Guided Ideographic Spin System Model Optimization

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Mixture Simulation

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Simulation: simulation_1

BMRB entry

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Download entry NMR-STAR

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External links:

NMRFAM Servers

pKa (R. Williams)

1H NMR (Hans J. Reich)

Cytidine

Simulation outputs:

InChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1 Parameter Value
Field strength 499.84(MHz)
RMSD of the fit 0.00737
Temperature 298 K
pH 7.4
InChI InChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1
pKa 4.22
pKa 12.5
Note 1 None

Sample description:

Compound Type Concentration
Cytidine Solute 100mM
D2O Solvent 100%
sodium phosphate Buffer 50mM
sodium azide Cytocide 500uM
DSS Reference 500uM
Show/Hide Spin System Matrix

Spin System Matrix

18 19 25 24 23 22 20 21
18 7.835 7.416 0 0 0 0 0 0
19 0 6.034 0 0 0 0 0 0
25 0 0 5.894 3.864 0 0 0 0
24 0 0 0 4.299 5.172 0 0 0
23 0 0 0 0 4.2 5.999 0 0
22 0 0 0 0 0 4.123 2.637 4.353
20 0 0 0 0 0 0 3.923 -12.882
21 0 0 0 0 0 0 0 3.81

Spectra

Select field strength to view simulated spectra and peak lists (standard and GSD): Autoscale

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PPM Amplitude Peak Type
3.79136 0.381306 standard
3.79996 0.403659 standard
3.81712 0.593 standard
3.82574 0.62247 standard
3.90945 0.634026 standard
3.91456 0.663628 standard
3.93521 0.411907 standard
3.94034 0.424368 standard
4.10984 0.266773 standard
4.11527 0.322149 standard
4.1187 0.378973 standard
4.12196 0.498611 standard
4.12686 0.448369 standard
4.13002 0.410426 standard
4.1354 0.324428 standard
4.18942 0.532004 standard
4.2001 0.834942 standard
4.21163 0.483458 standard
4.29019 0.570386 standard
4.29822 0.723059 standard
4.30814 0.471114 standard
5.8899 1.00014 standard
5.89749 1.00019 standard
6.02656 0.959223 standard
6.04143 0.959147 standard
7.82798 0.958822 standard
7.84285 0.958822 standard
3.5765 0.0247741 standard
3.8892 0.960745 standard
3.98069 0.2605 standard
4.01282 0.253135 standard
4.10094 0.431822 standard
4.21459 1.0 standard
4.29776 0.451997 standard
5.85539 0.415534 standard
5.93581 0.741526 standard
6.12186 0.49155 standard
7.74747 0.480536 standard
7.93286 0.396263 standard
3.63631 0.0338401 standard
3.66552 0.039 standard
3.87998 1.0 standard
4.00029 0.130509 standard
4.03058 0.13172 standard
4.12233 0.456337 standard
4.14844 0.488413 standard
4.20225 0.861848 standard
4.23341 0.554597 standard
4.29412 0.484633 standard
5.86582 0.472996 standard
5.92334 0.48833 standard
5.96972 0.537405 standard
6.09366 0.542177 standard
7.77573 0.535282 standard
7.89925 0.471805 standard
3.66384 0.046196 standard
3.70921 0.0580502 standard
3.82382 0.42921 standard
3.87089 1.00001 standard
4.04906 0.175039 standard
4.14455 0.585988 standard
4.19964 0.732427 standard
4.2569 0.505694 standard
4.29757 0.42272 standard
4.34936 0.15058 standard
5.87249 0.547966 standard
5.91557 0.537991 standard
5.98639 0.552469 standard
6.07919 0.582179 standard
7.79031 0.577358 standard
7.8829 0.527694 standard
3.68217 0.060596 standard
3.72322 0.0738432 standard
3.82455 0.476831 standard
3.86931 1.00001 standard
3.89574 0.674845 standard
4.01721 0.105293 standard
4.04448 0.202422 standard
4.11256 0.34862 standard
4.14889 0.640349 standard
4.19992 0.729097 standard
4.25802 0.618678 standard
4.29894 0.457224 standard
4.34803 0.174522 standard
5.87458 0.619294 standard
5.91336 0.60662 standard
5.99192 0.605059 standard
6.07424 0.63761 standard
7.79517 0.633153 standard
7.87755 0.587914 standard
3.6969 0.0879436 standard
3.73403 0.103913 standard
3.82495 0.591259 standard
3.86562 1.00001 standard
3.89765 0.80122 standard
4.00429 0.127394 standard
4.02871 0.154662 standard
4.05602 0.187927 standard
4.11255 0.419389 standard
4.15331 0.790272 standard
4.19987 0.839713 standard
4.25828 0.724635 standard
4.29985 0.572025 standard
4.3449 0.231384 standard
5.87622 0.779304 standard
5.91161 0.76511 standard
5.9962 0.748434 standard
6.07037 0.78791 standard
7.79913 0.78331 standard
7.87318 0.733576 standard
3.75883 0.243905 standard
3.7792 0.270691 standard
3.82299 0.689203 standard
3.84367 0.794528 standard
3.89344 0.75516 standard
3.90579 0.833663 standard
3.95763 0.269834 standard
3.97028 0.286343 standard
4.08936 0.241013 standard
4.10333 0.271485 standard
4.11895 0.518532 standard
4.13198 0.510561 standard
4.13841 0.496748 standard
4.1517 0.401978 standard
4.17451 0.596554 standard
4.19963 0.866532 standard
4.22865 0.476456 standard
4.27877 0.640509 standard
4.29836 0.760294 standard
4.32235 0.404831 standard
5.88434 0.999368 standard
5.90315 1.00002 standard
6.01536 0.952653 standard
6.05233 0.966571 standard
7.81708 0.964713 standard
7.85415 0.949544 standard
3.77747 0.314371 standard
3.79154 0.340939 standard
3.82031 0.643711 standard
3.83448 0.703454 standard
3.90166 0.693821 standard
3.91007 0.746203 standard
3.94454 0.341615 standard
3.95304 0.357668 standard
4.10074 0.252603 standard
4.10987 0.295167 standard
4.12083 0.506723 standard
4.12921 0.471476 standard
4.13415 0.444525 standard
4.1431 0.349722 standard
4.18253 0.556876 standard
4.19983 0.845621 standard
4.21924 0.476174 standard
4.28484 0.602103 standard
4.29801 0.737422 standard
4.31442 0.439138 standard
5.88739 1.0 standard
5.90007 0.999807 standard
6.0216 0.960076 standard
6.04629 0.959718 standard
7.82312 0.958868 standard
7.84781 0.958868 standard
3.78631 0.355427 standard
3.79698 0.379866 standard
3.81844 0.613767 standard
3.82918 0.653691 standard
3.9064 0.658269 standard
3.91276 0.696392 standard
3.93858 0.384583 standard
3.94499 0.398757 standard
4.10645 0.261447 standard
4.11323 0.31173 standard
4.11749 0.366691 standard
4.1216 0.502326 standard
4.12785 0.455442 standard
4.13169 0.423437 standard
4.13839 0.334119 standard
4.18681 0.541984 standard
4.19998 0.836585 standard
4.21447 0.480109 standard
4.28816 0.583389 standard
4.29812 0.730438 standard
4.31047 0.45994 standard
5.88892 1.0001 standard
5.89847 1.00018 standard
6.02467 0.960165 standard
6.04321 0.960016 standard
7.8262 0.959519 standard
7.84473 0.959519 standard
3.79136 0.38134 standard
3.79996 0.403687 standard
3.81712 0.592973 standard
3.82574 0.622434 standard
3.90945 0.63337 standard
3.91458 0.66311 standard
3.93521 0.411938 standard
3.94034 0.424394 standard
4.10984 0.266758 standard
4.11527 0.322104 standard
4.1187 0.378899 standard
4.12196 0.498526 standard
4.12686 0.448282 standard
4.13002 0.410348 standard
4.1354 0.32439 standard
4.18942 0.531992 standard
4.2001 0.834886 standard
4.21163 0.48346 standard
4.29019 0.570359 standard
4.29822 0.722977 standard
4.30814 0.471116 standard
5.8899 1.00014 standard
5.89749 1.00019 standard
6.02656 0.959246 standard
6.04143 0.95917 standard
7.82798 0.958845 standard
7.84285 0.958845 standard
3.79468 0.400084 standard
3.80187 0.42036 standard
3.81613 0.579854 standard
3.82331 0.603125 standard
3.9116 0.61818 standard
3.91588 0.642602 standard
3.93309 0.436876 standard
3.93733 0.443973 standard
4.11206 0.27121 standard
4.11655 0.328734 standard
4.11938 0.382238 standard
4.12226 0.498433 standard
4.12625 0.447293 standard
4.12891 0.403876 standard
4.13344 0.31839 standard
4.19122 0.527348 standard
4.20013 0.830382 standard
4.20974 0.486678 standard
4.29162 0.563751 standard
4.29827 0.717374 standard
4.30658 0.479654 standard
5.89049 1.00015 standard
5.8969 1.00018 standard
6.02785 0.96053 standard
6.04024 0.960486 standard
7.82927 0.960503 standard
7.84156 0.960503 standard
3.79696 0.420152 standard
3.80318 0.4242 standard
3.81541 0.569239 standard
3.82153 0.581894 standard
3.91315 0.616237 standard
3.91681 0.623567 standard
3.93159 0.452084 standard
3.93525 0.44804 standard
4.11363 0.26868 standard
4.11751 0.332228 standard
4.11993 0.386234 standard
4.1224 0.489913 standard
4.12578 0.436674 standard
4.12816 0.390452 standard
4.13196 0.323293 standard
4.19251 0.523614 standard
4.20018 0.830053 standard
4.20835 0.488698 standard
4.29261 0.5562 standard
4.2984 0.718679 standard
4.30544 0.485616 standard
5.89099 1.00018 standard
5.8964 1.00019 standard
6.02874 0.959266 standard
6.03935 0.959238 standard
7.83016 0.959357 standard
7.84067 0.959357 standard
3.7979 0.424892 standard
3.80368 0.429627 standard
3.81511 0.570117 standard
3.82083 0.572183 standard
3.91384 0.61206 standard
3.91721 0.614928 standard
3.93099 0.45754 standard
3.93441 0.453351 standard
4.11427 0.265412 standard
4.11789 0.332206 standard
4.12017 0.383839 standard
4.12252 0.494439 standard
4.12566 0.43681 standard
4.12776 0.397128 standard
4.13143 0.320317 standard
4.19301 0.522236 standard
4.20017 0.8259 standard
4.20786 0.489186 standard
4.293 0.554234 standard
4.29837 0.712978 standard
4.305 0.487152 standard
5.89113 0.998738 standard
5.8962 1.00019 standard
6.02904 0.959538 standard
6.03895 0.959515 standard
7.83046 0.959366 standard
7.84037 0.959366 standard
3.79874 0.43119 standard
3.80408 0.435345 standard
3.81481 0.571144 standard
3.82024 0.568187 standard
3.91443 0.607627 standard
3.91761 0.610431 standard
3.9305 0.463686 standard
3.93367 0.460219 standard
4.11481 0.268097 standard
4.11817 0.333288 standard
4.12034 0.38699 standard
4.12262 0.497503 standard
4.12551 0.437906 standard
4.12747 0.397027 standard
4.13088 0.319235 standard
4.19347 0.520841 standard
4.20024 0.834786 standard
4.20736 0.491036 standard
4.2934 0.553451 standard
4.29842 0.712955 standard
4.29938 0.682653 standard
4.3046 0.490112 standard
5.89128 1.00016 standard
5.89611 1.00017 standard
6.02943 0.961273 standard
6.03865 0.961254 standard
7.83076 0.960793 standard
7.84007 0.960793 standard
3.80003 0.437619 standard
3.80482 0.441045 standard
3.81431 0.562957 standard
3.81915 0.559719 standard
3.91531 0.596249 standard
3.91821 0.598938 standard
3.9297 0.471888 standard
3.93249 0.468724 standard
4.11575 0.269796 standard
4.11875 0.338685 standard
4.1206 0.388205 standard
4.1227 0.492598 standard
4.1252 0.436807 standard
4.127 0.391256 standard
4.13005 0.315309 standard
4.1942 0.518674 standard
4.20024 0.83558 standard
4.20657 0.491452 standard
4.29399 0.549248 standard
4.29843 0.705583 standard
4.29939 0.676019 standard
4.30396 0.493611 standard
5.89158 1.00018 standard
5.89581 1.00019 standard
6.02993 0.959865 standard
6.03816 0.959852 standard
7.83125 0.959382 standard
7.83958 0.959382 standard
3.80055 0.439831 standard
3.80514 0.444278 standard
3.81411 0.560657 standard
3.81866 0.55733 standard
3.91571 0.594973 standard
3.91841 0.597572 standard
3.9293 0.473834 standard
3.932 0.470705 standard
4.11609 0.271087 standard
4.11894 0.33758 standard
4.12077 0.390758 standard
4.12266 0.491895 standard
4.12511 0.432924 standard
4.12681 0.390077 standard
4.12965 0.315224 standard
4.19449 0.517894 standard
4.20023 0.823223 standard
4.20628 0.492041 standard
4.29424 0.546848 standard
4.29851 0.717432 standard
4.30366 0.495356 standard
5.89167 1.00017 standard
5.89571 1.00018 standard
6.03013 0.960366 standard
6.03796 0.960355 standard
7.83155 0.960655 standard
7.83928 0.960655 standard
3.80102 0.4436 standard
3.80537 0.448021 standard
3.81391 0.557554 standard
3.81826 0.554152 standard
3.9161 0.590342 standard
3.91871 0.592942 standard
3.929 0.47563 standard
3.9316 0.472513 standard
4.11648 0.272702 standard
4.11919 0.339971 standard
4.12093 0.398471 standard
4.12262 0.493132 standard
4.12502 0.429822 standard
4.12661 0.388508 standard
4.12936 0.312868 standard
4.19479 0.517266 standard
4.20022 0.810568 standard
4.20598 0.492643 standard
4.29448 0.54657 standard
4.29854 0.714208 standard
4.29928 0.690192 standard
4.30347 0.496475 standard
5.89177 1.00017 standard
5.89561 1.00018 standard
6.03033 0.960513 standard
6.03776 0.960504 standard
7.83175 0.960834 standard
7.83908 0.960834 standard
3.80191 0.447904 standard
3.80586 0.45239 standard
3.81362 0.551952 standard
3.81757 0.548394 standard
3.9168 0.586815 standard
3.91911 0.589287 standard
3.9285 0.482176 standard
3.93081 0.479246 standard
4.11707 0.274049 standard
4.11951 0.340771 standard
4.12109 0.394826 standard
4.12274 0.492921 standard
4.1248 0.428361 standard
4.12634 0.382944 standard
4.12877 0.3118 standard
4.19529 0.514832 standard
4.2003 0.844336 standard
4.20548 0.49263 standard
4.29488 0.544406 standard
4.29851 0.708295 standard
4.29923 0.684833 standard
4.30307 0.49677 standard
5.89197 1.00019 standard
5.89542 1.00019 standard
6.03062 0.959296 standard
6.03736 0.959289 standard
7.83204 0.959218 standard
7.83879 0.959218 standard
3.8032 0.455903 standard
3.80656 0.460456 standard
3.81312 0.544929 standard
3.81648 0.541163 standard
3.91779 0.58117 standard
3.91971 0.583497 standard
3.9277 0.492296 standard
3.92962 0.489589 standard
4.11795 0.275175 standard
4.12011 0.34737 standard
4.12135 0.396444 standard
4.1228 0.486241 standard
4.12449 0.429932 standard
4.12586 0.377585 standard
4.12788 0.310081 standard
4.19608 0.513857 standard
4.20028 0.810261 standard
4.20469 0.494767 standard
4.29547 0.540768 standard
4.2986 0.711351 standard
4.29918 0.693191 standard
4.30238 0.502186 standard
5.89217 1.00018 standard
5.89512 1.00018 standard
6.03122 0.960885 standard
6.03687 0.960881 standard
7.83254 0.960293 standard
7.83829 0.960293 standard
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