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)	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	17463
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
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 (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
17276	None	-	-	24	-1	Manual	Public	N/A	Compare with
17174	None	-	-	25	0	Manual	Public	N/A	Compare with
17167	None	-	-	27	0	Manual	Public	N/A	Compare with
17160	None	-	-	20	0	Manual	Public	N/A	Compare with
17152	None	-	-	16	-1	Manual	Public	N/A	Compare with
17145	None	-	-	33	1	Manual	Public	N/A	Compare with
17322	None	-	-	18	0	Manual	Public	N/A	Compare with
17315	None	-	-	32	0	Manual	Public	N/A	Compare with
17307	None	-	-	23	0	Manual	Public	N/A	Compare with
17300	None	-	-	18	0	Manual	Public	N/A	Compare with
17291	None	-	-	28	0	Manual	Public	N/A	Compare with
17180	None	-	-	20	-1	Manual	Public	N/A	Compare with
17185	None	-	-	15	0	Manual	Public	N/A	Compare with
17192	None	-	-	44	0	Manual	Public	N/A	Compare with
17268	None	-	-	19	0	Manual	Public	N/A	Compare with
17262	None	-	-	17	0	Manual	Public	N/A	Compare with
17251	None	-	-	23	-2	Manual	Public	N/A	Compare with
17244	None	-	-	26	-1	Manual	Public	N/A	Compare with
17236	None	-	-	26	0	Manual	Public	N/A	Compare with
17229	None	-	-	27	0	Manual	Public	N/A	Compare with
17221	None	-	-	22	0	Manual	Public	N/A	Compare with
17217	None	-	-	31	1	Manual	Public	N/A	Compare with
17209	None	-	-	27	-2	Manual	Public	N/A	Compare with
17202	None	-	-	33	1	Manual	Public	N/A	Compare with
17284	None	-	-	23	0	Manual	Public	N/A	Compare with
17275	None	-	-	24	-1	Manual	Public	N/A	Compare with
17227	None	-	-	20	0	Manual	Public	N/A	Compare with
17200	None	-	-	26	1	Manual	Public	N/A	Compare with
17172	None	-	-	28	0	Manual	Public	N/A	Compare with
6461	None	-	-	15	0	Manual	Public	N/A	Compare with
17298	None	-	-	18	0	Manual	Public	N/A	Compare with
17259	None	-	-	15	-1	Manual	Public	N/A	Compare with
17199	None	-	-	26	1	Manual	Public	N/A	Compare with
6460	None	-	-	12	0	Manual	Public	N/A	Compare with
17258	None	-	-	15	-1	Manual	Public	N/A	Compare with
6459	None	-	-	16	0	Manual	Public	N/A	Compare with
17260	None	-	-	15	-1	Manual	Public	N/A	Compare with
17283	None	-	-	23	0	Manual	Public	N/A	Compare with
17299	None	-	-	18	0	Manual	Public	N/A	Compare with
17261	None	-	-	17	0	Manual	Public	N/A	Compare with
17243	None	-	-	26	-1	Manual	Public	N/A	Compare with
17228	None	-	-	20	0	Manual	Public	N/A	Compare with
17216	None	-	-	29	0	Manual	Public	N/A	Compare with
17201	None	-	-	33	1	Manual	Public	N/A	Compare with
17184	None	-	-	23	0	Manual	Public	N/A	Compare with
17173	None	-	-	25	0	Manual	Public	N/A	Compare with
17159	None	-	-	20	0	Manual	Public	N/A	Compare with
9643	None	-	-	103	1	Manual	Public	N/A	Compare with
17314	None	-	-	32	0	Manual	Public	N/A	Compare with
6458	None	-	-	13	0	Manual	Public	N/A	Compare with
17280	None	-	-	24	1	Manual	Public	N/A	Compare with
17277	None	-	-	24	1	Manual	Public	N/A	Compare with
17222	None	-	-	22	0	Manual	Public	N/A	Compare with
17219	None	-	-	31	1	Manual	Public	N/A	Compare with
17218	None	-	-	31	1	Manual	Public	N/A	Compare with
17213	None	-	-	29	0	Manual	Public	N/A	Compare with
17210	None	-	-	27	-2	Manual	Public	N/A	Compare with
17206	None	-	-	18	0	Manual	Public	N/A	Compare with
17203	None	-	-	33	1	Manual	Public	N/A	Compare with
17196	None	-	-	28	0	Manual	Public	N/A	Compare with
17193	None	-	-	28	0	Manual	Public	N/A	Compare with
17189	None	-	-	44	0	Manual	Public	N/A	Compare with
17224	None	-	-	22	0	Manual	Public	N/A	Compare with
17230	None	-	-	27	0	Manual	Public	N/A	Compare with
17233	None	-	-	26	0	Manual	Public	N/A	Compare with
17272	None	-	-	18	0	Manual	Public	N/A	Compare with
17269	None	-	-	18	0	Manual	Public	N/A	Compare with
17265	None	-	-	19	0	Manual	Public	N/A	Compare with
17263	None	-	-	17	0	Manual	Public	N/A	Compare with
17255	None	-	-	27	0	Manual	Public	N/A	Compare with
17252	None	-	-	23	-2	Manual	Public	N/A	Compare with
17248	None	-	-	27	-2	Manual	Public	N/A	Compare with
17245	None	-	-	27	-2	Manual	Public	N/A	Compare with
17240	None	-	-	16	-1	Manual	Public	N/A	Compare with
17237	None	-	-	16	-1	Manual	Public	N/A	Compare with
17186	None	-	-	15	0	Manual	Public	N/A	Compare with
17183	None	-	-	23	0	Manual	Public	N/A	Compare with
17323	None	-	-	18	0	Manual	Public	N/A	Compare with
17319	None	-	-	24	0	Manual	Public	N/A	Compare with
17316	None	-	-	32	0	Manual	Public	N/A	Compare with
17311	None	-	-	25	-1	Manual	Public	N/A	Compare with
17308	None	-	-	23	0	Manual	Public	N/A	Compare with
17304	None	-	-	25	0	Manual	Public	N/A	Compare with
17301	None	-	-	25	0	Manual	Public	N/A	Compare with
17295	None	-	-	9	-1	Manual	Public	N/A	Compare with
17292	None	-	-	28	0	Manual	Public	N/A	Compare with
17288	None	-	-	17	0	Manual	Public	N/A	Compare with
17326	None	-	-	25	0	Manual	Public	N/A	Compare with
17146	None	-	-	33	1	Manual	Public	N/A	Compare with
17149	None	-	-	16	-1	Manual	Public	N/A	Compare with
17181	None	-	-	23	0	Manual	Public	N/A	Compare with
17177	None	-	-	20	-1	Manual	Public	N/A	Compare with
17175	None	-	-	25	0	Manual	Public	N/A	Compare with
17171	None	-	-	28	0	Manual	Public	N/A	Compare with
17168	None	-	-	27	0	Manual	Public	N/A	Compare with
17164	None	-	-	23	0	Manual	Public	N/A	Compare with
17161	None	-	-	23	0	Manual	Public	N/A	Compare with
17156	None	-	-	17	0	Manual	Public	N/A	Compare with
17153	None	-	-	17	0	Manual	Public	N/A	Compare with
17285	None	-	-	17	0	Manual	Public	N/A	Compare with