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 Typeheteromolecule
Residue Name (RNME)URA
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms12
Net Charge0
Forcefieldmultiple
Molecule ID6460
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version53A6 (IFP53A6.dat / 53A6.ifp)
Upload Date2012-10-30 23:45:42
Literature Reference

Topology History

Other conformers for this molecule (101-200 of 634)

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 (634)RMSD Matrix (634)

Molid  Formula  Iupac  Atoms  Charge  Curation > Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17275 None - 24 -1 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17314 None - 32 0 Manual N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17191 None - 44 0 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17198 None - 26 1 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17298 None - 18 0 Manual N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17313 None - 32 0 Manual N/A Compare with
6454 None - 15 0 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17264 None - 17 0 Manual N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17322 None - 18 0 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17284 None - 23 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)