1、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RCSB protein data bank 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) * *
2、 * Version 4.0 * * Copyright (c) 1996-2004 * * Planaria Software LLC * ALL RIGHTS RESERVED * * infoplanaria- * http:/www.planaria- * *WARNING - ArgusLab may not be used in any manner that competes with the business of Planaria Software LLC or will provide assistance to any competitor of Planaria Sof
3、tware LLC. The licensee of this program is prohibited from giving any competitor of Planaria Software LLC. access to this program. By using this program, the user acknowledges that Planaria Software LLC. is engaged in the business of creating and licensing software in the field of computational chem
4、istry and represents and warrants to Planaria Software LLC that it is not a competitor of Planaria Software LLC. and that it will not use this program in any manner prohibited above. *Calculation start time: Tue Jun 18 00:19:58 2013* Docking ligand: Unnamed* Ligand atom type information*1. (3768) C
5、: Hydrophobic2. (3769) C : Polar3. (3770) C : Hydrophobic4. (3771) C : Hydrophobic5. (3772) C : Hydrophobic6. (3773) C : Hydrophobic7. (3774) N : Polar8. (3775) C : Polar9. (3776) C : Polar10. (3777) N : Polar11. (3778) C : Polar12. (3779) C : Hydrophobic13. (3780) O : H-bond acceptor14. (3781) O :
6、H-bond acceptor15. (3782) C : Polar16. (3783) C : Hydrophobic17. (3784) C : Polar18. (3785) C : Hydrophobic19. (3786) C : Hydrophobic20. (3787) C : Hydrophobic21. (3788) C : Hydrophobic22. (3789) C : Hydrophobic23. (3790) Cl : Hydrophobic24. (3791) C : Hydrophobic25. (3792) C : Hydrophobic26. (3793)
7、 C : Hydrophobic27. (3794) C : Hydrophobic28. (3795) C : Hydrophobic29. (3796) Cl : Hydrophobic30. (3797) I : Hydrophobic31. (3798) C : Polar32. (3799) C : Polar33. (3800) N : Polar34. (3801) C : Polar35. (3802) C : Polar36. (3803) O : H-bond acceptor37. (3804) C : Polar38. (3805) C : Polar39. (3806
8、) O : H-bond acceptor40. (3807) N : Polar41. (3808) H : atom type none42. (3809) H : atom type none43. (3810) H : atom type none44. (3811) H : atom type none45. (3812) H : atom type none46. (3813) H : atom type none47. (3814) H : atom type none48. (3815) H : atom type none49. (3816) H : atom type no
9、ne50. (3817) H : atom type none51. (3818) H : atom type none52. (3819) H : atom type none53. (3820) H : atom type none54. (3821) H : atom type none55. (3822) H : atom type none56. (3823) H : atom type none57. (3824) H : atom type none58. (3825) H : atom type none59. (3826) H : atom type none60. (382
10、7) H : atom type none61. (3828) H : atom type none62. (3829) H : atom type none63. (3830) H : atom type none64. (3831) H : atom type none65. (3832) H : atom type none66. (3833) H : atom type none67. (3834) H : atom type none* ArgusDock Search Engine*Settings for the docking run*Number of Ligand tors
11、ions = 5Number of Target torsions = 0Precision = Regular PrecisionAugment root node with inner torsions = falseMaximum number of poses = 150Start the dockingLigand extended root node radii: primary = 5.02069, secondary =3.10689, tertiary =2.24397 search points from a total of 232 grid pointsRoot nod
12、e configuration 0Number of candidate poses found = 01 sec. to complete the initial search.No acceptable ligand poses were foundDocking run: elapsed time = 1 seconds(2) * * * ArgusLab (tm) * * Version 4.0 * * Copyright (c) 1996-2004 * * Planaria Software LLC * ALL RIGHTS RESERVED * * infoplanaria- *
13、http:/www.planaria- * *WARNING - ArgusLab may not be used in any manner that competes with the business of Planaria Software LLC or will provide assistance to any competitor of Planaria Software LLC. The licensee of this program is prohibited from giving any competitor of Planaria Software LLC. acce
14、ss to this program. By using this program, the user acknowledges that Planaria Software LLC. is engaged in the business of creating and licensing software in the field of computational chemistry and represents and warrants to Planaria Software LLC that it is not a competitor of Planaria Software LLC
15、. and that it will not use this program in any manner prohibited above. *Calculation start time: Sat Jun 29 22:53:33 2013* Docking ligand: Fragment* Ligand atom type information*1. (3768) C : Hydrophobic2. (3769) C : Hydrophobic3. (3770) C : Hydrophobic4. (3771) C : Hydrophobic5. (3772) C : Hydropho
16、bic6. (3773) C : Hydrophobic7. (3774) C : Polar8. (3775) N : Polar9. (3776) C : Hydrophobic10. (3777) C : Polar11. (3778) N : H-bond acceptor12. (3779) C : Polar13. (3780) C : Polar14. (3781) C : Hydrophobic15. (3782) C : Hydrophobic16. (3783) C : Hydrophobic17. (3784) C : Hydrophobic18. (3785) C :
17、Hydrophobic19. (3786) C : Hydrophobic20. (3787) C : Hydrophobic21. (3788) C : Polar22. (3789) O : H-bond acceptor charged23. (3790) O : Polar24. (3791) H : atom type none25. (3792) H : atom type none26. (3793) H : atom type none27. (3794) H : atom type none28. (3795) H : atom type none29. (3796) H :
18、 atom type none30. (3797) H : atom type none31. (3798) H : atom type none32. (3799) H : atom type none33. (3800) H : atom type none34. (3801) H : atom type none35. (3802) H : atom type none36. (3803) H : atom type none37. (3804) H : atom type none38. (3805) H : atom type none39. (3806) H : atom type
19、 none40. (3807) H : atom type none41. (3808) H : atom type none* ArgusDock Search Engine*Settings for the docking run*Number of Ligand torsions = 6Number of Target torsions = 0Precision = Regular PrecisionAugment root node with inner torsions = falseMaximum number of poses = 150Start the dockingLiga
20、nd extended root node radii: primary = 2.72634, secondary =2.48889, tertiary = 0.02378871 search points from a total of 219 grid pointsRoot node configuration 0Number of candidate poses found = 1501 sec. to complete the initial search. pose 0 fitness = -11.0079 pose 1 fitness = -11.0077 pose 2 fitne
21、ss = -11.0049 pose 3 fitness = -10.9749 pose 4 fitness = -10.9615 pose 5 fitness = -10.9551 pose 6 fitness = -10.8503 pose 7 fitness = -10.85 pose 8 fitness = -10.8167 pose 9 fitness = -10.8032 pose 10 fitness = -10.7961 pose 11 fitness = -10.7767 pose 12 fitness = -10.7765 pose 13 fitness = -10.746
22、3 pose 14 fitness = -10.7442 pose 15 fitness = -10.7307 pose 16 fitness = -10.6191 pose 17 fitness = -10.6189 pose 18 fitness = -10.586 pose 19 fitness = -10.5725 pose 20 fitness = -10.5166 pose 21 fitness = -10.488 pose 22 fitness = -10.4668 pose 23 fitness = -10.4668 pose 24 fitness = -10.4666 pos
23、e 25 fitness = -10.4382 pose 26 fitness = -10.4161 pose 27 fitness = -10.416 pose 28 fitness = -10.3894 pose 29 fitness = -10.3894 pose 30 fitness = -10.3869 pose 31 fitness = -10.352 pose 32 fitness = -10.352 pose 33 fitness = -10.3474 pose 34 fitness = -10.3071 pose 35 fitness = -10.3047 pose 36 f
24、itness = -10.2884 pose 37 fitness = -10.2687 pose 38 fitness = -10.2487 pose 39 fitness = -10.2458 pose 40 fitness = -10.225 pose 41 fitness = -10.2063 pose 42 fitness = -10.1981 pose 43 fitness = -10.1952 pose 44 fitness = -10.1702 pose 45 fitness = -10.166 pose 46 fitness = -10.1461 pose 47 fitnes
25、s = -10.1421 pose 48 fitness = -10.1406 pose 49 fitness = -10.1166 pose 50 fitness = -10.0838 pose 51 fitness = -10.0769 pose 52 fitness = -10.069 pose 53 fitness = -10.0188 pose 54 fitness = -10.0058 pose 55 fitness = -10.0008 pose 56 fitness = -9.97695 pose 57 fitness = -9.97689 pose 58 fitness =
26、-9.97517 pose 59 fitness = -9.94081 pose 60 fitness = -9.93779 pose 61 fitness = -9.93042 pose 62 fitness = -9.92628 pose 63 fitness = -9.92628 pose 64 fitness = -9.90153 pose 65 fitness = -9.90093 pose 66 fitness = -9.89019 pose 67 fitness = -9.88712 pose 68 fitness = -9.87681 pose 69 fitness = -9.
27、85249 pose 70 fitness = -9.84514 pose 71 fitness = -9.84514 pose 72 fitness = -9.81921 pose 73 fitness = -9.80355 pose 74 fitness = -9.77883 pose 75 fitness = -9.76205 pose 76 fitness = -9.67817 pose 77 fitness = -9.67242 pose 78 fitness = -9.67231 pose 79 fitness = -9.67153 pose 80 fitness = -9.67153 pose 81 fitness = -9.65614 pose 82 fitness = -9.62655 pose 83 fitness = -9.58561 pose 84 fitness = -9.54429 pose 85 fitness = -9.54393 pose 86 fitness = -9.53493 pos
