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 building block
Residue Name (RNME)WBR
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge0
Forcefieldmultiple
Molecule ID17256
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:15
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 (501-600 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 
17222 None - 22 0 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17207 None - 18 0 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
4213 None - 61 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
5181 None - 56 -6 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
9377 None - 12 -2 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
5639 None - 127 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
5797 None - 18 -1 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
6252 None - 89 0 Manual* N/A Compare with
6451 None - 27 0 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
6461 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)