MD Topology | NMR | X-Ray

Visualize with JSmol

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
Residue Name (RNME)	ECA
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	20
Net Charge	-2
Forcefield	multiple
Molecule ID	17385
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2014-02-03 13:07:17
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
17551	None	-	-	15	-1	Manual	Public	N/A	Compare with
17283	None	-	-	23	0	Manual	Public	N/A	Compare with
17196	None	-	-	28	0	Manual	Public	N/A	Compare with
1526	None	-	-	143	0	Manual*	Public	N/A	Compare with
17349	None	-	-	15	0	Manual	Public	N/A	Compare with
1581	None	-	-	149	0	Manual*	Public	N/A	Compare with
17381	None	-	-	23	0	Manual	Public	N/A	Compare with
17534	None	-	-	24	0	Manual	Public	N/A	Compare with
17298	None	-	-	18	0	Manual	Public	N/A	Compare with
17330	None	-	-	17	-2	Manual	Public	N/A	Compare with
562	None	-	-	9	0	Manual*	Public	N/A	Compare with
5797	None	-	-	18	-1	Manual*	Public	N/A	Compare with
17483	None	-	-	15	0	Manual	Public	N/A	Compare with
17155	None	-	-	17	0	Manual	Public	N/A	Compare with
17515	None	-	-	26	0	Manual	Public	N/A	Compare with
17247	None	-	-	27	-2	Manual	Public	N/A	Compare with
17279	None	-	-	24	1	Manual	Public	N/A	Compare with
2694	None	-	-	77	-3	Manual	Public	N/A	Compare with
17432	None	-	-	15	0	Manual	Public	N/A	Compare with
4580	None	-	-	161	-8	Manual*	Public	N/A	Compare with
17466	None	-	-	31	0	Manual	Public	N/A	Compare with
578	None	-	-	10	0	Manual*	Public	N/A	Compare with
7283	None	-	-	87	1	Manual*	Public	N/A	Compare with
17498	None	-	-	25	0	Manual	Public	N/A	Compare with
17230	None	-	-	27	0	Manual	Public	N/A	Compare with
17262	None	-	-	17	0	Manual	Public	N/A	Compare with
1680	None	-	-	30	0	Manual*	Public	N/A	Compare with
17415	None	-	-	24	1	Manual	Public	N/A	Compare with
3487	None	-	-	12	0	Manual*	Public	N/A	Compare with
17447	None	-	-	28	0	Manual	Public	N/A	Compare with
17179	None	-	-	20	-1	Manual	Public	N/A	Compare with
17211	None	-	-	27	-2	Manual	Public	N/A	Compare with
1558	None	-	-	137	0	Manual*	Public	N/A	Compare with
17364	None	-	-	12	0	Manual	Public	N/A	Compare with
1601	None	-	-	17	0	Manual*	Public	N/A	Compare with
17396	None	-	-	24	-1	Manual	Public	N/A	Compare with
17549	None	-	-	15	-1	Manual	Public	N/A	Compare with
17313	None	-	-	32	0	Manual	Public	N/A	Compare with
175	None	-	-	19	0	Manual*	Public	N/A	Compare with
4582	None	-	-	161	-8	Manual*	Public	N/A	Compare with
17194	None	-	-	28	0	Manual	Public	N/A	Compare with
17347	None	-	-	20	-2	Manual	Public	N/A	Compare with
1578	None	-	-	144	0	Manual*	Public	N/A	Compare with
17379	None	-	-	28	-1	Manual	Public	N/A	Compare with
17532	None	-	-	18	0	Manual	Public	N/A	Compare with
17296	None	-	-	9	-1	Manual	Public	N/A	Compare with
17328	None	-	-	25	0	Manual	Public	N/A	Compare with
215	None	-	-	19	0	Manual*	Public	N/A	Compare with
5795	None	-	-	18	-1	Manual*	Public	N/A	Compare with
17481	None	-	-	15	0	Manual	Public	N/A	Compare with
17153	None	-	-	17	0	Manual	Public	N/A	Compare with
17513	None	-	-	26	0	Manual	Public	N/A	Compare with
17245	None	-	-	27	-2	Manual	Public	N/A	Compare with
17277	None	-	-	24	1	Manual	Public	N/A	Compare with
2671	None	-	-	47	-3	Manual	Public	N/A	Compare with
17430	None	-	-	15	0	Manual	Public	N/A	Compare with
4578	None	-	-	161	-8	Manual*	Public	N/A	Compare with
17496	None	-	-	19	0	Manual	Public	N/A	Compare with
17228	None	-	-	20	0	Manual	Public	N/A	Compare with
17260	None	-	-	15	-1	Manual	Public	N/A	Compare with
1678	None	-	-	35	0	Manual*	Public	N/A	Compare with
17413	None	-	-	24	1	Manual	Public	N/A	Compare with
3485	None	-	-	6	0	Manual*	Public	N/A	Compare with
17445	None	-	-	28	0	Manual	Public	N/A	Compare with
17177	None	-	-	20	-1	Manual	Public	N/A	Compare with
17209	None	-	-	27	-2	Manual	Public	N/A	Compare with
1556	None	-	-	143	0	Manual*	Public	N/A	Compare with
17362	None	-	-	12	0	Manual	Public	N/A	Compare with
1596	None	-	-	3	0	Manual*	Public	N/A	Compare with
17394	None	-	-	24	-1	Manual	Public	N/A	Compare with
17547	None	-	-	26	1	Manual	Public	N/A	Compare with
17311	None	-	-	25	-1	Manual	Public	N/A	Compare with
173	None	-	-	20	0	Manual*	Public	N/A	Compare with
17464	None	-	-	22	0	Manual	Public	N/A	Compare with
576	None	-	-	26	0	Manual*	Public	N/A	Compare with
7281	None	-	-	62	1	Manual*	Public	N/A	Compare with
17345	None	-	-	20	-2	Manual	Public	N/A	Compare with
1576	None	-	-	129	0	Manual*	Public	N/A	Compare with
17377	None	-	-	28	-1	Manual	Public	N/A	Compare with
17530	None	-	-	18	0	Manual	Public	N/A	Compare with
17294	None	-	-	9	-1	Manual	Public	N/A	Compare with
17326	None	-	-	25	0	Manual	Public	N/A	Compare with
213	None	-	-	27	0	Manual*	Public	N/A	Compare with
5471	None	-	-	130	-10	Manual*	Public	N/A	Compare with
17479	None	-	-	27	-1	Manual	Public	N/A	Compare with
1511	None	-	-	131	0	Manual*	Public	N/A	Compare with
17151	None	-	-	16	-1	Manual	Public	N/A	Compare with
17511	None	-	-	27	0	Manual	Public	N/A	Compare with
17243	None	-	-	26	-1	Manual	Public	N/A	Compare with
17275	None	-	-	24	-1	Manual	Public	N/A	Compare with
2276	None	-	-	363	-2	Manual*	Public	N/A	Compare with
17428	None	-	-	34	1	Manual	Public	N/A	Compare with
4182	None	-	-	5	0	Manual*	Public	N/A	Compare with
17192	None	-	-	44	0	Manual	Public	N/A	Compare with
17226	None	-	-	20	0	Manual	Public	N/A	Compare with
17258	None	-	-	15	-1	Manual	Public	N/A	Compare with
1668	None	-	-	27	0	Manual*	Public	N/A	Compare with
17411	None	-	-	18	0	Manual	Public	N/A	Compare with
3411	None	-	-	18	0	Manual*	Public	N/A	Compare with
17443	None	-	-	28	1	Manual	Public	N/A	Compare with