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)	RMC
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	30
Net Charge	1
Forcefield	multiple
Molecule ID	17336
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
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 (401-500 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 >
17161	None	-	-	23	0	Manual	Public	N/A	Compare with
17160	None	-	-	20	0	Manual	Public	N/A	Compare with
17159	None	-	-	20	0	Manual	Public	N/A	Compare with
17158	None	-	-	20	0	Manual	Public	N/A	Compare with
17157	None	-	-	20	0	Manual	Public	N/A	Compare with
17156	None	-	-	17	0	Manual	Public	N/A	Compare with
17155	None	-	-	17	0	Manual	Public	N/A	Compare with
17154	None	-	-	17	0	Manual	Public	N/A	Compare with
17153	None	-	-	17	0	Manual	Public	N/A	Compare with
17152	None	-	-	16	-1	Manual	Public	N/A	Compare with
17151	None	-	-	16	-1	Manual	Public	N/A	Compare with
17150	None	-	-	16	-1	Manual	Public	N/A	Compare with
17149	None	-	-	16	-1	Manual	Public	N/A	Compare with
17148	None	-	-	33	1	Manual	Public	N/A	Compare with
17147	None	-	-	33	1	Manual	Public	N/A	Compare with
17146	None	-	-	33	1	Manual	Public	N/A	Compare with
17145	None	-	-	33	1	Manual	Public	N/A	Compare with
9643	None	-	-	103	1	Manual	Public	N/A	Compare with
9411	None	-	-	17	-2	Manual*	Public	N/A	Compare with
9377	None	-	-	12	-2	Manual*	Public	N/A	Compare with
9371	None	-	-	11	-2	Manual*	Public	N/A	Compare with
8099	None	-	-	3218	0	Manual*	Public	N/A	Compare with
7284	None	-	-	71	1	Manual*	Public	N/A	Compare with
7283	None	-	-	87	1	Manual*	Public	N/A	Compare with
7282	None	-	-	113	0	Manual*	Public	N/A	Compare with
7281	None	-	-	62	1	Manual*	Public	N/A	Compare with
6871	None	-	-	108	0	Manual*	Public	N/A	Compare with
6870	None	-	-	24	0	Manual*	Public	N/A	Compare with
6461	None	-	-	15	0	Manual	Public	N/A	Compare with
6460	None	-	-	12	0	Manual	Public	N/A	Compare with
6459	None	-	-	16	0	Manual	Public	N/A	Compare with
6458	None	-	-	13	0	Manual	Public	N/A	Compare with
6451	None	-	-	27	0	Manual	Public	N/A	Compare with
6252	None	-	-	89	0	Manual*	Public	N/A	Compare with
5838	None	-	-	43	-1	Manual*	Public	N/A	Compare with
5814	None	-	-	381	1	Manual*	Public	N/A	Compare with
5810	None	-	-	156	-12	Manual*	Public	N/A	Compare with
5798	None	-	-	19	0	Manual*	Public	N/A	Compare with
5797	None	-	-	18	-1	Manual*	Public	N/A	Compare with
5796	None	-	-	19	0	Manual*	Public	N/A	Compare with
5795	None	-	-	18	-1	Manual*	Public	N/A	Compare with
5639	None	-	-	127	0	Manual	Public	N/A	Compare with
5471	None	-	-	130	-10	Manual*	Public	N/A	Compare with
5182	None	-	-	110	-8	Manual*	Public	N/A	Compare with
5181	None	-	-	56	-6	Manual*	Public	N/A	Compare with
5100	None	-	-	58	-6	Manual*	Public	N/A	Compare with
5089	None	-	-	41	1	Manual*	Public	N/A	Compare with
5031	None	-	-	78	0	Manual*	Public	N/A	Compare with
5011	None	-	-	40	-4	Manual*	Public	N/A	Compare with
4908	None	-	-	40	-4	Manual*	Public	N/A	Compare with
4604	None	-	-	217	0	Manual*	Public	N/A	Compare with
4603	None	-	-	113	0	Manual*	Public	N/A	Compare with
4602	None	-	-	113	0	Manual*	Public	N/A	Compare with
4593	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4592	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4582	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4581	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4580	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4579	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4578	None	-	-	161	-8	Manual*	Public	N/A	Compare with
4213	None	-	-	61	0	Manual	Public	N/A	Compare with
4182	None	-	-	5	0	Manual*	Public	N/A	Compare with
4013	None	-	-	176	0	Manual*	Public	N/A	Compare with
3947	None	-	-	127	-1	Manual	Public	N/A	Compare with
3924	None	-	-	176	0	Manual	Public	N/A	Compare with
3923	None	-	-	4	0	Manual	Public	N/A	Compare with
3587	None	-	-	9	0	Manual*	Public	N/A	Compare with
3505	None	-	-	18	0	Manual*	Public	N/A	Compare with
3504	None	-	-	15	0	Manual*	Public	N/A	Compare with
3502	None	-	-	19	0	Manual*	Public	N/A	Compare with
3501	None	-	-	21	0	Manual*	Public	N/A	Compare with
3500	None	-	-	18	0	Manual*	Public	N/A	Compare with
3496	None	-	-	15	0	Manual*	Public	N/A	Compare with
3488	None	-	-	12	0	Manual*	Public	N/A	Compare with
3487	None	-	-	12	0	Manual*	Public	N/A	Compare with
3486	None	-	-	9	0	Manual*	Public	N/A	Compare with
3485	None	-	-	6	0	Manual*	Public	N/A	Compare with
3412	None	-	-	18	0	Manual*	Public	N/A	Compare with
3411	None	-	-	18	0	Manual*	Public	N/A	Compare with
3410	None	-	-	15	0	Manual*	Public	N/A	Compare with
3409	None	-	-	27	0	Manual*	Public	N/A	Compare with
3408	None	-	-	24	0	Manual*	Public	N/A	Compare with
2921	None	-	-	75	-2	Manual	Public	N/A	Compare with
2920	None	-	-	27	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