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 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
Tautomer Group IDNone
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 (1-100 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  Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17505 None - 29 0 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17269 None - 18 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17288 None - 17 0 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17320 None - 24 0 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17335 None - 30 1 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17488 None - 21 0 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
17437 None - 25 0 Manual N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17235 None - 26 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17267 None - 19 0 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17420 None - 21 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17318 None - 24 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17471 None - 24 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17333 None - 30 1 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17486 None - 21 0 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
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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)