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 (501-600 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
2919	None	-	-	52	-1	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
17447	None	-	-	28	0	Manual	Public	N/A	Compare with
1547	None	-	-	24	0	Manual*	Public	N/A	Compare with
1587	None	-	-	155	0	Manual*	Public	N/A	Compare with
17179	None	-	-	20	-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
177	None	-	-	20	0	Manual*	Public	N/A	Compare with
17396	None	-	-	24	-1	Manual	Public	N/A	Compare with
581	None	-	-	16	0	Manual*	Public	N/A	Compare with
17549	None	-	-	15	-1	Manual	Public	N/A	Compare with
17430	None	-	-	15	0	Manual	Public	N/A	Compare with
1564	None	-	-	143	0	Manual*	Public	N/A	Compare with
1606	None	-	-	20	0	Manual*	Public	N/A	Compare with
17194	None	-	-	28	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
562	None	-	-	9	0	Manual*	Public	N/A	Compare with
17532	None	-	-	18	0	Manual	Public	N/A	Compare with
4604	None	-	-	217	0	Manual*	Public	N/A	Compare with
9411	None	-	-	17	-2	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
17513	None	-	-	26	0	Manual	Public	N/A	Compare with
1738	None	-	-	77	0	Manual*	Public	N/A	Compare with
3502	None	-	-	19	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
17158	None	-	-	20	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
2749	None	-	-	14	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
17445	None	-	-	28	0	Manual	Public	N/A	Compare with
1539	None	-	-	137	0	Manual*	Public	N/A	Compare with
1584	None	-	-	137	0	Manual*	Public	N/A	Compare with
17177	None	-	-	20	-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
175	None	-	-	19	0	Manual*	Public	N/A	Compare with
17394	None	-	-	24	-1	Manual	Public	N/A	Compare with
578	None	-	-	10	0	Manual*	Public	N/A	Compare with
17547	None	-	-	26	1	Manual	Public	N/A	Compare with
5814	None	-	-	381	1	Manual*	Public	N/A	Compare with
1562	None	-	-	125	0	Manual*	Public	N/A	Compare with
1604	None	-	-	16	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
17377	None	-	-	28	-1	Manual	Public	N/A	Compare with
215	None	-	-	19	0	Manual*	Public	N/A	Compare with
17530	None	-	-	18	0	Manual	Public	N/A	Compare with
4602	None	-	-	113	0	Manual*	Public	N/A	Compare with
9371	None	-	-	11	-2	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
17511	None	-	-	27	0	Manual	Public	N/A	Compare with
1733	None	-	-	81	0	Manual*	Public	N/A	Compare with
3500	None	-	-	18	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
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
2745	None	-	-	24	0	Manual*	Public	N/A	Compare with
4581	None	-	-	161	-8	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
17443	None	-	-	28	1	Manual	Public	N/A	Compare with
1532	None	-	-	149	0	Manual*	Public	N/A	Compare with
1582	None	-	-	119	0	Manual*	Public	N/A	Compare with
17175	None	-	-	25	0	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
173	None	-	-	20	0	Manual*	Public	N/A	Compare with
17392	None	-	-	18	0	Manual	Public	N/A	Compare with
576	None	-	-	26	0	Manual*	Public	N/A	Compare with
17545	None	-	-	26	1	Manual	Public	N/A	Compare with
5798	None	-	-	19	0	Manual*	Public	N/A	Compare with
17156	None	-	-	17	0	Manual	Public	N/A	Compare with
1602	None	-	-	20	0	Manual*	Public	N/A	Compare with
17190	None	-	-	44	0	Manual	Public	N/A	Compare with
17222	None	-	-	22	0	Manual	Public	N/A	Compare with
17343	None	-	-	23	-2	Manual	Public	N/A	Compare with
17375	None	-	-	30	-1	Manual	Public	N/A	Compare with
213	None	-	-	27	0	Manual*	Public	N/A	Compare with
17528	None	-	-	18	0	Manual	Public	N/A	Compare with
1511	None	-	-	131	0	Manual*	Public	N/A	Compare with
21025	None	-	-	209	-4	Manual*	Public	N/A	Compare with
4592	None	-	-	161	-8	Manual*	Public	N/A	Compare with