in silico tethering 5 (human TS)

Tethering with dimer of human TS (1hvy.pdb, chain A and B)

download 1hvy.pdb
remove chain C and D, remove all HETATM - 1hvy-AB.pdb
load in pymol and addH - 1hvy-AB_addH.pdb
protonation with whatif (whatif.sh 1hvy-AB) - 1hvy-AB_addH.wi.pdb
load 1hvy-AB_addH.wi.pdb in pymol and save again - 1hvy-AB_addH.wi.pdb
(this step is important otherwise GOLD has problems with atom types)
load 1hvy-AB_addH.wi.pdb in pymol and remove side chain of C195 in monomer A - 1hvy-AB-C195G.wi.pdb
center Ca-C195: 2710
radius: 25 A
linking atom of receptor 1hvy-AB-C195G.wi.pdb: 2710
linking atom of ligand CID_445503-cys3D.sdf: 43
start GOLD 3.1.1: gold_di1hvyC195G_wi.conf
WARNING: problems with atom types in mol2 for CME
output: docking_di1hvyC195G_wi_445503.25A.sdf

/home/henricsn/LIGHTS/results/docking3_C195/

GoldScore

gold_analysis.sh -xray1 1f4c_CID_445503-cys3D.pdb -file docking_di1hvyC195G_wi_445503.25A.sdf

# res RMSD Fit iVDW iTOR eVDW iHB eHB covENE ENE iVDWw eVDWw iHBw eHBw covENEw

1 xray 4.055 -62.8230 1.3323 -6.2609 -39.1031 0.0000 0.0000 -4.1278 1.3323 -6.2609 -53.7667 0.0000 0.0000 -4.1278

2 xray 2.604 -63.6710 0.9784 -7.3613 -40.3971 0.0000 0.0000 -1.7421 0.9784 -7.3613 -55.5460 0.0000 0.0000 -1.7421

3 xray 3.601 -63.7446 2.4519 -6.3737 -38.9745 0.0000 0.0634 -6.2961 2.4519 -6.3737 -53.5900 0.0000 0.0634 -6.2961

4 xray 2.677 -64.5006 3.0205 -6.6253 -43.1369 0.0000 0.0000 -1.5825 3.0205 -6.6253 -59.3133 0.0000 0.0000 -1.5825

5 xray 2.770 -64.8253 0.7088 -9.2115 -38.8219 0.0000 0.0000 -2.9425 0.7088 -9.2115 -53.3801 0.0000 0.0000 -2.9425

6 xray 4.703 -64.9171 4.7280 -5.9889 -44.6867 0.0000 0.0000 -2.2121 4.7280 -5.9889 -61.4442 0.0000 0.0000 -2.2121

7 xray 5.971 -65.4486 1.3970 -10.6061 -40.5492 0.0000 0.9765 -1.4610 1.3970 -10.6061 -55.7551 0.0000 0.9765 -1.4610

8 xray 3.613 -66.4313 3.5888 -9.7684 -42.8230 0.0000 0.0000 -1.3701 3.5888 -9.7684 -58.8817 0.0000 0.0000 -1.3701

9 xray 2.840 -66.7561 2.5434 -9.1796 -42.2038 0.0000 0.0000 -2.0897 2.5434 -9.1796 -58.0302 0.0000 0.0000 -2.0897

10 xray 4.394 -67.2942 4.5140 -7.4001 -45.6146 0.0000 0.0000 -1.6880 4.5140 -7.4001 -62.7201 0.0000 0.0000 -1.6880

ChemScore

gold_analysis.sh -xray1 1f4c_CID_445503-cys3D.pdb -file docking_di1hvyC195G_wi_445503.CS25A.sdf

#  res  RMSD   Fit      DG      ZeCo    HB     MET     LIPO   iHB     DEC    DEI     ROT   COVA    HBw     METw   LIPOw   iHBw   DECw   DEIw   ROTw
1 xray 2.970 27.6035 -28.5315 -5.4800 0.9909 0.0000 203.5008 0.0000 -2.5486 2.7656 1.5889 0.7110 -3.3095 -0.0000 -23.8096 0.0000 -2.5486 2.7656 4.0676
2 xray 3.071 27.3111 -25.9856 -5.4800 0.0000 0.0000 210.0268 0.0000 -4.0692 2.5345 1.5889 0.2091 -0.0000 -0.0000 -24.5731 0.0000 -4.0692 2.5345 4.0676
3 xray 2.111 27.1902 -27.3617 -5.4800 0.7800 0.0000 199.5215 0.0000 -4.0543 4.1380 1.5889 0.0879 -2.6052 -0.0000 -23.3440 0.0000 -4.0543 4.1380 4.0676
4 xray 3.384 27.1419 -26.3246 -5.4800 0.9975 0.0000 184.4479 0.0000 -4.5729 3.5722 1.5889 0.1835 -3.3318 -0.0000 -21.5804 0.0000 -4.5729 3.5722 4.0676
5 xray 2.489 26.4371 -25.0277 -5.4800 0.0000 0.0000 201.8401 0.0000 -4.2024 2.6448 1.5889 0.1482 -0.0000 -0.0000 -23.6153 0.0000 -4.2024 2.6448 4.0676
6 xray 2.446 26.3775 -28.2369 -5.4800 0.9121 0.0000 203.2328 0.0000 -1.8107 2.9759 1.5889 0.6941 -3.0463 -0.0000 -23.7782 0.0000 -1.8107 2.9759 4.0676
7 xray 2.870 26.3377 -24.2788 -5.4800 0.0000 0.0000 195.4388 0.0000 -5.1053 2.9634 1.5889 0.0829 -0.0000 -0.0000 -22.8663 0.0000 -5.1053 2.9634 4.0676
8 xray 3.440 26.0938 -27.0845 -5.4800 0.8465 0.0000 195.2542 0.0000 -4.1761 4.7190 1.5889 0.4478 -2.8273 -0.0000 -22.8447 0.0000 -4.1761 4.7190 4.0676
9 xray 2.678 25.9856 -26.5399 -5.4800 0.5860 0.0000 198.0370 0.0000 -3.4596 3.8882 1.5889 0.1257 -1.9572 -0.0000 -23.1703 0.0000 -3.4596 3.8882 4.0676
10 xray 2.624 24.1333 -23.7122 -5.4800 0.1138 0.0000 187.3470 0.0000 -4.9108 4.4308 1.5889 0.0589 -0.3802 -0.0000 -21.9196 0.0000 -4.9108 4.4308 4.0676

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