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)	YCH
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	24
Net Charge	0
Forcefield	multiple
Molecule ID	17534
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:19
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	Curation	Visibility	Δ Qm Optimized Energy (kJ.mol^-1)	Compare
3408	None	-	-	24	Manual*	Public	N/A	Compare with
3488	None	-	-	12	Manual*	Public	N/A	Compare with
3496	None	-	-	15	Manual*	Public	N/A	Compare with
3924	None	-	-	176	Manual	Public	N/A	Compare with
3923	None	-	-	4	Manual	Public	N/A	Compare with
3587	None	-	-	9	Manual*	Public	N/A	Compare with
3505	None	-	-	18	Manual*	Public	N/A	Compare with
3504	None	-	-	15	Manual*	Public	N/A	Compare with
3502	None	-	-	19	Manual*	Public	N/A	Compare with
3501	None	-	-	21	Manual*	Public	N/A	Compare with
3500	None	-	-	18	Manual*	Public	N/A	Compare with
6451	None	-	-	27	Manual	Public	N/A	Compare with
1510	None	-	-	161	Manual*	Public	N/A	Compare with
578	None	-	-	10	Manual*	Public	N/A	Compare with
577	None	-	-	37	Manual*	Public	N/A	Compare with
576	None	-	-	26	Manual*	Public	N/A	Compare with
575	None	-	-	20	Manual*	Public	N/A	Compare with
574	None	-	-	17	Manual*	Public	N/A	Compare with
573	None	-	-	20	Manual*	Public	N/A	Compare with
572	None	-	-	17	Manual*	Public	N/A	Compare with
571	None	-	-	14	Manual*	Public	N/A	Compare with
570	None	-	-	11	Manual*	Public	N/A	Compare with
580	None	-	-	12	Manual*	Public	N/A	Compare with
581	None	-	-	16	Manual*	Public	N/A	Compare with
1507	None	-	-	138	Manual*	Public	N/A	Compare with
1506	None	-	-	134	Manual*	Public	N/A	Compare with
1505	None	-	-	130	Manual*	Public	N/A	Compare with
1503	None	-	-	118	Manual*	Public	N/A	Compare with
1502	None	-	-	106	Manual*	Public	N/A	Compare with
619	None	-	-	16	Manual*	Public	N/A	Compare with
584	None	-	-	15	Manual*	Public	N/A	Compare with
583	None	-	-	15	Manual*	Public	N/A	Compare with
582	None	-	-	12	Manual*	Public	N/A	Compare with
564	None	-	-	6	Manual*	Public	N/A	Compare with
562	None	-	-	9	Manual*	Public	N/A	Compare with
176	None	-	-	20	Manual*	Public	N/A	Compare with
175	None	-	-	19	Manual*	Public	N/A	Compare with
17165	None	-	-	27	Manual	Public	N/A	Compare with
173	None	-	-	20	Manual*	Public	N/A	Compare with
172	None	-	-	14	Manual*	Public	N/A	Compare with
171	None	-	-	14	Manual*	Public	N/A	Compare with
169	None	-	-	13	Manual*	Public	N/A	Compare with
168	None	-	-	15	Manual*	Public	N/A	Compare with
166	None	-	-	17	Manual*	Public	N/A	Compare with
177	None	-	-	20	Manual*	Public	N/A	Compare with
205	None	-	-	24	Manual*	Public	N/A	Compare with
216	None	-	-	13	Manual*	Public	N/A	Compare with
215	None	-	-	19	Manual*	Public	N/A	Compare with
214	None	-	-	24	Manual*	Public	N/A	Compare with
213	None	-	-	27	Manual*	Public	N/A	Compare with
212	None	-	-	17	Manual*	Public	N/A	Compare with
211	None	-	-	14	Manual*	Public	N/A	Compare with
210	None	-	-	17	Manual*	Public	N/A	Compare with
208	None	-	-	23	Manual*	Public	N/A	Compare with
207	None	-	-	20	Manual*	Public	N/A	Compare with
165	None	-	-	26	Manual*	Public	N/A	Compare with
1511	None	-	-	131	Manual*	Public	N/A	Compare with
1605	None	-	-	23	Manual*	Public	N/A	Compare with
1589	None	-	-	131	Manual*	Public	N/A	Compare with
1588	None	-	-	125	Manual*	Public	N/A	Compare with
1587	None	-	-	155	Manual*	Public	N/A	Compare with
1586	None	-	-	149	Manual*	Public	N/A	Compare with
1584	None	-	-	137	Manual*	Public	N/A	Compare with
1583	None	-	-	125	Manual*	Public	N/A	Compare with
1582	None	-	-	119	Manual*	Public	N/A	Compare with
1581	None	-	-	149	Manual*	Public	N/A	Compare with
1579	None	-	-	143	Manual*	Public	N/A	Compare with
1590	None	-	-	147	Manual*	Public	N/A	Compare with
1591	None	-	-	137	Manual*	Public	N/A	Compare with
1604	None	-	-	16	Manual*	Public	N/A	Compare with
1603	None	-	-	17	Manual*	Public	N/A	Compare with
1602	None	-	-	20	Manual*	Public	N/A	Compare with
1601	None	-	-	17	Manual*	Public	N/A	Compare with
1598	None	-	-	6	Manual*	Public	N/A	Compare with
1596	None	-	-	3	Manual*	Public	N/A	Compare with
1595	None	-	-	5	Manual*	Public	N/A	Compare with
1594	None	-	-	10	Manual*	Public	N/A	Compare with
1593	None	-	-	3	Manual*	Public	N/A	Compare with
1578	None	-	-	144	Manual*	Public	N/A	Compare with
1577	None	-	-	138	Manual*	Public	N/A	Compare with
1561	None	-	-	119	Manual*	Public	N/A	Compare with
1560	None	-	-	123	Manual*	Public	N/A	Compare with
1558	None	-	-	137	Manual*	Public	N/A	Compare with
1557	None	-	-	131	Manual*	Public	N/A	Compare with
1556	None	-	-	143	Manual*	Public	N/A	Compare with
1538	None	-	-	161	Manual*	Public	N/A	Compare with
1532	None	-	-	149	Manual*	Public	N/A	Compare with
1526	None	-	-	143	Manual*	Public	N/A	Compare with
1525	None	-	-	147	Manual*	Public	N/A	Compare with
1562	None	-	-	125	Manual*	Public	N/A	Compare with
1563	None	-	-	137	Manual*	Public	N/A	Compare with
1576	None	-	-	129	Manual*	Public	N/A	Compare with
1574	None	-	-	123	Manual*	Public	N/A	Compare with
1572	None	-	-	153	Manual*	Public	N/A	Compare with
1571	None	-	-	147	Manual*	Public	N/A	Compare with
1570	None	-	-	125	Manual*	Public	N/A	Compare with
1567	None	-	-	119	Manual*	Public	N/A	Compare with
1566	None	-	-	129	Manual*	Public	N/A	Compare with
1565	None	-	-	113	Manual*	Public	N/A	Compare with
1564	None	-	-	143	Manual*	Public	N/A	Compare with