Crystallography Open Database

Information card for entry 2001562

2001561 << 2001562 >> 2001563

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Coordinates	2001562.cif
Original IUCr paper	HTML

Structure parameters

Chemical name	2-(α-hydroxybenzyl)-methyl-8-azabicyclo[3.2.1]octan-3-one
Formula	C15 H19 N O2
Calculated formula	C15 H19 N O2
SMILES	[C@H]12[C@H](C(=O)C[C@H](CC1)N2C)[C@H](c1ccccc1)O.[C@@H]12[C@@H](C(=O)C[C@@H](CC1)N2C)[C@@H](c1ccccc1)O
Title of publication	Structure of 2-(α-hydroxybenzyl)-8-methyl-8-azabicyclo[3.2.1]octan-3-one
Authors of publication	Li, J.; Quail, J. W.; Zheng, G. Z.; Majewski, M.
Journal of publication	Acta Crystallographica Section C
Year of publication	1993
Journal volume	49
Journal issue	7
Pages of publication	1410 - 1412
a	8.1213 ± 0.0007 Å
b	17.514 ± 0.003 Å
c	18.903 ± 0.003 Å
α	90 ± 0.01°
β	90 ± 0.009°
γ	90 ± 0.01°
Cell volume	2688.7 ± 0.7 Å³
Cell temperature	287 K
Ambient diffraction temperature	287 K
Number of distinct elements	4
Space group number	61
Hermann-Mauguin space group symbol	P b c a
Hall space group symbol	-P 2ac 2ab
Residual factor for all reflections	0.072
Residual factor for significantly intense reflections	0.048
Weighted residual factors for all reflections	0.062
Weighted residual factors for significantly intense reflections	0.059
Goodness-of-fit parameter for all reflections	2.219
Goodness-of-fit parameter for significantly intense reflections	2.619
Diffraction radiation wavelength	1.5418 Å
Diffraction radiation type	CuKα
Has coordinates	Yes
Has disorder	No
Has F_obs	No

Version history

Revision	Date	Message	Files
176435 (current)	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.	2001562.cif
134621	2015-04-02	The 'cif_fix_values' script with an option '--fix-only-weighting-scheme' and 'cif_filter' script were run over CIF files which included an incorrect value of the data item '_refine_ls_weighting_scheme'. Read the log for more details. There were more than 18k CIF files with values to modify. Usually these incorrect values include comment with formulas, but values of this data item must be an enumerator. The script creates new data item '_refine_ls_weighting_details' to store these comments with formulas, and writes the enumerator 'calc' as a value of data item '_refine_ls_weighting_scheme'. There exists some exceptions in the script.	2001562.cif
131841	2015-02-13	cod/ (robertas@burundukas) Removed commas, inserted missing spaces and newlines between values in the loop '_diffrn_standard_refln_index_' (h k l). No more messages from the 'cif_validate' cod-tools validator about this loop. codsql 'select codid, message from validation where message like "%_diffrn_standard_refln_index_%value%" ' \ \| perl -ne '/\d+,/ and print' \ \| awk '{print $1}' \| uniq \| codid2file \ \| xargs perl -0777 -i -pe 's/^loop_\s^_diffrn_standard_refln_index_.?^loop_/ \ $target = $&, \ $target =~ s! (?: (-?\d+) \s* (?:,\s*)? ) ! \ "$1 " !gxeims , \ $target =~ s!((?:-?\d+ ??){3}) ! "$1\n" !geims, \ $target /iems	2001562.cif
91933	2013-12-28	cif/ (saulius@koala.ibt.lt) Adding DOIs that could be assigned unambiguously to the range 2x CIFs.	2001562.cif
32112	2012-02-03	cif/: committing an update of 45+ thous files, with information appended from the originals.	2001562.cif
26848	2011-09-28	cif/2/, hkl/2/, html/ Reorganising CIFs of the range 2* into the "prefix-directory" tree.	2001562.cif
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).	2001562.cif
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.	2001562.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.	2001562.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	2001562.cif
665	2009-04-21	Redepositing COD files reprocessed in the Acta-Cryst-C-1991-1993-redeposition/ directory. Although all structures were present in COD already, this redeposition enhances and improves the deposited files in several aspects: 1) full bibliographies, with diacrytic marks, are added from the IUCr BibTeX files; 2) chemical formula information is checked and fixed were necessary; 3) symmetry operators were checked for syntactic correctness, fixed were necessary, and spacegroup information was derived from these operators whenever possible; the original spacegroup was checked against the determined spacegroup and the differences were marked if present; 4) missing cell constants were restored, 5) at least in one entry, corrent coordinates were restored, 6) in entries where problems were detected, _code_depositor_comments and _cod_error_... tags were added, 7) information necessary to generate Acta Cryst. paper back-links was added, and the comment header agreed with IUCr was inserted.	2001562.cif
481	2008-11-20	Changing volume number in numerous Acta Cryst. C published CIFs from 'C[0-9]?[0-9]' into '[0-9]?[0-9]'. This makes the COD CIF collection more uniform, and also helps the deposition scripts to spot potential duplicates more accurately. The command for this transformation was: for i in 2/.cif; \ do ( \ if grep -q '_journal_volume C' $i && \ grep -q '_journal_name_full .Acta Cryst' $i; \ then \ echo === $i ===; \ perl -i -pe 's/_journal_volume C/_journal_volume /' $i; \ perl -i -pe \ "s/_journal_name_full ./_journal_name_full 'Acta Crystallographica Section C'/" $i ; \ fi \ ) done	2001562.cif
268	2008-03-14	14 files corrected.	2001562.cif
19	2008-01-26	Changing all end-of-line codes from DOS style to UNIX style in all COD CIF files, for more convenient processing: In the cod/cif/ directory: ff \*.cif \| xargs perl -i -pe 's/\r\n/\n/'	2001562.cif
14	2008-01-14	Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files.	2001562.cif
13	2008-01-13	Setting the svn:keywords property to "Author Date Revision URL Id" for all CIF files in the cod/cif directory.	2001562.cif
1	2007-11-30	Adding all .cif files from the COD, downloaded in a Cod.zip file on 2007.02.07 (and the same Cod.zip is downloadable today, on 2007.11.29)	2001562.cif