Subject: Summary: Cyclodextrin.

From: Yubo Fan <[email-masked]>
Date: Wed, 03 Jun 1998 08:55:39 +0800

Hi, everyone,

I sent an email to ask the structures of cyclodextrin several days ago. Till now
I have received many emails. Thanks a lot.

> Hi, everyone,
>
> I have been looking for the structure of cyclodextrin in the Web but
> failed. Is there cyclodextrin structure file (for example, PDB file) in
> the InterNet? Or, if someone have, could you please send me one copy by
> email? I need the structures of alpha-cyclodextrin, beta-cyclodextrin
> and gamma-cyclodextrin. The precise structure data is preferred, for
> instance, the data from monocrystal or by calculation.
>
> With best regards
>
> Y. Fan

Dear Dr. Fan,

please have a look at:

http://caramel.oc.chemie.tu-darmstadt.de/~lemmi/molcad/cyc_iso1.html

and ask Dr. Immel (at the bottom of the WWW-page) by e-mail for the structure
data you need.

Best regards from Stuttgart, Germany,
Heinz Poehlmann
 .-------------------------------------------------------------------------.
 | Dr. Heinz W. Poehlmann                     Regionales Rechenzentrum     |
 | Manager Applications Department            der Universitaet Stuttgart   |
 | Computational Chemistry Support            (University Computer Center) |
 | phone:   (49)-711-685-5992                 RUS / HLRS                   |
 | fax:     (49)-711-6787626                  Allmandring 30               |
 | e-mail:  [email-masked]                 D-70550 Stuttgart            |
 | e-mail:  [email-masked]    Germany                      |
 '-------------------------------------------------------------------------'

Dear Yubo,
        have a look to our electronic poster page at:
http://antas.agraria.uniss.it
You'll find some papers on beta-cyclodextrin and you could download the
pdb file
bye
Bruno

Dr Bruno Manunza
Molecular Modeling Lab
DISAABA (Dept. of Agricultural Environm. Sci)
University of Sassari
V.le Italia 39 07100 Sassari, ITALY
phone: 39 79 229215
fax:   39 79 229276
e-mail: [email-masked]
web: http://antas.agraria.uniss.it

Subject:
        Re: CCL:Cyclodextrin.
   Date:
        Thu, 28 May 1998 17:45:21 +0100
   From:
        Peter Tebbutt <[email-masked]>
     To:
        [email-masked]

Hi Yubo Fan,

I know there is a structure of cyclodextrin shipped with the latest version
of Chem3D Ultra (which we supply) but I don't expect you'd want to buy
*just* for the structure, but you may be able to contact someone at
CambridgeSoft and ask them where and how they got it.

the web site is www.camsoft.com and all contacts are here.

With regards

Peter Tebbutt
ChemSymphony Consultant
Cherwell Scientific Publishing

Subject:
   Date:         Thu, 28 May 1998 22:38:38 -0400
   From:         "Genbin Shi" <[email-masked]>
     To:         [email-masked]

HETATM 2864  C11 BCD   371     -10.695  -3.048   2.018  1.00 44.16
     1DMB2978
HETATM 2865  C21 BCD   371      -9.822  -2.557   0.835  1.00 41.96
     1DMB2979
HETATM 2866  O21 BCD   371     -10.292  -3.169  -0.384  1.00 41.22
     1DMB2980
HETATM 2867  C31 BCD   371      -8.347  -2.840   1.090  1.00 39.24
     1DMB2981
HETATM 2868  O31 BCD   371      -7.539  -2.239   0.055  1.00 37.29
     1DMB2982
HETATM 2869  C41 BCD   371      -7.919  -2.296   2.440  1.00 38.31
     1DMB2983
HETATM 2870  O41 BCD   371      -6.611  -2.820   2.694  1.00 35.68
     1DMB2984
HETATM 2871  C51 BCD   371      -8.844  -2.756   3.560  1.00 38.64
     1DMB2985
HETATM 2872  O51 BCD   371     -10.233  -2.402   3.204  1.00 41.49
     1DMB2986
HETATM 2873  C61 BCD   371      -8.606  -2.123   4.910  1.00 38.11
     1DMB2987
HETATM 2874  O61 BCD   371      -9.468  -2.752   5.872  1.00 38.72
     1DMB2988
HETATM 2875  C12 BCD   371      -5.613  -1.953   3.133  1.00 33.23
     1DMB2989
HETATM 2876  C22 BCD   371      -4.333  -2.133   2.309  1.00 31.78
     1DMB2990
HETATM 2877  O22 BCD   371      -4.676  -1.971   0.924  1.00 30.82
     1DMB2991
HETATM 2878  C32 BCD   371      -3.686  -3.461   2.647  1.00 32.17
     1DMB2992
HETATM 2879  O32 BCD   371      -2.455  -3.571   1.909  1.00 29.27
     1DMB2993
HETATM 2880  C42 BCD   371      -3.395  -3.532   4.144  1.00 33.44
     1DMB2994
HETATM 2881  O42 BCD   371      -2.841  -4.818   4.436  1.00 36.32
     1DMB2995
HETATM 2882  C52 BCD   371      -4.686  -3.107   4.929  1.00 33.06
     1DMB2996
HETATM 2883  O52 BCD   371      -5.344  -2.160   4.511  1.00 33.51
     1DMB2997
HETATM 2884  C62 BCD   371      -4.549  -3.315   6.415  1.00 32.59
     1DMB2998
HETATM 2885  O62 BCD   371      -5.883  -3.621   6.808  1.00 33.01
     1DMB2999
HETATM 2886  C13 BCD   371      -1.517  -5.001   4.857  1.00 38.44
     1DMB3000
HETATM 2887  C23 BCD   371      -0.932  -6.211   4.128  1.00 39.94
     1DMB3001
HETATM 2888  O23 BCD   371      -1.137  -6.034   2.698  1.00 41.05
     1DMB3002
HETATM 2889  C33 BCD   371      -1.625  -7.480   4.573  1.00 41.82
     1DMB3003
HETATM 2890  O33 BCD   371      -1.047  -8.602   3.875  1.00 43.17
     1DMB3004
HETATM 2891  C43 BCD   371      -1.553  -7.642   6.070  1.00 41.98
     1DMB3005
HETATM 2892  O43 BCD   371      -2.369  -8.742   6.418  1.00 45.81
     1DMB3006
HETATM 2893  C53 BCD   371      -2.142  -6.400   6.742  1.00 40.30
     1DMB3007
HETATM 2894  O53 BCD   371      -1.493  -5.234   6.262  1.00 39.57
     1DMB3008
HETATM 2895  C63 BCD   371      -1.916  -6.454   8.275  1.00 39.59
     1DMB3009
HETATM 2896  O63 BCD   371      -2.099  -5.298   8.983  1.00 38.96
     1DMB3010
HETATM 2897  C14 BCD   371      -1.964  -9.647   7.437  1.00 47.95
     1DMB3011
HETATM 2898  C24 BCD   371      -1.402 -10.903   6.699  1.00 49.38
     1DMB3012
HETATM 2899  O24 BCD   371      -0.248 -10.584   5.947  1.00 48.08
     1DMB3013
HETATM 2900  C34 BCD   371      -2.519 -11.412   5.791  1.00 50.04
     1DMB3014
HETATM 2901  O34 BCD   371      -2.054 -12.478   4.960  1.00 53.04
     1DMB3015
HETATM 2902  C44 BCD   371      -3.690 -11.818   6.656  1.00 50.60
     1DMB3016
HETATM 2903  O44 BCD   371      -4.781 -12.155   5.775  1.00 51.64
     1DMB3017
HETATM 2904  C54 BCD   371      -4.138 -10.630   7.509  1.00 50.75
     1DMB3018
HETATM 2905  O54 BCD   371      -3.073 -10.004   8.199  1.00 48.61
     1DMB3019
HETATM 2906  C64 BCD   371      -5.102 -11.149   8.634  1.00 51.84
     1DMB3020
HETATM 2907  O64 BCD   371      -5.390 -10.038   9.471  1.00 54.82
     1DMB3021
HETATM 2908  C15 BCD   371      -5.419 -13.414   5.945  1.00 52.23
     1DMB3022
HETATM 2909  C25 BCD   371      -5.707 -13.994   4.576  1.00 52.24
     1DMB3023
HETATM 2910  O25 BCD   371      -4.546 -13.981   3.725  1.00 52.16
     1DMB3024
HETATM 2911  C35 BCD   371      -6.800 -13.172   3.886  1.00 53.12
     1DMB3025
HETATM 2912  O35 BCD   371      -7.171 -13.786   2.640  1.00 52.81
     1DMB3026
HETATM 2913  C45 BCD   371      -8.010 -13.090   4.780  1.00 52.87
     1DMB3027
HETATM 2914  O45 BCD   371      -8.930 -12.190   4.114  1.00 52.91
     1DMB3028
HETATM 2915  C55 BCD   371      -7.665 -12.498   6.169  1.00 52.76
     1DMB3029
HETATM 2916  O55 BCD   371      -6.571 -13.255   6.733  1.00 53.32
     1DMB3030
HETATM 2917  C65 BCD   371      -8.818 -12.637   7.086  1.00 52.15
     1DMB3031
HETATM 2918  O65 BCD   371      -8.706 -11.845   8.242  1.00 52.49
     1DMB3032
HETATM 2919  C16 BCD   371     -10.304 -12.590   4.018  1.00 53.25
     1DMB3033
HETATM 2920  C26 BCD   371     -10.713 -12.447   2.599  1.00 53.73
     1DMB3034
HETATM 2921  O26 BCD   371      -9.633 -12.943   1.788  1.00 53.90
     1DMB3035
HETATM 2922  C36 BCD   371     -10.959 -10.996   2.183  1.00 53.67
     1DMB3036
HETATM 2923  O36 BCD   371     -11.798 -11.037   0.979  1.00 54.50
     1DMB3037
HETATM 2924  C46 BCD   371     -11.608 -10.162   3.187  1.00 53.38
     1DMB3038
HETATM 2925  O46 BCD   371     -11.342  -8.781   2.766  1.00 53.24
     1DMB3039
HETATM 2926  C56 BCD   371     -11.029 -10.352   4.581  1.00 53.59
     1DMB3040
HETATM 2927  O56 BCD   371     -11.092 -11.766   4.871  1.00 53.68
     1DMB3041
HETATM 2928  C66 BCD   371     -11.772  -9.657   5.726  1.00 54.48
     1DMB3042
HETATM 2929  O66 BCD   371     -12.379 -10.540   6.427  1.00 56.29
     1DMB3043
HETATM 2930  C17 BCD   371     -12.461  -8.130   2.145  1.00 52.98
     1DMB3044
HETATM 2931  C27 BCD   371     -12.023  -7.621   0.792  1.00 52.83
     1DMB3045
HETATM 2932  O27 BCD   371     -11.276  -8.655   0.107  1.00 53.92
     1DMB3046
HETATM 2933  C37 BCD   371     -11.132  -6.390   0.892  1.00 53.08
     1DMB3047
HETATM 2934  O37 BCD   371     -11.049  -5.776  -0.411  1.00 54.19
     1DMB3048
HETATM 2935  C47 BCD   371     -11.670  -5.344   1.883  1.00 52.00
     1DMB3049
HETATM 2936  O47 BCD   371     -10.554  -4.443   2.051  1.00 48.88
     1DMB3050
HETATM 2937  C57 BCD   371     -11.910  -6.045   3.225  1.00 53.05
     1DMB3051
HETATM 2938  O57 BCD   371     -12.888  -7.112   3.002  1.00 53.07
     1DMB3052
HETATM 2939  C67 BCD   371     -12.545  -5.111   4.255  1.00 54.33
     1DMB3053
HETATM 2940  O67 BCD   371     -11.847  -5.338   5.480  1.00 56.68
     1DMB3054

 Subject:         it is another BCD
   Date:         Thu, 28 May 1998 22:40:42 -0400
   From:        "Genbin Shi" <[email-masked]>
     To:         [email-masked]

HETATM 5267  C11 BCD   701      58.178  14.795   3.335  1.00 70.57           C
HETATM 5268  C21 BCD   701      59.711  14.744   3.251  1.00 70.08           C
HETATM 5269  O21 BCD   701      60.151  13.491   2.753  1.00 68.12           O
HETATM 5270  C31 BCD   701      60.339  14.990   4.620  1.00 71.70           C
HETATM 5271  O31 BCD   701      61.755  15.064   4.481  1.00 73.17           O
HETATM 5272  C41 BCD   701      59.815  16.281   5.272  1.00 71.24           C
HETATM 5273  O41 BCD   701      60.198  16.268   6.675  1.00 67.96           O
HETATM 5274  C51 BCD   701      58.268  16.381   5.170  1.00 72.03           C
HETATM 5275  O51 BCD   701      57.787  16.067   3.839  1.00 71.27           O
HETATM 5276  C61 BCD   701      57.775  17.786   5.469  1.00 72.02           C
HETATM 5277  O61 BCD   701      58.010  18.136   6.824  1.00 74.16           O
HETATM 5278  C12 BCD   701      61.002  17.304   7.183  1.00 65.43           C
HETATM 5279  C22 BCD   701      62.303  16.715   7.743  1.00 64.11           C
HETATM 5280  O22 BCD   701      62.961  15.950   6.747  1.00 64.84           O
HETATM 5281  C32 BCD   701      62.026  15.822   8.959  1.00 64.20           C
HETATM 5282  O32 BCD   701      63.264  15.411   9.536  1.00 60.82           O
HETATM 5283  C42 BCD   701      61.159  16.553  10.010  1.00 64.64           C
HETATM 5284  O42 BCD   701      60.726  15.611  11.028  1.00 63.48           O
HETATM 5285  C52 BCD   701      59.923  17.174   9.327  1.00 63.39           C
HETATM 5286  O52 BCD   701      60.332  18.010   8.219  1.00 65.37           O
HETATM 5287  C62 BCD   701      59.051  18.028  10.244  1.00 59.96           C
HETATM 5288  O62 BCD   701      59.720  19.214  10.658  1.00 58.04           O
HETATM 5289  C13 BCD   701      60.690  16.082  12.351  1.00 65.83           C
HETATM 5290  C23 BCD   701      61.969  15.702  13.079  1.00 67.15           C
HETATM 5291  O23 BCD   701      63.086  16.197  12.360  1.00 68.24           O
HETATM 5292  C33 BCD   701      62.087  14.178  13.217  1.00 69.41           C
HETATM 5293  O33 BCD   701      63.160  13.859  14.098  1.00 68.93           O
HETATM 5294  C43 BCD   701      60.814  13.531  13.761  1.00 69.78           C
HETATM 5295  O43 BCD   701      60.891  12.112  13.473  1.00 65.43           O
HETATM 5296  C53 BCD   701      59.517  14.130  13.145  1.00 70.39           C
HETATM 5297  O53 BCD   701      59.581  15.574  13.063  1.00 67.09           O
HETATM 5298  C63 BCD   701      58.297  13.825  14.005  1.00 69.56           C
HETATM 5299  O63 BCD   701      58.447  14.365  15.314  1.00 63.90           O
HETATM 5300  C14 BCD   701      60.650  11.225  14.532  1.00 63.03           C
HETATM 5301  C24 BCD   701      61.481   9.940  14.337  1.00 61.25           C
HETATM 5302  O24 BCD   701      62.825  10.281  14.008  1.00 61.24           O
HETATM 5303  C34 BCD   701      60.894   9.060  13.226  1.00 60.24           C
HETATM 5304  O34 BCD   701      61.553   7.801  13.188  1.00 58.92           O
HETATM 5305  C44 BCD   701      59.400   8.835  13.433  1.00 61.38           C
HETATM 5306  O44 BCD   701      58.884   8.110  12.299  1.00 65.50           O
HETATM 5307  C54 BCD   701      58.705  10.193  13.549  1.00 61.65           C
HETATM 5308  O54 BCD   701      59.261  10.922  14.665  1.00 62.66           O
HETATM 5309  C64 BCD   701      57.191  10.117  13.744  1.00 59.06           C
HETATM 5310  O64 BCD   701      56.834   9.148  14.716  1.00 59.30           O
HETATM 5311  C15 BCD   701      58.093   6.985  12.557  1.00 66.61           C
HETATM 5312  C25 BCD   701      58.378   5.937  11.494  1.00 66.33           C
HETATM 5313  O25 BCD   701      59.777   5.668  11.448  1.00 65.04           O
HETATM 5314  C35 BCD   701      57.905   6.447  10.136  1.00 64.90           C
HETATM 5315  O35 BCD   701      58.126   5.438   9.166  1.00 62.58           O
HETATM 5316  C45 BCD   701      56.412   6.823  10.173  1.00 68.60           C
HETATM 5317  O45 BCD   701      56.049   7.474   8.925  1.00 73.83           O
HETATM 5318  C55 BCD   701      56.132   7.790  11.345  1.00 68.27           C
HETATM 5319  O55 BCD   701      56.697   7.293  12.589  1.00 69.34           O
HETATM 5320  C65 BCD   701      54.634   8.002  11.595  1.00 66.79           C
HETATM 5321  O65 BCD   701      54.354   8.289  12.964  1.00 60.09           O
HETATM 5322  C16 BCD   701      54.996   6.930   8.158  1.00 77.25           C
HETATM 5323  C26 BCD   701      55.545   6.380   6.840  1.00 79.46           C
HETATM 5324  O26 BCD   701      56.534   5.392   7.086  1.00 82.77           O
HETATM 5325  C36 BCD   701      56.144   7.523   6.021  1.00 79.00           C
HETATM 5326  O36 BCD   701      56.677   7.014   4.802  1.00 77.18           O
HETATM 5327  C46 BCD   701      55.077   8.608   5.743  1.00 76.30           C
HETATM 5328  O46 BCD   701      55.728   9.771   5.155  1.00 75.01           O
HETATM 5329  C56 BCD   701      54.389   9.039   7.068  1.00 77.02           C
HETATM 5330  O56 BCD   701      53.973   7.892   7.871  1.00 78.19           O
HETATM 5331  C66 BCD   701      53.145   9.914   6.844  1.00 76.48           C
HETATM 5332  O66 BCD   701      52.042   9.170   6.330  1.00 69.20           O
HETATM 5333  C17 BCD   701      55.301  10.241   3.896  1.00 74.81           C
HETATM 5334  C27 BCD   701      56.498  10.316   2.945  1.00 75.34           C
HETATM 5335  O27 BCD   701      57.195   9.075   2.953  1.00 75.29           O
HETATM 5336  C37 BCD   701      57.462  11.438   3.354  1.00 73.43           C
HETATM 5337  O37 BCD   701      58.477  11.566   2.370  1.00 71.99           O
HETATM 5338  C47 BCD   701      56.748  12.786   3.516  1.00 72.74           C
HETATM 5339  O47 BCD   701      57.678  13.733   4.123  1.00 71.60           O
HETATM 5340  C57 BCD   701      55.496  12.622   4.414  1.00 72.45           C
HETATM 5341  O57 BCD   701      54.659  11.519   3.969  1.00 74.88           O
HETATM 5342  C67 BCD   701      54.606  13.862   4.421  1.00 72.56           C
HETATM 5343  O67 BCD   701      53.899  14.008   3.192  1.00 68.22           O

Ni hao,

by seraching the PDB website at: http://www.pdb.bnl.gov/pdb-bin/pdbmain
with the keyword "cyclodextrin" you will find the following entries:
# 3DB database, Fri May 29 02:48:02 EDT 1998
# Query: kw=cyclodextrin&m=du
# Hits: 16 (search time 0 sec)
1AC0 Glucoamylase, Granular Starch-Binding Doma... Sorimachi
1ACZ Glucoamylase, Granular Starch-Binding Doma... Sorimachi
1BTC Beta-Amylase with Alpha-Cyclodextrin (Alph... Mikami             2.00
1CDG Cyclodextrin Glycosyltransferase (Cgtase)     Lawson             2.00
1CGT Cyclodextrin Glycosyltransferase              Klein              2.00
1CGU Cyclodextrin Glycosyltransferase mutant As... Klein              2.50
1CIU Thermostable Cgtase From Thermoanaerobacte... Knegtel            2.30
1CXE Complex Of Cgtase With Maltotetraose At Ro... Knegtel            2.10
1CXF Complex Of A (D229n E257q) Double Mutant C... Knegtel            2.60
1CXH Complex Of Cgtase With Maltotetraose At Ro... Knegtel            2.40
1CXI Wild-Type Cgtase From Bacillus Circulans S... Knegtel            2.20
1CYG Cyclodextrin Glucanotransferase (Cgtase)      Kubota             2.50
1DIJ Complex Of A Y195f Mutant Cgtase From B. C... Strokopytov        2.60
1PAM Cyclodextrin Glucanotransferase               Harata             1.80
1TCM Cyclodextrin Glycosyltransferase W616a Mut... Knegtel            2.20
3CGT Structure Of Cyclodextrin Glycosyltransfer... Schmidt            2.40

Some of these structures are complexes of enzymes complexed with alpha and
beta cyclodextrins. Small molecule structures in the PDB are usually
less accurate than those in the CSD (which also contains several cyclo-
dextrin structures) but unfortunately the CSD requires a license that
you will have to pay for before you can access their structures.
I hope this helps you out.

Best regards,

Ronald Knegtel

-------------------------------------------------------------------------------
Dr. Ronald M. A. Knegtel                     Research Scientist
Dept. of Molecular Design and Informatics    Phone  : +31-412-661469
N.V. Organon, RK2340                         Fax    : +31-412-662539
P.O. Box 20  5340 BH Oss                     http://www.organon.nl/
The Netherlands                     E-Mail : [email-masked]
-------------------------------------------------------------------------------

Subject:         Alpha and Beta cyclodextrin PDB files
   Date:         Tue, 02 Jun 1998 14:27:33 +0900
   From:         "Tomasz Girek" <[email-masked]>
     To:         [email-masked]

Dear Yubo,
I have the pdb files of alpha and beta cyclodextrin and bellow I added it, but I
am also looking for optimized ctruktures of all cyclodextrins. If somebody others
sended to you this data, plesa send it to me
I will be very obliged

Sincerelly Yours

Tom

Tomasz Girek Ph.D.

Graduate School of Biotechnology
Korea University
5-1, Anam-dong, Sungbuk-ku
136-701 Seoul, Korea

e-mail:
[email-masked]
[email-masked]

COMPND ACX ALPHA-CYCLODEXTRIN (CYCLOHEXA-AMYLOSE)
REMARK ACX Extracted from PDB file 1cxf.pdb
REMARK ACX Formula C36 H60 O30
REMARK ACX Nr of non-hydrogen atoms  66
REMARK ACX Residue type ACX
REMARK ACX Residue name     90
REMARK ACX Original residue name (for O) $688
REMARK ACX  RESOLUTION. 2.6  ANGSTROMS.                                  1CXF  61

REMARK ==> Deduced formula : (C 36 O 30)
REMARK Est. total nr of hydrogens : ( 60)
ATOM      1  C1A ACX    90      -4.386   2.634   0.411  1.00 20.00
ATOM      2  C2A ACX    90      -5.059   1.442   1.047  1.00 20.00
ATOM      3  C3A ACX    90      -4.501   0.157   0.497  1.00 20.00
ATOM      4  C4A ACX    90      -4.561   0.122  -1.008  1.00 20.00
ATOM      5  C5A ACX    90      -3.831   1.333  -1.522  1.00 20.00
ATOM      6  C6A ACX    90      -3.940   1.462  -3.002  1.00 20.00
ATOM      7  O1A ACX    90      -3.055   2.660   0.836  1.00 20.00
ATOM      8  O2A ACX    90      -4.853   1.490   2.447  1.00 20.00
ATOM      9  O3A ACX    90      -5.169  -0.993   1.009  1.00 20.00
ATOM     10  O5A ACX    90      -4.412   2.515  -0.994  1.00 20.00
ATOM     11  O6A ACX    90      -3.607   2.780  -3.427  1.00 20.00
ATOM     12  C1B ACX    90      -0.071   4.817   2.535  1.00 20.00
ATOM     13  C2B ACX    90      -1.239   4.524   3.431  1.00 20.00
ATOM     14  C3B ACX    90      -2.099   3.458   2.809  1.00 20.00
ATOM     15  C4B ACX    90      -2.495   3.844   1.408  1.00 20.00
ATOM     16  C5B ACX    90      -1.267   4.215   0.589  1.00 20.00
ATOM     17  C6B ACX    90      -1.651   4.848  -0.719  1.00 20.00
ATOM     18  O1B ACX    90       0.639   3.653   2.369  1.00 20.00
ATOM     19  O2B ACX    90      -0.805   4.060   4.712  1.00 20.00
ATOM     20  O3B ACX    90      -3.219   3.264   3.649  1.00 20.00
ATOM     21  O5B ACX    90      -0.576   5.243   1.281  1.00 20.00
ATOM     22  O6B ACX    90      -0.561   4.752  -1.631  1.00 20.00
ATOM     23  C1C ACX    90       4.327   1.923   2.339  1.00 20.00
ATOM     24  C2C ACX    90       3.748   2.112   3.726  1.00 20.00
ATOM     25  C3C ACX    90       2.271   2.414   3.602  1.00 20.00
ATOM     26  C4C ACX    90       2.019   3.598   2.691  1.00 20.00
ATOM     27  C5C ACX    90       2.779   3.489   1.372  1.00 20.00
ATOM     28  C6C ACX    90       2.856   4.808   0.666  1.00 20.00
ATOM     29  O1C ACX    90       3.664   0.842   1.714  1.00 20.00
ATOM     30  O2C ACX    90       3.993   0.955   4.523  1.00 20.00
ATOM     31  O3C ACX    90       1.676   2.740   4.857  1.00 20.00
ATOM     32  O5C ACX    90       4.141   3.124   1.595  1.00 20.00
ATOM     33  O6C ACX    90       4.025   5.547   1.034  1.00 20.00
ATOM     34  C1D ACX    90       4.218  -2.793  -0.163  1.00 20.00
ATOM     35  C2D ACX    90       4.301  -2.780   1.337  1.00 20.00
ATOM     36  C3D ACX    90       3.717  -1.510   1.903  1.00 20.00
ATOM     37  C4D ACX    90       4.430  -0.311   1.316  1.00 20.00
ATOM     38  C5D ACX    90       4.486  -0.346  -0.219  1.00 20.00
ATOM     39  C6D ACX    90       5.553   0.597  -0.719  1.00 20.00
ATOM     40  O1D ACX    90       2.910  -2.986  -0.570  1.00 20.00
ATOM     41  O2D ACX    90       3.574  -3.883   1.881  1.00 20.00
ATOM     42  O3D ACX    90       3.828  -1.559   3.323  1.00 20.00
ATOM     43  O5D ACX    90       4.864  -1.639  -0.726  1.00 20.00
ATOM     44  O6D ACX    90       6.412   0.935   0.379  1.00 20.00
ATOM     45  C1E ACX    90      -0.085  -4.865  -2.733  1.00 20.00
ATOM     46  C2E ACX    90       0.557  -5.689  -1.630  1.00 20.00
ATOM     47  C3E ACX    90       1.262  -4.773  -0.672  1.00 20.00
ATOM     48  C4E ACX    90       2.368  -4.020  -1.388  1.00 20.00
ATOM     49  C5E ACX    90       1.858  -3.338  -2.650  1.00 20.00
ATOM     50  C6E ACX    90       3.024  -3.036  -3.555  1.00 20.00
ATOM     51  O1E ACX    90      -1.030  -3.974  -2.156  1.00 20.00
ATOM     52  O2E ACX    90      -0.387  -6.487  -0.924  1.00 20.00
ATOM     53  O3E ACX    90       1.835  -5.535   0.393  1.00 20.00
ATOM     54  O5E ACX    90       0.942  -4.149  -3.423  1.00 20.00
ATOM     55  O6E ACX    90       2.685  -2.276  -4.727  1.00 20.00
ATOM     56  C1F ACX    90      -4.413  -1.748  -2.527  1.00 20.00
ATOM     57  C2F ACX    90      -4.662  -3.099  -1.975  1.00 20.00
ATOM     58  C3F ACX    90      -3.334  -3.690  -1.552  1.00 20.00
ATOM     59  C4F ACX    90      -2.354  -3.772  -2.726  1.00 20.00
ATOM     60  C5F ACX    90      -2.295  -2.433  -3.475  1.00 20.00
ATOM     61  C6F ACX    90      -1.686  -2.561  -4.850  1.00 20.00
ATOM     62  O1F ACX    90      -3.852  -0.992  -1.526  1.00 20.00
ATOM     63  O2F ACX    90      -5.498  -2.927  -0.837  1.00 20.00
ATOM     64  O3F ACX    90      -3.554  -4.929  -0.884  1.00 20.00
ATOM     65  O5F ACX    90      -3.594  -1.878  -3.686  1.00 20.00
ATOM     66  O6F ACX    90      -0.863  -1.413  -5.083  1.00 20.00
END

COMPND BCD BETA-CYCLODEXTRIN
REMARK BCD Extracted from PDB file 1dmb.pdb
REMARK BCD Formula C42 H70 O35
REMARK BCD Nr of non-hydrogen atoms  77
REMARK BCD Residue type BCD
REMARK BCD Residue name    180
REMARK BCD Original residue name (for O) $371
REMARK BCD  RESOLUTION. 1.80 ANGSTROMS.                                  1DMB  32

REMARK ==> Deduced formula : (C 42 O 35)
REMARK Est. total nr of hydrogens : ( 67)
ATOM      1  C11 BCD   180      -3.833   4.636  -2.253  1.00 20.00
ATOM      2  C21 BCD   180      -2.960   5.127  -3.436  1.00 20.00
ATOM      3  O21 BCD   180      -3.430   4.515  -4.655  1.00 20.00
ATOM      4  C31 BCD   180      -1.485   4.844  -3.181  1.00 20.00
ATOM      5  O31 BCD   180      -0.677   5.445  -4.216  1.00 20.00
ATOM      6  C41 BCD   180      -1.057   5.388  -1.831  1.00 20.00
ATOM      7  O41 BCD   180       0.251   4.864  -1.577  1.00 20.00
ATOM      8  C51 BCD   180      -1.982   4.928  -0.711  1.00 20.00
ATOM      9  O51 BCD   180      -3.371   5.282  -1.067  1.00 20.00
ATOM     10  C61 BCD   180      -1.744   5.561   0.639  1.00 20.00
ATOM     11  O61 BCD   180      -2.606   4.932   1.601  1.00 20.00
ATOM     12  C12 BCD   180       1.249   5.731  -1.138  1.00 20.00
ATOM     13  C22 BCD   180       2.529   5.551  -1.962  1.00 20.00
ATOM     14  O22 BCD   180       2.186   5.713  -3.347  1.00 20.00
ATOM     15  C32 BCD   180       3.176   4.223  -1.624  1.00 20.00
ATOM     16  O32 BCD   180       4.407   4.113  -2.362  1.00 20.00
ATOM     17  C42 BCD   180       3.467   4.152  -0.127  1.00 20.00
ATOM     18  O42 BCD   180       4.021   2.866   0.165  1.00 20.00
ATOM     19  C52 BCD   180       2.176   4.577   0.658  1.00 20.00
ATOM     20  O52 BCD   180       1.518   5.524   0.240  1.00 20.00
ATOM     21  C62 BCD   180       2.313   4.369   2.144  1.00 20.00
ATOM     22  O62 BCD   180       0.979   4.063   2.537  1.00 20.00
ATOM     23  C13 BCD   180       5.345   2.683   0.586  1.00 20.00
ATOM     24  C23 BCD   180       5.930   1.473  -0.143  1.00 20.00
ATOM     25  O23 BCD   180       5.725   1.650  -1.573  1.00 20.00
ATOM     26  C33 BCD   180       5.237   0.204   0.302  1.00 20.00
ATOM     27  O33 BCD   180       5.815  -0.918  -0.396  1.00 20.00
ATOM     28  C43 BCD   180       5.309   0.042   1.799  1.00 20.00
ATOM     29  O43 BCD   180       4.493  -1.058   2.147  1.00 20.00
ATOM     30  C53 BCD   180       4.720   1.284   2.471  1.00 20.00
ATOM     31  O53 BCD   180       5.369   2.450   1.991  1.00 20.00
ATOM     32  C63 BCD   180       4.946   1.230   4.004  1.00 20.00
ATOM     33  O63 BCD   180       4.763   2.386   4.712  1.00 20.00
ATOM     34  C14 BCD   180       4.898  -1.963   3.166  1.00 20.00
ATOM     35  C24 BCD   180       5.460  -3.219   2.428  1.00 20.00
ATOM     36  O24 BCD   180       6.614  -2.900   1.676  1.00 20.00
ATOM     37  C34 BCD   180       4.343  -3.728   1.520  1.00 20.00
ATOM     38  O34 BCD   180       4.808  -4.794   0.689  1.00 20.00
ATOM     39  C44 BCD   180       3.172  -4.134   2.385  1.00 20.00
ATOM     40  O44 BCD   180       2.081  -4.471   1.504  1.00 20.00
ATOM     41  C54 BCD   180       2.724  -2.946   3.238  1.00 20.00
ATOM     42  O54 BCD   180       3.789  -2.320   3.928  1.00 20.00
ATOM     43  C64 BCD   180       1.760  -3.465   4.363  1.00 20.00
ATOM     44  O64 BCD   180       1.472  -2.354   5.200  1.00 20.00
ATOM     45  C15 BCD   180       1.443  -5.730   1.674  1.00 20.00
ATOM     46  C25 BCD   180       1.155  -6.310   0.305  1.00 20.00
ATOM     47  O25 BCD   180       2.316  -6.297  -0.546  1.00 20.00
ATOM     48  C35 BCD   180       0.062  -5.488  -0.385  1.00 20.00
ATOM     49  O35 BCD   180      -0.309  -6.102  -1.631  1.00 20.00
ATOM     50  C45 BCD   180      -1.148  -5.406   0.509  1.00 20.00
ATOM     51  O45 BCD   180      -2.068  -4.506  -0.157  1.00 20.00
ATOM     52  C55 BCD   180      -0.803  -4.814   1.898  1.00 20.00
ATOM     53  O55 BCD   180       0.291  -5.571   2.462  1.00 20.00
ATOM     54  C65 BCD   180      -1.956  -4.953   2.815  1.00 20.00
ATOM     55  O65 BCD   180      -1.844  -4.161   3.971  1.00 20.00
ATOM     56  C16 BCD   180      -3.442  -4.906  -0.253  1.00 20.00
ATOM     57  C26 BCD   180      -3.851  -4.763  -1.672  1.00 20.00
ATOM     58  O26 BCD   180      -2.771  -5.259  -2.483  1.00 20.00
ATOM     59  C36 BCD   180      -4.097  -3.312  -2.088  1.00 20.00
ATOM     60  O36 BCD   180      -4.936  -3.353  -3.292  1.00 20.00
ATOM     61  C46 BCD   180      -4.746  -2.478  -1.084  1.00 20.00
ATOM     62  O46 BCD   180      -4.480  -1.097  -1.505  1.00 20.00
ATOM     63  C56 BCD   180      -4.167  -2.668   0.310  1.00 20.00
ATOM     64  O56 BCD   180      -4.230  -4.082   0.600  1.00 20.00
ATOM     65  C66 BCD   180      -4.910  -1.973   1.455  1.00 20.00
ATOM     66  O66 BCD   180      -5.517  -2.856   2.156  1.00 20.00
ATOM     67  C17 BCD   180      -5.599  -0.446  -2.126  1.00 20.00
ATOM     68  C27 BCD   180      -5.161   0.063  -3.479  1.00 20.00
ATOM     69  O27 BCD   180      -4.414  -0.971  -4.164  1.00 20.00
ATOM     70  C37 BCD   180      -4.270   1.294  -3.379  1.00 20.00
ATOM     71  O37 BCD   180      -4.187   1.908  -4.682  1.00 20.00
ATOM     72  C47 BCD   180      -4.808   2.340  -2.388  1.00 20.00
ATOM     73  O47 BCD   180      -3.692   3.241  -2.220  1.00 20.00
ATOM     74  C57 BCD   180      -5.048   1.639  -1.046  1.00 20.00
ATOM     75  O57 BCD   180      -6.026   0.572  -1.269  1.00 20.00
ATOM     76  C67 BCD   180      -5.683   2.573  -0.016  1.00 20.00
ATOM     77  O67 BCD   180      -4.985   2.346   1.209  1.00 20.00
END

Here, I attached the beta-cyclodextrin file from Chem3D software. I have changed
its original file format into PDB format.

COMPND  BCycloDextrin.PDB
HETATM    1  C                  -5.934   0.982   0.623
HETATM    2  C                  -6.300   2.170  -0.263
HETATM    3  C                  -5.060   3.036  -0.531
HETATM    4  C                  -4.409   3.416   0.802
HETATM    5  C                  -4.073   2.163   1.609
HETATM    6  C                  -3.623   2.541   3.027
HETATM    7  C                  -4.444  -3.915  -0.833
HETATM    8  C                  -5.281  -3.160  -1.803
HETATM    9  C                  -5.136  -1.645  -1.627
HETATM   10  C                  -5.331  -1.271  -0.219
HETATM   11  C                  -4.366  -2.054   0.670
HETATM   12  C                  -4.418  -1.785   2.175
HETATM   13  C                   0.332  -6.035  -1.594
HETATM   14  C                  -0.446  -5.768  -2.864
HETATM   15  C                  -1.403  -4.598  -2.614
HETATM   16  C                  -2.278  -4.939  -1.435
HETATM   17  C                  -1.459  -5.288  -0.183
HETATM   18  C                  -2.282  -5.832   0.918
HETATM   19  C                   4.882  -3.634  -0.274
HETATM   20  C                   4.791  -4.391  -1.617
HETATM   21  C                   3.330  -4.446  -2.035
HETATM   22  C                   2.502  -5.070  -0.938
HETATM   23  C                   2.732  -4.349   0.388
HETATM   24  C                   2.075  -5.133   1.565
HETATM   25  C                   5.641   1.615   0.117
HETATM   26  C                   6.072   0.913  -1.172
HETATM   27  C                   5.213  -0.304  -1.440
HETATM   28  C                   5.267  -1.229  -0.248
HETATM   29  C                   4.823  -0.463   0.986
HETATM   30  C                   4.900  -1.294   2.290
HETATM   31  C                   2.224   5.651   0.597
HETATM   32  C                   3.126   5.587  -0.641
HETATM   33  C                   3.461   4.137  -0.957
HETATM   34  C                   4.100   3.497   0.257
HETATM   35  C                   3.153   3.598   1.457
HETATM   36  C                   3.746   3.079   2.755
HETATM   37  C                  -3.054   5.422   0.908
HETATM   38  C                  -2.463   6.238  -0.248
HETATM   39  C                  -1.064   5.726  -0.600
HETATM   40  C                  -0.200   5.729   0.647
HETATM   41  C                  -0.851   4.995   1.816
HETATM   42  C                  -0.133   5.227   3.137
HETATM   43  O                  -6.861   1.696  -1.487
HETATM   44  O                  -5.451   4.239  -1.200
HETATM   45  O                  -3.184   4.087   0.450
HETATM   46  O                  -5.322   1.425   1.814
HETATM   47  O                  -3.193   1.377   3.682
HETATM   48  O                  -4.907  -3.550  -3.139
HETATM   49  O                  -6.100  -0.978  -2.494
HETATM   50  O                  -5.040   0.148  -0.112
HETATM   51  O                  -4.722  -3.453   0.442
HETATM   52  O                  -3.443  -2.320   2.766
HETATM   53  O                  -5.507  -1.857   2.936
HETATM   54  O                   0.435  -5.478  -3.957
HETATM   55  O                  -2.243  -4.389  -3.758
HETATM   56  O                  -3.063  -3.738  -1.181
HETATM   57  O                  -0.525  -6.343  -0.529
HETATM   58  O                  -2.992  -6.912   0.486
HETATM   59  O                   5.564  -3.729  -2.616
HETATM   60  O                   3.188  -5.200  -3.252
HETATM   61  O                   1.118  -4.889  -1.315
HETATM   62  O                   4.117  -4.290   0.689
HETATM   63  O                   2.203  -4.410   2.763
HETATM   64  O                   6.012   1.858  -2.266
HETATM   65  O                   5.682  -0.961  -2.618
HETATM   66  O                   4.393  -2.312  -0.494
HETATM   67  O                   5.660   0.689   1.200
HETATM   68  O                   6.136  -1.912   2.471
HETATM   69  O                   2.411   6.229  -1.730
HETATM   70  O                   4.377   4.100  -2.070
HETATM   71  O                   4.326   2.119  -0.069
HETATM   72  O                   2.877   5.006   1.686
HETATM   73  O                   4.958   3.730   3.114
HETATM   74  O                  -3.325   6.164  -1.400
HETATM   75  O                  -0.468   6.571  -1.602
HETATM   76  O                   0.993   5.034   0.302
HETATM   77  O                  -2.210   5.507   2.031
HETATM   78  O                  -0.112   6.625   3.432
HETATM   79  H                  -6.858   0.446   0.920
HETATM   80  H                  -7.075   2.783   0.243
HETATM   81  H                  -4.335   2.461  -1.145
HETATM   82  H                  -5.107   4.054   1.386
HETATM   83  H                  -3.258   1.604   1.100
HETATM   84  H                  -4.492   2.928   3.600
HETATM   85  H                  -2.743   3.217   2.967
HETATM   86  H                  -4.732  -4.986  -0.854
HETATM   87  H                  -6.346  -3.446  -1.672
HETATM   88  H                  -4.122  -1.330  -1.955
HETATM   89  H                  -6.377  -1.498   0.082
HETATM   90  H                  -3.324  -1.878   0.327
HETATM   91  H                   0.986  -6.918  -1.742
HETATM   92  H                  -1.033  -6.672  -3.135
HETATM   93  H                  -0.815  -3.683  -2.384
HETATM   94  H                  -2.933  -5.797  -1.698
HETATM   95  H                  -0.922  -4.382   0.171
HETATM   96  H                  -3.024  -5.069   1.237
HETATM   97  H                  -1.617  -6.192   1.732
HETATM   98  H                   5.931  -3.651   0.087
HETATM   99  H                   5.177  -5.424  -1.486
HETATM  100  H                   2.964  -3.417  -2.234
HETATM  101  H                   2.779  -6.141  -0.829
HETATM  102  H                   2.294  -3.330   0.335
HETATM  103  H                   2.612  -6.095   1.714
HETATM  104  H                   0.986  -5.243   1.373
HETATM  105  H                   6.372   2.411   0.366
HETATM  106  H                   7.135   0.602  -1.084
HETATM  107  H                   4.163   0.016  -1.611
HETATM  108  H                   6.309  -1.587  -0.105
HETATM  109  H                   3.782  -0.100   0.841
HETATM  110  H                   4.140  -2.103   2.257
HETATM  111  H                   4.747  -0.625   3.163
HETATM  112  H                   2.080   6.710   0.893
HETATM  113  H                   4.065   6.148  -0.442
HETATM  114  H                   2.529   3.590  -1.214
HETATM  115  H                   5.051   4.021   0.492
HETATM  116  H                   2.214   3.046   1.234
HETATM  117  H                   3.984   2.000   2.647
HETATM  118  H                   3.030   3.257   3.586
HETATM  119  H                  -4.079   5.784   1.128
HETATM  120  H                  -2.400   7.307   0.049
HETATM  121  H                  -1.139   4.690  -0.993
HETATM  122  H                   0.015   6.778   0.944
HETATM  123  H                  -0.878   3.906   1.598
HETATM  124  H                   0.926   4.905   3.043
HETATM  125  H                  -0.700   4.737   3.957
HETATM  126  H                  -7.072   2.455  -2.004
HETATM  127  H                  -4.666   4.739  -1.344
HETATM  128  H                  -2.923   1.634   4.547
HETATM  129  H                  -5.451  -3.058  -3.730
HETATM  130  H                  -5.989  -0.052  -2.366
HETATM  131  H                  -5.221  -1.634   3.838
HETATM  132  H                  -0.106  -5.322  -4.712
HETATM  133  H                  -2.808  -3.663  -3.554
HETATM  134  H                  -3.496  -7.220   1.220
HETATM  135  H                   5.473  -4.229  -3.409
HETATM  136  H                   2.270  -5.203  -3.466
HETATM  137  H                   1.793  -4.923   3.438
HETATM  138  H                   6.283   1.396  -3.042
HETATM  139  H                   5.126  -1.710  -2.753
HETATM  140  H                   6.088  -2.389   3.281
HETATM  141  H                   2.970   6.187  -2.487
HETATM  142  H                   4.564   3.193  -2.241
HETATM  143  H                   5.247   3.345   3.923
HETATM  144  H                  -2.920   6.678  -2.079
HETATM  145  H                   0.387   6.218  -1.784
HETATM  146  H                   0.339   6.725   4.253
CONECT    1    2   46   50   79
CONECT    2    1    3   43   80
CONECT    3    2    4   44   81
CONECT    4    3    5   45   82
CONECT    5    4    6   46   83
CONECT    6    5   47   84   85
CONECT    7    8   51   56   86
CONECT    8    7    9   48   87
CONECT    9    8   10   49   88
CONECT   10    9   11   50   89
CONECT   11   10   12   51   90
CONECT   12   11   52   53
CONECT   13   14   57   61   91
CONECT   14   13   15   54   92
CONECT   15   14   16   55   93
CONECT   16   15   17   56   94
CONECT   17   16   18   57   95
CONECT   18   17   58   96   97
CONECT   19   20   62   66   98
CONECT   20   19   21   59   99
CONECT   21   20   22   60  100
CONECT   22   21   23   61  101
CONECT   23   22   24   62  102
CONECT   24   23   63  103  104
CONECT   25   26   67   71  105
CONECT   26   25   27   64  106
CONECT   27   26   28   65  107
CONECT   28   27   29   66  108
CONECT   29   28   30   67  109
CONECT   30   29   68  110  111
CONECT   31   32   72   76  112
CONECT   32   31   33   69  113
CONECT   33   32   34   70  114
CONECT   34   33   35   71  115
CONECT   35   34   36   72  116
CONECT   36   35   73  117  118
CONECT   37   38   45   77  119
CONECT   38   37   39   74  120
CONECT   39   38   40   75  121
CONECT   40   39   41   76  122
CONECT   41   40   42   77  123
CONECT   42   41   78  124  125
CONECT   43    2  126
CONECT   44    3  127
CONECT   45    4   37
CONECT   46    1    5
CONECT   47    6  128
CONECT   48    8  129
CONECT   49    9  130
CONECT   50    1   10
CONECT   51    7   11
CONECT   52   12
CONECT   53   12  131
CONECT   54   14  132
CONECT   55   15  133
CONECT   56    7   16
CONECT   57   13   17
CONECT   58   18  134
CONECT   59   20  135
CONECT   60   21  136
CONECT   61   13   22
CONECT   62   19   23
CONECT   63   24  137
CONECT   64   26  138
CONECT   65   27  139
CONECT   66   19   28
CONECT   67   25   29
CONECT   68   30  140
CONECT   69   32  141
CONECT   70   33  142
CONECT   71   25   34
CONECT   72   31   35
CONECT   73   36  143
CONECT   74   38  144
CONECT   75   39  145
CONECT   76   31   40
CONECT   77   37   41
CONECT   78   42  146
CONECT   79    1
CONECT   80    2
CONECT   81    3
CONECT   82    4
CONECT   83    5
CONECT   84    6
CONECT   85    6
CONECT   86    7
CONECT   87    8
CONECT   88    9
CONECT   89   10
CONECT   90   11
CONECT   91   13
CONECT   92   14
CONECT   93   15
CONECT   94   16
CONECT   95   17
CONECT   96   18
CONECT   97   18
CONECT   98   19
CONECT   99   20
CONECT  100   21
CONECT  101   22
CONECT  102   23
CONECT  103   24
CONECT  104   24
CONECT  105   25
CONECT  106   26
CONECT  107   27
CONECT  108   28
CONECT  109   29
CONECT  110   30
CONECT  111   30
CONECT  112   31
CONECT  113   32
CONECT  114   33
CONECT  115   34
CONECT  116   35
CONECT  117   36
CONECT  118   36
CONECT  119   37
CONECT  120   38
CONECT  121   39
CONECT  122   40
CONECT  123   41
CONECT  124   42
CONECT  125   42
CONECT  126   43
CONECT  127   44
CONECT  128   47
CONECT  129   48
CONECT  130   49
CONECT  131   53
CONECT  132   54
CONECT  133   55
CONECT  134   58
CONECT  135   59
CONECT  136   60
CONECT  137   63
CONECT  138   64
CONECT  139   65
CONECT  140   68
CONECT  141   69
CONECT  142   70
CONECT  143   73
CONECT  144   74
CONECT  145   75
CONECT  146   78
END

--
=============================================================
Yubo Fan                         Email: [email-masked]
Organic Synthesis Lab                   [email-masked]
The Department of Chemistry
Fudan University                 Phone: 8621-65648139
No. 220 Handan Road              Fax:   8621-65641740
Shanghai, 200433
P. R. China
=============================================================