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	17233
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:15
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 (101-200 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
3924	None	-	-	176	0	Manual	Public	N/A	Compare with
17250	None	-	-	23	-2	Manual	Public	N/A	Compare with
17282	None	-	-	23	0	Manual	Public	N/A	Compare with
17403	None	-	-	16	-1	Manual	Public	N/A	Compare with
17435	None	-	-	21	-1	Manual	Public	N/A	Compare with
1571	None	-	-	147	0	Manual*	Public	N/A	Compare with
1649	None	-	-	5	0	Manual*	Public	N/A	Compare with
17167	None	-	-	27	0	Manual	Public	N/A	Compare with
17199	None	-	-	26	1	Manual	Public	N/A	Compare with
17352	None	-	-	15	0	Manual	Public	N/A	Compare with
165	None	-	-	26	0	Manual*	Public	N/A	Compare with
17384	None	-	-	23	0	Manual	Public	N/A	Compare with
568	None	-	-	16	0	Manual*	Public	N/A	Compare with
17537	None	-	-	19	-2	Manual	Public	N/A	Compare with
5100	None	-	-	58	-6	Manual*	Public	N/A	Compare with
17148	None	-	-	33	1	Manual	Public	N/A	Compare with
17301	None	-	-	25	0	Manual	Public	N/A	Compare with
17182	None	-	-	23	0	Manual	Public	N/A	Compare with
17214	None	-	-	29	0	Manual	Public	N/A	Compare with
17367	None	-	-	29	0	Manual	Public	N/A	Compare with
204	None	-	-	22	0	Manual*	Public	N/A	Compare with
17399	None	-	-	21	0	Manual	Public	N/A	Compare with
17520	None	-	-	28	0	Manual	Public	N/A	Compare with
584	None	-	-	15	0	Manual*	Public	N/A	Compare with
17552	None	-	-	15	-1	Manual	Public	N/A	Compare with
6459	None	-	-	16	0	Manual	Public	N/A	Compare with
17163	None	-	-	23	0	Manual	Public	N/A	Compare with
17284	None	-	-	23	0	Manual	Public	N/A	Compare with
17316	None	-	-	32	0	Manual	Public	N/A	Compare with
17469	None	-	-	24	0	Manual	Public	N/A	Compare with
17501	None	-	-	32	0	Manual	Public	N/A	Compare with
1655	None	-	-	9	0	Manual*	Public	N/A	Compare with
3408	None	-	-	24	0	Manual*	Public	N/A	Compare with
17233	None	-	-	26	0	Manual	Public	N/A	Compare with
17265	None	-	-	19	0	Manual	Public	N/A	Compare with
17418	None	-	-	21	0	Manual	Public	N/A	Compare with
17450	None	-	-	23	0	Manual	Public	N/A	Compare with
1551	None	-	-	153	0	Manual*	Public	N/A	Compare with
1590	None	-	-	147	0	Manual*	Public	N/A	Compare with
17484	None	-	-	15	0	Manual	Public	N/A	Compare with
17516	None	-	-	26	0	Manual	Public	N/A	Compare with
2018	None	-	-	90	-1	Manual*	Public	N/A	Compare with
3587	None	-	-	9	0	Manual*	Public	N/A	Compare with
17248	None	-	-	27	-2	Manual	Public	N/A	Compare with
17280	None	-	-	24	1	Manual	Public	N/A	Compare with
17401	None	-	-	16	-1	Manual	Public	N/A	Compare with
17433	None	-	-	21	-1	Manual	Public	N/A	Compare with
1567	None	-	-	119	0	Manual*	Public	N/A	Compare with
1642	None	-	-	18	0	Manual*	Public	N/A	Compare with
17165	None	-	-	27	0	Manual	Public	N/A	Compare with
17197	None	-	-	26	1	Manual	Public	N/A	Compare with
17350	None	-	-	15	0	Manual	Public	N/A	Compare with
163	None	-	-	13	0	Manual*	Public	N/A	Compare with
17382	None	-	-	23	0	Manual	Public	N/A	Compare with
566	None	-	-	12	0	Manual*	Public	N/A	Compare with
17535	None	-	-	24	0	Manual	Public	N/A	Compare with
5031	None	-	-	78	0	Manual*	Public	N/A	Compare with
17146	None	-	-	33	1	Manual	Public	N/A	Compare with
17299	None	-	-	18	0	Manual	Public	N/A	Compare with
17331	None	-	-	17	-2	Manual	Public	N/A	Compare with
17212	None	-	-	27	-2	Manual	Public	N/A	Compare with
17365	None	-	-	29	0	Manual	Public	N/A	Compare with
178	None	-	-	21	1	Manual*	Public	N/A	Compare with
17397	None	-	-	21	0	Manual	Public	N/A	Compare with
582	None	-	-	12	0	Manual*	Public	N/A	Compare with
17550	None	-	-	15	-1	Manual	Public	N/A	Compare with
6451	None	-	-	27	0	Manual	Public	N/A	Compare with
17161	None	-	-	23	0	Manual	Public	N/A	Compare with
17314	None	-	-	32	0	Manual	Public	N/A	Compare with
17467	None	-	-	31	0	Manual	Public	N/A	Compare with
17499	None	-	-	25	0	Manual	Public	N/A	Compare with
2920	None	-	-	27	1	Manual	Public	N/A	Compare with
17231	None	-	-	27	0	Manual	Public	N/A	Compare with
17263	None	-	-	17	0	Manual	Public	N/A	Compare with
17416	None	-	-	24	1	Manual	Public	N/A	Compare with
17448	None	-	-	28	0	Manual	Public	N/A	Compare with
1548	None	-	-	24	0	Manual*	Public	N/A	Compare with
1588	None	-	-	125	0	Manual*	Public	N/A	Compare with
17180	None	-	-	20	-1	Manual	Public	N/A	Compare with
17514	None	-	-	26	0	Manual	Public	N/A	Compare with
1771	None	-	-	186	-1	Manual*	Public	N/A	Compare with
3504	None	-	-	15	0	Manual*	Public	N/A	Compare with
17246	None	-	-	27	-2	Manual	Public	N/A	Compare with
17278	None	-	-	24	1	Manual	Public	N/A	Compare with
17431	None	-	-	15	0	Manual	Public	N/A	Compare with
1565	None	-	-	113	0	Manual*	Public	N/A	Compare with
1608	None	-	-	20	0	Manual*	Public	N/A	Compare with
17195	None	-	-	28	0	Manual	Public	N/A	Compare with
17348	None	-	-	20	-2	Manual	Public	N/A	Compare with
17380	None	-	-	28	-1	Manual	Public	N/A	Compare with
564	None	-	-	6	0	Manual*	Public	N/A	Compare with
17533	None	-	-	24	0	Manual	Public	N/A	Compare with
4908	None	-	-	40	-4	Manual*	Public	N/A	Compare with
9643	None	-	-	103	1	Manual	Public	N/A	Compare with
17297	None	-	-	18	0	Manual	Public	N/A	Compare with
17329	None	-	-	17	-2	Manual	Public	N/A	Compare with
17482	None	-	-	15	0	Manual	Public	N/A	Compare with
17363	None	-	-	12	0	Manual	Public	N/A	Compare with
176	None	-	-	20	0	Manual*	Public	N/A	Compare with
17395	None	-	-	24	-1	Manual	Public	N/A	Compare with