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 building block
Residue Name (RNME)	H31
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	24
Net Charge	-1
Forcefield	multiple
Molecule ID	17394
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:17
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 (601-633 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
17364	None	-	-	12	0	Manual	Public	N/A	Compare with
566	None	-	-	12	0	Manual*	Public	N/A	Compare with
6460	None	-	-	12	0	Manual	Public	N/A	Compare with
9377	None	-	-	12	-2	Manual*	Public	N/A	Compare with
3488	None	-	-	12	0	Manual*	Public	N/A	Compare with
9371	None	-	-	11	-2	Manual*	Public	N/A	Compare with
570	None	-	-	11	0	Manual*	Public	N/A	Compare with
1594	None	-	-	10	0	Manual*	Public	N/A	Compare with
567	None	-	-	10	0	Manual*	Public	N/A	Compare with
578	None	-	-	10	0	Manual*	Public	N/A	Compare with
1651	None	-	-	10	0	Manual*	Public	N/A	Compare with
3587	None	-	-	9	0	Manual*	Public	N/A	Compare with
17296	None	-	-	9	-1	Manual	Public	N/A	Compare with
3486	None	-	-	9	0	Manual*	Public	N/A	Compare with
1655	None	-	-	9	0	Manual*	Public	N/A	Compare with
17294	None	-	-	9	-1	Manual	Public	N/A	Compare with
17293	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
569	None	-	-	8	0	Manual*	Public	N/A	Compare with
1664	None	-	-	8	0	Manual*	Public	N/A	Compare with
564	None	-	-	6	0	Manual*	Public	N/A	Compare with
1598	None	-	-	6	0	Manual*	Public	N/A	Compare with
3485	None	-	-	6	0	Manual*	Public	N/A	Compare with
1649	None	-	-	5	0	Manual*	Public	N/A	Compare with
1595	None	-	-	5	0	Manual*	Public	N/A	Compare with
1657	None	-	-	5	0	Manual*	Public	N/A	Compare with
4182	None	-	-	5	0	Manual*	Public	N/A	Compare with
3923	None	-	-	4	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
1596	None	-	-	3	0	Manual*	Public	N/A	Compare with