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Pseudobond parameters for QM/MM studies involving nucleosides, nucleotides, and their analogs
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10.1063/1.4772182
/content/aip/journal/jcp/138/4/10.1063/1.4772182
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/4/10.1063/1.4772182

Figures

Image of FIG. 1.
FIG. 1.

(a) Example of a truncated nucleoside (deoxycytidine) analog used in the training set during pseudobond parameter optimization. Atoms in the QM subsystem are shown in black, the Nps boundary atom in blue, and MM atoms in red. (b) Representation of the different training and test sets used in this work.

Image of FIG. 2.
FIG. 2.

Correlations of (a) bond distances (in Å) and (b) angles (in º) between pseudobond-containing molecules (PsMol) and corresponding standard molecules (StdMol) for the total test set using the Tot parameters.

Image of FIG. 3.
FIG. 3.

Correlation between pseudobond containing molecules (PsMol) and standard molecules (StdMol) for (a) ESP charges, (b) NBO charges, (c) AIM charges, and (d) AIM M1 computed using the Total testing set.

Image of FIG. 4.
FIG. 4.

Representations of the molecules used for pseudobond testing: (a) acyclovir, (b) clofarabine, (c) emtricitabine, (d) tenofovir, and (e) GLY3 (triglycine) polypeptide. Atoms in the QM subsystem are shown in black, the Nps boundary atom in blue, and MM atoms in red.

Tables

Generic image for table
Table I.

Five sets of optimized pseudobond parameters from the total test set (Tot), the purine test sets (Pur1 and Pur2), and the pyrimidine test sets (Pyr1 and Pyr2).

Generic image for table
Table II.

RMS error for ESP, NBO, and AIM charges, AIM M1, bond distances, and bond angles for the different optimized parameters. The tables summarize the rmse values obtained for the purine (a), pyrimidine (b), and total (c) test sets.

Generic image for table
Table III.

RMS error for charges, first moments M1 (a.u.), bond distances (Å), and angles (degrees) and the dihedrals for adenosine monophosphate computed using various basis sets.

Generic image for table
Table IV.

RMS errors for partial charges (a.u.), M1 (a.u.), bond distances (Å), and angles (degrees) for acyclovir, clofarabin, emtricitabine, tenofovir, and triglycine polypeptide.

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/content/aip/journal/jcp/138/4/10.1063/1.4772182
2013-01-24
2014-04-25
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Pseudobond parameters for QM/MM studies involving nucleosides, nucleotides, and their analogs
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/4/10.1063/1.4772182
10.1063/1.4772182
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