The ground state coordinates of the QM domain in the “dye-4nt+sugar” model for DFHBI-aptamer complex optimized using the ONIOM(DFT:MM) method with the M06-2X/6-31G* functional:
103
DFHBI and 4 nucleotides with 1 sugar optimized in the ground state
H 12.69382 5.72527 10.18095
C 12.76830 4.65322 9.88449
H 11.94474 4.13440 10.38269
O 12.56362 4.54497 8.47157
C 13.62889 3.80841 7.89485
H 13.36344 2.75679 7.76064
N 13.88550 4.37702 6.58692
C 14.06752 5.72586 6.39661
H 14.16780 6.39345 7.24333
N 14.09522 6.07116 5.13929
C 13.95139 4.88525 4.46617
C 13.89359 4.65945 3.06136
O 13.74509 5.48541 2.16659
N 13.97504 3.28426 2.77967
H 14.20736 3.02281 1.81756
C 13.93063 2.28363 3.72266
N 14.14677 1.01228 3.22533
H 13.73147 0.85946 2.29752
H 13.75018 0.27222 3.82112
N 13.80543 2.49539 5.00654
C 13.84716 3.81292 5.33484
C 14.11187 3.96337 10.21596
H 14.68411 4.54479 10.94831
C 14.80791 3.99342 8.85991
H 15.16385 5.02550 8.71707
O 15.83358 3.08527 8.68660
H 16.45507 3.59530 8.09348
O 13.98328 2.62637 10.60168
H 13.74564 2.41226 11.43841
H 15.74103 -1.52303 -3.42139
N 15.91699 -1.09075 -2.49316
C 15.75441 -1.65532 -1.23782
H 15.40267 -2.66886 -1.12414
N 16.03390 -0.83434 -0.26354
C 16.37721 0.33020 -0.90574
C 16.79245 1.57559 -0.32549
O 16.93739 1.81177 0.86387
N 17.09286 2.51172 -1.33150
H 17.35108 3.45990 -1.02544
C 16.99925 2.27460 -2.67939
N 17.37672 3.28575 -3.48767
H 17.56585 4.21963 -3.15032
H 17.24542 3.14065 -4.48609
N 16.62452 1.13274 -3.21628
C 16.32427 0.20405 -2.28103
H 20.92420 8.26452 3.63783
N 20.82542 7.24332 3.56282
C 20.59818 6.34423 4.57937
H 20.51868 6.67383 5.60718
N 20.49870 5.11256 4.16966
C 20.65439 5.20334 2.80762
C 20.68692 4.21814 1.81614
N 20.46559 2.88349 2.10017
H 21.22276 2.29643 1.73503
H 20.38414 2.70868 3.10442
N 20.89665 4.59164 0.55307
C 21.13843 5.88605 0.30577
H 21.35511 6.12360 -0.73429
N 21.13011 6.93133 1.14082
C 20.86964 6.51975 2.39441
H 15.84073 12.47775 0.48679
N 15.73012 11.53488 0.05500
C 15.84533 11.23437 -1.29157
H 16.04523 12.01016 -2.02108
N 15.70180 9.96088 -1.55150
C 15.45568 9.39749 -0.32043
C 15.23679 8.01258 0.01853
O 15.24638 7.05037 -0.73028
N 14.99623 7.86217 1.39225
H 14.75569 6.92213 1.72300
C 15.06582 8.86208 2.31917
N 14.93365 8.50039 3.61542
H 14.60499 7.57292 3.88811
H 14.58854 9.22687 4.24007
N 15.28586 10.12446 2.01497
C 15.46376 10.33712 0.69535
C 17.05107 3.93962 3.82731
H 16.93567 3.02726 3.24541
C 17.34306 5.16793 3.17765
C 17.47054 6.33257 3.98167
H 17.68764 7.29145 3.52691
C 17.34914 6.23854 5.33495
C 17.05759 5.03517 6.04764
C 16.87624 3.90767 5.18437
C 17.52947 5.17241 1.76357
H 17.42214 4.20021 1.27795
C 17.84185 6.23192 0.95266
C 18.29176 8.24390 0.31608
O 17.81885 5.25548 -1.31488
C 17.95833 6.17987 -0.50234
N 18.27988 7.48499 -0.85010
C 18.40434 7.97307 -2.20086
H 18.22918 7.13637 -2.88033
H 19.40964 8.36815 -2.38974
H 17.66165 8.75140 -2.40148
C 18.59334 9.69793 0.33160
H 18.19662 10.11811 1.26233
H 18.12823 10.22628 -0.50836
H 19.66454 9.88741 0.30464
N 18.05999 7.54766 1.37384
F 16.51869 2.75902 5.80285
O 16.99217 4.99359 7.31001
F 17.52798 7.33214 6.10613
The excited state coordinates of the QM domain in the “dye-4nt+sugar” model for DFHBI-aptamer complex optimized using the ONIOM(TD-DFT:MM) method with the CAM-B3LYP/6-31G* functional:
103
DFHBI and 4 nucleotides with 1 sugar, optimized for the 1st excited state
H 12.72925 5.79549 10.40763
C 12.76864 4.73651 10.06752
H 11.96021 4.21644 10.58719
O 12.49277 4.70005 8.66244
C 13.48316 3.91707 8.01774
H 13.15847 2.88037 7.89573
N 13.69321 4.46853 6.70225
C 13.98555 5.78632 6.45017
H 14.13417 6.48780 7.25960
N 14.05363 6.06076 5.17823
C 13.82999 4.85466 4.55800
C 13.75323 4.55803 3.17013
O 13.70447 5.33830 2.22546
N 13.67580 3.16153 2.96867
H 13.84085 2.81806 2.02090
C 13.54090 2.23052 3.96866
N 13.60556 0.91819 3.58373
H 13.27512 0.68782 2.64287
H 13.17839 0.25785 4.23961
N 13.46692 2.52954 5.23801
C 13.63334 3.84878 5.48333
C 14.10861 4.00107 10.30349
H 14.73831 4.54937 11.01184
C 14.72556 4.02702 8.91086
H 15.12645 5.04038 8.76486
O 15.69275 3.06790 8.66145
H 16.27725 3.52948 7.99819
O 13.96688 2.66094 10.67083
H 13.73996 2.43004 11.50402
H 15.81237 -1.51857 -3.51087
N 15.97421 -1.07046 -2.58870
C 15.82855 -1.62667 -1.32756
H 15.47450 -2.63811 -1.20218
N 16.12353 -0.80070 -0.36447
C 16.45942 0.36027 -1.01918
C 16.91250 1.59359 -0.45311
O 17.11140 1.81248 0.73313
N 17.18830 2.53234 -1.46120
H 17.46350 3.48269 -1.17326
C 17.07497 2.28946 -2.80544
N 17.44824 3.29711 -3.61956
H 17.65915 4.22684 -3.28180
H 17.30245 3.16023 -4.61684
N 16.68361 1.14782 -3.32976
C 16.38659 0.22511 -2.38966
H 21.11841 8.36458 3.68278
N 21.07202 7.34142 3.60446
C 20.87145 6.43780 4.62115
H 20.84705 6.75847 5.65387
N 20.73524 5.21461 4.19971
C 20.84485 5.31235 2.83275
C 20.83787 4.33239 1.83457
N 20.63594 2.98736 2.10974
H 21.41374 2.42175 1.75358
H 20.57199 2.81168 3.11487
N 21.03497 4.71752 0.57254
C 21.28189 6.00752 0.32826
H 21.49066 6.24833 -0.71209
N 21.30328 7.04880 1.17331
C 21.06633 6.62730 2.42786
H 15.75043 12.46425 0.52843
N 15.62849 11.51891 0.10522
C 15.77499 11.20163 -1.23414
H 15.98490 11.96991 -1.96920
N 15.64675 9.92626 -1.48051
C 15.38013 9.37316 -0.24727
C 15.16825 7.99266 0.10017
O 15.20351 7.02425 -0.64093
N 14.90336 7.84649 1.47299
H 14.65475 6.90862 1.80306
C 14.95520 8.85920 2.38854
N 14.83967 8.51697 3.69092
H 14.52565 7.59341 3.99683
H 14.49916 9.25389 4.30577
N 15.15902 10.11863 2.06872
C 15.35941 10.32467 0.75293
C 17.08446 3.81817 3.62687
H 16.95526 2.92668 3.02244
C 17.47377 5.04399 3.00354
C 17.59726 6.20338 3.83271
H 17.87348 7.15072 3.38960
C 17.39154 6.10670 5.17394
C 17.00789 4.90842 5.85279
C 16.84424 3.78464 4.96547
C 17.71641 5.05033 1.60402
H 17.63741 4.09328 1.10084
C 17.97391 6.17993 0.81755
C 18.37678 8.21486 0.21191
O 17.89996 5.25378 -1.46562
C 18.06203 6.17193 -0.63801
N 18.35834 7.49128 -0.96113
C 18.47239 8.00026 -2.30445
H 18.29017 7.17156 -2.99027
H 19.47535 8.39715 -2.49937
H 17.72789 8.77932 -2.48921
C 18.64163 9.66952 0.29357
H 18.14920 10.06044 1.19030
H 18.25111 10.21479 -0.57142
H 19.70327 9.89915 0.38985
N 18.15967 7.46215 1.26192
F 16.41188 2.64967 5.55223
O 16.84396 4.84678 7.10362
F 17.55755 7.18954 5.96061