MD Topology | NMR | X-Ray

Visualize with JSmol

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
Residue Name (RNME)	S1P
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	18
Net Charge	-1
Forcefield	multiple
Molecule ID	17371
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	45A3 (IFP45A3.dat)
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 (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
17440	None	-	-	25	0	Manual	Public	N/A	Compare with
1555	None	-	-	167	0	Manual*	Public	N/A	Compare with
17172	None	-	-	28	0	Manual	Public	N/A	Compare with
17506	None	-	-	29	0	Manual	Public	N/A	Compare with
2182	None	-	-	41	-4	Manual*	Public	N/A	Compare with
17238	None	-	-	16	-1	Manual	Public	N/A	Compare with
4013	None	-	-	176	0	Manual*	Public	N/A	Compare with
17270	None	-	-	18	0	Manual	Public	N/A	Compare with
17423	None	-	-	21	0	Manual	Public	N/A	Compare with
17455	None	-	-	28	0	Manual	Public	N/A	Compare with
1574	None	-	-	123	0	Manual*	Public	N/A	Compare with
17187	None	-	-	15	0	Manual	Public	N/A	Compare with
17219	None	-	-	31	1	Manual	Public	N/A	Compare with
17372	None	-	-	18	-1	Manual	Public	N/A	Compare with
17525	None	-	-	18	0	Manual	Public	N/A	Compare with
167	None	-	-	14	-1	Manual*	Public	N/A	Compare with
18623	None	-	-	139	-3	Manual	Public	N/A	Compare with
570	None	-	-	11	0	Manual*	Public	N/A	Compare with
7281	None	-	-	62	1	Manual*	Public	N/A	Compare with
17289	None	-	-	28	0	Manual	Public	N/A	Compare with
17321	None	-	-	18	0	Manual	Public	N/A	Compare with
17474	None	-	-	23	0	Manual	Public	N/A	Compare with
17355	None	-	-	23	0	Manual	Public	N/A	Compare with
17387	None	-	-	20	-2	Manual	Public	N/A	Compare with
17540	None	-	-	19	-2	Manual	Public	N/A	Compare with
206	None	-	-	25	1	Manual*	Public	N/A	Compare with
5471	None	-	-	130	-10	Manual*	Public	N/A	Compare with
1502	None	-	-	106	0	Manual*	Public	N/A	Compare with
17151	None	-	-	16	-1	Manual	Public	N/A	Compare with
17304	None	-	-	25	0	Manual	Public	N/A	Compare with
17336	None	-	-	30	1	Manual	Public	N/A	Compare with
17489	None	-	-	22	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
17253	None	-	-	27	0	Manual	Public	N/A	Compare with
17406	None	-	-	28	-1	Manual	Public	N/A	Compare with
17438	None	-	-	25	0	Manual	Public	N/A	Compare with
1553	None	-	-	155	0	Manual*	Public	N/A	Compare with
17170	None	-	-	28	0	Manual	Public	N/A	Compare with
1593	None	-	-	3	0	Manual*	Public	N/A	Compare with
17202	None	-	-	33	1	Manual	Public	N/A	Compare with
2166	None	-	-	186	-1	Manual*	Public	N/A	Compare with
17236	None	-	-	26	0	Manual	Public	N/A	Compare with
3924	None	-	-	176	0	Manual	Public	N/A	Compare with
17268	None	-	-	19	0	Manual	Public	N/A	Compare with
17421	None	-	-	21	0	Manual	Public	N/A	Compare with
17453	None	-	-	28	0	Manual	Public	N/A	Compare with
1571	None	-	-	147	0	Manual*	Public	N/A	Compare with
17185	None	-	-	15	0	Manual	Public	N/A	Compare with
1649	None	-	-	5	0	Manual*	Public	N/A	Compare with
17217	None	-	-	31	1	Manual	Public	N/A	Compare with
17370	None	-	-	18	-1	Manual	Public	N/A	Compare with
17523	None	-	-	21	-1	Manual	Public	N/A	Compare with
165	None	-	-	26	0	Manual*	Public	N/A	Compare with
18621	None	-	-	49	-3	Manual*	Public	N/A	Compare with
568	None	-	-	16	0	Manual*	Public	N/A	Compare with
6870	None	-	-	24	0	Manual*	Public	N/A	Compare with
17287	None	-	-	17	0	Manual	Public	N/A	Compare with
17319	None	-	-	24	0	Manual	Public	N/A	Compare with
17472	None	-	-	24	0	Manual	Public	N/A	Compare with
17504	None	-	-	32	0	Manual	Public	N/A	Compare with
17385	None	-	-	20	-2	Manual	Public	N/A	Compare with
17538	None	-	-	19	-2	Manual	Public	N/A	Compare with
204	None	-	-	22	0	Manual*	Public	N/A	Compare with
5181	None	-	-	56	-6	Manual*	Public	N/A	Compare with
584	None	-	-	15	0	Manual*	Public	N/A	Compare with
17149	None	-	-	16	-1	Manual	Public	N/A	Compare with
17302	None	-	-	25	0	Manual	Public	N/A	Compare with
17334	None	-	-	30	1	Manual	Public	N/A	Compare with
17487	None	-	-	21	0	Manual	Public	N/A	Compare with
1655	None	-	-	9	0	Manual*	Public	N/A	Compare with
3408	None	-	-	24	0	Manual*	Public	N/A	Compare with
17251	None	-	-	23	-2	Manual	Public	N/A	Compare with
17404	None	-	-	16	-1	Manual	Public	N/A	Compare with
17436	None	-	-	21	-1	Manual	Public	N/A	Compare with
1551	None	-	-	153	0	Manual*	Public	N/A	Compare with
17168	None	-	-	27	0	Manual	Public	N/A	Compare with
1590	None	-	-	147	0	Manual*	Public	N/A	Compare with
17200	None	-	-	26	1	Manual	Public	N/A	Compare with
17353	None	-	-	23	0	Manual	Public	N/A	Compare with
2018	None	-	-	90	-1	Manual*	Public	N/A	Compare with
17234	None	-	-	26	0	Manual	Public	N/A	Compare with
3587	None	-	-	9	0	Manual*	Public	N/A	Compare with
17266	None	-	-	19	0	Manual	Public	N/A	Compare with
17419	None	-	-	21	0	Manual	Public	N/A	Compare with
17451	None	-	-	23	0	Manual	Public	N/A	Compare with
1567	None	-	-	119	0	Manual*	Public	N/A	Compare with
17183	None	-	-	23	0	Manual	Public	N/A	Compare with
1642	None	-	-	18	0	Manual*	Public	N/A	Compare with
17215	None	-	-	29	0	Manual	Public	N/A	Compare with
17368	None	-	-	29	0	Manual	Public	N/A	Compare with
17400	None	-	-	21	0	Manual	Public	N/A	Compare with
17521	None	-	-	21	-1	Manual	Public	N/A	Compare with
163	None	-	-	13	0	Manual*	Public	N/A	Compare with
18619	None	-	-	49	-3	Manual	Public	N/A	Compare with
566	None	-	-	12	0	Manual*	Public	N/A	Compare with
6460	None	-	-	12	0	Manual	Public	N/A	Compare with
17164	None	-	-	23	0	Manual	Public	N/A	Compare with
17285	None	-	-	17	0	Manual	Public	N/A	Compare with
17317	None	-	-	24	0	Manual	Public	N/A	Compare with