Crystallography Open Database

Information card for entry 2210546

Preview

Coordinates	2210546.cif
Structure factors	2210546.hkl
Original IUCr paper	HTML
External links	ChemSpider; PubChem

Structure parameters

Common name	Desmethylbergenin
Chemical name	3,4,8,9,10-pentahydroxy-2-hydroxymethyl-2,3,4,4a,6,10b- hexahydropyrano[3,2-<i>c</i>]isochromen-6-one hemihydrate
Formula	C13 H15 O9.5
Calculated formula	C13 H15 O9.5
SMILES	O.O[C@@H]1[C@H](O[C@@H]2[C@H](OC(=O)c3cc(O)c(O)c(O)c23)[C@H]1O)CO
Title of publication	Desmethylbergenin hemihydrate
Authors of publication	Zamarrud; Viqar Uddin Ahmad; Shazia Anjum; Farayl Vali Mohammad; M. Qaiser
Journal of publication	Acta Crystallographica Section E
Year of publication	2006
Journal volume	62
Journal issue	10
Pages of publication	o4626 - o4628
a	8.282 ± 0.0019 Å
b	11.566 ± 0.003 Å
c	13.959 ± 0.003 Å
α	90°
β	97.545 ± 0.005°
γ	90°
Cell volume	1325.6 ± 0.5 Å³
Cell temperature	293 ± 2 K
Ambient diffraction temperature	293 ± 2 K
Number of distinct elements	3
Space group number	5
Hermann-Mauguin space group symbol	C 1 2 1
Hall space group symbol	C 2y
Residual factor for all reflections	0.0322
Residual factor for significantly intense reflections	0.0306
Weighted residual factors for significantly intense reflections	0.0771
Weighted residual factors for all reflections included in the refinement	0.0788
Goodness-of-fit parameter for all reflections included in the refinement	1.222
Diffraction radiation wavelength	0.71073 Å
Diffraction radiation type	MoKα
Has coordinates	Yes
Has disorder	No
Has F_obs	Yes

Version history

Revision	Date	Message	Files
301804 (current)	2025-08-19	Add cross-references to PubChem compounds in COD range 2/21 Each referenced PubChem compound corresponds to the full crystal structure.	2210546.cif 2210546.hkl
201974	2017-10-13	cif/2/ Marking COD entries in range 2/21 that are known to be related to ChemSpider entries using the _cod_related_entry data loop.	2210546.cif 2210546.hkl
181025	2016-04-03	hkl/2/21/ (antanas@echidna) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in subrange 2/21/05.	2210546.cif 2210546.hkl
176435	2016-02-14	cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries from ranges 1, 2.	2210546.cif 2210546.hkl
91933	2013-12-28	cif/ (saulius@koala.ibt.lt) Adding DOIs that could be assigned unambiguously to the range 2x CIFs.	2210546.cif 2210546.hkl
88064	2013-08-29	Adding _cod_database_fobs_code data item to all COD CIFs that have Fobs deposited and did not have this data item yet.	2210546.cif 2210546.hkl
32112	2012-02-03	cif/: committing an update of 45+ thous files, with information appended from the originals.	2210546.cif 2210546.hkl
26848	2011-09-28	cif/2/, hkl/2/, html/ Reorganising CIFs of the range 2* into the "prefix-directory" tree.	2210546.cif 2210546.hkl
26029	2011-09-17	cif/2/ Reverting changes of revision 25271: ( cd cif/2/; svn merge -r25271:25270 . ) The problem was that the reprocessed files from IUCr, although were more complete, "resurrected" data errors that were corrected in the previous recisions. The additional data that have been extracted during the reprocessing will have to be merged without overwriting the existing values in COD files, except some explicit and controlled cases (such as publication titles and chemical names).	2210546.cif 2210546.hkl
26025	2011-09-16	hkl/2/ Adding assigned Fobs files for the 1980-2010 IUCr data.	2210546.cif 2210546.hkl
25271	2011-09-10	cif/2/ Adding reporocessed IUCr CIFs for the years 1980-2010. The CIFs now contain more complete bibliography, substance names, correctly unfolded text fields (using the CIF line unfolding protocol), explicitely set cell angles, and _cod_data_source_block fields.	2210546.cif
5310	2011-01-02	cif/ Running cif_fix_enum with the core CIF dictionary on COD ranges 2, 8 and 9. Range 9 remained unchanged, and in ranges 2 and 8 there were 17309 modified files, most changes were fixes enumerator case.	2210546.cif
966	2010-01-30	cif/ Adding _cod_database_code tags to all COD entries. Adding tag description to the cif_cod.dic dictionary so that COD entries can be validated.	2210546.cif
858	2009-11-18	cod/cif/ Changing all _chemical_formula_sum values, were necessary, to conform IUCr recommended syntax and sorting order. After this operation, it will be easier to search for structures using the _chemical_formula_sum values. Only those files and thos lines that really needed to be changed were changed; otehrwise the CIFs were not reformatted. The procedure was as follows: first, all files were passed through a 'cif_filter --parse-formula-sum' command, and the lines containing _cif_formula_sum matching tags were extracted. The extracted tags were "spliced" into the CIF files using the ./bin/{un,}grepciftag commands and awk to filter out old tags and add new tags in their place; the replacement was only done if the new tags contained "_cod_" tags ('grep -q _cod_ tmp-$$'), indicating that cif_filter has altered the formula, or the original file did not contain the _chemical_formula_sum tag ('! grep -q _chemical_formula_sum X'), indicating that cif_filter has guessed the chemical_formula_sum from the file (which should not have happened, actually). If the file was different, disregarding spaces, from the original one ('if ! diff -wb X tmp2-$$'), the original was replaced by the new file, to be committed to the repository. The full command for this step was: ( \ set -x; \ find ? -name \.cif \ \| xargs -n1 -iX \ sh -c 'cif_filter --parse-formula-sum X \ \| ./bin/grepciftag _chemical_formula_sum > tmp-$$; \ if grep -q _cod_ tmp-$$ \|\| ! grep -q _chemical_formula_sum X; \ then \ awk "/^#/,/_chemical_formula_sum/{print} /_chemical_formula_sum/{exit}" X \ \| ./bin/ungrepciftag _chemical_formula_sum > tmp2-$$; \ cat tmp-$$ >> tmp2-$$; \ awk "/_chemical_formula_sum/,/\$eof/" X \ \| ./bin/ungrepciftag _chemical_formula_sum >> tmp2-$$; \ if ! diff -wb X tmp2-$$; \ then \ mv -fv tmp2-$$ X; \ fi; \ fi; \ rm -f tmp-$$ tmp2-$$' \ ) >& sort-chemical-formulae-2009.11.16.log Next, the files were searched that differ from their originals only by the order of CIF tags: svn st \ \| awk '/^M/{print $NF}' \ \| sort \| xargs -n1 -iX \ bash -c 'if diff -q <(svn cat X\|sort) <(sort X) >& /dev/null; \ then echo X; \ fi' \ >& only-reordered.lst These files, after manual inspection ('cat only-reordered.lst \| xargs svn diff \| less'), were reverted to the originals: cat only-reordered.lst \| xargs svn revert Finally, a syntax check was performed using 'vcif': svn st \| awk '/^M/{print $NF}' \ \| sort \| xargs -n1 -iX \ sh -c 'echo -n X"\r"; vcif -l 2048 X \|\| { echo == X == ; echo X >&2; }' \ 2> vcif-check-2009.11.18.err A check on the whole COD archive showed the same files as recorded in vcif-check-2009.11.18.err: find ? -name \.cif \ \| sort \ \| xargs -n1 -iX \ sh -c 'echo -n X"\r"; \ vcif -l 2048 X \|\| { echo == X == ; echo X >&2; }' \ 2> vcif-all-check-`-date`.err diff vcif-check-2009.11.18.err vcif-all-check-2009.11.18.err Since no differences were detected in between vcif-check-2009.11.18.err and vcif-all-check-2009.11.18.err, the latter was deleted and is not committed. The check reveled two broken files, 2/2000267.cif and 2/2001000.cif; these were corrected manually. Afther this, one more 'vcif' check showed no syntax errors, and the changes are committed into the COD repository. 19798 files have modifications in this commit, according to svn st \| grep '^M' \| wc -l	2210546.cif
853	2009-11-16	cif/ Reconstructing spacegroup designators from the symmetry operators were possible. The comands used can be found in the log file reformat-spacegroups-2009.11.14.log committed with the current revision. Only lines that contained spacegroup designators were changed, and all files pass vcif test after the conversion.	2210546.cif
326	2008-04-03	Adding all Acta Cryst. B, C, and E missing retrospective CIF files up to 2008 February, generated from the files that were automatically downloaded from the IUCr site.	2210546.cif