5.093
-7.831
A
N1
OXI
0
HETATM
C
N1
OXI
2
1.00
1
N
0.00
1.351
6.359
-5.427
A
C4
OXI
0
HETATM
C
C4
OXI
2
1.00
1
C
0.00
1.071
7.014
-4.454
A
O4
OXI
0
HETATM
C
O4
OXI
2
1.00
1
O
0.00
0.493
6.371
-6.531
A
C10
OXI
0
HETATM
C
C10
OXI
2
1.00
1
C
0.00
0.851
5.632
-7.683
A
C9
OXI
0
HETATM
C
C9
OXI
2
1.00
1
C
0.00
-0.072
5.692
-8.754
A
C8
OXI
0
HETATM
C
C8
OXI
2
1.00
1
C
0.00
-0.793
6.915
-6.354
A
C5
OXI
0
HETATM
C
C5
OXI
2
1.00
1
C
0.00
-1.312
6.297
-8.604
A
C7
OXI
0
HETATM
C
C7
OXI
2
1.00
1
C
0.00
-1.668
6.919
-7.433
A
C6
OXI
0
HETATM
C
C6
OXI
2
1.00
1
C
0.00
-2.937
7.377
-7.536
A
O6
OXI
0
HETATM
C
O6
OXI
2
1.00
1
O
0.00
-2.306
6.455
-9.506
A
O7
OXI
0
HETATM
C
O7
OXI
2
1.00
1
O
0.00
-3.380
7.122
-8.863
A
C11
OXI
0
HETATM
C
C11
OXI
2
1.00
1
C
0.00
2.495
4.232
-8.976
A
C12
OXI
0
HETATM
C
C12
OXI
2
1.00
1
C
0.00
1.470
3.351
-9.715
A
C13
OXI
0
HETATM
C
C13
OXI
2
1.00
1
C
0.00
3.911
4.729
-6.887
A
H2
OXI
0
HETATM
C
H2
OXI
2
1.00
1
H
0.00
0.060
5.174
-9.707
A
H8
OXI
0
HETATM
C
H8
OXI
2
1.00
1
H
0.00
-1.075
7.492
-5.459
A
H5
OXI
0
HETATM
C
H5
OXI
2
1.00
1
H
0.00
-3.604
8.084
-9.389
A
H111
OXI
0
HETATM
C
H111
OXI
2
1.00
1
H
0.00
-4.274
6.448
-8.841
A
H112
OXI
0
HETATM
C
H112
OXI
2
1.00
1
H
0.00
2.959
4.885
-9.749
A
H121
OXI
0
HETATM
C
H121
OXI
2
1.00
1
H
0.00
3.280
3.527
-8.607
A
H122
OXI
0
HETATM
C
H122
OXI
2
1.00
1
H
0.00
1.285
3.739
-10.744
A
H131
OXI
0
HETATM
C
H131
OXI
2
1.00
1
H
0.00
1.841
2.304
-9.803
A
H132
OXI
0
HETATM
C
H132
OXI
2
1.00
1
H
0.00
0.497
3.327
-9.174
A
H133
OXI
0
HETATM
C
H133
OXI
2
1.00
1
H
0.00
2.732
-5.300
5.357
B
C1
OXI
0
HETATM
D
C1
OXI
2
1.00
1
C
0.00
2.865
-5.782
4.262
B
O1
OXI
0
HETATM
D
O1
OXI
2
1.00
1
O
0.00
1.392
-5.360
5.996
B
C3
OXI
0
HETATM
D
C3
OXI
2
1.00
1
C
0.00
1.156
-4.803
7.250
B
C2
OXI
0
HETATM
D
C2
OXI
2
1.00
1
C
0.00
0.026
-4.956
7.953
B
N1
OXI
0
HETATM
D
N1
OXI
2
1.00
1
N
0.00
0.291
-5.861
5.308
B
C4
OXI
0
HETATM
D
C4
OXI
2
1.00
1
C
0.00
0.423
-6.355
4.216
B
O4
OXI
0
HETATM
D
O4
OXI
2
1.00
1
O
0.00
-0.903
-6.061
6.013
B
C10
OXI
0
HETATM
D
C10
OXI
2
1.00
1
C
0.00
-1.033
-5.481
7.292
B
C9
OXI
0
HETATM
D
C9
OXI
2
1.00
1
C
0.00
-2.261
-5.702
7.951
B
C8
OXI
0
HETATM
D
C8
OXI
2
1.00
1
C
0.00
-2.005
-6.606
5.326
B
C5
OXI
0
HETATM
D
C5
OXI
2
1.00
1
C
0.00
-3.294
-6.385
7.331
B
C7
OXI
0
HETATM
D
C7
OXI
2
1.00
1
C
0.00
-3.172
-6.850
6.044
B
C6
OXI
0
HETATM
D
C6
OXI
2
1.00
1
C
0.00
-4.355
-7.369
5.648
B
O6
OXI
0
HETATM
D
O6
OXI
2
1.00
1
O
0.00
-4.521
-6.700
7.802
B
O7
OXI
0
HETATM
D
O7
OXI
2
1.00
1
O
0.00
-5.218
-7.385
6.776
B
C11
OXI
0
HETATM
D
C11
OXI
2
1.00
1
C
0.00
-0.124
-4.302
9.275
B
C12
OXI
0
HETATM
D
C12
OXI
2
1.00
1
C
0.00
-0.529
-5.158
10.486
B
C13
OXI
0
HETATM
D
C13
OXI
2
1.00
1
C
0.00
2.031
-4.401
7.803
B
H2
OXI
0
HETATM
D
H2
OXI
2
1.00
1
H
0.00
-2.505
-5.305
8.940
B
H8
OXI
0
HETATM
D
H8
OXI
2
1.00
1
H
0.00
-1.920
-7.060
4.324
B
H5
OXI
0
HETATM
D
H5
OXI
2
1.00
1
H
0.00
-5.432
-8.437
7.091
B
H111
OXI
0
HETATM
D
H111
OXI
2
1.00
1
H
0.00
-6.158
-6.826
6.536
B
H112
OXI
0
HETATM
D
H112
OXI
2
1.00
1
H
0.00
-0.903
-3.506
9.178
B
H121
OXI
0
HETATM
D
H121
OXI
2
1.00
1
H
0.00
0.847
-3.818
9.541
B
H122
OXI
0
HETATM
D
H122
OXI
2
1.00
1
H
0.00
0.263
-5.137
11.271
B
H131
OXI
0
HETATM
D
H131
OXI
2
1.00
1
H
0.00
-1.475
-4.772
10.935
B
H132
OXI
0
HETATM
D
H132
OXI
2
1.00
1
H
0.00
-0.693
-6.219
10.186
B
H133
OXI
0
HETATM
D
H133
OXI
2
1.00
1
H
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Tuma, J.
Connors, W.H.
Stitelman, D.H.
Richert, C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H15 N3 O4
241.244
n
5'-AMINO-5'-DEOXYTHYMIDINE
DNA linking
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C13 H11 N O5
261.230
OXOLINIC ACID
non-polymer
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
124
4236
4246
10.1021/ja0125117
11960452
On the effect of covalently appended quinolones on termini of DNA duplexes.
2002
10.2210/pdb1kse/pdb
pdb_00001kse
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
Quinolone-DNA hybrid
1728.254
5'-D(*(5AT)P*GP*CP*GP*CP*A)-3'
2
syn
polymer
261.230
OXOLINIC ACID
2
syn
non-polymer
no
yes
(5AT)(DG)(DC)(DG)(DC)(DA)
TGCGCA
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
-7.550
1
19
A
2
B
5
-2.740
A_DG2:DC5_B
1
-7.786
-1.510
0.378
-0.658
-5.593
1
19
A
3
B
4
-1.682
A_DC3:DG4_B
2
-5.073
-0.157
0.390
-0.184
7.058
1
19
A
4
B
3
-1.487
A_DG4:DC3_B
3
-2.748
0.001
0.439
-0.194
12.265
1
19
A
5
B
2
-1.904
A_DC5:DG2_B
4
-12.002
0.957
-0.004
-0.427
3.159
47.332
A
A
2
3
12.647
B
B
5
4
3.238
10.060
0.100
0.112
AA_DG2DC3:DG4DC5_BB
1
-5.886
7.399
45.955
-0.673
-0.599
2.924
33.276
A
A
3
4
10.548
B
B
4
3
2.831
6.009
0.143
0.786
AA_DC3DG4:DC3DG4_BB
2
-0.282
0.495
32.743
0.484
-0.292
3.077
43.925
A
A
4
5
18.153
B
B
3
2
3.233
13.276
-0.306
0.432
AA_DG4DC5:DG2DC3_BB
3
9.785
-13.379
40.853
-0.684
1.340
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2002-05-08
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2002-01-12
REL
OXI
OXOLINIC ACID
Custom synthesized by the authors
sample
closest to the average
1
2D NOESY, DQF-COSY, TOCSY
2D NOESY
165 mM Phosphate buffer(KH2PO4/K2HPO4), NaCl at pH 7 (uncorrected for deuterium effect)
7
ambient
283
K
Torsion-Angle Molecular Dynamics
analyte buffer, salt, D2O
D2O
analyte buffer, salt, H2O/D2O (85:15)
H2O/D2O (85:15)
Brunger
structure solution
CNS
1.0
Brunger
refinement
CNS
1.0
600
Bruker
DPX
T
1
2
OXI
OXI
0
A
T
1
2
OXI
OXI
0
B
T
1
n
1
5AT
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
G
4
n
4
DG
4
A
C
5
n
5
DC
5
A
A
6
n
6
DA
6
A
T
1
n
1
5AT
1
B
G
2
n
2
DG
2
B
C
3
n
3
DC
3
B
G
4
n
4
DG
4
B
C
5
n
5
DC
5
B
A
6
n
6
DA
6
B
author_defined_assembly
2
dimeric
A
5AT
1
5'-AMINO-5'-DEOXYTHYMIDINE
A
5AT
1
DT
B
5AT
1
5'-AMINO-5'-DEOXYTHYMIDINE
B
5AT
1
DT
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
Solution Structure of a quinolone-capped DNA duplex
1
N
N
1
N
N
2
N
N
2
N
N
covale
1.350
none
A
OXI
0
C
C1
OXI
1_555
A
5AT
1
A
N5'
5AT
1
1_555
covale
1.607
both
A
5AT
1
A
O3'
5AT
1
1_555
A
DG
2
A
P
DG
2
1_555
covale
1.357
none
B
OXI
0
D
C1
OXI
1_555
B
5AT
1
B
N5'
5AT
1
1_555
covale
1.611
both
B
5AT
1
B
O3'
5AT
1
1_555
B
DG
2
B
P
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
5
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
5
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
5
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
4
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
4
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
4
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
3
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
3
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
3
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
2
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
2
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
2
B
N2
DG
2
1_555
DNA
DNA, quinolone, Synthetic hybrid, disrupted terminal basepairs
1KSE
PDB
1
1KSE
1
6
1KSE
1
6
1KSE
A
1
1
6
1
6
1KSE
1
6
1KSE
B
1
1
6
BINDING SITE FOR RESIDUE OXI A 0
A
OXI
0
Software
4
BINDING SITE FOR RESIDUE OXI B 0
B
OXI
0
Software
4
A
5AT
1
A
5AT
1
4
1_555
A
DG
2
A
DG
2
4
1_555
B
DC
5
B
DC
5
4
1_555
B
DA
6
B
DA
6
4
1_555
A
DC
5
A
DC
5
4
1_555
A
DA
6
A
DA
6
4
1_555
B
5AT
1
B
5AT
1
4
1_555
B
DG
2
B
DG
2
4
1_555