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)	W7H
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	28
Net Charge	0
Forcefield	multiple
Molecule ID	17456
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
Upload Date	2014-02-03 13:07:18
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 (301-400 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
17466	None	-	-	31	0	Manual	Public	N/A	Compare with
2921	None	-	-	75	-2	Manual	Public	N/A	Compare with
17402	None	-	-	16	-1	Manual	Public	N/A	Compare with
17404	None	-	-	16	-1	Manual	Public	N/A	Compare with
17405	None	-	-	28	-1	Manual	Public	N/A	Compare with
3923	None	-	-	4	0	Manual	Public	N/A	Compare with
3924	None	-	-	176	0	Manual	Public	N/A	Compare with
3947	None	-	-	127	-1	Manual	Public	N/A	Compare with
17410	None	-	-	18	0	Manual	Public	N/A	Compare with
17413	None	-	-	24	1	Manual	Public	N/A	Compare with
4213	None	-	-	61	0	Manual	Public	N/A	Compare with
17415	None	-	-	24	1	Manual	Public	N/A	Compare with
17401	None	-	-	16	-1	Manual	Public	N/A	Compare with
17398	None	-	-	21	0	Manual	Public	N/A	Compare with
17397	None	-	-	21	0	Manual	Public	N/A	Compare with
17377	None	-	-	28	-1	Manual	Public	N/A	Compare with
17378	None	-	-	28	-1	Manual	Public	N/A	Compare with
17380	None	-	-	28	-1	Manual	Public	N/A	Compare with
17381	None	-	-	23	0	Manual	Public	N/A	Compare with
17384	None	-	-	23	0	Manual	Public	N/A	Compare with
17385	None	-	-	20	-2	Manual	Public	N/A	Compare with
17387	None	-	-	20	-2	Manual	Public	N/A	Compare with
17388	None	-	-	20	-2	Manual	Public	N/A	Compare with
17394	None	-	-	24	-1	Manual	Public	N/A	Compare with
17395	None	-	-	24	-1	Manual	Public	N/A	Compare with
17416	None	-	-	24	1	Manual	Public	N/A	Compare with
17421	None	-	-	21	0	Manual	Public	N/A	Compare with
17446	None	-	-	28	0	Manual	Public	N/A	Compare with
17447	None	-	-	28	0	Manual	Public	N/A	Compare with
5639	None	-	-	127	0	Manual	Public	N/A	Compare with
17454	None	-	-	28	0	Manual	Public	N/A	Compare with
17456	None	-	-	28	0	Manual	Public	N/A	Compare with
17457	None	-	-	28	0	Manual	Public	N/A	Compare with
17460	None	-	-	28	0	Manual	Public	N/A	Compare with
17461	None	-	-	22	0	Manual	Public	N/A	Compare with
17463	None	-	-	22	0	Manual	Public	N/A	Compare with
17464	None	-	-	22	0	Manual	Public	N/A	Compare with
17444	None	-	-	28	1	Manual	Public	N/A	Compare with
17443	None	-	-	28	1	Manual	Public	N/A	Compare with
17440	None	-	-	25	0	Manual	Public	N/A	Compare with
17422	None	-	-	21	0	Manual	Public	N/A	Compare with
17424	None	-	-	21	0	Manual	Public	N/A	Compare with
17425	None	-	-	34	1	Manual	Public	N/A	Compare with
17428	None	-	-	34	1	Manual	Public	N/A	Compare with
17429	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
17436	None	-	-	21	-1	Manual	Public	N/A	Compare with
17437	None	-	-	25	0	Manual	Public	N/A	Compare with
17439	None	-	-	25	0	Manual	Public	N/A	Compare with
17468	None	-	-	31	0	Manual	Public	N/A	Compare with
17469	None	-	-	24	0	Manual	Public	N/A	Compare with
17506	None	-	-	29	0	Manual	Public	N/A	Compare with
17509	None	-	-	27	0	Manual	Public	N/A	Compare with
17510	None	-	-	27	0	Manual	Public	N/A	Compare with
17512	None	-	-	27	0	Manual	Public	N/A	Compare with
17513	None	-	-	26	0	Manual	Public	N/A	Compare with
17517	None	-	-	28	0	Manual	Public	N/A	Compare with
17518	None	-	-	28	0	Manual	Public	N/A	Compare with
17520	None	-	-	28	0	Manual	Public	N/A	Compare with
17521	None	-	-	21	-1	Manual	Public	N/A	Compare with
17524	None	-	-	21	-1	Manual	Public	N/A	Compare with
17505	None	-	-	29	0	Manual	Public	N/A	Compare with
17503	None	-	-	32	0	Manual	Public	N/A	Compare with
17502	None	-	-	32	0	Manual	Public	N/A	Compare with
17471	None	-	-	24	0	Manual	Public	N/A	Compare with
17472	None	-	-	24	0	Manual	Public	N/A	Compare with
17478	None	-	-	27	-1	Manual	Public	N/A	Compare with
17481	None	-	-	15	0	Manual	Public	N/A	Compare with
17485	None	-	-	21	0	Manual	Public	N/A	Compare with
17488	None	-	-	21	0	Manual	Public	N/A	Compare with
17493	None	-	-	19	0	Manual	Public	N/A	Compare with
17494	None	-	-	19	0	Manual	Public	N/A	Compare with
17496	None	-	-	19	0	Manual	Public	N/A	Compare with
17497	None	-	-	25	0	Manual	Public	N/A	Compare with
17525	None	-	-	18	0	Manual	Public	N/A	Compare with
17527	None	-	-	18	0	Manual	Public	N/A	Compare with
17359	None	-	-	30	0	Manual	Public	N/A	Compare with
17360	None	-	-	30	0	Manual	Public	N/A	Compare with
2671	None	-	-	47	-3	Manual	Public	N/A	Compare with
2672	None	-	-	39	0	Manual	Public	N/A	Compare with
2694	None	-	-	77	-3	Manual	Public	N/A	Compare with
17366	None	-	-	29	0	Manual	Public	N/A	Compare with
17368	None	-	-	29	0	Manual	Public	N/A	Compare with
17369	None	-	-	18	-1	Manual	Public	N/A	Compare with
17372	None	-	-	18	-1	Manual	Public	N/A	Compare with
2919	None	-	-	52	-1	Manual	Public	N/A	Compare with
17356	None	-	-	23	0	Manual	Public	N/A	Compare with
17355	None	-	-	23	0	Manual	Public	N/A	Compare with
17353	None	-	-	23	0	Manual	Public	N/A	Compare with
17337	None	-	-	18	0	Manual	Public	N/A	Compare with
17338	None	-	-	18	0	Manual	Public	N/A	Compare with
17340	None	-	-	18	0	Manual	Public	N/A	Compare with
17341	None	-	-	23	-2	Manual	Public	N/A	Compare with
17344	None	-	-	23	-2	Manual	Public	N/A	Compare with
17345	None	-	-	20	-2	Manual	Public	N/A	Compare with
17347	None	-	-	20	-2	Manual	Public	N/A	Compare with
17348	None	-	-	20	-2	Manual	Public	N/A	Compare with
17352	None	-	-	15	0	Manual	Public	N/A	Compare with
2920	None	-	-	27	1	Manual	Public	N/A	Compare with