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	lipid
Residue Name (RNME)	POPC
Formula	None
IUPAC InChI Key	None
IUPAC InChI	None
IUPAC Name
Common Name
Canonical SMILES (Daylight)	NULL
Number of atoms	134
Net Charge	0
Forcefield	multiple
Molecule ID	1506
Visibility	Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version	54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date	2010-07-08 11:44:56
Literature Reference	Link

Affiliated Pre-Equilibrated Systems

Author	Name	Description	Link
David Poger	POPC bilayer	Hydrated 128-POPC bilayer	Link
Megan O'Mara	P-gp with NCP, ATP in a Cholesterol & POPC bilayer ...	P-gp with NCP, ATP in a Cholesterol & POPC bilayer ...	Link
ZhiGuang Jia, Megan L. O'Mara, ...	Vancomycin and lipid II forms 2:2 complexes in POPC membrane ...	Vancomycin spontenoursly attac ...	Link
Megan L. O'Mara	ATP-bound P-gp inward facing, membrane-embedded conformation, Run B ...	P-gp with Mg2+ and ATP in a PO ...	Link
Megan L. O'Mara	Membrane-embedded P-gp with AT ...	P-gp with Mg2+ and ATP in a PO ...	Link
Megan L. O'Mara	ATP-bound P-gp asymmetric membrane-embedded conformation, Run C ...	P-gp with Mg2+ and ATP in a PO ...	Link
Megan L. O'Mara	ATP-bound P-gp asymmetric membrane-embedded conformation, Run C ...	P-gp with Mg2+ and ATP in a PO ...	Link
ZG Jia, ML O'Mara, J Zuegg, MA Cooper, AE Mark ...	Lipid II in POPC membrane	System contain 3 lipid II and 125 POPC molocule ...	Link

Topology History

Other conformers for this molecule (201-300 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
17189	None	-	-	44	0	Manual	Public	N/A	Compare with
2671	None	-	-	47	-3	Manual	Public	N/A	Compare with
4578	None	-	-	161	-8	Manual*	Public	N/A	Compare with
17255	None	-	-	27	0	Manual	Public	N/A	Compare with
17408	None	-	-	28	-1	Manual	Public	N/A	Compare with
17440	None	-	-	25	0	Manual	Public	N/A	Compare with
1578	None	-	-	144	0	Manual*	Public	N/A	Compare with
17172	None	-	-	28	0	Manual	Public	N/A	Compare with
17204	None	-	-	33	1	Manual	Public	N/A	Compare with
17357	None	-	-	30	0	Manual	Public	N/A	Compare with
170	None	-	-	14	0	Manual*	Public	N/A	Compare with
17389	None	-	-	18	0	Manual	Public	N/A	Compare with
573	None	-	-	20	0	Manual*	Public	N/A	Compare with
17542	None	-	-	29	0	Manual	Public	N/A	Compare with
5795	None	-	-	18	-1	Manual*	Public	N/A	Compare with
17153	None	-	-	17	0	Manual	Public	N/A	Compare with
17306	None	-	-	23	0	Manual	Public	N/A	Compare with
17338	None	-	-	18	0	Manual	Public	N/A	Compare with
17491	None	-	-	22	0	Manual	Public	N/A	Compare with
17372	None	-	-	18	-1	Manual	Public	N/A	Compare with
210	None	-	-	17	0	Manual*	Public	N/A	Compare with
17525	None	-	-	18	0	Manual	Public	N/A	Compare with
1506	None	-	-	134	0	Manual*	Public	N/A	Compare with
18623	None	-	-	139	-3	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
17506	None	-	-	29	0	Manual	Public	N/A	Compare with
1678	None	-	-	35	0	Manual*	Public	N/A	Compare with
3485	None	-	-	6	0	Manual*	Public	N/A	Compare with
17238	None	-	-	16	-1	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
1556	None	-	-	143	0	Manual*	Public	N/A	Compare with
1596	None	-	-	3	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
4182	None	-	-	5	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
1576	None	-	-	129	0	Manual*	Public	N/A	Compare with
17170	None	-	-	28	0	Manual	Public	N/A	Compare with
17202	None	-	-	33	1	Manual	Public	N/A	Compare with
17355	None	-	-	23	0	Manual	Public	N/A	Compare with
168	None	-	-	15	0	Manual*	Public	N/A	Compare with
17387	None	-	-	20	-2	Manual	Public	N/A	Compare with
571	None	-	-	14	0	Manual*	Public	N/A	Compare with
17540	None	-	-	19	-2	Manual	Public	N/A	Compare with
5471	None	-	-	130	-10	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
2276	None	-	-	363	-2	Manual*	Public	N/A	Compare with
207	None	-	-	20	0	Manual*	Public	N/A	Compare with
17523	None	-	-	21	-1	Manual	Public	N/A	Compare with
1503	None	-	-	118	0	Manual*	Public	N/A	Compare with
18621	None	-	-	49	-3	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
1668	None	-	-	27	0	Manual*	Public	N/A	Compare with
3411	None	-	-	18	0	Manual*	Public	N/A	Compare with
17236	None	-	-	26	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
1554	None	-	-	155	0	Manual*	Public	N/A	Compare with
1594	None	-	-	10	0	Manual*	Public	N/A	Compare with
17185	None	-	-	15	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
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
1572	None	-	-	153	0	Manual*	Public	N/A	Compare with
17168	None	-	-	27	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
166	None	-	-	17	0	Manual*	Public	N/A	Compare with
17385	None	-	-	20	-2	Manual	Public	N/A	Compare with
569	None	-	-	8	0	Manual*	Public	N/A	Compare with
17538	None	-	-	19	-2	Manual	Public	N/A	Compare with
5181	None	-	-	56	-6	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
2172	None	-	-	26	-1	Manual*	Public	N/A	Compare with
3947	None	-	-	127	-1	Manual	Public	N/A	Compare with
619	None	-	-	16	0	Manual*	Public	N/A	Compare with
18619	None	-	-	49	-3	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