MD Topology | NMR | X-Ray

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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)		2000	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	NA (hh:mm:ss)

Molecule Information
Molecular Dynamics (MD) Files

Molecule Information


Molecule Type	amino acid
Residue Name (RNME)	YNN
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	26
Net Charge	0
Forcefield	multiple
Molecule ID	17235
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
Upload Date	2014-02-03 13:07:15
Literature Reference	Drazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, Bojan Zagrovic; A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications; PLOS Computational Biology, 2013, 9 (7), e1003154

Topology History

Other conformers for this molecule (1-100 of 633)

The highlighted row is the currently viewed molecule with the following conditions:
Green: the current molecule has the lowest QM energy in the set.
Yellow: the current molecule is within 2 kJ.mol^-1 of the minimum energy.
Red: the current molecule is above 2 kJ.mol^-1 of the minimum energy.

Compare All Topologies (633)RMSD Matrix (633)

Molid	Formula	Iupac	Common Name	Atoms >	Charge	Curation	Visibility	Δ Qm Optimized Energy (kJ.mol^-1)	Compare
1596	None	-	-	3	0	Manual*	Public	N/A	Compare with
1646	None	-	-	3	0	Manual*	Public	N/A	Compare with
1593	None	-	-	3	0	Manual*	Public	N/A	Compare with
3923	None	-	-	4	0	Manual	Public	N/A	Compare with
1657	None	-	-	5	0	Manual*	Public	N/A	Compare with
1595	None	-	-	5	0	Manual*	Public	N/A	Compare with
4182	None	-	-	5	0	Manual*	Public	N/A	Compare with
1649	None	-	-	5	0	Manual*	Public	N/A	Compare with
1598	None	-	-	6	0	Manual*	Public	N/A	Compare with
564	None	-	-	6	0	Manual*	Public	N/A	Compare with
3485	None	-	-	6	0	Manual*	Public	N/A	Compare with
569	None	-	-	8	0	Manual*	Public	N/A	Compare with
1664	None	-	-	8	0	Manual*	Public	N/A	Compare with
3587	None	-	-	9	0	Manual*	Public	N/A	Compare with
1655	None	-	-	9	0	Manual*	Public	N/A	Compare with
17293	None	-	-	9	-1	Manual	Public	N/A	Compare with
17296	None	-	-	9	-1	Manual	Public	N/A	Compare with
562	None	-	-	9	0	Manual*	Public	N/A	Compare with
565	None	-	-	9	0	Manual*	Public	N/A	Compare with
17295	None	-	-	9	-1	Manual	Public	N/A	Compare with
17294	None	-	-	9	-1	Manual	Public	N/A	Compare with
3486	None	-	-	9	0	Manual*	Public	N/A	Compare with
1651	None	-	-	10	0	Manual*	Public	N/A	Compare with
567	None	-	-	10	0	Manual*	Public	N/A	Compare with
1594	None	-	-	10	0	Manual*	Public	N/A	Compare with
578	None	-	-	10	0	Manual*	Public	N/A	Compare with
570	None	-	-	11	0	Manual*	Public	N/A	Compare with
9371	None	-	-	11	-2	Manual*	Public	N/A	Compare with
566	None	-	-	12	0	Manual*	Public	N/A	Compare with
17364	None	-	-	12	0	Manual	Public	N/A	Compare with
3487	None	-	-	12	0	Manual*	Public	N/A	Compare with
17363	None	-	-	12	0	Manual	Public	N/A	Compare with
17362	None	-	-	12	0	Manual	Public	N/A	Compare with
17361	None	-	-	12	0	Manual	Public	N/A	Compare with
9377	None	-	-	12	-2	Manual*	Public	N/A	Compare with
582	None	-	-	12	0	Manual*	Public	N/A	Compare with
6460	None	-	-	12	0	Manual	Public	N/A	Compare with
580	None	-	-	12	0	Manual*	Public	N/A	Compare with
3488	None	-	-	12	0	Manual*	Public	N/A	Compare with
216	None	-	-	13	0	Manual*	Public	N/A	Compare with
169	None	-	-	13	0	Manual*	Public	N/A	Compare with
163	None	-	-	13	0	Manual*	Public	N/A	Compare with
6458	None	-	-	13	0	Manual	Public	N/A	Compare with
211	None	-	-	14	0	Manual*	Public	N/A	Compare with
172	None	-	-	14	0	Manual*	Public	N/A	Compare with
571	None	-	-	14	0	Manual*	Public	N/A	Compare with
171	None	-	-	14	0	Manual*	Public	N/A	Compare with
167	None	-	-	14	-1	Manual*	Public	N/A	Compare with
170	None	-	-	14	0	Manual*	Public	N/A	Compare with
2749	None	-	-	14	0	Manual*	Public	N/A	Compare with
17551	None	-	-	15	-1	Manual	Public	N/A	Compare with
3496	None	-	-	15	0	Manual*	Public	N/A	Compare with
17186	None	-	-	15	0	Manual	Public	N/A	Compare with
3504	None	-	-	15	0	Manual*	Public	N/A	Compare with
17352	None	-	-	15	0	Manual	Public	N/A	Compare with
17483	None	-	-	15	0	Manual	Public	N/A	Compare with
17349	None	-	-	15	0	Manual	Public	N/A	Compare with
17482	None	-	-	15	0	Manual	Public	N/A	Compare with
17552	None	-	-	15	-1	Manual	Public	N/A	Compare with
17260	None	-	-	15	-1	Manual	Public	N/A	Compare with
17351	None	-	-	15	0	Manual	Public	N/A	Compare with
17429	None	-	-	15	0	Manual	Public	N/A	Compare with
583	None	-	-	15	0	Manual*	Public	N/A	Compare with
17258	None	-	-	15	-1	Manual	Public	N/A	Compare with
17259	None	-	-	15	-1	Manual	Public	N/A	Compare with
6461	None	-	-	15	0	Manual	Public	N/A	Compare with
17185	None	-	-	15	0	Manual	Public	N/A	Compare with
17187	None	-	-	15	0	Manual	Public	N/A	Compare with
17549	None	-	-	15	-1	Manual	Public	N/A	Compare with
17481	None	-	-	15	0	Manual	Public	N/A	Compare with
17257	None	-	-	15	-1	Manual	Public	N/A	Compare with
584	None	-	-	15	0	Manual*	Public	N/A	Compare with
17431	None	-	-	15	0	Manual	Public	N/A	Compare with
17432	None	-	-	15	0	Manual	Public	N/A	Compare with
17430	None	-	-	15	0	Manual	Public	N/A	Compare with
17350	None	-	-	15	0	Manual	Public	N/A	Compare with
168	None	-	-	15	0	Manual*	Public	N/A	Compare with
17188	None	-	-	15	0	Manual	Public	N/A	Compare with
17550	None	-	-	15	-1	Manual	Public	N/A	Compare with
17484	None	-	-	15	0	Manual	Public	N/A	Compare with
3410	None	-	-	15	0	Manual*	Public	N/A	Compare with
1604	None	-	-	16	0	Manual*	Public	N/A	Compare with
6459	None	-	-	16	0	Manual	Public	N/A	Compare with
619	None	-	-	16	0	Manual*	Public	N/A	Compare with
17401	None	-	-	16	-1	Manual	Public	N/A	Compare with
17151	None	-	-	16	-1	Manual	Public	N/A	Compare with
17240	None	-	-	16	-1	Manual	Public	N/A	Compare with
17237	None	-	-	16	-1	Manual	Public	N/A	Compare with
17403	None	-	-	16	-1	Manual	Public	N/A	Compare with
17149	None	-	-	16	-1	Manual	Public	N/A	Compare with
17150	None	-	-	16	-1	Manual	Public	N/A	Compare with
17152	None	-	-	16	-1	Manual	Public	N/A	Compare with
581	None	-	-	16	0	Manual*	Public	N/A	Compare with
17402	None	-	-	16	-1	Manual	Public	N/A	Compare with
17239	None	-	-	16	-1	Manual	Public	N/A	Compare with
17404	None	-	-	16	-1	Manual	Public	N/A	Compare with
568	None	-	-	16	0	Manual*	Public	N/A	Compare with
17238	None	-	-	16	-1	Manual	Public	N/A	Compare with
17332	None	-	-	17	-2	Manual	Public	N/A	Compare with
17154	None	-	-	17	0	Manual	Public	N/A	Compare with