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)	NME
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	20
Net Charge	0
Forcefield	multiple
Molecule ID	17227
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
Upload Date	2014-02-03 13:07:15
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
7284	None	-	-	71	1	Manual*	Public	N/A	Compare with
17425	None	-	-	34	1	Manual	Public	N/A	Compare with
17427	None	-	-	34	1	Manual	Public	N/A	Compare with
17428	None	-	-	34	1	Manual	Public	N/A	Compare with
17443	None	-	-	28	1	Manual	Public	N/A	Compare with
17545	None	-	-	26	1	Manual	Public	N/A	Compare with
17442	None	-	-	28	1	Manual	Public	N/A	Compare with
17415	None	-	-	24	1	Manual	Public	N/A	Compare with
17334	None	-	-	30	1	Manual	Public	N/A	Compare with
17279	None	-	-	24	1	Manual	Public	N/A	Compare with
17219	None	-	-	31	1	Manual	Public	N/A	Compare with
17204	None	-	-	33	1	Manual	Public	N/A	Compare with
17199	None	-	-	26	1	Manual	Public	N/A	Compare with
17148	None	-	-	33	1	Manual	Public	N/A	Compare with
17416	None	-	-	24	1	Manual	Public	N/A	Compare with
17336	None	-	-	30	1	Manual	Public	N/A	Compare with
17335	None	-	-	30	1	Manual	Public	N/A	Compare with
9643	None	-	-	103	1	Manual	Public	N/A	Compare with
17146	None	-	-	33	1	Manual	Public	N/A	Compare with
17147	None	-	-	33	1	Manual	Public	N/A	Compare with
17197	None	-	-	26	1	Manual	Public	N/A	Compare with
17198	None	-	-	26	1	Manual	Public	N/A	Compare with
17200	None	-	-	26	1	Manual	Public	N/A	Compare with
17201	None	-	-	33	1	Manual	Public	N/A	Compare with
17217	None	-	-	31	1	Manual	Public	N/A	Compare with
17218	None	-	-	31	1	Manual	Public	N/A	Compare with
17220	None	-	-	31	1	Manual	Public	N/A	Compare with
17277	None	-	-	24	1	Manual	Public	N/A	Compare with
17280	None	-	-	24	1	Manual	Public	N/A	Compare with
17333	None	-	-	30	1	Manual	Public	N/A	Compare with
17145	None	-	-	33	1	Manual	Public	N/A	Compare with
7283	None	-	-	87	1	Manual*	Public	N/A	Compare with
17444	None	-	-	28	1	Manual	Public	N/A	Compare with
17203	None	-	-	33	1	Manual	Public	N/A	Compare with
7281	None	-	-	62	1	Manual*	Public	N/A	Compare with
178	None	-	-	21	1	Manual*	Public	N/A	Compare with
2920	None	-	-	27	1	Manual	Public	N/A	Compare with
17548	None	-	-	26	1	Manual	Public	N/A	Compare with
17414	None	-	-	24	1	Manual	Public	N/A	Compare with
17202	None	-	-	33	1	Manual	Public	N/A	Compare with
5814	None	-	-	381	1	Manual*	Public	N/A	Compare with
17413	None	-	-	24	1	Manual	Public	N/A	Compare with
164	None	-	-	27	1	Manual*	Public	N/A	Compare with
17278	None	-	-	24	1	Manual	Public	N/A	Compare with
206	None	-	-	25	1	Manual*	Public	N/A	Compare with
17441	None	-	-	28	1	Manual	Public	N/A	Compare with
17546	None	-	-	26	1	Manual	Public	N/A	Compare with
17547	None	-	-	26	1	Manual	Public	N/A	Compare with
5089	None	-	-	41	1	Manual*	Public	N/A	Compare with
17426	None	-	-	34	1	Manual	Public	N/A	Compare with
1584	None	-	-	137	0	Manual*	Public	N/A	Compare with
1582	None	-	-	119	0	Manual*	Public	N/A	Compare with
1590	None	-	-	147	0	Manual*	Public	N/A	Compare with
1581	None	-	-	149	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
1574	None	-	-	123	0	Manual*	Public	N/A	Compare with
1576	None	-	-	129	0	Manual*	Public	N/A	Compare with
1578	None	-	-	144	0	Manual*	Public	N/A	Compare with
1583	None	-	-	125	0	Manual*	Public	N/A	Compare with
1579	None	-	-	143	0	Manual*	Public	N/A	Compare with
1586	None	-	-	149	0	Manual*	Public	N/A	Compare with
1577	None	-	-	138	0	Manual*	Public	N/A	Compare with
1538	None	-	-	161	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
30988	None	-	-	1456	0	Template	Public	N/A	Compare with
177	None	-	-	20	0	Manual*	Public	N/A	Compare with
176	None	-	-	20	0	Manual*	Public	N/A	Compare with
175	None	-	-	19	0	Manual*	Public	N/A	Compare with
169	None	-	-	13	0	Manual*	Public	N/A	Compare with
168	None	-	-	15	0	Manual*	Public	N/A	Compare with
1591	None	-	-	137	0	Manual*	Public	N/A	Compare with
577	None	-	-	37	0	Manual*	Public	N/A	Compare with
578	None	-	-	10	0	Manual*	Public	N/A	Compare with
580	None	-	-	12	0	Manual*	Public	N/A	Compare with
1532	None	-	-	149	0	Manual*	Public	N/A	Compare with
1526	None	-	-	143	0	Manual*	Public	N/A	Compare with
1525	None	-	-	147	0	Manual*	Public	N/A	Compare with
1524	None	-	-	137	0	Manual*	Public	N/A	Compare with
1511	None	-	-	131	0	Manual*	Public	N/A	Compare with
1510	None	-	-	161	0	Manual*	Public	N/A	Compare with
1507	None	-	-	138	0	Manual*	Public	N/A	Compare with
1506	None	-	-	134	0	Manual*	Public	N/A	Compare with
1505	None	-	-	130	0	Manual*	Public	N/A	Compare with
1503	None	-	-	118	0	Manual*	Public	N/A	Compare with
1502	None	-	-	106	0	Manual*	Public	N/A	Compare with
619	None	-	-	16	0	Manual*	Public	N/A	Compare with
584	None	-	-	15	0	Manual*	Public	N/A	Compare with
583	None	-	-	15	0	Manual*	Public	N/A	Compare with
582	None	-	-	12	0	Manual*	Public	N/A	Compare with
581	None	-	-	16	0	Manual*	Public	N/A	Compare with