From owner-chemistry@ccl.net Fri Jul 13 16:10:01 2007 From: "HarryBGottlieb#comcast.net" To: CCL Subject: CCL: Where to find FDA drug database Message-Id: <-34735-070713120458-13541-eJX8e3k/uaMacvxBZLCB/g---server.ccl.net> X-Original-From: HarryBGottlieb=-=comcast.net Content-Type: multipart/alternative; boundary="NextPart_Webmail_9m3u9jl4l_1312_1184340838_0" Date: Fri, 13 Jul 2007 15:33:58 +0000 MIME-Version: 1.0 Sent to CCL by: HarryBGottlieb**comcast.net --NextPart_Webmail_9m3u9jl4l_1312_1184340838_0 Content-Type: text/plain Content-Transfer-Encoding: 8bit Steven, A recent overview of DrugBank by John Proudfoot appeared in CHEMISTRY International, May-June 2007, page 24. He wrote that, "This free resource pulls together a surprisingly comprehensive amount of information on drugs and drug targets and contains data on over 1 000 marketed and over 3 000 additional experimental drug substances." That is about the size of the Comprehensive Medicinal Chemistry 3D (CMC3D) database that I was familiar with from MDL in the early-mid 1990's. I'd also guess that "pieces of information" exceeds the count of "drugs" in the other source. Best, Harry Gottlieb -------------- Original message -------------- > From: "Yuan Zhao ccl|-|mail.sioc.ac.cn" > > Sent to CCL by: "Yuan Zhao" [ccl ~~ mail.sioc.ac.cn] > Thanks! > I've downloaded the database in DrugBank. It contains 1066 molecules in the > sdf file, of which 11 are blank molecules and 10 contain '*' in atomic > name. However, I searched in google and found a software named as "Synapse > EMR Express SERVER" which seemed to be able to download and install FDA > drug database. It imported about 21000 pieces of infomation but I could not > find them. Does it mean that there are over 21000 drugs in FDA database? If > it is the truth, the molecules in DrugBank seem too few to summarize the > property of FDA database. > > Steven > > ======================================================================== > CCL: Where to find FDA drug database > > > Sent to CCL by: [DSprous*redpointbio.com] > In reply to "Yuan Zhao" [ccl=-=mail.sioc.ac.cn] query summarized as: > > "I wonder how many drugs FDA have approved till now or this year?" > > To my knowledge: > > The FDA Orange Book (http://www.fda.gov/cder/ob/) is closest publicly > available answer to this question. It is a list of approved drug > formulations and does not have structures. Further, since it is a list > of approved formulations, children's motrin is distinct from adult > strength which is different from extra strength. The FDA apparently > simply does not seem to be interested in an actual molecular database of > approved active ingredients. You would need to download a copy of the > list, develop a script to generate a unique list of active ingredients > and then use something like LexiChem to convert the chemical and trade > names to SMILES. This gives one about 1300 to 1400 compounds. > > An alternative which is easier to work with is the DrugBank > (http://redpoll.pharmacy.ualberta.ca/drugbank/) datasets maintained by > Wishart [University of Alberta]. This too is a list of ~1300 to 1400 > compounds. > > If anyone knows better public sources, please post. > > Dennis G. Sprous, PhD > Chemoinformatics/Computational Chemistry > RedPointBio Inc. > 7 Graphics Drive Ewing NJ 08628 > 609-637-9700 > -----Original Message----- > > From: owner-chemistry],[ccl.net [mailto:owner-chemistry],[ccl.net] > Sent: Wednesday, July 11, 2007 10:40 AM > To: Dennis Sprous > Subject: CCL: Where to find FDA drug database > > > Sent to CCL by: "Yuan Zhao" [ccl=-=mail.sioc.ac.cn] > Hi all, > > I wonder how many drugs FDA have approved till now or this year. > If possible, where can I download the FDA drug database in sd, mol > or other chemical formats? Does anyone know how many drugs in FDA > are fit for Lipinski rule of five? Any clue will be appreciate. > > Thanks. > > Stevenhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistr > y/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/s > end_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/sp > ammers.txt------------------------------------------------------------ > ------------------------------------------------------------> > > --NextPart_Webmail_9m3u9jl4l_1312_1184340838_0 Content-Type: text/html Content-Transfer-Encoding: 8bit
Steven,
A recent overview of DrugBank by John Proudfoot appeared in CHEMISTRY International, May-June 2007, page 24.  He wrote that, "This free resource pulls together a surprisingly comprehensive amount of information on drugs and drug targets and contains data on over 1 000 marketed and over 3 000 additional experimental drug substances."  That is about the size of the Comprehensive Medicinal Chemistry 3D (CMC3D) database that I was familiar with from MDL in the early-mid 1990's.
 
I'd also guess that "pieces of information" exceeds the count of "drugs" in the other source.
 
Best,
Harry Gottlieb
-------------- Original message --------------
From: "Yuan Zhao ccl|-|mail.sioc.ac.cn" <owner-chemistry=-=ccl.net>

>
> Sent to CCL by: "Yuan Zhao" [ccl ~~ mail.sioc.ac.cn]
> Thanks!
> I've downloaded the database in DrugBank. It contains 1066 molecules in the
> sdf file, of which 11 are blank molecules and 10 contain '*' in atomic
> name. However, I searched in google and found a software named as "Synapse
> EMR Express SERVER" which seemed to be able to download and install FDA
> drug database. It imported about 21000 pieces of infomation but I could not
> find them. Does it mean that there are over 21000 drugs in FDA database? If
> it is the truth, the molecules in DrugBank seem too few to summarize the
> property of FDA database.
>
> Steven
>
> ================================= =======================================
> CCL: Where to find FDA drug database
>
>
> Sent to CCL by: [DSprous*redpointbio.com]
> In reply to "Yuan Zhao" [ccl=-=mail.sioc.ac.cn] query summarized as:
>
> "I wonder how many drugs FDA have approved till now or this year?"
>
> To my knowledge:
>
> The FDA Orange Book (http://www.fda.gov/cder/ob/) is closest publicly
> available answer to this question. It is a list of approved drug
> formulations and does not have structures. Further, since it is a list
> of approved formulations, children's motrin is distinct from adult
> strength which is different from extra strength. The FDA apparently
> simply does not seem to be interested in an actual molecular database of
> approved active ingredients. You would need to download a copy of the
> list, develop a script to generate a unique list of active ingredients
> ; and then use something like LexiChem to convert the chemical and trade
> names to SMILES. This gives one about 1300 to 1400 compounds.
>
> An alternative which is easier to work with is the DrugBank
> (http://redpoll.pharmacy.ualberta.ca/drugbank/) datasets maintained by
> Wishart [University of Alberta]. This too is a list of ~1300 to 1400
> compounds.
>
> If anyone knows better public sources, please post.
>
> Dennis G. Sprous, PhD
> Chemoinformatics/Computational Chemistry
> RedPointBio Inc.
> 7 Graphics Drive Ewing NJ 08628
> 609-637-9700
> -----Original Message-----
> > From: owner-chemistry],[ccl.net [mailto:owner-chemistry],[ccl.net]
> Sent: Wednesday, July 11, 2007 10:40 AM
> To: Dennis Sprous
> Subject: CCL: Where to find FDA drug database
>
>
> Sent to CCL by: "Yuan Zhao" [ccl=-=mail.sioc.ac.cn]
> Hi all,
>
> I wonder how many drugs FDA have approved till now or this year.
> If possible, where can I download the FDA drug database in sd, mol
> or other chemical formats? Does anyone know how many drugs in FDA
> are fit for Lipinski rule of five? Any clue will be appreciate.
>
> Thanks.
>
> Stevenhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistr
> y/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/s
> end_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/sp
> ammers.txt------------------------------------------------------------
> ------------------------------------------------------------
>
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>
>
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--NextPart_Webmail_9m3u9jl4l_1312_1184340838_0-- From owner-chemistry@ccl.net Fri Jul 13 16:58:00 2007 From: "Stefan Motiu talposanul-,-yahoo.com" To: CCL Subject: CCL:G: Does Gaussian create temporary UFF charges? Message-Id: <-34736-070713165505-6619-9Tyl6CneRRwjmCU0Pp8z3w_._server.ccl.net> X-Original-From: Stefan Motiu Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1222593528-1184360079=:18402" Date: Fri, 13 Jul 2007 13:54:39 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Stefan Motiu [talposanul,yahoo.com] --0-1222593528-1184360079=:18402 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello: On p. 1, of the Gaussian ’03 Online Manual, the following route section is given: # ONIOM (HF/6-31(d):AM1:UFF). My question is does Gaussian create charges in the UFF force filed while running (for I have found only zeroes when tried retrieving them), and thus, can one publish such results, or, on the other hand, should one, say, use UFF=Q.EQ (charge equilibration) for publications? Thanks, Stefan --------------------------------- Don't pick lemons. See all the new 2007 cars at Yahoo! Autos. --0-1222593528-1184360079=:18402 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hello:
On p. 1, of the Gaussian ’03 Online Manual, the following route section is given: # ONIOM (HF/6-31(d):AM1:UFF). My question is does Gaussian create charges in the UFF force filed while running (for I have found only zeroes when tried retrieving them), and thus, can one publish such results, or, on the other hand, should one, say, use UFF=Q.EQ (charge equilibration) for publications?
Thanks,
Stefan

Don't pick lemons.
See all the new 2007 cars at Yahoo! Autos. --0-1222593528-1184360079=:18402-- From owner-chemistry@ccl.net Fri Jul 13 18:34:00 2007 From: "Rick Venable venabler|nhlbi.nih.gov" To: CCL Subject: CCL: Where to find FDA drug database Message-Id: <-34737-070713173849-3640-td4/YbMf2/5NDjTMCsIafg]^[server.ccl.net> X-Original-From: Rick Venable Content-type: multipart/alternative; boundary="B_3267191155_7006633" Date: Fri, 13 Jul 2007 17:05:55 -0400 Mime-version: 1.0 Sent to CCL by: Rick Venable [venabler-,-nhlbi.nih.gov] > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3267191155_7006633 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable There are ca. 21,000 formulations in the =B3orange book=B2; a given drug substance will have many formulations (different dosages, tablet vs. caplet= , single-use vs. multi-use vials, etc.). One of the earlier posts (included below) indicated that these 21,000 formulations represent ca. 1300-1400 dru= g substances, comparable in number and scope to those listed in DrugBank. --=20 Rick Venable 29/500 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-8014 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 7/13/07 11:33 AM, "HarryBGottlieb#comcast.net" wrote: > A recent overview of DrugBank by John Proudfoot appeared in CHEMISTRY > International, May-June 2007, page 24. He wrote that, "This free resourc= e > pulls together a surprisingly comprehensive amount of information on drug= s and > drug targets and contains data on over 1 000 marketed and over 3 000 > additional experimental drug substances." That is about the size of the > Comprehensive Medicinal Chemistry 3D (CMC3D) database that I was familiar= with > from MDL in the early-mid 1990's. > =20 > I'd also guess that "pieces of information" exceeds the count of "drugs" = in > the other source. > =20 > Best, > Harry Gottlieb >=20 >> -------------- Original message -------------- >> From: "Yuan Zhao ccl|-|mail.sioc.ac.cn" >>=20 >>> >=20 >>> > Sent to CCL by: "Yuan Zhao" [ccl ~~ mail.sioc.ac.cn] >>> > Thanks!=20 >>> > I've downloaded the database in DrugBank. It contains 1066 molecules = in >>> the=20 >>> > sdf file, of which 11 are blank molecules and 10 contain '*' in atomi= c >>> > name. However, I searched in google and found a software named as "Sy= napse >>> > EMR Express SERVER" which seemed to be able to download and install F= DA >>> > drug database. It imported about 21000 pieces of infomation but I cou= ld >>> not=20 >>> > find them. Does it mean that there are over 21000 drugs in FDA databa= se? >>> If=20 >>> > it is the truth, the molecules in DrugBank seem too few to summarize = the >>> > property of FDA database. >>> >=20 >>> > Steven=20 >>=20 >> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D >>> > CCL: Where to find FDA drug database >>> > Sent to CCL by: [DSprous*redpointbio.com] >>> > In reply to "Yuan Zhao" [ccl=3D-=3Dmail.sioc.ac.cn] query summarized as: >>> >=20 >>> > "I wonder how many drugs FDA have approved till now or this year?" >>> >=20 >>> > To my knowledge: >>> >=20 >>> > The FDA Orange Book (http://www.fda.gov/cder/ob/) is closest publicly >>> > available answer to this question. It is a list of approved drug >>> > formulations and does not have structures. Further, since it is a lis= t >>> > of approved formulations, children's motrin is distinct from adult >>> > strength which is different from extra strength. The FDA apparently >>> > simply does not seem to be interested in an actual molecular database= of >>> > approved active ingredients. You would need to download a copy of the >>> > list, develop a script to generate a unique list of active ingredient= s ! >>> > ; and then use something like LexiChem to convert the chemical and tr= ade >>> > names to SMILES. This gives one about 1300 to 1400 compounds. >>> >=20 >>> > An alternative which is easier to work with is the DrugBank >>> > (http://redpoll.pharmacy.ualberta.ca/drugbank/) datasets maintained b= y >>> > Wishart [University of Alberta]. This too is a list of ~1300 to 1400 >>> > compounds.=20 >>> >=20 >>> > If anyone knows better public sources, please post. >>> >=20 >>> > Dennis G. Sprous, PhD >>> > Chemoinformatics/Computational Chemistry >>> > RedPointBio Inc. >>> > 7 Graphics Drive Ewing NJ 08628 >>> > 609-637-9700=20 >>> > -----Original Message----- >>>> > > From: owner-chemistry],[ccl.net [mailto:owner-chemistry],[ccl.net] >>> > Sent: Wednesday, July 11, 2007 10:40 AM >>> > To: Dennis Sprous >>> > Subject: CCL: Where to find FDA drug database >>> >=20 >>> >=20 >>> > Sent to CCL by: "Yuan Zhao" [ccl=3D-=3Dmail.sioc.ac.cn] >>> > Hi a! ll,=20 >>> >=20 >>> > I wonder how many drugs FDA have approved till now or this year. >>> > If possible, where can I download the FDA drug database in sd, mol >>> > or other chemical formats? Does anyone know how many drugs in FDA >>> > are fit for Lipinski rule of five? Any clue will be appreciate.=20 --B_3267191155_7006633 Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Re: CCL: Where to find FDA drug database There are ca. 21,000 f= ormulations in the “orange book”; a given drug substance will ha= ve many formulations (different dosages, tablet vs. caplet, single-use vs. m= ulti-use vials, etc.).   One of the earlier posts (included below)= indicated that these 21,000 formulations represent ca. 1300-1400 drug subst= ances, comparable in number and scope to those listed in DrugBank.

--
Rick Venable        29/500
Membrane Biophysics Section
NIH/NHLBI Lab. of Computational Biology
Bethesda, MD  20892-8014   U.S.A.
(301) 496-1905   venabler AT nhlbi*nih*gov


On 7/13/07 11:33 AM, "HarryBGottlieb#comcast.net" <owner-chemi= stry\a/ccl.net> wrote:
A recent overview of DrugBank by John Proudfoot appeared in CHEMISTRY In= ternational, May-June 2007, page 24.  He wrote that, "This free re= source pulls together a surprisingly comprehensive amount of information on = drugs and drug targets and contains data on over 1 000 marketed and over 3 0= 00 additional experimental drug substances."  That is about the si= ze of the Comprehensive Medicinal Chemistry 3D (CMC3D) database that I was f= amiliar with from MDL in the early-mid 1990's.
 
I'd also guess that "pieces of information" exceeds the count of = "drugs" in the other source.
 
Best,
Harry Gottlieb

-------------- Original message --------------
> From: "Yuan Zhao ccl|-|mail.sioc.ac.cn" <owner-chemistry-.-ccl= .net>

>
> Sent to CCL by: "Yuan Zhao" [ccl ~~ mail.sioc.ac.cn]
> Thanks!
> I've downloaded the database in DrugBank. It contains 1066 molecules i= n the
> sdf file, of which 11 are blank molecules and 10 contain '*' in atomic=
> name. However, I searched in google and found a software named as &quo= t;Synapse
> EMR Express SERVER" which seemed to be able to download and insta= ll FDA
> drug database. It imported about 21000 pieces of infomation but I coul= d not
> find them. Does it mean that there are over 21000 drugs in FDA databas= e? If
> it is the truth, the molecules in DrugBank seem too few to summarize t= he
> property of FDA database.
>
> Steven

 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> CCL: Where to find FDA drug database
> Sent to CCL by: [DSprous*redpointbio.com]
> In reply to "Yuan Zhao" [ccl=3D-=3Dmail.sioc.ac.cn] query summar= ized as:
>
> "I wonder how many drugs FDA have approved till now or this year?= "
>
> To my knowledge:
>
> The FDA Orange Book (http://www= .fda.gov/cder/ob/) is closest publicly
> available answer to this question. It is a list of approved drug
> formulations and does not have structures. Further, since it is a list=
> of approved formulations, children's motrin is distinct from adult > strength which is different from extra strength. The FDA apparently > simply does not seem to be interested in an actual molecular database = of
> approved active ingredients. You would need to download a copy of the =
> list, develop a script to generate a unique list of active ingredients= !
> ; and then use something like LexiChem to convert the chemical and tra= de
> names to SMILES. This gives one about 1300 to 1400 compounds.
>
> An alternative which is easier to work with is the DrugBank
> (http://redpo= ll.pharmacy.ualberta.ca/drugbank/) datasets maintained by
> Wishart [University of Alberta]. This too is a list of ~1300 to 1400 <= BR> > compounds.
>
> If anyone knows better public sources, please post.
>
> Dennis G. Sprous, PhD
> Chemoinformatics/Computational Chemistry
> RedPointBio Inc.
> 7 Graphics Drive Ewing NJ 08628
> 609-637-9700
> -----Original Message-----
> > From: owner-chemistry],[ccl.net [mailto:owner-chemistry],[ccl.net]
> Sent: Wednesday, July 11, 2007 10:40 AM
> To: Dennis Sprous
> Subject: CCL: Where to find FDA drug database
>
>
> Sent to CCL by: "Yuan Zhao" [ccl=3D-=3Dmail.sioc.ac.cn]
> Hi a! ll,
>
> I wonder how many drugs FDA have approved till now or this year.
> If possible, where can I download the FDA drug database in sd, mol > or other chemical formats? Does anyone know how many drugs in FDA
> are fit for Lipinski rule of five? Any clue will be appreciate.
--B_3267191155_7006633-- From owner-chemistry@ccl.net Fri Jul 13 19:08:00 2007 From: "Yousef Sharifi ysharifi||gmail.com" To: CCL Subject: CCL: MP2 Calculation Error Message-Id: <-34738-070713183701-16658-ZimWDxG6+muC48MoJ2hOcA]_[server.ccl.net> X-Original-From: "Yousef Sharifi" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0004_01C7C57C.B610F650" Date: Fri, 13 Jul 2007 18:36:20 -0400 MIME-Version: 1.0 Sent to CCL by: "Yousef Sharifi" [ysharifi(-)gmail.com] This is a multipart message in MIME format. ------=_NextPart_000_0004_01C7C57C.B610F650 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit I am trying to run MP2/6-31g optimization on Benzene molecule but it exits with no specific reason. I would really appreciate any comments. Here are the last couple of lines: ExpMin= 1.03D-01 ExpMax= 4.56D+03 ExpMxC= 6.82D+02 IAcc=1 IRadAn= 1 AccDes= 1.00D-06 HarFok: IExCor= 205 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 ScaDFX= 1.000000 1.000000 1.000000 1.000000 Range of M.O.s used for correlation: 7 144 NBasis= 144 NAE= 21 NBE= 21 NFC= 6 NFV= 0 NROrb= 138 NOA= 15 NOB= 15 NVA= 123 NVB= 123 **** Warning!!: The largest alpha MO coefficient is 0.17744602D+02 Estimate disk for full transformation 350596100 words. Semi-Direct transformation. ModeAB= 2 MOrb= 138 LenV= 99146315 LASXX= 75467172 LTotXX= 104541297 LenRXX= 108618075 LTotAB= 18624915 MaxLAS= 108618075 LenRXY= 18624915 NonZer= 150934344 LenScr= 315701760 LnRSAI= 0 LnScr1= 0 LExtra= 0 Total= 442944750 MaxDsk= -1 SrtSym= F ITran= 5 JobTyp=0 Pass 1: I= 1 to 138. writwa Best regards, Yousef Sharifi ------=_NextPart_000_0004_01C7C57C.B610F650 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

 

I am trying to run MP2/6-31g optimization on Benzene = molecule but it exits with no specific reason.  I would really appreciate = any comments. Here are the last couple of lines:

 

ExpMin=3D 1.03D-01 ExpMax=3D 4.56D+03 ExpMxC=3D 6.82D+02 = IAcc=3D1 IRadAn=3D         1 AccDes=3D = 1.00D-06

 HarFok:  IExCor=3D 205 AccDes=3D 1.00D-06 = IRadAn=3D         1 = IDoV=3D1

 ScaDFX=3D  1.000000  1.000000  = 1.000000  1.000000

 Range of M.O.s used for = correlation:     7   = 144

 NBasis=3D   144 NAE=3D    = 21 NBE=3D    21 NFC=3D     6 = NFV=3D     0

 NROrb=3D    138 = NOA=3D    15 NOB=3D    15 = NVA=3D   123 NVB=3D   123

 

 **** Warning!!: The largest alpha MO coefficient = is  0.17744602D+02

 

 Estimate disk for full transformation   = 350596100 words.

 Semi-Direct transformation.

 ModeAB=3D       &= nbsp;   2 = MOrb=3D           138 = LenV=3D      99146315

 LASXX=3D     75467172 = LTotXX=3D   104541297 LenRXX=3D   = 108618075

 LTotAB=3D    18624915 = MaxLAS=3D   108618075 LenRXY=3D    = 18624915

 NonZer=3D   150934344 = LenScr=3D   315701760 LnRSAI=3D    =        0

 LnScr1=3D       &= nbsp;   0 = LExtra=3D           0 = Total=3D    442944750

 MaxDsk=3D       &= nbsp;  -1 = SrtSym=3D           F = ITran=3D           = ; 5

 JobTyp=3D0 Pass  1:  I=3D   1 = to 138.

writwa

 

Best regards,

 

Yousef Sharifi

 

 

------=_NextPart_000_0004_01C7C57C.B610F650--