comparing acedrg vs csd · • run refmac5 to assess geometry (idealisation mode) compare with csd...
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![Page 2: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/2.jpg)
AceDRG vs CSDSuggested by Oliver Smart
Monomer library update CCD entries in the CSD
323 5073 1517
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AceDRG vs CSD323 Comp IDs from the CCD
Establish Baseline – original PDB files:• Take PDBs• Extract ligand coordinates• Run REFMAC5 to assess geometry (idealisation mode)
![Page 4: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/4.jpg)
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AceDRG vs CSD323 Comp IDs from the CCD
Establish Baseline – original PDB files:• Take PDBs• Extract ligand coordinates• Run REFMAC5 to assess geometry (idealisation mode)
Re-refined PDB using AceDRG dictionary (monomer library update)• Extract ligand coordinates• Run REFMAC5 to assess geometry (idealisation mode)
![Page 5: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/5.jpg)
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AceDRG vs CSD323 Comp IDs from the CCD
Establish Baseline – original PDB files:• Take PDBs• Extract ligand coordinates• Run REFMAC5 to assess geometry (idealisation mode)
Re-refined PDB using AceDRG dictionary (monomer library update)• Extract ligand coordinates• Run REFMAC5 to assess geometry (idealisation mode)
Compare with CSD model:• Take coordinates• Run REFMAC5 to assess geometry (idealisation mode)
![Page 6: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/6.jpg)
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PDB ligands
REFMAC5 function value
Frequency
010
2030
4050
10 100 1000 10000
![Page 7: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/7.jpg)
PDB ligands
REFMAC5 function value
Frequency
010
2030
4050
10 100 1000 10000
7
![Page 8: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/8.jpg)
PDB ligands
REFMAC5 function value
Frequency
010
2030
4050
10 100 1000 10000
8
![Page 9: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/9.jpg)
PDB ligands
REFMAC5 function value per atom
Frequency
020
4060
80
0.1 1 10 100 1000
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DifferentnumbersofmoleculesinPDBfile.OnlyeveroneinCCD/CSDfile.Differentnumberofatomsindifferentligands.SoluGon:scalebynumberofatoms.
Mostligands(250/323)presentonce.Somearepresent2-11Gmes.3h6ihas102DMFligands.
![Page 10: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/10.jpg)
PDB ligands
REFMAC5 function value per atom
Frequency
020
4060
80
0.1 1 10 100 1000
10
![Page 11: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/11.jpg)
PDB ligands
REFMAC5 function value per atom
Frequency
020
4060
80
0.1 1 10 100 1000
11
![Page 12: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/12.jpg)
PDB ligands
REFMAC5 function value per atom
Frequency
020
4060
80
0.1 1 10 100 1000
12
ANL : 2ov47 atomsf = 3435
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PDB ligands Re-Refined with AceDRG
REFMAC5 function value per atom
Frequency
020
4060
80100
0.1 1 10 100 1000
13
![Page 14: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/14.jpg)
CSD ligands (CCD representatives)
REFMAC5 function value per atom
Frequency
020
4060
80100
0.1 1 10 100 1000
14
![Page 15: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/15.jpg)
-0.5 0.0 0.5 1.0
-10
12
3
QQ-Plot - REFMAC5 function value per atom
PDB ligands Re-Refined with AceDRG
CS
D li
gand
s (C
CD
repr
esen
tativ
es)
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![Page 16: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/16.jpg)
-0.5 0.0 0.5 1.0
-10
12
3
REFMAC5 function value per atom
PDB ligands Re-Refined with AceDRG
CS
D li
gand
s (C
CD
repr
esen
tativ
es)
16
![Page 17: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/17.jpg)
-0.5 0.0 0.5 1.0
-10
12
3
REFMAC5 function value per atom
PDB ligands Re-Refined with AceDRG
CS
D li
gand
s (C
CD
repr
esen
tativ
es)
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AOM4OA1AN3C0
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AOM : 1lho
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AOM : 1lho
AOM (CSD)
![Page 20: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/20.jpg)
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AOM : 1lho
AOM (CSD)
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AOM : 1lho
AOM (CSD)Refined 1cyc
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4OA: 4q0a
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4OA: 4q0a
4OA (CSD)
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4OA: 4q0a
4OA (CSD)
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4OA: 4q0a
4OA (CSD)Refined 1cyc
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1AN: 1lgw
![Page 27: Comparing AceDRG vs CSD · • Run REFMAC5 to assess geometry (idealisation mode) Compare with CSD model: • Take coordinates • Run REFMAC5 to assess geometry (idealisation mode)](https://reader034.vdocuments.us/reader034/viewer/2022050402/5f7fe98c364e4550893034cb/html5/thumbnails/27.jpg)
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1AN: 1lgw
1AN (CSD)
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1AN: 1lgw
1AN (CSD)Refined 1cyc
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3C0: 4u16
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3C0: 4u16
3C0 (CSD)
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3C0: 4u16
3C0 (CSD)
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3C0: 4u16
3C0 (CSD)Refined 1cyc
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SummaryNotes:• LigandmaybeinaparGcularconformaGonduetoenvironment–notscoringidealconformaGons
• RidinghydrogensareaddedbyREFMACandusedforscoring.• MadeadifferenceforafeworiginalPDBentries(3AQin4txs).• Nodifferenceinre-refinedorCSDligands.
Conclusions:• ThereareproblemsintheCSDmodels.
• CouldinvesGgatefurther,andreporttoCSD.• Noteissuescouldbeinintermediatesteps–CCD,Coot,etc.
• Nomenclatureinconsistencies–howdowedealwiththis?
• NothingconcerningidenGfiedthatshouldmakeuseworriedaboutAceDRG.• Noextremeoutliersa_erre-refinementwithAceDRG.• ThereareissuesinthemodelsdepositedinthePDB(nosurprise).