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)	SDH
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	12
Net Charge	0
Forcefield	multiple
Molecule ID	17364
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
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
17426	None	-	-	34	1	Manual	Public	N/A	Compare with
17443	None	-	-	28	1	Manual	Public	N/A	Compare with
17444	None	-	-	28	1	Manual	Public	N/A	Compare with
17414	None	-	-	24	1	Manual	Public	N/A	Compare with
7281	None	-	-	62	1	Manual*	Public	N/A	Compare with
7283	None	-	-	87	1	Manual*	Public	N/A	Compare with
7284	None	-	-	71	1	Manual*	Public	N/A	Compare with
17333	None	-	-	30	1	Manual	Public	N/A	Compare with
17334	None	-	-	30	1	Manual	Public	N/A	Compare with
17335	None	-	-	30	1	Manual	Public	N/A	Compare with
17336	None	-	-	30	1	Manual	Public	N/A	Compare with
9643	None	-	-	103	1	Manual	Public	N/A	Compare with
17145	None	-	-	33	1	Manual	Public	N/A	Compare with
17146	None	-	-	33	1	Manual	Public	N/A	Compare with
17147	None	-	-	33	1	Manual	Public	N/A	Compare with
17442	None	-	-	28	1	Manual	Public	N/A	Compare with
17441	None	-	-	28	1	Manual	Public	N/A	Compare with
17197	None	-	-	26	1	Manual	Public	N/A	Compare with
17427	None	-	-	34	1	Manual	Public	N/A	Compare with
17428	None	-	-	34	1	Manual	Public	N/A	Compare with
17219	None	-	-	31	1	Manual	Public	N/A	Compare with
17218	None	-	-	31	1	Manual	Public	N/A	Compare with
17217	None	-	-	31	1	Manual	Public	N/A	Compare with
5089	None	-	-	41	1	Manual*	Public	N/A	Compare with
17198	None	-	-	26	1	Manual	Public	N/A	Compare with
5814	None	-	-	381	1	Manual*	Public	N/A	Compare with
17204	None	-	-	33	1	Manual	Public	N/A	Compare with
17203	None	-	-	33	1	Manual	Public	N/A	Compare with
17202	None	-	-	33	1	Manual	Public	N/A	Compare with
17201	None	-	-	33	1	Manual	Public	N/A	Compare with
17200	None	-	-	26	1	Manual	Public	N/A	Compare with
17199	None	-	-	26	1	Manual	Public	N/A	Compare with
17148	None	-	-	33	1	Manual	Public	N/A	Compare with