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)	NH3
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	18
Net Charge	0
Forcefield	multiple
Molecule ID	17337
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:16
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 (1-100 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
4592	None	-	-	161	-8	Manual*	Public	N/A	Compare with
7284	None	-	-	71	1	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
1731	None	-	-	74	0	Manual*	Public	N/A	Compare with
3488	None	-	-	12	0	Manual*	Public	N/A	Compare with
17241	None	-	-	26	-1	Manual	Public	N/A	Compare with
17365	None	-	-	29	0	Manual	Public	N/A	Compare with
17273	None	-	-	24	-1	Manual	Public	N/A	Compare with
17397	None	-	-	21	0	Manual	Public	N/A	Compare with
17550	None	-	-	15	-1	Manual	Public	N/A	Compare with
1560	None	-	-	123	0	Manual*	Public	N/A	Compare with
1602	None	-	-	20	0	Manual*	Public	N/A	Compare with
17190	None	-	-	44	0	Manual	Public	N/A	Compare with
17314	None	-	-	32	0	Manual	Public	N/A	Compare with
17222	None	-	-	22	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
213	None	-	-	27	0	Manual*	Public	N/A	Compare with
1511	None	-	-	131	0	Manual*	Public	N/A	Compare with
17533	None	-	-	24	0	Manual	Public	N/A	Compare with
1525	None	-	-	147	0	Manual*	Public	N/A	Compare with
1579	None	-	-	143	0	Manual*	Public	N/A	Compare with
17173	None	-	-	25	0	Manual	Public	N/A	Compare with
17297	None	-	-	18	0	Manual	Public	N/A	Compare with
17205	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
171	None	-	-	14	0	Manual*	Public	N/A	Compare with
17514	None	-	-	26	0	Manual	Public	N/A	Compare with
574	None	-	-	17	0	Manual*	Public	N/A	Compare with
5796	None	-	-	19	0	Manual*	Public	N/A	Compare with
17154	None	-	-	17	0	Manual	Public	N/A	Compare with
17431	None	-	-	15	0	Manual	Public	N/A	Compare with
2672	None	-	-	39	0	Manual	Public	N/A	Compare with
4579	None	-	-	161	-8	Manual*	Public	N/A	Compare with
17224	None	-	-	22	0	Manual	Public	N/A	Compare with
17348	None	-	-	20	-2	Manual	Public	N/A	Compare with
17256	None	-	-	27	0	Manual	Public	N/A	Compare with
17380	None	-	-	28	-1	Manual	Public	N/A	Compare with
17414	None	-	-	24	1	Manual	Public	N/A	Compare with
17446	None	-	-	28	0	Manual	Public	N/A	Compare with
1679	None	-	-	31	0	Manual*	Public	N/A	Compare with
3486	None	-	-	9	0	Manual*	Public	N/A	Compare with
17239	None	-	-	16	-1	Manual	Public	N/A	Compare with
17363	None	-	-	12	0	Manual	Public	N/A	Compare with
17271	None	-	-	18	0	Manual	Public	N/A	Compare with
17395	None	-	-	24	-1	Manual	Public	N/A	Compare with
17548	None	-	-	26	1	Manual	Public	N/A	Compare with
1557	None	-	-	131	0	Manual*	Public	N/A	Compare with
1598	None	-	-	6	0	Manual*	Public	N/A	Compare with
17188	None	-	-	15	0	Manual	Public	N/A	Compare with
17312	None	-	-	25	-1	Manual	Public	N/A	Compare with
17220	None	-	-	31	1	Manual	Public	N/A	Compare with
17465	None	-	-	31	0	Manual	Public	N/A	Compare with
17497	None	-	-	25	0	Manual	Public	N/A	Compare with
211	None	-	-	14	0	Manual*	Public	N/A	Compare with
1507	None	-	-	138	0	Manual*	Public	N/A	Compare with
7282	None	-	-	113	0	Manual*	Public	N/A	Compare with
1577	None	-	-	138	0	Manual*	Public	N/A	Compare with
17171	None	-	-	28	0	Manual	Public	N/A	Compare with
17295	None	-	-	9	-1	Manual	Public	N/A	Compare with
17203	None	-	-	33	1	Manual	Public	N/A	Compare with
17327	None	-	-	25	0	Manual	Public	N/A	Compare with
17480	None	-	-	27	-1	Manual	Public	N/A	Compare with
169	None	-	-	13	0	Manual*	Public	N/A	Compare with
17512	None	-	-	27	0	Manual	Public	N/A	Compare with
572	None	-	-	17	0	Manual*	Public	N/A	Compare with
5639	None	-	-	127	0	Manual	Public	N/A	Compare with
17152	None	-	-	16	-1	Manual	Public	N/A	Compare with
17429	None	-	-	15	0	Manual	Public	N/A	Compare with
2280	None	-	-	186	-1	Manual*	Public	N/A	Compare with
4213	None	-	-	61	0	Manual	Public	N/A	Compare with
17346	None	-	-	20	-2	Manual	Public	N/A	Compare with
17254	None	-	-	27	0	Manual	Public	N/A	Compare with
17378	None	-	-	28	-1	Manual	Public	N/A	Compare with
17531	None	-	-	18	0	Manual	Public	N/A	Compare with
17412	None	-	-	18	0	Manual	Public	N/A	Compare with
17444	None	-	-	28	1	Manual	Public	N/A	Compare with
1677	None	-	-	34	0	Manual*	Public	N/A	Compare with
3412	None	-	-	18	0	Manual*	Public	N/A	Compare with
17237	None	-	-	16	-1	Manual	Public	N/A	Compare with
17361	None	-	-	12	0	Manual	Public	N/A	Compare with
17269	None	-	-	18	0	Manual	Public	N/A	Compare with
17393	None	-	-	24	-1	Manual	Public	N/A	Compare with
17546	None	-	-	26	1	Manual	Public	N/A	Compare with
1555	None	-	-	167	0	Manual*	Public	N/A	Compare with
1595	None	-	-	5	0	Manual*	Public	N/A	Compare with
17186	None	-	-	15	0	Manual	Public	N/A	Compare with
17310	None	-	-	25	-1	Manual	Public	N/A	Compare with
17218	None	-	-	31	1	Manual	Public	N/A	Compare with
17463	None	-	-	22	0	Manual	Public	N/A	Compare with
17495	None	-	-	19	0	Manual	Public	N/A	Compare with
208	None	-	-	23	0	Manual*	Public	N/A	Compare with
1505	None	-	-	130	0	Manual*	Public	N/A	Compare with
6871	None	-	-	108	0	Manual*	Public	N/A	Compare with
17169	None	-	-	28	0	Manual	Public	N/A	Compare with
17293	None	-	-	9	-1	Manual	Public	N/A	Compare with
17201	None	-	-	33	1	Manual	Public	N/A	Compare with
17325	None	-	-	25	0	Manual	Public	N/A	Compare with