Click on the PDB geometries, then when the JSmol page opens, click on "Specific Script" to see the site of interest. To reproduce these results, download the ZIP file, then run the <filename>.mop file using MOPAC. Then use MOPAC to run the <filename>.arc file newly created.
PDB geometry |
Nature of problem |
Effect |
How the problem was corrected |
| 5UIZ ZIP | The side-chain oxygen on Asn-42 is only 1.45
Å from HOH-402, a water oxygen. |
The resulting O-O bond
caused the water to have only one hydrogen atom |
SITE was used to define
HOH-402 as a cation, this caused a second hydrogen to be added to the water oxygen. |
| 5UGD
ZIP 5N7V ZIP |
Phenyl-methyl C-C distances too short. | A methyl was incorrectly interpreted as a methylene, i.e., as =CH2, not -CH3 |
SITE was used to add a hydrogen atom to the methyl carbon. |
| 5L6Q ZIP | CO3 groups were present. | These were misread as [CO3]2- | SITE was used to define an oxygen on each CO3 as being neutral, this resulted in [HCO3]- . |
| 5LYC
ZIP 5UG2 ZIP |
The Lewis structure for a heme complex was incorrect |
The Lewis structure for a heme complex was incorrect. |
Using CVB,
bonds were deleted between Fe and two N atoms on opposite sides of the ring. This produced spurious charges on one C4N ring. Using SETPI, a p-bond was defined between C2 and C3 in that ring. The resulting heme system had the correct Lewis structure. |
| 5VPS ZIP | The geometry of a piperidine ring was nearer to
a pyridinium than to a piperidine. |
The ring was incorrectly hydrogenated to make it a pyridinium. |
SITE was used to add hydrogen atoms to four carbon atoms. |