Re: CCL:probe used in GRID
- From: Patrik Rydberg <patrik.rydberg$at$teokem.lu.se>
- Subject: Re: CCL:probe used in GRID
- Date: Thu, 18 Nov 2004 10:04:56 +0100
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
>
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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
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