CCL: What is the format of this file containing Cartesian coordinates?



 Sent to CCL by: "Tamas Gunda" [tgunda2[#]puma.unideb.hu]
 Hi,
 
Mol2Mol has been made just for the input of files with unknown formats. Any kind of format can be inputted with it using the appropriate format string.
 Look at:  www.gunda.hu/mol2mol
 
In this case copy the coordinates to the clipboard, open the file input window as general user input format,
 and create and select  the following input format string:
 x y z d e d
 (this is for x y z coodinates, dummy, element symbol, dummy)
 and choose input from the clipboard
 
The data are inputted. The molecule looks quite odd as apart from two OH groups all of the z coordinates of carbon atoms are nearly zero.
 Hope this helps
 Tamas Gunda
 --------------------------------------------------
 
From: "Andrew DeYoung andrewdaviddeyoung- -gmail.com"
 <owner-chemistry(0)ccl.net>
 Sent: Sunday, January 08, 2012 20:50 PM
 To: "Gunda, Gunda " <tgunda2(0)puma.unideb.hu>
 
Subject: CCL: What is the format of this file containing Cartesian coordinates?
 
 Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung*|*gmail.com]
 Hi,
 I have been reading the paper "Modeling of Graphite Oxide,"
 Boukhvalov, D. W.; Katsnelson, M. I., J. Am. Chem. Soc. 2008, 130,
 10697-10701.  This paper has Supporting Information associated with
 it, located here: http://pubs.acs.org/doi/suppl/10.1021/ja8021686 .
 This Supporting Information contains the Cartesian coordinates for
 various chemical species discussed in the paper (obtained by ab initio
 calculations).  For example, one of the series of coordinates that
 this Supporting Information provides is the following:
 -0.02689401 0.05432733 1.07516282 3 H 1
 0.03282702 -0.01179385 0.68330051 2 O 2
 0.60586594 -0.05478650 -1.06215854 3 H 3
 0.54625340 0.01126245 -0.67028541 2 O 4
 -0.00037430 0.00545262 0.11451905 1 C 5
 -0.87007097 0.50375034 -0.04749619 1 C 6
 -0.86607388 -0.50142967 -0.04692549 1 C 7
 0.87536552 0.51049597 0.02025204 1 C 8
 0.87795979 -0.51877321 0.02366501 1 C 9
 -0.00283324 1.00386837 -0.01257709 1 C 10
 0.00039748 -1.00136092 -0.01066833 1 C 11
 -1.73307292 0.00197123 -0.03871588 1 C 12
 -0.86683173 1.50543512 -0.02856670 1 C 13
 -0.86909689 -1.50476823 -0.02691608 1 C 14
 1.73809709 0.00167020 0.06437659 1 C 15
 0.86891453 1.50286912 0.03907748 1 C 16
 0.87181125 -1.50614862 0.04060303 1 C 17
 -1.73625671 1.00707540 -0.04218536 1 C 18
 -1.73743458 -1.00321958 -0.04099753 1 C 19
 1.73948240 1.00519036 0.06254294 1 C 20
 1.73748379 -1.00684011 0.06397068 1 C 21
 -0.00097315 2.00519687 -0.00474136 1 C 22
 -0.00025493 -2.00481803 -0.00256281 1 C 23
 -2.60679486 0.50744858 -0.05730558 1 C 24
 -2.60244033 -0.49997860 -0.05660149 1 C 25
 -1.73600183 2.00826255 -0.03828653 1 C 26
 -1.73589004 -2.00632024 -0.03581581 1 C 27
 -0.86809971 2.50743539 -0.01969374 1 C 28
 -0.86743107 -2.50800945 -0.01663035 1 C 29
 1.73739025 -2.00803386 0.03602309 1 C 30
 0.86918912 -2.50605556 0.01898868 1 C 31
 -2.60674237 1.50998962 -0.06149746 1 C 32
 -2.60337977 -1.50359739 -0.05952099 1 C 33
 -0.00151756 3.01254125 0.00026303 1 C 34
 -1.73833995 3.01353076 -0.04134158 1 C 35
 1.73896850 -3.01089377 0.04144619 1 C 36
 -2.60747482 2.51319434 -0.06379837 1 C 37
 0.87160242 -3.51651549 0.01963025 1 C 38
 -2.60959081 3.52137327 -0.06444686 1 C 39
 1.74167046 -4.01903762 0.03732286 1 C 40
 0.57935253 -0.00591929 -0.10150666 1 C 41
 -0.29895259 0.51824224 -0.01065610 1 C 42
 -0.29637000 -0.51095564 -0.00724144 1 C 43
 -1.15911004 -0.00215128 -0.05137018 1 C 44
 0.57861451 1.00085598 0.02367761 1 C 45
 0.58190077 -1.00453933 0.02559150 1 C 46
 -1.15848220 1.00634128 -0.05096692 1 C 47
 -1.16048708 -1.00566650 -0.04953595 1 C 48
 1.44505788 0.50095217 0.05994684 1 C 49
 1.44905447 -0.50423433 0.06052232 1 C 50
 -0.29287191 1.50575663 -0.02758935 1 C 51
 -0.28990959 -1.50337425 -0.02606221 1 C 52
 -2.02697593 0.50391544 -0.04217217 1 C 53
 -2.02491349 -0.50419505 -0.04152028 1 C 54
 1.44809109 1.50425324 0.03991273 1 C 55
 1.44587383 -1.50598582 0.04156281 1 C 56
 0.57921418 2.00435850 0.01557045 1 C 57
 0.58001551 -2.00575731 0.01775155 1 C 58
 -1.15838843 2.00756158 -0.02302302 1 C 59
 -1.15757535 -2.00795444 -0.02057379 1 C 60
 2.31207394 -0.00245438 0.05172946 1 C 61
 -2.02776434 1.50719055 -0.04446594 1 C 62
 -2.02602610 -1.50572182 -0.04269775 1 C 63
 2.31642963 1.00271453 0.05400912 1 C 64
 2.31524228 -1.00755964 0.05519446 1 C 65
 -0.29021505 2.50557497 -0.00598370 1 C 66
 -0.28747789 -2.51054533 -0.00287556 1 C 67
 1.44708230 -2.50791413 0.03270193 1 C 68
 2.31499473 -2.00876451 0.05130262 1 C 69
 0.58051995 -3.01303700 0.01275161 1 C 70
 -2.02771967 2.50972812 -0.04865231 1 C 71
 -1.15998355 3.01040245 -0.02842868 1 C 72
 2.31732484 -3.01400623 0.05435683 1 C 73
 1.45151430 -3.51897104 0.03339008 1 C 74
 -2.03208004 3.51717648 -0.04935652 1 C 75
 2.31999134 -4.02068999 0.05257440 1 C 76
 However, the Supporting Information (nor the article itself) appears
 to specify the type of coordinate file that they are providing.  For
 example, is this in PDB format, XYZ format, or another format?  Can
 anyone please help me know which format this might be so that I can
 save it in an appropriate file type and visualize the structure using
 VMD?
 Thank you kindly!
 Andrew DeYoung
 Carnegie Mellon University>