MD Topology | NMR | X-Ray

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Processing Information

QM Processing Stage

Click table to toggle details.

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)	EME
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	22
Net Charge	0
Forcefield	multiple
Molecule ID	17462
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:18
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 (201-300 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
169	None	-	-	13	0	Manual*	Public	N/A	Compare with
168	None	-	-	15	0	Manual*	Public	N/A	Compare with
167	None	-	-	14	-1	Manual*	Public	N/A	Compare with
166	None	-	-	17	0	Manual*	Public	N/A	Compare with
165	None	-	-	26	0	Manual*	Public	N/A	Compare with
164	None	-	-	27	1	Manual*	Public	N/A	Compare with
204	None	-	-	22	0	Manual*	Public	N/A	Compare with
205	None	-	-	24	0	Manual*	Public	N/A	Compare with
206	None	-	-	25	1	Manual*	Public	N/A	Compare with
569	None	-	-	8	0	Manual*	Public	N/A	Compare with
568	None	-	-	16	0	Manual*	Public	N/A	Compare with
567	None	-	-	10	0	Manual*	Public	N/A	Compare with
566	None	-	-	12	0	Manual*	Public	N/A	Compare with
565	None	-	-	9	0	Manual*	Public	N/A	Compare with
564	None	-	-	6	0	Manual*	Public	N/A	Compare with
562	None	-	-	9	0	Manual*	Public	N/A	Compare with
216	None	-	-	13	0	Manual*	Public	N/A	Compare with
215	None	-	-	19	0	Manual*	Public	N/A	Compare with
214	None	-	-	24	0	Manual*	Public	N/A	Compare with
213	None	-	-	27	0	Manual*	Public	N/A	Compare with
212	None	-	-	17	0	Manual*	Public	N/A	Compare with
211	None	-	-	14	0	Manual*	Public	N/A	Compare with
210	None	-	-	17	0	Manual*	Public	N/A	Compare with
208	None	-	-	23	0	Manual*	Public	N/A	Compare with
207	None	-	-	20	0	Manual*	Public	N/A	Compare with
30988	None	-	-	1456	0	Template	Public	N/A	Compare with
2920	None	-	-	27	1	Manual	Public	N/A	Compare with
1733	None	-	-	81	0	Manual*	Public	N/A	Compare with
1732	None	-	-	73	0	Manual*	Public	N/A	Compare with
1731	None	-	-	74	0	Manual*	Public	N/A	Compare with
1680	None	-	-	30	0	Manual*	Public	N/A	Compare with
1679	None	-	-	31	0	Manual*	Public	N/A	Compare with
1678	None	-	-	35	0	Manual*	Public	N/A	Compare with
1677	None	-	-	34	0	Manual*	Public	N/A	Compare with
1668	None	-	-	27	0	Manual*	Public	N/A	Compare with
1664	None	-	-	8	0	Manual*	Public	N/A	Compare with
1657	None	-	-	5	0	Manual*	Public	N/A	Compare with
1655	None	-	-	9	0	Manual*	Public	N/A	Compare with
1651	None	-	-	10	0	Manual*	Public	N/A	Compare with
1649	None	-	-	5	0	Manual*	Public	N/A	Compare with
1646	None	-	-	3	0	Manual*	Public	N/A	Compare with
1642	None	-	-	18	0	Manual*	Public	N/A	Compare with
1611	None	-	-	18	0	Manual*	Public	N/A	Compare with
1736	None	-	-	80	0	Manual*	Public	N/A	Compare with
1738	None	-	-	77	0	Manual*	Public	N/A	Compare with
1771	None	-	-	186	-1	Manual*	Public	N/A	Compare with
2919	None	-	-	52	-1	Manual	Public	N/A	Compare with
2752	None	-	-	19	0	Manual*	Public	N/A	Compare with
2749	None	-	-	14	0	Manual*	Public	N/A	Compare with
2747	None	-	-	20	0	Manual*	Public	N/A	Compare with
2745	None	-	-	24	0	Manual*	Public	N/A	Compare with
2694	None	-	-	77	-3	Manual	Public	N/A	Compare with
2672	None	-	-	39	0	Manual	Public	N/A	Compare with
2671	None	-	-	47	-3	Manual	Public	N/A	Compare with
2280	None	-	-	186	-1	Manual*	Public	N/A	Compare with
2276	None	-	-	363	-2	Manual*	Public	N/A	Compare with
2182	None	-	-	41	-4	Manual*	Public	N/A	Compare with
2172	None	-	-	26	-1	Manual*	Public	N/A	Compare with
2166	None	-	-	186	-1	Manual*	Public	N/A	Compare with
2109	None	-	-	171	-2	Manual*	Public	N/A	Compare with
2018	None	-	-	90	-1	Manual*	Public	N/A	Compare with
2002	None	-	-	24	0	Manual*	Public	N/A	Compare with
1608	None	-	-	20	0	Manual*	Public	N/A	Compare with
1606	None	-	-	20	0	Manual*	Public	N/A	Compare with
1605	None	-	-	23	0	Manual*	Public	N/A	Compare with
1579	None	-	-	143	0	Manual*	Public	N/A	Compare with
1578	None	-	-	144	0	Manual*	Public	N/A	Compare with
1577	None	-	-	138	0	Manual*	Public	N/A	Compare with
1576	None	-	-	129	0	Manual*	Public	N/A	Compare with
1574	None	-	-	123	0	Manual*	Public	N/A	Compare with
1572	None	-	-	153	0	Manual*	Public	N/A	Compare with
1571	None	-	-	147	0	Manual*	Public	N/A	Compare with
1570	None	-	-	125	0	Manual*	Public	N/A	Compare with
1567	None	-	-	119	0	Manual*	Public	N/A	Compare with
1566	None	-	-	129	0	Manual*	Public	N/A	Compare with
1565	None	-	-	113	0	Manual*	Public	N/A	Compare with
1564	None	-	-	143	0	Manual*	Public	N/A	Compare with
1563	None	-	-	137	0	Manual*	Public	N/A	Compare with
1562	None	-	-	125	0	Manual*	Public	N/A	Compare with
1561	None	-	-	119	0	Manual*	Public	N/A	Compare with
1560	None	-	-	123	0	Manual*	Public	N/A	Compare with
1581	None	-	-	149	0	Manual*	Public	N/A	Compare with
1582	None	-	-	119	0	Manual*	Public	N/A	Compare with
1583	None	-	-	125	0	Manual*	Public	N/A	Compare with
1604	None	-	-	16	0	Manual*	Public	N/A	Compare with
1603	None	-	-	17	0	Manual*	Public	N/A	Compare with
1602	None	-	-	20	0	Manual*	Public	N/A	Compare with
1601	None	-	-	17	0	Manual*	Public	N/A	Compare with
1598	None	-	-	6	0	Manual*	Public	N/A	Compare with
1596	None	-	-	3	0	Manual*	Public	N/A	Compare with
1595	None	-	-	5	0	Manual*	Public	N/A	Compare with
1594	None	-	-	10	0	Manual*	Public	N/A	Compare with
1593	None	-	-	3	0	Manual*	Public	N/A	Compare with
1591	None	-	-	137	0	Manual*	Public	N/A	Compare with
1590	None	-	-	147	0	Manual*	Public	N/A	Compare with
1589	None	-	-	131	0	Manual*	Public	N/A	Compare with
1588	None	-	-	125	0	Manual*	Public	N/A	Compare with
1587	None	-	-	155	0	Manual*	Public	N/A	Compare with
1586	None	-	-	149	0	Manual*	Public	N/A	Compare with
1584	None	-	-	137	0	Manual*	Public	N/A	Compare with