MD Topology | NMR | X-Ray

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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 building block
Residue Name (RNME)	CSA
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	15
Net Charge	-1
Forcefield	multiple
Molecule ID	17552
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
Upload Date	2014-02-03 13:07:19
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
7282	None	-	-	113	0	Manual*	Public	N/A	Compare with
17498	None	-	-	25	0	Manual	Public	N/A	Compare with
1577	None	-	-	138	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
17415	None	-	-	24	1	Manual	Public	N/A	Compare with
169	None	-	-	13	0	Manual*	Public	N/A	Compare with
17447	None	-	-	28	0	Manual	Public	N/A	Compare with
572	None	-	-	17	0	Manual*	Public	N/A	Compare with
5639	None	-	-	127	0	Manual	Public	N/A	Compare with
17179	None	-	-	20	-1	Manual	Public	N/A	Compare with
17152	None	-	-	16	-1	Manual	Public	N/A	Compare with
17211	None	-	-	27	-2	Manual	Public	N/A	Compare with
17364	None	-	-	12	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
2280	None	-	-	186	-1	Manual*	Public	N/A	Compare with
4213	None	-	-	61	0	Manual	Public	N/A	Compare with
17313	None	-	-	32	0	Manual	Public	N/A	Compare with
17466	None	-	-	31	0	Manual	Public	N/A	Compare with
17347	None	-	-	20	-2	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
1677	None	-	-	34	0	Manual*	Public	N/A	Compare with
3412	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
17481	None	-	-	15	0	Manual	Public	N/A	Compare with
1555	None	-	-	167	0	Manual*	Public	N/A	Compare with
17513	None	-	-	26	0	Manual	Public	N/A	Compare with
1595	None	-	-	5	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
17430	None	-	-	15	0	Manual	Public	N/A	Compare with
208	None	-	-	23	0	Manual*	Public	N/A	Compare with
1505	None	-	-	130	0	Manual*	Public	N/A	Compare with
6871	None	-	-	108	0	Manual*	Public	N/A	Compare with
17194	None	-	-	28	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
17413	None	-	-	24	1	Manual	Public	N/A	Compare with
167	None	-	-	14	-1	Manual*	Public	N/A	Compare with
17445	None	-	-	28	0	Manual	Public	N/A	Compare with
570	None	-	-	11	0	Manual*	Public	N/A	Compare with
5182	None	-	-	110	-8	Manual*	Public	N/A	Compare with
17177	None	-	-	20	-1	Manual	Public	N/A	Compare with
17150	None	-	-	16	-1	Manual	Public	N/A	Compare with
17209	None	-	-	27	-2	Manual	Public	N/A	Compare with
17362	None	-	-	12	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
2182	None	-	-	41	-4	Manual*	Public	N/A	Compare with
4013	None	-	-	176	0	Manual*	Public	N/A	Compare with
17311	None	-	-	25	-1	Manual	Public	N/A	Compare with
17464	None	-	-	22	0	Manual	Public	N/A	Compare with
17496	None	-	-	19	0	Manual	Public	N/A	Compare with
1574	None	-	-	123	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
1664	None	-	-	8	0	Manual*	Public	N/A	Compare with
3410	None	-	-	15	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
17479	None	-	-	27	-1	Manual	Public	N/A	Compare with
1553	None	-	-	155	0	Manual*	Public	N/A	Compare with
17511	None	-	-	27	0	Manual	Public	N/A	Compare with
1593	None	-	-	3	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
17428	None	-	-	34	1	Manual	Public	N/A	Compare with
206	None	-	-	25	1	Manual*	Public	N/A	Compare with
1502	None	-	-	106	0	Manual*	Public	N/A	Compare with
6461	None	-	-	15	0	Manual	Public	N/A	Compare with
17192	None	-	-	44	0	Manual	Public	N/A	Compare with
17345	None	-	-	20	-2	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
17411	None	-	-	18	0	Manual	Public	N/A	Compare with
165	None	-	-	26	0	Manual*	Public	N/A	Compare with
17443	None	-	-	28	1	Manual	Public	N/A	Compare with
568	None	-	-	16	0	Manual*	Public	N/A	Compare with
5100	None	-	-	58	-6	Manual*	Public	N/A	Compare with
17175	None	-	-	25	0	Manual	Public	N/A	Compare with
17148	None	-	-	33	1	Manual	Public	N/A	Compare with
17207	None	-	-	18	0	Manual	Public	N/A	Compare with
17360	None	-	-	30	0	Manual	Public	N/A	Compare with
17392	None	-	-	18	0	Manual	Public	N/A	Compare with
17545	None	-	-	26	1	Manual	Public	N/A	Compare with
2166	None	-	-	186	-1	Manual*	Public	N/A	Compare with
3924	None	-	-	176	0	Manual	Public	N/A	Compare with
17309	None	-	-	25	-1	Manual	Public	N/A	Compare with
17341	None	-	-	23	-2	Manual	Public	N/A	Compare with
17462	None	-	-	22	0	Manual	Public	N/A	Compare with
17494	None	-	-	19	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
1655	None	-	-	9	0	Manual*	Public	N/A	Compare with
21025	None	-	-	209	-4	Manual*	Public	N/A	Compare with
3408	None	-	-	24	0	Manual*	Public	N/A	Compare with
17292	None	-	-	28	0	Manual	Public	N/A	Compare with