From chemistry-request \\at// ccl.net Thu Nov 18 03:51:00 2004 Received: from nomina.net.lu.se (nomina.net.lu.se [130.235.132.90]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAI8owMh007392 for ; Thu, 18 Nov 2004 03:50:59 -0500 Received: from teokem.lu.se (atle.teokem.lu.se [130.235.1.29]) by nomina.net.lu.se (8.9.3/8.9.0) with ESMTP id KAA02627; Thu, 18 Nov 2004 10:06:54 +0100 (MET) Message-ID: <419C65B8.2040102$at$teokem.lu.se> Date: Thu, 18 Nov 2004 10:04:56 +0100 From: Patrik Rydberg User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.5) Gecko/20030925 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL CC: Jinsong Zhao Subject: Re: CCL:probe used in GRID References: <20041117193721.49864.qmail$at$web15401.mail.cnb.yahoo.com> In-Reply-To: <20041117193721.49864.qmail$at$web15401.mail.cnb.yahoo.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.9 required=7.5 tests=FCS_URI_NODOTS, FVGT_m_MULTI_ODD2,FVGT_m_MULTI_ODD3,MK_YAHOO_REDIR_01,WLS_URI_OPT_150 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Here's a list of all probes I know of and what they describe N3+ sp3 Amine NH3 cation N2+ sp3 Amine NH2 cation N2: sp3 NH2 with lone pair N2= sp2 Amine NH2 cation N2 Neutral flat NH2 eg amide N1+ sp3 Amine NH cation N1: sp3 NH with lone pair N1= sp2 Amine NH cation N1 Neutral flat NH eg amide NH= sp2 NH with lone pair N1# sp NH with one hydrogen N: sp3 N with lone pair N:= sp2 N with lone pair N:# sp N with lone pair N-: Anionic tetrazole N NM3 Trimethyl-ammonium cation O sp2 carbonyl oxygen O:: sp2 Carboxy oxygen atom O- sp2 phenolate oxygen O= O of SO4 or sulfonamide OH Phenol or carboxy OH O1 Alkyl hydroxy OH group OC2 Ether oxygen OES sp3 ester oxygen atom ON Oxygen of nitro group OS O of sulfone / sulfoxide OH2 Water OFU Furan oxygen atom C3 Methyl CH3 group C1= sp2 CH aromatic or vinyl PO4 PO4 phosphate dianion PO4H PO4H phosphate anion S1 Neutral SH group H Neutral hydrogen atom F Organic fluorine atom F- Fluoride anion CL Organic chlorine atom CL- Chlorine anion BR Organic bromine atom BR- Bromine anion I Organic iodine atom I- Iodine anion LI+ Lithium cation NA+ Sodium cation K+ Potassium cation RB+ Rubidium cation CS+ Caesium cation MG+2 Magnesium cation CA+2 Calcium cation xxxx Reserved for future use ZN+2 Zinc cation CU+2 Cupric copper cation FE+2 Ferrous iron cation FE+3 Ferric iron cation BOTH The amphipathic Probe DRY The hydrophobic Probe COO- Ionised alkyl carboxy group AR.COO- Ionised aryl carboxy group CONH2 Alkyl amide AR.CONH2 Aryl amide CONHR * Alkyl N-alkyl amide R.CONHR AR.CONHR * Aryl N-alkyl amide AR.CONHR AMIDINE Alkyl amidine R.C(NH2)2 AR.AMIDINE Aryl amidine AR.C(NH2)2 M-DIAMINE meta-diamino-benzene best regards Patrik Rydberg Jinsong Zhao wrote: > Dear all, > > In GRID (ver 22, www.moldiscovery.com), I just kown the probe DRY is > used to identify hydrophobic regions, and H or water probe, etc. > However, I can not find the similar informaton for C3, C1= and many > other probes. I mean the type of interaction between probe and ligand > represented by the probe. > > Would you like to give me a brief description on this aspects or point > me out where I can find those information. > > Additional question, where I can find the information about those > probe, such as radius, charge and something else. > > Thank you very much for your consideration on this matter. > > Best wishes, > Jinsong > > ===== > (Mr.) Jinsong Zhao > Ph.D. Candidate > School of the Environment > Nanjing University > No.22 Hankou Road, Najing 210093 > P.R. China > E-mail: zh_jinsong$at$yahoo.com.cn > > _________________________________________________________ > Do You Yahoo!? > 150MrGzMP37h?qKQ#,4xDz43HkRt |-at-| V5nLC > http://cn.rd.yahoo.com/mail_cn/tag/yisou/music/*http://music.yisou.com/ > C$at$E.CwPGS&SP>!SP#,KQ1iC -A_T- M http://cn.rd.yahoo.com/mail_cn/tag/yisou/image/*http://image.yisou.com > 1G>MJG1000UW#,QE;"5gSJWTVz {*at*} )H]#! > http://cn.rd.yahoo.com/mail_cn/tag/1g/*http://cn.mail.yahoo.com/event/mail_1g/ > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY$at$ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST$at$ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow$at$nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > -------------------------------------------------------------------- Patrik Rydberg Tel: +46-46-222 8236 Theoretical Chemistry Fax: +46-46-222 4543 Chemical Center, P.O.B 124 patrik.rydberg$at$teokem.lu.se S-221 00 Lund, Sweden http://www.teokem.lu.se/~patrik --------------------------------------------------------------------