PERANCANGAN PEPTIDA SIKLIS SEBAGAI INHIBITOR POTENSIAL UNTUK ENZIM NS3-NS2B PROTEASE VIRUS DENGUE SECARA IN SILICO MELALUI MOLECULAR DOCKING SAMIRA 0305030573 UNIVERSITAS INDONESIA FAKULTAS MATEMATIKA DAN ILMU PENGETAHUAN ALAM DEPARTEMEN KIMIA DEPOK 2009 Perencanaan peptida..., Samira, FMIPA UI, 2009
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PERANCANGAN PEPTIDA SIKLIS SEBAGAI INHIBITOR POTENSIAL UNTUK ENZIM NS3-NS2B PROTEASE VIRUS
DENGUE SECARA IN SILICO MELALUI MOLECULAR DOCKING
SAMIRA 0305030573
UNIVERSITAS INDONESIA
FAKULTAS MATEMATIKA DAN ILMU PENGETAHUAN ALAM DEPARTEMEN KIMIA
DEPOK
2009
Perencanaan peptida..., Samira, FMIPA UI, 2009
PERANCANGAN PEPTIDA SIKLIS SEBAGAI INHIBITOR
POTENSIAL UNTUK ENZIM NS3-NS2B PROTEASE VIRUS DENGUE SECARA IN SILICO MELALUI
MOLECULAR DOCKING
Skripsi diajukan sebagai salah satu syarat
untuk memperoleh gelar Sarjana Sains
SAMIRA 0305030573
UNIVERSITAS INDONESIA
FAKULTAS MATEMATIKA DAN ILMU PENGETAHUAN ALAM DEPARTEMEN KIMIA
DEPOK
2009
Perencanaan peptida..., Samira, FMIPA UI, 2009
SKRIPSI : PERANCANGAN PEPTIDA SIKLIS SEBAGAI INHIBITOR
POTENSIAL UNTUK ENZIM NS3-NS2B PROTEASE VIRUS
DENGUE SECARA IN SILICO MELALUI MOLECULAR
DOCKING
NAMA : SAMIRA
NPM : 0305030573
SKRIPSI INI TELAH DIPERIKSA DAN DISETUJUI
DEPOK, 7 JULI 2009
PROF. DR. USMAN SUMO FRIEND TAMBUNAN, M.Sc
PEMBIMBING
Tanggal lulus ujian sarjana : ........................................................................................... Penguji I : Prof. Dr. Soleh Kosela,.M.Sc............................................................... Penguji II : Dra. Sri Handayani,.M.Biomed............................................................ Penguji III : Dr. Amarila Malik, Apt,.M.Si.............................................................
Perencanaan peptida..., Samira, FMIPA UI, 2009
Perencanaan peptida..., Samira, FMIPA UI, 2009
KATA PENGANTAR
Puji syukur penulis panjatkan kepada kehadirat Allah SWT yang
senantiasa memberikan berkah dan kenikmatan dalam kehidupan penulis.
Alhamdulillah berkat rahmat dan karuniaNya penulis dapat menyelesaikan
penelitian dan penulisan skripsi sebagai syarat menempuh ujian akhir Sarjana
di Departemen Kimia Fakultas Matematika dan Ilmu Pengetahuan Alam
Universitas Indonesia.
Penulis mempersembahkan karya ini untuk keluarga, terutama mama
dan aba atas ketulusan, kesabaran, dan kasih sayang yang luar biasa indah
sehingga mengantarkan penulis sampai pada jenjang ini. Juga kepada adik-
adik tersayang Usama, Fatma, dan Abdu. Sungguh kalian menjadi inspirasi
utama dan pembangkit semangat penulis. Semoga apa yang telah penulis
lakukan dapat memberikan kebanggaan bagi keluarga.
Penulis mengucapkan terima kasih kepada Prof. Dr. Usman Sumo F.T.,
M.Sc selaku pembimbing yang telah membimbing penulis dengan penuh
kesabaran, kebapakan, dan perhatian. Terima kasih atas kepercayaan yang
diberikan. Terima kasih telah menjadi dosen, bapak, dan partner yang
membuka lebih luas cakrawala penulis mengenai hidup.
Pada kesempatan ini pula, penulis ingin mengucapkan terima kasih
yang sebesarnya kepada:
1. Dr. Ridla Bakri selaku Ketua Departemen Kimia FMIPA UI
iPerencanaan peptida..., Samira, FMIPA UI, 2009
2. Ir. Widyastuti Samadi, M.Si selaku Koordinator Pendidikan sekaligus
Pembimbing Akademik penulis yang selalu menebarkan aura bahagia
Lampiran 9. Data Energi Hasil Docking 9.1 Ligan Standar Keeping original residue number (specified in the input PDBQ file) for outputting. MODEL 70 USER Run = 70 USER Cluster Rank = 1 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 19.094 A USER USER Estimated Free Energy of Binding = -6.14 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 31.54 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -11.63 kcal/mol USER vdW + Hbond + desolv Energy = -9.95 kcal/mol USER Electrostatic Energy = -1.68 kcal/mol USER (2) Final Total Internal Energy = -2.70 kcal/mol USER (3) Torsional Free Energy = +6.86 kcal/mol USER (4) Unbound System's Energy = -1.33 kcal/mol USER MODEL 62 USER Run = 62 USER Cluster Rank = 2 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 21.454 A USER USER Estimated Free Energy of Binding = -5.71 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 64.78 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -11.65 kcal/mol USER vdW + Hbond + desolv Energy = -9.76 kcal/mol USER Electrostatic Energy = -1.89 kcal/mol USER (2) Final Total Internal Energy = -2.26 kcal/mol USER (3) Torsional Free Energy = +6.86 kcal/mol USER (4) Unbound System's Energy = -1.33 kcal/mol USER MODEL 94 USER Run = 94 USER Cluster Rank = 3 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 21.345 A USER USER Estimated Free Energy of Binding = -5.53 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 88.96 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -9.50 kcal/mol USER vdW + Hbond + desolv Energy = -8.22 kcal/mol USER Electrostatic Energy = -1.29 kcal/mol USER (2) Final Total Internal Energy = -4.21 kcal/mol USER (3) Torsional Free Energy = +6.86 kcal/mol USER (4) Unbound System's Energy = -1.33 kcal/mol USER USER MODEL 95 USER Run = 95 USER Cluster Rank = 4
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USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 23.464 A USER USER Estimated Free Energy of Binding = -5.50 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 92.46 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -10.42 kcal/mol USER vdW + Hbond + desolv Energy = -9.33 kcal/mol USER Electrostatic Energy = -1.09 kcal/mol USER (2) Final Total Internal Energy = -3.27 kcal/mol USER (3) Torsional Free Energy = +6.86 kcal/mol USER (4) Unbound System's Energy = -1.33 kcal/mol USER MODEL 35 USER Run = 35 USER Cluster Rank = 5 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 22.130 A USER USER Estimated Free Energy of Binding = -5.48 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 95.42 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -10.32 kcal/mol USER vdW + Hbond + desolv Energy = -8.41 kcal/mol USER Electrostatic Energy = -1.91 kcal/mol USER (2) Final Total Internal Energy = -3.36 kcal/mol USER (3) Torsional Free Energy = +6.86 kcal/mol USER (4) Unbound System's Energy = -1.33 kcal/mol USER MODEL 56 USER Run = 56 USER Cluster Rank = 6 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 21.104 A USER USER Estimated Free Energy of Binding = -5.12 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 177.50 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -10.20 kcal/mol USER vdW + Hbond + desolv Energy = -9.04 kcal/mol USER Electrostatic Energy = -1.16 kcal/mol USER (2) Final Total Internal Energy = -3.11 kcal/mol USER (3) Torsional Free Energy = +6.86 kcal/mol USER (4) Unbound System's Energy = -1.33 kcal/mol USER MODEL 52 USER Run = 52 USER Cluster Rank = 7 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 20.284 A USER USER Estimated Free Energy of Binding = -5.09 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 186.65 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -10.85 kcal/mol USER vdW + Hbond + desolv Energy = -9.85 kcal/mol USER Electrostatic Energy = -1.00 kcal/mol USER (2) Final Total Internal Energy = -2.43 kcal/mol USER (3) Torsional Free Energy = +6.86 kcal/mol USER (4) Unbound System's Energy = -1.33 kcal/mol
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USER MODEL 60 USER Run = 60 USER Cluster Rank = 8 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 19.222 A USER USER Estimated Free Energy of Binding = -4.94 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 238.64 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -9.66 kcal/mol USER vdW + Hbond + desolv Energy = -8.61 kcal/mol USER Electrostatic Energy = -1.04 kcal/mol USER (2) Final Total Internal Energy = -3.48 kcal/mol USER (3) Torsional Free Energy = +6.86 kcal/mol USER (4) Unbound System's Energy = -1.33 kcal/mol USER MODEL 40 USER Run = 40 USER Cluster Rank = 9 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 20.524 A USER USER Estimated Free Energy of Binding = -4.79 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 309.67 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -9.02 kcal/mol USER vdW + Hbond + desolv Energy = -7.83 kcal/mol USER Electrostatic Energy = -1.19 kcal/mol USER (2) Final Total Internal Energy = -3.96 kcal/mol USER (3) Torsional Free Energy = +6.86 kcal/mol USER (4) Unbound System's Energy = -1.33 kcal/mol USER MODEL 7 USER Run = 7 USER Cluster Rank = 10 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 20.156 A USER USER Estimated Free Energy of Binding = -4.54 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 470.79 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -9.75 kcal/mol USER vdW + Hbond + desolv Energy = -8.79 kcal/mol USER Electrostatic Energy = -0.96 kcal/mol USER (2) Final Total Internal Energy = -2.98 kcal/mol USER (3) Torsional Free Energy = +6.86 kcal/mol USER (4) Unbound System's Energy = -1.33 kcal/mol USER
9.2 Ligan KRR LOWEST ENERGY DOCKED CONFORMATION from EACH CLUSTER Keeping original residue number (specified in the input PDBQ file) for outputting. MODEL 82 USER Run = 82 USER Cluster Rank = 1 USER Number of conformations in this cluster = 8 USER USER RMSD from reference structure = 21.447 A
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USER USER Estimated Free Energy of Binding = -7.01 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 7.32 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -10.16 kcal/mol USER vdW + Hbond + desolv Energy = -8.08 kcal/mol USER Electrostatic Energy = -2.08 kcal/mol USER (2) Final Total Internal Energy = -1.56 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.60 kcal/mol USER MODEL 81 USER Run = 81 USER Cluster Rank = 2 USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 18.939 A USER USER Estimated Free Energy of Binding = -6.86 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 9.40 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -10.05 kcal/mol USER vdW + Hbond + desolv Energy = -7.21 kcal/mol USER Electrostatic Energy = -2.84 kcal/mol USER (2) Final Total Internal Energy = -1.53 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.60 kcal/mol USER MODEL 47 USER Run = 47 USER Cluster Rank = 3 USER Number of conformations in this cluster = 4 USER USER RMSD from reference structure = 21.544 A USER USER Estimated Free Energy of Binding = -6.72 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 11.77 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -10.15 kcal/mol USER vdW + Hbond + desolv Energy = -8.37 kcal/mol USER Electrostatic Energy = -1.78 kcal/mol USER (2) Final Total Internal Energy = -1.29 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.60 kcal/mol USER MODEL 74 USER Run = 74 USER Cluster Rank = 4 USER Number of conformations in this cluster = 3 USER USER RMSD from reference structure = 21.841 A USER USER Estimated Free Energy of Binding = -6.13 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 32.38 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -9.76 kcal/mol USER vdW + Hbond + desolv Energy = -7.07 kcal/mol USER Electrostatic Energy = -2.69 kcal/mol USER (2) Final Total Internal Energy = -1.08 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.60 kcal/mol USER MODEL 72 USER Run = 72
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USER Cluster Rank = 5 USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 20.606 A USER USER Estimated Free Energy of Binding = -5.98 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 41.13 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -10.30 kcal/mol USER vdW + Hbond + desolv Energy = -7.79 kcal/mol USER Electrostatic Energy = -2.51 kcal/mol USER (2) Final Total Internal Energy = -0.40 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.60 kcal/mol USER MODEL 13 USER Run = 13 USER Cluster Rank = 6 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 21.801 A USER USER Estimated Free Energy of Binding = -5.95 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 43.45 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.94 kcal/mol USER vdW + Hbond + desolv Energy = -7.55 kcal/mol USER Electrostatic Energy = -1.39 kcal/mol USER (2) Final Total Internal Energy = -1.72 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.60 kcal/mol USER MODEL 68 USER Run = 68 USER Cluster Rank = 7 USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 20.780 A USER USER Estimated Free Energy of Binding = -5.94 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 43.88 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.62 kcal/mol USER vdW + Hbond + desolv Energy = -7.35 kcal/mol USER Electrostatic Energy = -1.27 kcal/mol USER (2) Final Total Internal Energy = -2.04 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.60 kcal/mol USER MODEL 33 USER Run = 33 USER Cluster Rank = 8 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 22.680 A USER USER Estimated Free Energy of Binding = -5.68 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 68.30 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -9.68 kcal/mol USER vdW + Hbond + desolv Energy = -8.03 kcal/mol USER Electrostatic Energy = -1.66 kcal/mol USER (2) Final Total Internal Energy = -0.72 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol
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USER (4) Unbound System's Energy = -0.60 kcal/mol USER MODEL 90 USER Run = 90 USER Cluster Rank = 9 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 21.452 A USER USER Estimated Free Energy of Binding = -5.57 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 82.82 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -9.45 kcal/mol USER vdW + Hbond + desolv Energy = -8.02 kcal/mol USER Electrostatic Energy = -1.44 kcal/mol USER (2) Final Total Internal Energy = -0.83 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.60 kcal/mol USER MODEL 12 USER Run = 12 USER Cluster Rank = 10 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 20.272 A USER USER Estimated Free Energy of Binding = -5.54 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 87.47 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -7.88 kcal/mol USER vdW + Hbond + desolv Energy = -6.39 kcal/mol USER Electrostatic Energy = -1.49 kcal/mol USER (2) Final Total Internal Energy = -2.37 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.60 kcal/mol 9.3 Ligan GRR LOWEST ENERGY DOCKED CONFORMATION from EACH CLUSTER Keeping original residue number (specified in the input PDBQ file) for outputting. MODEL 81 USER Run = 81 USER Cluster Rank = 1 USER Number of conformations in this cluster = 4 USER USER RMSD from reference structure = 22.144 A USER USER Estimated Free Energy of Binding = -8.12 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 1.11 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.17 kcal/mol USER vdW + Hbond + desolv Energy = -7.10 kcal/mol USER Electrostatic Energy = -1.07 kcal/mol USER (2) Final Total Internal Energy = -3.73 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -1.03 kcal/mol
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MODEL 1 USER Run = 1 USER Cluster Rank = 2 USER Number of conformations in this cluster = 4 USER USER RMSD from reference structure = 22.308 A USER USER Estimated Free Energy of Binding = -7.94 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 1.52 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.34 kcal/mol USER vdW + Hbond + desolv Energy = -7.19 kcal/mol USER Electrostatic Energy = -1.15 kcal/mol USER (2) Final Total Internal Energy = -3.38 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -1.03 kcal/mol USER MODEL 20 USER Run = 20 USER Cluster Rank = 3 USER Number of conformations in this cluster = 5 USER USER RMSD from reference structure = 20.966 A USER USER Estimated Free Energy of Binding = -7.58 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 2.77 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -10.28 kcal/mol USER vdW + Hbond + desolv Energy = -8.41 kcal/mol USER Electrostatic Energy = -1.86 kcal/mol USER (2) Final Total Internal Energy = -1.08 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -1.03 kcal/mol USER MODEL 56 USER Run = 56 USER Cluster Rank = 4 USER Number of conformations in this cluster = 3 USER USER RMSD from reference structure = 21.800 A USER USER Estimated Free Energy of Binding = -7.56 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 2.89 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.20 kcal/mol USER vdW + Hbond + desolv Energy = -7.06 kcal/mol USER Electrostatic Energy = -1.14 kcal/mol USER (2) Final Total Internal Energy = -3.13 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -1.03 kcal/mol USER MODEL 99 USER Run = 99 USER Cluster Rank = 5 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 23.171 A USER USER Estimated Free Energy of Binding = -7.53 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 3.01 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.16 kcal/mol USER vdW + Hbond + desolv Energy = -6.75 kcal/mol USER Electrostatic Energy = -1.41 kcal/mol
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USER (2) Final Total Internal Energy = -3.15 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -1.03 kcal/mol USER MODEL 79 USER Run = 79 USER Cluster Rank = 6 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 19.850 A USER USER Estimated Free Energy of Binding = -7.50 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 3.16 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -7.91 kcal/mol USER vdW + Hbond + desolv Energy = -7.00 kcal/mol USER Electrostatic Energy = -0.91 kcal/mol USER (2) Final Total Internal Energy = -3.37 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -1.03 kcal/mol USER MODEL 42 USER Run = 42 USER Cluster Rank = 7 USER Number of conformations in this cluster = 4 USER USER RMSD from reference structure = 21.997 A USER USER Estimated Free Energy of Binding = -7.31 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 4.36 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -7.93 kcal/mol USER vdW + Hbond + desolv Energy = -6.45 kcal/mol USER Electrostatic Energy = -1.48 kcal/mol USER (2) Final Total Internal Energy = -3.16 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -1.03 kcal/mol USER MODEL 67 USER Run = 67 USER Cluster Rank = 8 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 22.002 A USER USER Estimated Free Energy of Binding = -7.15 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 5.75 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -7.27 kcal/mol USER vdW + Hbond + desolv Energy = -6.07 kcal/mol USER Electrostatic Energy = -1.20 kcal/mol USER (2) Final Total Internal Energy = -3.65 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -1.03 kcal/mol USER MODEL 92 USER Run = 92 USER Cluster Rank = 9 USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 19.252 A USER USER Estimated Free Energy of Binding = -7.07 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 6.57 uM (micromolar) [Temperature = 298.15 K]
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USER USER (1) Final Intermolecular Energy = -8.66 kcal/mol USER vdW + Hbond + desolv Energy = -7.25 kcal/mol USER Electrostatic Energy = -1.41 kcal/mol USER (2) Final Total Internal Energy = -2.18 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -1.03 kcal/mol USER MODEL 66 USER Run = 66 USER Cluster Rank = 10 USER Number of conformations in this cluster = 6 USER USER RMSD from reference structure = 18.394 A USER USER Estimated Free Energy of Binding = -7.04 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 6.96 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.51 kcal/mol USER vdW + Hbond + desolv Energy = -7.56 kcal/mol USER Electrostatic Energy = -0.95 kcal/mol USER (2) Final Total Internal Energy = -2.30 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -1.03 kcal/mol
9.4 Ligan RGR LOWEST ENERGY DOCKED CONFORMATION from EACH CLUSTER Keeping original residue number (specified in the input PDBQ file) for outputting. MODEL 90 USER Run = 90 USER Cluster Rank = 1 USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 21.400 A USER USER Estimated Free Energy of Binding = -7.50 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 3.20 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.61 kcal/mol USER vdW + Hbond + desolv Energy = -7.47 kcal/mol USER Electrostatic Energy = -1.14 kcal/mol USER (2) Final Total Internal Energy = -2.48 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -0.84 kcal/mol USER MODEL 89 USER Run = 89 USER Cluster Rank = 2 USER Number of conformations in this cluster = 9 USER USER RMSD from reference structure = 20.933 A USER USER Estimated Free Energy of Binding = -7.35 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 4.12 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -10.18 kcal/mol USER vdW + Hbond + desolv Energy = -7.85 kcal/mol USER Electrostatic Energy = -2.33 kcal/mol USER (2) Final Total Internal Energy = -0.76 kcal/mol
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USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -0.84 kcal/mol USER MODEL 19 USER Run = 19 USER Cluster Rank = 3 USER Number of conformations in this cluster = 5 USER USER RMSD from reference structure = 20.333 A USER USER Estimated Free Energy of Binding = -7.16 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 5.67 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.06 kcal/mol USER vdW + Hbond + desolv Energy = -7.04 kcal/mol USER Electrostatic Energy = -1.02 kcal/mol USER (2) Final Total Internal Energy = -2.69 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -0.84 kcal/mol USER MODEL 82 USER Run = 82 USER Cluster Rank = 4 USER Number of conformations in this cluster = 4 USER USER RMSD from reference structure = 19.309 A USER USER Estimated Free Energy of Binding = -7.08 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 6.46 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.66 kcal/mol USER vdW + Hbond + desolv Energy = -7.29 kcal/mol USER Electrostatic Energy = -1.37 kcal/mol USER (2) Final Total Internal Energy = -2.01 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -0.84 kcal/mol USER MODEL 99 USER Run = 99 USER Cluster Rank = 5 USER Number of conformations in this cluster = 4 USER USER RMSD from reference structure = 19.248 A USER USER Estimated Free Energy of Binding = -6.86 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 9.42 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.56 kcal/mol USER vdW + Hbond + desolv Energy = -6.91 kcal/mol USER Electrostatic Energy = -1.65 kcal/mol USER (2) Final Total Internal Energy = -1.88 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -0.84 kcal/mol USER MODEL 50 USER Run = 50 USER Cluster Rank = 6 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 20.285 A USER USER Estimated Free Energy of Binding = -6.86 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 9.42 uM (micromolar) [Temperature = 298.15 K] USER
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USER (1) Final Intermolecular Energy = -9.75 kcal/mol USER vdW + Hbond + desolv Energy = -7.92 kcal/mol USER Electrostatic Energy = -1.83 kcal/mol USER (2) Final Total Internal Energy = -0.70 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -0.84 kcal/mol USER MODEL 79 USER Run = 79 USER Cluster Rank = 7 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 21.439 A USER USER Estimated Free Energy of Binding = -6.85 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 9.60 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.12 kcal/mol USER vdW + Hbond + desolv Energy = -7.21 kcal/mol USER Electrostatic Energy = -0.91 kcal/mol USER (2) Final Total Internal Energy = -2.32 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -0.84 kcal/mol USER MODEL 1 USER Run = 1 USER Cluster Rank = 8 USER Number of conformations in this cluster = 3 USER USER RMSD from reference structure = 22.714 A USER USER Estimated Free Energy of Binding = -6.61 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 14.40 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -7.25 kcal/mol USER vdW + Hbond + desolv Energy = -6.22 kcal/mol USER Electrostatic Energy = -1.03 kcal/mol USER (2) Final Total Internal Energy = -2.95 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -0.84 kcal/mol USER MODEL 91 USER Run = 91 USER Cluster Rank = 9 USER Number of conformations in this cluster = 3 USER USER RMSD from reference structure = 21.049 A USER USER Estimated Free Energy of Binding = -6.58 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 15.07 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.24 kcal/mol USER vdW + Hbond + desolv Energy = -6.23 kcal/mol USER Electrostatic Energy = -2.01 kcal/mol USER (2) Final Total Internal Energy = -1.93 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -0.84 kcal/mol USER MODEL 17 USER Run = 17 USER Cluster Rank = 10 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 20.532 A USER
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USER Estimated Free Energy of Binding = -6.58 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 15.12 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -7.08 kcal/mol USER vdW + Hbond + desolv Energy = -5.31 kcal/mol USER Electrostatic Energy = -1.78 kcal/mol USER (2) Final Total Internal Energy = -3.08 kcal/mol USER (3) Torsional Free Energy = +2.74 kcal/mol USER (4) Unbound System's Energy = -0.84 kcal/mol
9.5 Ligan RTR LOWEST ENERGY DOCKED CONFORMATION from EACH CLUSTER Keeping original residue number (specified in the input PDBQ file) for outputting. MODEL 26 USER Run = 26 USER Cluster Rank = 1 USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 23.466 A USER USER Estimated Free Energy of Binding = -7.69 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 2.31 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -10.06 kcal/mol USER vdW + Hbond + desolv Energy = -8.35 kcal/mol USER Electrostatic Energy = -1.71 kcal/mol USER (2) Final Total Internal Energy = -1.72 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.79 kcal/mol USER MODEL 59 USER Run = 59 USER Cluster Rank = 2 USER Number of conformations in this cluster = 3 USER USER RMSD from reference structure = 22.148 A USER USER Estimated Free Energy of Binding = -7.06 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 6.66 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -9.98 kcal/mol USER vdW + Hbond + desolv Energy = -8.32 kcal/mol USER Electrostatic Energy = -1.66 kcal/mol USER (2) Final Total Internal Energy = -1.17 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.79 kcal/mol USER MODEL 35 USER Run = 35 USER Cluster Rank = 3 USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 17.414 A USER USER Estimated Free Energy of Binding = -6.86 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 9.38 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.04 kcal/mol USER vdW + Hbond + desolv Energy = -6.70 kcal/mol USER Electrostatic Energy = -1.33 kcal/mol USER (2) Final Total Internal Energy = -2.91 kcal/mol
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USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.79 kcal/mol USER MODEL 45 USER Run = 45 USER Cluster Rank = 4 USER Number of conformations in this cluster = 3 USER USER RMSD from reference structure = 20.368 A USER USER Estimated Free Energy of Binding = -6.82 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 9.96 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.44 kcal/mol USER vdW + Hbond + desolv Energy = -7.27 kcal/mol USER Electrostatic Energy = -1.17 kcal/mol USER (2) Final Total Internal Energy = -2.47 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.79 kcal/mol USER MODEL 20 USER Run = 20 USER Cluster Rank = 5 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 21.583 A USER USER Estimated Free Energy of Binding = -6.39 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 20.54 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -7.15 kcal/mol USER vdW + Hbond + desolv Energy = -6.48 kcal/mol USER Electrostatic Energy = -0.67 kcal/mol USER (2) Final Total Internal Energy = -3.33 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.79 kcal/mol USER MODEL 76 USER Run = 76 USER Cluster Rank = 6 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 19.552 A USER USER Estimated Free Energy of Binding = -6.34 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 22.40 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -7.66 kcal/mol USER vdW + Hbond + desolv Energy = -6.74 kcal/mol USER Electrostatic Energy = -0.92 kcal/mol USER (2) Final Total Internal Energy = -2.77 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.79 kcal/mol USER MODEL 4 USER Run = 4 USER Cluster Rank = 7 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 21.274 A USER USER Estimated Free Energy of Binding = -6.30 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 23.93 uM (micromolar) [Temperature = 298.15 K] USER
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USER (1) Final Intermolecular Energy = -7.49 kcal/mol USER vdW + Hbond + desolv Energy = -6.55 kcal/mol USER Electrostatic Energy = -0.94 kcal/mol USER (2) Final Total Internal Energy = -2.90 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.79 kcal/mol USER MODEL 31 USER Run = 31 USER Cluster Rank = 8 USER Number of conformations in this cluster = 3 USER USER RMSD from reference structure = 21.139 A USER USER Estimated Free Energy of Binding = -6.27 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 25.18 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.85 kcal/mol USER vdW + Hbond + desolv Energy = -7.46 kcal/mol USER Electrostatic Energy = -1.39 kcal/mol USER (2) Final Total Internal Energy = -1.51 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.79 kcal/mol USER MODEL 52 USER Run = 52 USER Cluster Rank = 9 USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 18.053 A USER USER Estimated Free Energy of Binding = -6.26 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 25.82 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.02 kcal/mol USER vdW + Hbond + desolv Energy = -7.22 kcal/mol USER Electrostatic Energy = -0.80 kcal/mol USER (2) Final Total Internal Energy = -2.33 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.79 kcal/mol USER MODEL 62 USER Run = 62 USER Cluster Rank = 10 USER Number of conformations in this cluster = 3 USER USER RMSD from reference structure = 22.118 A USER USER Estimated Free Energy of Binding = -6.23 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 27.32 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -6.96 kcal/mol USER vdW + Hbond + desolv Energy = -6.70 kcal/mol USER Electrostatic Energy = -0.27 kcal/mol USER (2) Final Total Internal Energy = -3.35 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.79 kcal/mol
9.6 Ligan TRR LOWEST ENERGY DOCKED CONFORMATION from EACH CLUSTER Keeping original residue number (specified in the input PDBQ file) for outputting.
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MODEL 11 USER Run = 11 USER Cluster Rank = 1 USER Number of conformations in this cluster = 4 USER USER RMSD from reference structure = 20.116 A USER USER Estimated Free Energy of Binding = -7.08 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 6.45 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -9.11 kcal/mol USER vdW + Hbond + desolv Energy = -7.86 kcal/mol USER Electrostatic Energy = -1.26 kcal/mol USER (2) Final Total Internal Energy = -2.19 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.93 kcal/mol USER MODEL 25 USER Run = 25 USER Cluster Rank = 2 USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 22.117 A USER USER Estimated Free Energy of Binding = -6.88 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 8.99 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.09 kcal/mol USER vdW + Hbond + desolv Energy = -7.22 kcal/mol USER Electrostatic Energy = -0.87 kcal/mol USER (2) Final Total Internal Energy = -3.01 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.93 kcal/mol USER MODEL 32 USER Run = 32 USER Cluster Rank = 3 USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 18.845 A USER USER Estimated Free Energy of Binding = -6.61 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 14.35 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -7.92 kcal/mol USER vdW + Hbond + desolv Energy = -6.90 kcal/mol USER Electrostatic Energy = -1.02 kcal/mol USER (2) Final Total Internal Energy = -2.91 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.93 kcal/mol USER MODEL 61 USER Run = 61 USER Cluster Rank = 4 USER Number of conformations in this cluster = 4 USER USER RMSD from reference structure = 21.306 A USER USER Estimated Free Energy of Binding = -6.34 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 22.43 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -7.06 kcal/mol USER vdW + Hbond + desolv Energy = -6.14 kcal/mol
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USER Electrostatic Energy = -0.92 kcal/mol USER (2) Final Total Internal Energy = -3.50 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.93 kcal/mol USER MODEL 92 USER Run = 92 USER Cluster Rank = 5 USER Number of conformations in this cluster = 3 USER USER RMSD from reference structure = 19.643 A USER USER Estimated Free Energy of Binding = -6.33 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 22.93 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.08 kcal/mol USER vdW + Hbond + desolv Energy = -7.16 kcal/mol USER Electrostatic Energy = -0.92 kcal/mol USER (2) Final Total Internal Energy = -2.46 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.93 kcal/mol USER MODEL 98 USER Run = 98 USER Cluster Rank = 6 USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 21.850 A USER USER Estimated Free Energy of Binding = -6.29 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 24.37 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -7.13 kcal/mol USER vdW + Hbond + desolv Energy = -6.34 kcal/mol USER Electrostatic Energy = -0.79 kcal/mol USER (2) Final Total Internal Energy = -3.38 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.93 kcal/mol USER MODEL 22 USER Run = 22 USER Cluster Rank = 7 USER Number of conformations in this cluster = 3 USER USER RMSD from reference structure = 19.138 A USER USER Estimated Free Energy of Binding = -6.25 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 26.03 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -7.87 kcal/mol USER vdW + Hbond + desolv Energy = -6.26 kcal/mol USER Electrostatic Energy = -1.62 kcal/mol USER (2) Final Total Internal Energy = -2.60 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.93 kcal/mol USER MODEL 75 USER Run = 75 USER Cluster Rank = 8 USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 20.372 A USER USER Estimated Free Energy of Binding = -6.19 kcal/mol [=(1)+(2)+(3)-(4)]
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USER Estimated Inhibition Constant, Ki = 28.81 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -7.22 kcal/mol USER vdW + Hbond + desolv Energy = -6.15 kcal/mol USER Electrostatic Energy = -1.07 kcal/mol USER (2) Final Total Internal Energy = -3.19 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.93 kcal/mol USER MODEL 76 USER Run = 76 USER Cluster Rank = 9 USER Number of conformations in this cluster = 5 USER USER RMSD from reference structure = 18.898 A USER USER Estimated Free Energy of Binding = -6.15 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 30.90 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.85 kcal/mol USER vdW + Hbond + desolv Energy = -7.93 kcal/mol USER Electrostatic Energy = -0.92 kcal/mol USER (2) Final Total Internal Energy = -1.52 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.93 kcal/mol USER MODEL 29 USER Run = 29 USER Cluster Rank = 10 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 18.667 A USER USER Estimated Free Energy of Binding = -6.00 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 39.92 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -7.09 kcal/mol USER vdW + Hbond + desolv Energy = -6.44 kcal/mol USER Electrostatic Energy = -0.66 kcal/mol USER (2) Final Total Internal Energy = -3.13 kcal/mol USER (3) Torsional Free Energy = +3.29 kcal/mol USER (4) Unbound System's Energy = -0.93 kcal/mol
9.7 Ligan KRK LOWEST ENERGY DOCKED CONFORMATION from EACH CLUSTER Keeping original residue number (specified in the input PDBQ file) for outputting. MODEL 47 USER Run = 47 USER Cluster Rank = 1 USER Number of conformations in this cluster = 6 USER USER RMSD from reference structure = 21.220 A USER USER Estimated Free Energy of Binding = -8.39 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 707.25 nM (nanomolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -11.32 kcal/mol USER vdW + Hbond + desolv Energy = -9.31 kcal/mol USER Electrostatic Energy = -2.00 kcal/mol USER (2) Final Total Internal Energy = -2.27 kcal/mol
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USER (3) Torsional Free Energy = +4.39 kcal/mol USER (4) Unbound System's Energy = -0.80 kcal/mol MODEL 20 USER Run = 20 USER Cluster Rank = 2 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 23.176 A USER USER Estimated Free Energy of Binding = -7.58 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 2.78 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -11.23 kcal/mol USER vdW + Hbond + desolv Energy = -8.98 kcal/mol USER Electrostatic Energy = -2.25 kcal/mol USER (2) Final Total Internal Energy = -1.54 kcal/mol USER (3) Torsional Free Energy = +4.39 kcal/mol USER (4) Unbound System's Energy = -0.80 kcal/mol USER MODEL 74 USER Run = 74 USER Cluster Rank = 3 USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 20.292 A USER USER Estimated Free Energy of Binding = -6.96 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 7.86 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -11.19 kcal/mol USER vdW + Hbond + desolv Energy = -9.16 kcal/mol USER Electrostatic Energy = -2.03 kcal/mol USER (2) Final Total Internal Energy = -0.97 kcal/mol USER (3) Torsional Free Energy = +4.39 kcal/mol USER (4) Unbound System's Energy = -0.80 kcal/mol USER MODEL 81 USER Run = 81 USER Cluster Rank = 4 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 21.222 A USER USER Estimated Free Energy of Binding = -6.83 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 9.83 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -9.27 kcal/mol USER vdW + Hbond + desolv Energy = -7.26 kcal/mol USER Electrostatic Energy = -2.01 kcal/mol USER (2) Final Total Internal Energy = -2.75 kcal/mol USER (3) Torsional Free Energy = +4.39 kcal/mol USER (4) Unbound System's Energy = -0.80 kcal/mol USER MODEL 6 USER Run = 6 USER Cluster Rank = 5 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 23.022 A USER USER Estimated Free Energy of Binding = -6.62 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 13.99 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.64 kcal/mol
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USER vdW + Hbond + desolv Energy = -7.16 kcal/mol USER Electrostatic Energy = -1.48 kcal/mol USER (2) Final Total Internal Energy = -3.18 kcal/mol USER (3) Torsional Free Energy = +4.39 kcal/mol USER (4) Unbound System's Energy = -0.80 kcal/mol USER MODEL 28 USER Run = 28 USER Cluster Rank = 6 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 19.990 A USER USER Estimated Free Energy of Binding = -6.42 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 19.70 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.96 kcal/mol USER vdW + Hbond + desolv Energy = -7.62 kcal/mol USER Electrostatic Energy = -1.34 kcal/mol USER (2) Final Total Internal Energy = -2.65 kcal/mol USER (3) Torsional Free Energy = +4.39 kcal/mol USER (4) Unbound System's Energy = -0.80 kcal/mol USER MODEL 32 USER Run = 32 USER Cluster Rank = 7 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 21.592 A USER USER Estimated Free Energy of Binding = -6.40 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 20.26 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -9.04 kcal/mol USER vdW + Hbond + desolv Energy = -7.45 kcal/mol USER Electrostatic Energy = -1.59 kcal/mol USER (2) Final Total Internal Energy = -2.55 kcal/mol USER (3) Torsional Free Energy = +4.39 kcal/mol USER (4) Unbound System's Energy = -0.80 kcal/mol USER MODEL 84 USER Run = 84 USER Cluster Rank = 8 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 21.459 A USER USER Estimated Free Energy of Binding = -6.32 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 23.40 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -9.40 kcal/mol USER vdW + Hbond + desolv Energy = -7.89 kcal/mol USER Electrostatic Energy = -1.51 kcal/mol USER (2) Final Total Internal Energy = -2.11 kcal/mol USER (3) Torsional Free Energy = +4.39 kcal/mol USER (4) Unbound System's Energy = -0.80 kcal/mol USER MODEL 83 USER Run = 83 USER Cluster Rank = 9 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 19.665 A USER USER Estimated Free Energy of Binding = -6.28 kcal/mol [=(1)+(2)+(3)-(4)]
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USER Estimated Inhibition Constant, Ki = 24.79 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.48 kcal/mol USER vdW + Hbond + desolv Energy = -7.45 kcal/mol USER Electrostatic Energy = -1.03 kcal/mol USER (2) Final Total Internal Energy = -3.00 kcal/mol USER (3) Torsional Free Energy = +4.39 kcal/mol USER (4) Unbound System's Energy = -0.80 kcal/mol USER MODEL 61 USER Run = 61 USER Cluster Rank = 10 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 22.954 A USER USER Estimated Free Energy of Binding = -6.25 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 26.24 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -10.58 kcal/mol USER vdW + Hbond + desolv Energy = -8.90 kcal/mol USER Electrostatic Energy = -1.68 kcal/mol USER (2) Final Total Internal Energy = -0.86 kcal/mol USER (3) Torsional Free Energy = +4.39 kcal/mol USER (4) Unbound System's Energy = -0.80 kcal/mol USER
9.8 Ligan RRK LOWEST ENERGY DOCKED CONFORMATION from EACH CLUSTER Keeping original residue number (specified in the input PDBQ file) for outputting. MODEL 12 USER Run = 12 USER Cluster Rank = 1 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 16.046 A USER USER Estimated Free Energy of Binding = -7.48 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 3.28 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -9.43 kcal/mol USER vdW + Hbond + desolv Energy = -7.11 kcal/mol USER Electrostatic Energy = -2.32 kcal/mol USER (2) Final Total Internal Energy = -3.03 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.86 kcal/mol USER MODEL 15 USER Run = 15 USER Cluster Rank = 2 USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 15.812 A USER USER Estimated Free Energy of Binding = -7.38 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 3.86 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -9.48 kcal/mol
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USER vdW + Hbond + desolv Energy = -7.54 kcal/mol USER Electrostatic Energy = -1.94 kcal/mol USER (2) Final Total Internal Energy = -2.88 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.86 kcal/mol USER MODEL 11 USER Run = 11 USER Cluster Rank = 3 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 17.991 A USER USER Estimated Free Energy of Binding = -6.90 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 8.71 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.70 kcal/mol USER vdW + Hbond + desolv Energy = -7.51 kcal/mol USER Electrostatic Energy = -1.19 kcal/mol USER (2) Final Total Internal Energy = -3.17 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.86 kcal/mol USER MODEL 18 USER Run = 18 USER Cluster Rank = 4 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 14.453 A USER USER Estimated Free Energy of Binding = -6.85 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 9.58 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.41 kcal/mol USER vdW + Hbond + desolv Energy = -6.79 kcal/mol USER Electrostatic Energy = -1.61 kcal/mol USER (2) Final Total Internal Energy = -3.41 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.86 kcal/mol USER MODEL 83 USER Run = 83 USER Cluster Rank = 5 USER Number of conformations in this cluster = 6 USER USER RMSD from reference structure = 17.766 A USER USER Estimated Free Energy of Binding = -6.83 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 9.83 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.73 kcal/mol USER vdW + Hbond + desolv Energy = -6.36 kcal/mol USER Electrostatic Energy = -2.37 kcal/mol USER (2) Final Total Internal Energy = -3.08 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.86 kcal/mol USER MODEL 68 USER Run = 68 USER Cluster Rank = 6 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 18.623 A USER
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USER Estimated Free Energy of Binding = -6.48 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 17.78 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.75 kcal/mol USER vdW + Hbond + desolv Energy = -6.96 kcal/mol USER Electrostatic Energy = -1.79 kcal/mol USER (2) Final Total Internal Energy = -2.71 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.86 kcal/mol USER MODEL 37 USER Run = 37 USER Cluster Rank = 7 USER Number of conformations in this cluster = 3 USER USER RMSD from reference structure = 17.264 A USER USER Estimated Free Energy of Binding = -6.46 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 18.52 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.60 kcal/mol USER vdW + Hbond + desolv Energy = -6.53 kcal/mol USER Electrostatic Energy = -2.07 kcal/mol USER (2) Final Total Internal Energy = -2.83 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.86 kcal/mol USER MODEL 40 USER Run = 40 USER Cluster Rank = 8 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 17.143 A USER USER Estimated Free Energy of Binding = -6.45 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 18.80 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.08 kcal/mol USER vdW + Hbond + desolv Energy = -5.81 kcal/mol USER Electrostatic Energy = -2.27 kcal/mol USER (2) Final Total Internal Energy = -3.34 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.86 kcal/mol USER MODEL 86 USER Run = 86 USER Cluster Rank = 9 USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 17.879 A USER USER Estimated Free Energy of Binding = -6.42 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 19.70 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -8.79 kcal/mol USER vdW + Hbond + desolv Energy = -7.31 kcal/mol USER Electrostatic Energy = -1.48 kcal/mol USER (2) Final Total Internal Energy = -2.60 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.86 kcal/mol USER MODEL 52 USER Run = 52 USER Cluster Rank = 10
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USER Number of conformations in this cluster = 2 USER USER RMSD from reference structure = 19.085 A USER USER Estimated Free Energy of Binding = -6.34 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 22.52 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -7.57 kcal/mol USER vdW + Hbond + desolv Energy = -6.16 kcal/mol USER Electrostatic Energy = -1.41 kcal/mol USER (2) Final Total Internal Energy = -3.74 kcal/mol USER (3) Torsional Free Energy = +4.12 kcal/mol USER (4) Unbound System's Energy = -0.86 kcal/mol
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Lampiran 10. Bagan Kerja Penelitian
Pencarian Data PDB Struktur Tiga Dimensi Enzim
NS3-NS2B Protease Virus Dengue
Visualisasi Letak Sisi Aktif dan Kofaktor
Enzim NS3-NS2B Protease
Analisis Binding Site dan Residu
Substrat Enzim NS3-NS2B Protease
Penentuan Sekuens Asam Amino Peptida sebagai
Inhibitor
Penentuan Nilai Log P Peptida Siklis
Perancangan Struktur Tiga Dimensi Peptida Siklis
Sebagai Ligan
Optimasi Geometri dan Minimisasi Energi
Struktur Tiga Dimensi Peptida Siklis
Optimasi Geometri dan Minimisasi Energi
Struktur Tiga Dimensi Enzim NS3-NS2B
Konformasi Ligan
Terhadap Binding Site
Energi Ikatan dan
Konstanta
Ikatan
Hidrogen
Preparasi File Docking
Contact
Residu
Docking
Analisis Docking
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Lampiran 11. Hubungan antara Nilai RMSD dengan Perbandingan Struktur