计算机辅助药物设计结课作业DUO.docx
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计算机辅助药物设计结课作业DUO
计算机辅助药物设计结课作业
学院：
生物工程
专业：
生物制药
学号：
10045116
姓名：
冯倩
一、利用chemdraw做5个分子结构或反应式，展示分子至少5种不同显示元素或显示方式
二、从RCSBproteindatabank下载蛋白文件，利用chimera显示其结构，至少包含ribbons，化学键，原子，表面和文字标记等显示元素
三、利用chem3d做至少2个分子3d图像，包含不同显示方式并标记个别原子或键参数
四、利用Arguslab对接至少2个分子，列出对接结果（对接输出结果文件里的内容，如能量等）
（1）
************************************************
**
*ArgusLab（tm）*
**
*Version4.0*
**
*Copyright（c）1996-2004*
**
*PlanariaSoftwareLLC*
*ALLRIGHTSRESERVED*
**
*info@planaria-*
*http:
//www.planaria-*
**
************************************************
***********************************************************************
WARNING--ArgusLabmaynotbeusedinanymannerthatcompeteswith
thebusinessofPlanariaSoftwareLLCorwillprovideassistanceto
anycompetitorofPlanariaSoftwareLLC.Thelicenseeofthisprogram
isprohibitedfromgivinganycompetitorofPlanariaSoftwareLLC.
accesstothisprogram.Byusingthisprogram,theuseracknowledges
thatPlanariaSoftwareLLC.isengagedinthebusinessofcreatingand
licensingsoftwareinthefieldofcomputationalchemistryand
representsandwarrantstoPlanariaSoftwareLLCthatitisnota
competitorofPlanariaSoftwareLLC.andthatitwillnotusethis
programinanymannerprohibitedabove.
***********************************************************************
Calculationstarttime:
TueJun1800:
19:
582013
***********************************************
Dockingligand:
Unnamed
***********************************************
Ligandatomtypeinformation
*****************************
1.（3768）C:
Hydrophobic
2.（3769）C:
Polar
3.（3770）C:
Hydrophobic
4.（3771）C:
Hydrophobic
5.（3772）C:
Hydrophobic
6.（3773）C:
Hydrophobic
7.（3774）N:
Polar
8.（3775）C:
Polar
9.（3776）C:
Polar
10.（3777）N:
Polar
11.（3778）C:
Polar
12.（3779）C:
Hydrophobic
13.（3780）O:
H-bondacceptor
14.（3781）O:
H-bondacceptor
15.（3782）C:
Polar
16.（3783）C:
Hydrophobic
17.（3784）C:
Polar
18.（3785）C:
Hydrophobic
19.（3786）C:
Hydrophobic
20.（3787）C:
Hydrophobic
21.（3788）C:
Hydrophobic
22.（3789）C:
Hydrophobic
23.（3790）Cl:
Hydrophobic
24.（3791）C:
Hydrophobic
25.（3792）C:
Hydrophobic
26.（3793）C:
Hydrophobic
27.（3794）C:
Hydrophobic
28.（3795）C:
Hydrophobic
29.（3796）Cl:
Hydrophobic
30.（3797）I:
Hydrophobic
31.（3798）C:
Polar
32.（3799）C:
Polar
33.（3800）N:
Polar
34.（3801）C:
Polar
35.（3802）C:
Polar
36.（3803）O:
H-bondacceptor
37.（3804）C:
Polar
38.（3805）C:
Polar
39.（3806）O:
H-bondacceptor
40.（3807）N:
Polar
41.（3808）H:
atomtypenone
42.（3809）H:
atomtypenone
43.（3810）H:
atomtypenone
44.（3811）H:
atomtypenone
45.（3812）H:
atomtypenone
46.（3813）H:
atomtypenone
47.（3814）H:
atomtypenone
48.（3815）H:
atomtypenone
49.（3816）H:
atomtypenone
50.（3817）H:
atomtypenone
51.（3818）H:
atomtypenone
52.（3819）H:
atomtypenone
53.（3820）H:
atomtypenone
54.（3821）H:
atomtypenone
55.（3822）H:
atomtypenone
56.（3823）H:
atomtypenone
57.（3824）H:
atomtypenone
58.（3825）H:
atomtypenone
59.（3826）H:
atomtypenone
60.（3827）H:
atomtypenone
61.（3828）H:
atomtypenone
62.（3829）H:
atomtypenone
63.（3830）H:
atomtypenone
64.（3831）H:
atomtypenone
65.（3832）H:
atomtypenone
66.（3833）H:
atomtypenone
67.（3834）H:
atomtypenone
***************************************************
ArgusDockSearchEngine
***************************************************
Settingsforthedockingrun
****************************
NumberofLigandtorsions=5
NumberofTargettorsions=0
Precision=RegularPrecision
Augmentrootnodewithinnertorsions=false
Maximumnumberofposes=150
Startthedocking
Ligandextendedrootnoderadii:
primary=5.02069,secondary=3.10689,tertiary=2.24397
searchpointsfromatotalof232gridpoints
Rootnodeconfiguration0
Numberofcandidateposesfound=0
1sec.tocompletetheinitialsearch.
Noacceptableligandposeswerefound
Dockingrun:
elapsedtime=1seconds
（2）
************************************************
**
*ArgusLab（tm）*
**
*Version4.0*
**
*Copyright（c）1996-2004*
**
*PlanariaSoftwareLLC*
*ALLRIGHTSRESERVED*
**
*info@planaria-*
*http:
//www.planaria-*
**
************************************************
***********************************************************************
WARNING--ArgusLabmaynotbeusedinanymannerthatcompeteswith
thebusinessofPlanariaSoftwareLLCorwillprovideassistanceto
anycompetitorofPlanariaSoftwareLLC.Thelicenseeofthisprogram
isprohibitedfromgivinganycompetitorofPlanariaSoftwareLLC.
accesstothisprogram.Byusingthisprogram,theuseracknowledges
thatPlanariaSoftwareLLC.isengagedinthebusinessofcreatingand
licensingsoftwareinthefieldofcomputationalchemistryand
representsandwarrantstoPlanariaSoftwareLLCthatitisnota
competitorofPlanariaSoftwareLLC.andthatitwillnotusethis
programinanymannerprohibitedabove.
***********************************************************************
Calculationstarttime:
SatJun2922:
53:
332013
***********************************************
Dockingligand:
Fragment
***********************************************
Ligandatomtypeinformation
*****************************
1.（3768）C:
Hydrophobic
2.（3769）C:
Hydrophobic
3.（3770）C:
Hydrophobic
4.（3771）C:
Hydrophobic
5.（3772）C:
Hydrophobic
6.（3773）C:
Hydrophobic
7.（3774）C:
Polar
8.（3775）N:
Polar
9.（3776）C:
Hydrophobic
10.（3777）C:
Polar
11.（3778）N:
H-bondacceptor
12.（3779）C:
Polar
13.（3780）C:
Polar
14.（3781）C:
Hydrophobic
15.（3782）C:
Hydrophobic
16.（3783）C:
Hydrophobic
17.（3784）C:
Hydrophobic
18.（3785）C:
Hydrophobic
19.（3786）C:
Hydrophobic
20.（3787）C:
Hydrophobic
21.（3788）C:
Polar
22.（3789）O:
H-bondacceptorcharged
23.（3790）O:
Polar
24.（3791）H:
atomtypenone
25.（3792）H:
atomtypenone
26.（3793）H:
atomtypenone
27.（3794）H:
atomtypenone
28.（3795）H:
atomtypenone
29.（3796）H:
atomtypenone
30.（3797）H:
atomtypenone
31.（3798）H:
atomtypenone
32.（3799）H:
atomtypenone
33.（3800）H:
atomtypenone
34.（3801）H:
atomtypenone
35.（3802）H:
atomtypenone
36.（3803）H:
atomtypenone
37.（3804）H:
atomtypenone
38.（3805）H:
atomtypenone
39.（3806）H:
atomtypenone
40.（3807）H:
atomtypenone
41.（3808）H:
atomtypenone
***************************************************
ArgusDockSearchEngine
***************************************************
Settingsforthedockingrun
****************************
NumberofLigandtorsions=6
NumberofTargettorsions=0
Precision=RegularPrecision
Augmentrootnodewithinnertorsions=false
Maximumnumberofposes=150
Startthedocking
Ligandextendedrootnoderadii:
primary=2.72634,secondary=2.48889,tertiary=0.0237887
1searchpointsfromatotalof219gridpoints
Rootnodeconfiguration0
Numberofcandidateposesfound=150
1sec.tocompletetheinitialsearch.
pose0fitness=-11.0079
pose1fitness=-11.0077
pose2fitness=-11.0049
pose3fitness=-10.9749
pose4fitness=-10.9615
pose5fitness=-10.9551
pose6fitness=-10.8503
pose7fitness=-10.85
pose8fitness=-10.8167
pose9fitness=-10.8032
pose10fitness=-10.7961
pose11fitness=-10.7767
pose12fitness=-10.7765
pose13fitness=-10.7463
pose14fitness=-10.7442
pose15fitness=-10.7307
pose16fitness=-10.6191
pose17fitness=-10.6189
pose18fitness=-10.586
pose19fitness=-10.5725
pose20fitness=-10.5166
pose21fitness=-10.488
pose22fitness=-10.4668
pose23fitness=-10.4668
pose24fitness=-10.4666
pose25fitness=-10.4382
pose26fitness=-10.4161
pose27fitness=-10.416
pose28fitness=-10.3894
pose29fitness=-10.3894
pose30fitness=-10.3869
pose31fitness=-10.352
pose32fitness=-10.352
pose33fitness=-10.3474
pose34fitness=-10.3071
pose35fitness=-10.3047
pose36fitness=-10.2884
pose37fitness=-10.2687
pose38fitness=-10.2487
pose39fitness=-10.2458
pose40fitness=-10.225
pose41fitness=-10.2063
pose42fitness=-10.1981
pose43fitness=-10.1952
pose44fitness=-10.1702
pose45fitness=-10.166
pose46fitness=-10.1461
pose47fitness=-10.1421
pose48fitness=-10.1406
pose49fitness=-10.1166
pose50fitness=-10.0838
pose51fitness=-10.0769
pose52fitness=-10.069
pose53fitness=-10.0188
pose54fitness=-10.0058
pose55fitness=-10.0008
pose56fitness=-9.97695
pose57fitness=-9.97689
pose58fitness=-9.97517
pose59fitness=-9.94081
pose60fitness=-9.93779
pose61fitness=-9.93042
pose62fitness=-9.92628
pose63fitness=-9.92628
pose64fitness=-9.90153
pose65fitness=-9.90093
pose66fitness=-9.89019
pose67fitness=-9.88712
pose68fitness=-9.87681
pose69fitness=-9.85249
pose70fitness=-9.84514
pose71fitness=-9.84514
pose72fitness=-9.81921
pose73fitness=-9.80355
pose74fitness=-9.77883
pose75fitness=-9.76205
pose76fitness=-9.67817
pose77fitness=-9.67242
pose78fitness=-9.67231
pose79fitness=-9.67153
pose80fitness=-9.67153
pose81fitness=-9.65614
pose82fitness=-9.62655
pose83fitness=-9.58561
pose84fitness=-9.54429
pose85fitness=-9.54393
pose86fitness=-9.53493
pos
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