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)	CAM
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	18
Net Charge	0
Forcefield	multiple
Molecule ID	17300
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
Upload Date	2014-02-03 13:07:16
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
1590	None	-	-	147	0	Manual*	Public	N/A	Compare with
1532	None	-	-	149	0	Manual*	Public	N/A	Compare with
1552	None	-	-	149	0	Manual*	Public	N/A	Compare with
1581	None	-	-	149	0	Manual*	Public	N/A	Compare with
1586	None	-	-	149	0	Manual*	Public	N/A	Compare with
1572	None	-	-	153	0	Manual*	Public	N/A	Compare with
1551	None	-	-	153	0	Manual*	Public	N/A	Compare with
1587	None	-	-	155	0	Manual*	Public	N/A	Compare with
1553	None	-	-	155	0	Manual*	Public	N/A	Compare with
1554	None	-	-	155	0	Manual*	Public	N/A	Compare with
5810	None	-	-	156	-12	Manual*	Public	N/A	Compare with
4580	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4582	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4581	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4593	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4579	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4578	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4592	None	-	-	161	-8	Manual*	Public	N/A	Compare with
1510	None	-	-	161	0	Manual*	Public	N/A	Compare with
1538	None	-	-	161	0	Manual*	Public	N/A	Compare with
1555	None	-	-	167	0	Manual*	Public	N/A	Compare with
2109	None	-	-	171	-2	Manual*	Public	N/A	Compare with
3924	None	-	-	176	0	Manual	Public	N/A	Compare with
4013	None	-	-	176	0	Manual*	Public	N/A	Compare with
1771	None	-	-	186	-1	Manual*	Public	N/A	Compare with
2280	None	-	-	186	-1	Manual*	Public	N/A	Compare with
2166	None	-	-	186	-1	Manual*	Public	N/A	Compare with
21025	None	-	-	209	-4	Manual*	Public	N/A	Compare with
4604	None	-	-	217	0	Manual*	Public	N/A	Compare with
2276	None	-	-	363	-2	Manual*	Public	N/A	Compare with
5814	None	-	-	381	1	Manual*	Public	N/A	Compare with
30988	None	-	-	1456	0	Template	Public	N/A	Compare with
8099	None	-	-	3218	0	Manual*	Public	N/A	Compare with