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)	GSA
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	17410
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 (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
1507	None	-	-	138	0	Manual*	Public	N/A	Compare with
18660	None	-	-	49	-3	Manual*	Public	N/A	Compare with
7282	None	-	-	113	0	Manual*	Public	N/A	Compare with
17290	None	-	-	28	0	Manual	Public	N/A	Compare with
17322	None	-	-	18	0	Manual	Public	N/A	Compare with
17475	None	-	-	23	0	Manual	Public	N/A	Compare with
17507	None	-	-	29	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
17271	None	-	-	18	0	Manual	Public	N/A	Compare with
17424	None	-	-	21	0	Manual	Public	N/A	Compare with
17456	None	-	-	28	0	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
17220	None	-	-	31	1	Manual	Public	N/A	Compare with
17373	None	-	-	30	-1	Manual	Public	N/A	Compare with
211	None	-	-	14	0	Manual*	Public	N/A	Compare with
17526	None	-	-	18	0	Manual	Public	N/A	Compare with
17407	None	-	-	28	-1	Manual	Public	N/A	Compare with
17439	None	-	-	25	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
17203	None	-	-	33	1	Manual	Public	N/A	Compare with
17356	None	-	-	23	0	Manual	Public	N/A	Compare with
169	None	-	-	13	0	Manual*	Public	N/A	Compare with
17388	None	-	-	20	-2	Manual	Public	N/A	Compare with
572	None	-	-	17	0	Manual*	Public	N/A	Compare with
17541	None	-	-	29	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
17305	None	-	-	23	0	Manual	Public	N/A	Compare with
17337	None	-	-	18	0	Manual	Public	N/A	Compare with
17490	None	-	-	22	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
17254	None	-	-	27	0	Manual	Public	N/A	Compare with
6871	None	-	-	108	0	Manual*	Public	N/A	Compare with
17288	None	-	-	17	0	Manual	Public	N/A	Compare with
17320	None	-	-	24	0	Manual	Public	N/A	Compare with
17473	None	-	-	23	0	Manual	Public	N/A	Compare with
17505	None	-	-	29	0	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
17269	None	-	-	18	0	Manual	Public	N/A	Compare with
17422	None	-	-	21	0	Manual	Public	N/A	Compare with
17454	None	-	-	28	0	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
17218	None	-	-	31	1	Manual	Public	N/A	Compare with
17371	None	-	-	18	-1	Manual	Public	N/A	Compare with
208	None	-	-	23	0	Manual*	Public	N/A	Compare with
17524	None	-	-	21	-1	Manual	Public	N/A	Compare with
1505	None	-	-	130	0	Manual*	Public	N/A	Compare with
18622	None	-	-	49	-3	Manual*	Public	N/A	Compare with
17437	None	-	-	25	0	Manual	Public	N/A	Compare with
1574	None	-	-	123	0	Manual*	Public	N/A	Compare with
17169	None	-	-	28	0	Manual	Public	N/A	Compare with
17201	None	-	-	33	1	Manual	Public	N/A	Compare with
17354	None	-	-	23	0	Manual	Public	N/A	Compare with
167	None	-	-	14	-1	Manual*	Public	N/A	Compare with
17386	None	-	-	20	-2	Manual	Public	N/A	Compare with
570	None	-	-	11	0	Manual*	Public	N/A	Compare with
17539	None	-	-	19	-2	Manual	Public	N/A	Compare with
5182	None	-	-	110	-8	Manual*	Public	N/A	Compare with
17150	None	-	-	16	-1	Manual	Public	N/A	Compare with
17303	None	-	-	25	0	Manual	Public	N/A	Compare with
17335	None	-	-	30	1	Manual	Public	N/A	Compare with
17488	None	-	-	21	0	Manual	Public	N/A	Compare with
2182	None	-	-	41	-4	Manual*	Public	N/A	Compare with
4013	None	-	-	176	0	Manual*	Public	N/A	Compare with
17252	None	-	-	23	-2	Manual	Public	N/A	Compare with
17405	None	-	-	28	-1	Manual	Public	N/A	Compare with
17286	None	-	-	17	0	Manual	Public	N/A	Compare with
17318	None	-	-	24	0	Manual	Public	N/A	Compare with
17471	None	-	-	24	0	Manual	Public	N/A	Compare with
17503	None	-	-	32	0	Manual	Public	N/A	Compare with
1664	None	-	-	8	0	Manual*	Public	N/A	Compare with
3410	None	-	-	15	0	Manual*	Public	N/A	Compare with
17235	None	-	-	26	0	Manual	Public	N/A	Compare with
17267	None	-	-	19	0	Manual	Public	N/A	Compare with
17420	None	-	-	21	0	Manual	Public	N/A	Compare with
17452	None	-	-	23	0	Manual	Public	N/A	Compare with
1553	None	-	-	155	0	Manual*	Public	N/A	Compare with
1593	None	-	-	3	0	Manual*	Public	N/A	Compare with
17184	None	-	-	23	0	Manual	Public	N/A	Compare with
17216	None	-	-	29	0	Manual	Public	N/A	Compare with
17369	None	-	-	18	-1	Manual	Public	N/A	Compare with
206	None	-	-	25	1	Manual*	Public	N/A	Compare with
17522	None	-	-	21	-1	Manual	Public	N/A	Compare with
1502	None	-	-	106	0	Manual*	Public	N/A	Compare with
18620	None	-	-	49	-3	Manual	Public	N/A	Compare with
6461	None	-	-	15	0	Manual	Public	N/A	Compare with
1571	None	-	-	147	0	Manual*	Public	N/A	Compare with
1649	None	-	-	5	0	Manual*	Public	N/A	Compare with
17167	None	-	-	27	0	Manual	Public	N/A	Compare with
17199	None	-	-	26	1	Manual	Public	N/A	Compare with