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 (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  Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
1554 None - 155 0 Manual* N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17528 None - 18 0 Manual N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
17441 None - 28 1 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
17543 None - 29 0 Manual N/A Compare with
205 None - 24 0 Manual* N/A Compare with
619 None - 16 0 Manual* N/A Compare with
17307 None - 23 0 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
17256 None - 27 0 Manual N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
17409 None - 18 0 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17290 None - 28 0 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17322 None - 18 0 Manual N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17271 None - 18 0 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17166 None - 27 0 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17526 None - 18 0 Manual N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
164 None - 27 1 Manual* N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
17541 None - 29 0 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
583 None - 15 0 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
17254 None - 27 0 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
5011 None - 40 -4 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)