C₁₀H₁₂N₅O₁₁P₂ | MD Topology | NMR | X-Ray

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Molecule Information


Molecule Type	nucleic acid
Residue Name (RNME)	_I1D
Formula	C₁₀H₁₂N₅O₁₁P₂
IUPAC InChI Key	VJIUZTHOGSFMJX-UUOKFMHZSA-N
IUPAC InChI	InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1,11H2,(H,14,18)(H,22,23)(H2,19,20,21)/t3-,5-,6-,9-/m1/s1
IUPAC Name
Common Name
Canonical SMILES (Daylight)	O[C@@H]1[C@@H](CO[P@@](=[O-])(O[P@](=O)(O)[O-])O)O[C@H]([C@@H]1O)N1C=[N]=C2C1=[N]=C(N)NC2=O
Number of atoms	40
Net Charge	-3
Forcefield	multiple
Molecule ID	49
PDB hetId	GDP
Visibility	Public
Molecule Tags

Format

Molecular Dynamics (MD) Files

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X-Ray - Docking Files

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NMR Parameters

¹H NMR Spectrum

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Fragment-Based Charges

No charge assignments available. Use the button above to use OFraMP fragment-based charge assignment.

Topology History

Processing Information

QM Processing Stage

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Processing Stage		Template	Semi-Empirical QM (QM0)	DFT QM (QM1)	DFT Hessian QM (QM2)
Calculation		None	Energy Minization	Energy Minization	Hessian
Level of Theory		None	Semi-Empirical / SCF	DFT (B3LYP/6-31G*)	DFT (B3LYP/6-31G*)
Default Size Limit (Atoms)		1000	500	50	40
Content of MD Topology
Charges Derived From		None	MOPAC	Merz-Singh-Kollman	Merz-Singh-Kollman
Geometry		User Provided	Optimized	Optimized	Optimized
Non-Bonded Interactions	Bonds	Rule Based: Parameters are asigned from existing parameters with a set of rules based on atom types and geometry.			Hessian Based: Force constant are calculated from the QM potential. New parameters are created when no suitable parameters exists.
	Angles
	Dihedrals

Data

Current Processing State	Completed
Total Processing Time	0:00:15 (hh:mm:ss)

Other conformers for this molecule (1-26 of 26)

Compare All Topologies (27)RMSD Matrix (27)

Molid	Formula	Iupac	Common Name	Atoms	Charge	Date	Curation	Visibility	Δ Qm Optimized Energy (kJ.mol^-1)	Compare
41614	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2017-04-09	ATB	Public	18.403	Compare with
35930	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2017-01-06	ATB	Public	23.880	Compare with
35916	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2017-01-06	ATB	Public	4.498	Compare with
35711	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-21	ATB	Public	-6.175	Compare with
35654	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-15	ATB	Public	14.635	Compare with
9111	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2014-06-24	ATB	Public	14.001	Compare with
289536	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-22	ATB	Public	27.859	Compare with
240219	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-22	ATB	Public	6.022	Compare with
240190	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-21	ATB	Public	6.220	Compare with
35945	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2017-01-23	ATB	Public	15.317	Compare with
35925	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2017-01-05	ATB	Public	12.603	Compare with
35787	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-25	ATB	Public	22.243	Compare with
35710	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-18	ATB	Public	18.655	Compare with
34818	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-11-07	ATB	Public	13.835	Compare with
366167	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2019-09-09	ATB	Public	-8.607	Compare with
288948	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-21	ATB	Public	8.181	Compare with
240211	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-22	ATB	Public	8.128	Compare with
240158	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-22	ATB	Public	13.441	Compare with
35938	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2017-01-15	ATB	Public	8.904	Compare with
35920	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2017-01-06	ATB	Public	16.700	Compare with
35763	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-23	ATB	Public	22.873	Compare with
35667	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-15	ATB	Public	26.346	Compare with
22219	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2014-11-27	ATB	Public	37.677	Compare with
289810	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-22	ATB	Public	27.709	Compare with
240232	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-22	ATB	Public	11.163	Compare with
240206	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-22	ATB	Public	26.344	Compare with

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Similar compounds (1-50 of 50)

Molid	Formula	Iupac	Common Name	Atoms	Charge	Date	Curation	Visibility	Details
240211	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-22	ATB	Public
32236	C₁₀H₁₅N₅O₁₁P₂	-	-	43	0	2016-07-02	ATB	Public
315148	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-06-06	ATB	Public
35667	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-15	ATB	Public
366167	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2019-09-09	ATB	Public
35925	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2017-01-05	ATB	Public
240158	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-22	ATB	Public
9111	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2014-06-24	ATB	Public
289536	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-22	ATB	Public
35654	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-15	ATB	Public
350234	C₁₀H₁₅N₅O₁₁P₂	-	-	43	0	2019-01-17	ATB	Public
35787	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-25	ATB	Public
240232	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-22	ATB	Public
35710	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-18	ATB	Public
35938	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2017-01-15	ATB	Public
240206	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-22	ATB	Public
28163	C₁₀H₁₁N₅O₁₁P₂	-	-	39	-2	2015-12-22	ATB	Public
303876	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-03-16	ATB	Public
360025	C₁₀H₁₃N₅O₁₁P₂	-	-	41	-2	2019-04-03	ATB	Public
35920	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2017-01-06	ATB	Public
288948	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-21	ATB	Public
35763	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-23	ATB	Public
41614	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2017-04-09	ATB	Public
240219	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-22	ATB	Public
34818	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-11-07	ATB	Public
35930	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2017-01-06	ATB	Public
240190	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-21	ATB	Public
22219	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2014-11-27	ATB	Public
289810	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-02-22	ATB	Public
360022	C₁₀H₁₅N₅O₁₁P₂	-	-	43	0	2019-04-03	ATB	Public
35916	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2017-01-06	ATB	Public
35711	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-21	ATB	Public
35945	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2017-01-23	ATB	Public
397302	C₁₀H₇N₅O₁₁P₂	-	-	35	-2	2019-12-31	Error	Public	Error
34964	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-11-10	Error	Public	Error
317594	C₁₀H₁₂N₅O₁₁P₂	-	-	40	0	2018-06-08	Error	Public	Error
367194	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-6	2019-10-15	Error	Public	Error
35663	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-15	Error	Public	Error
35650	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-13	Error	Public	Error
323649	C₁₀H₁₂N₅O₁₁P₂	-	-	40	0	2018-06-21	Error	Public	Error
379827	C₁₀H₇N₅O₁₁P₂	-	-	35	-2	2019-12-18	Error	Public	Error
317574	C₁₀H₁₂N₅O₁₁P₂	-	-	40	0	2018-06-08	Error	Public	Error
35669	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-19	Error	Public	Error
367193	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-4	2019-10-15	Error	Public	Error
35660	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-12-15	Error	Public	Error
397308	C₁₀H₇N₅O₁₁P₂	-	-	35	-2	2019-12-31	Error	Public	Error
268521	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-2	2017-11-02	Error	Public	Error
35063	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2016-11-16	Error	Public	Error
317596	C₁₀H₁₂N₅O₁₁P₂	-	-	40	-3	2018-06-08	Error	Public	Error
372916	C₁₀H₇N₅O₁₁P₂	-	-	35	-2	2019-12-15	Error	Public	Error

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Conditions of Use

ATB Pipeline Setting

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The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.

Experimental Solvation Free Energies (0-0 of 0)

Solvent >	Experimental Value (kJ.mol^-1)	Experimental Uncertainty (kJ.mol^-1)	Doi

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Calculated Solvation Free Energy

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Automated Topology Builder (ATB) and Repository
Version 3.0

C₁₀H₁₂N₅O₁₁P₂ | MD Topology | NMR | X-Ray

Visualize with JSmol

Molecule Information

Format

Molecular Dynamics (MD) Files

X-Ray - Docking Files

NMR Parameters

¹H NMR Spectrum

Fragment-Based Charges

Topology History

Processing Information

QM Processing Stage

Data

Other conformers for this molecule (1-26 of 26)

Similar compounds (1-50 of 50)

Conditions of Use

ATB Pipeline Setting

Experimental Solvation Free Energies (0-0 of 0)

Calculated Solvation Free Energy

Submit New Solvation Free Energy Computation

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Contributors

Automated Topology Builder (ATB) and Repository Version 3.0

C10H12N5O11P2 | MD Topology | NMR | X-Ray

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Molecule Information

Format

Molecular Dynamics (MD) Files

X-Ray - Docking Files

NMR Parameters

1H NMR Spectrum

Fragment-Based Charges

Topology History

Processing Information

QM Processing Stage

Data

Other conformers for this molecule (1-26 of 26)

Similar compounds (1-50 of 50)

Conditions of Use

ATB Pipeline Setting

Experimental Solvation Free Energies (0-0 of 0)

Calculated Solvation Free Energy

Submit New Solvation Free Energy Computation

Contact

Contributors

Automated Topology Builder (ATB) and Repository
Version 3.0

C₁₀H₁₂N₅O₁₁P₂ | MD Topology | NMR | X-Ray

¹H NMR Spectrum