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 StateCompleted
Total Processing TimeNA (hh:mm:ss)

Molecule Information
Molecule Typesolvent
Residue Name (RNME)H2O
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms3
Net Charge0
Forcefieldmultiple
Molecule ID1596
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version53A6 (IFP53A6.dat / 53A6.ifp)
Upload Date2010-07-19 10:01:45
Literature ReferenceLink

Affiliated Pre-Equilibrated Systems

Author Name Description Link
David Poger DPPC bilayer Hydrated 128-DPPC bilayer Link
Megan O'Mara Membrane-embedded P-glycoprote ... central P-gp structure from 30 ... Link
Megan L. O'Mara ATP-bound P-gp inward facing, ... 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 memb ... P-gp with Mg2+ and ATP in a PO ... Link
Megan L. O'Mara ATP-bound P-gp asymmetric memb ... P-gp with Mg2+ and ATP in a PO ... Link

Topology History

Other conformers for this molecule (101-200 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1)  		Compare 
17494 None - 19 0 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17496 None - 19 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17500 None - 25 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17502 None - 32 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
17534 None - 24 0 Manual N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17536 None - 24 0 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
17542 None - 29 0 Manual N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17544 None - 29 0 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17546 None - 26 1 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
17548 None - 26 1 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
17526 None - 18 0 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
17528 None - 18 0 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
17530 None - 18 0 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
17532 None - 18 0 Manual N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
17145 None - 33 1 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17147 None - 33 1 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17153 None - 17 0 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17155 None - 17 0 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17159 None - 20 0 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17165 None - 27 0 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
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Conditions of Use

ATB Pipeline Setting

Access to this feature is currently restricted

The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.

Experimental Solvation Free Energies (0-0 of 0)

Solvent > Experimental Value
(kJ.mol-1)  		Experimental Uncertainty
(kJ.mol-1)  		Doi 
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