Crystallography Open Database
- COD Home
- Accessing COD Data
- Add Your Data
- Documentation
Information card for entry 2216145
Preview
| Coordinates | 2216145.cif |
|---|---|
| Structure factors | 2216145.hkl |
| Original IUCr paper | HTML |
| External links | ChemSpider; PubChem |
| Chemical name | 2-Methylsulfanyl-1-(morpholin-4-ylmethyl)-1H-benzimidazole |
|---|---|
| Formula | C13 H17 N3 O S |
| Calculated formula | C13 H17 N3 O S |
| SMILES | n1(c(nc2ccccc12)SC)CN1CCOCC1 |
| Title of publication | 2-Methylsulfanyl-1-(morpholin-4-ylmethyl)-1<i>H</i>-benzimidazole |
| Authors of publication | Abou, Akoun; Bany, Guy E.; Kakou-Yao, Rita; Touré Seikou; Ebby, N'Dédé |
| Journal of publication | Acta Crystallographica Section E |
| Year of publication | 2007 |
| Journal volume | 63 |
| Journal issue | 11 |
| Pages of publication | o4218 - o4218 |
| a | 6.2461 ± 0.0002 Å |
| b | 9.7949 ± 0.0002 Å |
| c | 11.6966 ± 0.0005 Å |
| α | 75.475 ± 0.001° |
| β | 84.808 ± 0.001° |
| γ | 76.251 ± 0.002° |
| Cell volume | 672.51 ± 0.04 Å3 |
| Cell temperature | 294 K |
| Ambient diffraction temperature | 294 K |
| Number of distinct elements | 5 |
| Space group number | 2 |
| Hermann-Mauguin space group symbol | P -1 |
| Hall space group symbol | -P 1 |
| Residual factor for all reflections | 0.052 |
| Residual factor for significantly intense reflections | 0.043 |
| Weighted residual factors for all reflections | 0.096 |
| Weighted residual factors for significantly intense reflections | 0.086 |
| Weighted residual factors for all reflections included in the refinement | 0.096 |
| Goodness-of-fit parameter for all reflections included in the refinement | 0.917 |
| Diffraction radiation wavelength | 0.71073 Å |
| Diffraction radiation type | MoKα |
| Has coordinates | Yes |
| Has disorder | No |
| Has Fobs | Yes |
| 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. |
2216145.cif 2216145.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. |
2216145.cif 2216145.hkl |
| 181081 | 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 2/21/61. |
2216145.cif 2216145.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. |
2216145.cif 2216145.hkl |
| 91933 | 2013-12-28 | cif/ (saulius@koala.ibt.lt) Adding DOIs that could be assigned unambiguously to the range 2x CIFs. |
2216145.cif 2216145.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. | 2216145.cif 2216145.hkl |
| 32112 | 2012-02-03 | cif/: committing an update of 45+ thous files, with information appended from the originals. | 2216145.cif 2216145.hkl |
| 26848 | 2011-09-28 | cif/2/, hkl/2/, html/ Reorganising CIFs of the range 2* into the "prefix-directory" tree. |
2216145.cif 2216145.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). |
2216145.cif 2216145.hkl |
| 26025 | 2011-09-16 | hkl/2/ Adding assigned Fobs files for the 1980-2010 IUCr data. |
2216145.cif 2216145.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. |
2216145.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. |
2216145.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 |
2216145.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. |
2216145.cif |
All data in the COD and the database itself are dedicated to the
public domain and licensed under the
CC0
License
.
Users of the data should acknowledge the original authors of the
structural data.