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 Typeamino acid
Residue Name (RNME)L5H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms23
Net Charge0
Forcefieldmultiple
Molecule ID17163
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:14
Literature ReferenceDrazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, Bojan Zagrovic; A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications; PLOS Computational Biology, 2013, 9 (7), e1003154

Topology History

Other conformers for this molecule (401-500 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 
17161 None - 23 0 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17484 None - 15 0 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
564 None - 6 0 Manual* N/A Compare with
169 None - 13 0 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
177 None - 20 0 Manual* N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
212 None - 17 0 Manual* N/A Compare with
213 None - 27 0 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
215 None - 19 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
562 None - 9 0 Manual* N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
583 None - 15 0 Manual* N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
619 None - 16 0 Manual* N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
584 None - 15 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)