docking 6
(E. coli TS)
Docking of N-tosyl-D-proline to dimer of E. coli TS (1f4e.pdb, chain A and B)
- download 1f4e.pdb
- superimpose to 1hvy-AB_addH.wi.pdb
(sup2pdbs_sh
1hvy-AB_addH.wi.pdb 1f4e.pdb)
- 1f4e.pdbf
- load in pymol, correct bonds of ligand and addH - 1f4e_addH.wat.pdb
- protonation with whatif using water from X-ray structure (whatif.sh
1f4d_addh.wat) - 1f4e_addh.wat.wi.pdb
- remove water molecules but keeping sulfate - 1f4e_addh.wi.pdb
- load 1f4e_addh.wi.pdb in
pymol and save again
(this step is important otherwise GOLD has problems with
atom types)
- remove ligand, water and other small molecules -1f4e_addh.wi.pdb
- remove alternative conformation
of A of monomer A-GLN3
- center Ca-C146: 2355
(center 1hvy-Ca-C195: 3.002
2.973 11.352)
radius: 25 A
- start GOLD 3.1.1: gold_di1f4e_wi.conf
ligand: CID_445504-3D.sdf
- WARNING: problems with atom types in mol2
output: docking_di1f4e_wi_445504.25A.sdf
/home/henricsn/LIGHTS/results/docking3_C195/
GoldScore
gold_analysis.sh -xray1
1f4e_CID_445504-3D.pdb -file docking_di1f4e_wi_445504.25A.sdf
# res RMSD Fit iVDW iTOR eVDW iHB eHB covENE ENE iVDWw eVDWw iHBw eHBw covENEw
1 xray 1.483 46.6648 2.6326 -4.8347 28.3616 0.0000 9.8696 undef 2.6326 -4.8347 38.9972 0.0000 9.8696 undef
2 xray 1.502 46.5123 2.6514 -4.7948 28.6128 0.0000 9.3131 undef 2.6514 -4.7948 39.3426 0.0000 9.3131 undef
3 xray 1.468 45.5695 2.6542 -4.8344 27.9637 0.0000 9.2996 undef 2.6542 -4.8344 38.4501 0.0000 9.2996 undef
4 xray 1.506 45.2134 2.8279 -4.8302 27.3241 0.0000 9.6451 undef 2.8279 -4.8302 37.5707 0.0000 9.6451 undef
5 xray 6.030 44.4643 2.4124 -4.7978 26.0316 0.0000 11.0562 undef 2.4124 -4.7978 35.7935 0.0000 11.0562 undef
6 xray 6.054 44.2814 2.5478 -4.8317 26.2904 0.0000 10.4160 undef 2.5478 -4.8317 36.1493 0.0000 10.4160 undef
7 xray 6.130 44.0659 2.6558 -4.8021 26.5550 0.0000 9.6991 undef 2.6558 -4.8021 36.5131 0.0000 9.6991 undef
8 xray 6.060 44.0423 2.4690 -4.8299 26.3888 0.0000 10.1185 undef 2.4690 -4.8299 36.2846 0.0000 10.1185 undef
9 xray 6.024 44.0353 2.3374 -4.8283 26.2160 0.0000 10.4792 undef 2.3374 -4.8283 36.0470 0.0000 10.4792 undef
10 xray 5.990 43.9086 2.7175 -4.8304 25.7281 0.0000 10.6455 undef 2.7175 -4.8304 35.3761 0.0000 10.6455 undef
11 xray 6.105 43.8184 2.6842 -4.8260 25.8987 0.0000 10.3495 undef 2.6842 -4.8260 35.6107 0.0000 10.3495 undef
12 xray 1.504 43.7939 2.8730 -4.8097 26.4562 0.0000 9.3533 undef 2.8730 -4.8097 36.3773 0.0000 9.3533 undef
13 xray 6.094 43.7545 2.7975 -4.7967 25.8212 0.0000 10.2496 undef 2.7975 -4.7967 35.5041 0.0000 10.2496 undef
14 xray 6.153 43.4666 2.5757 -4.8302 26.2244 0.0000 9.6625 undef 2.5757 -4.8302 36.0586 0.0000 9.6625 undef
15 xray 6.031 43.4659 3.0568 -4.7948 27.8582 0.0000 6.8989 undef 3.0568 -4.7948 38.3050 0.0000 6.8989 undef
16 xray 6.098 43.3422 2.5300 -4.8305 26.3108 0.0000 9.4654 undef 2.5300 -4.8305 36.1773 0.0000 9.4654 undef
17 xray 6.092 43.2771 2.8606 -4.8316 25.8012 0.0000 9.7713 undef 2.8606 -4.8316 35.4767 0.0000 9.7713 undef
18 xray 6.041 43.2058 2.5013 -4.7974 25.6127 0.0000 10.2844 undef 2.5013 -4.7974 35.2175 0.0000 10.2844 undef
19 xray 6.088 43.1447 2.6266 -4.8302 25.3193 0.0000 10.5343 undef 2.6266 -4.8302 34.8140 0.0000 10.5343 undef
20 xray 1.413 43.1333 2.4999 -4.8345 27.6085 0.0000 7.5061 undef 2.4999 -4.8345 37.9617 0.0000 7.5061 undef
21 xray 6.092 43.0749 2.9560 -4.8292 25.7746 0.0000 9.5080 undef 2.9560 -4.8292 35.4400 0.0000 9.5080 undef
22 xray 6.107 42.8901 2.7225 -4.8283 27.3377 0.0000 7.4065 undef 2.7225 -4.8283 37.5894 0.0000 7.4065 undef
23 xray 6.056 42.8538 2.4875 -4.8286 25.9247 0.0000 9.5484 undef 2.4875 -4.8286 35.6465 0.0000 9.5484 undef
24 xray 6.012 42.8449 2.6317 -4.7975 27.1963 0.0000 7.6158 undef 2.6317 -4.7975 37.3949 0.0000 7.6158 undef
25 xray 5.981 42.8394 2.8197 -4.7999 26.9681 0.0000 7.7385 undef 2.8197 -4.7999 37.0812 0.0000 7.7385 undef
26 xray 1.813 42.6692 2.8119 -4.8253 26.6283 0.0000 8.0687 undef 2.8119 -4.8253 36.6139 0.0000 8.0687 undef
27 xray 6.114 42.6354 3.0550 -4.8363 25.9650 0.0000 8.7148 undef 3.0550 -4.8363 35.7018 0.0000 8.7148 undef
28 xray 6.017 42.4143 2.8505 -4.8335 26.4119 0.0000 8.0809 undef 2.8505 -4.8335 36.3163 0.0000 8.0809 undef
29 xray 6.067 42.3038 2.1482 -4.8281 27.1301 0.0000 7.6798 undef 2.1482 -4.8281 37.3039 0.0000 7.6798 undef
30 xray 6.064 40.9993 2.7151 -4.7935 25.4134 0.0000 8.1342 undef 2.7151 -4.7935 34.9435 0.0000 8.1342 undef
ChemScore
gold_analysis.sh -xray1 1f4e_CID_445504-3D.pdb -file docking_di1f4e_wi_445504.CS25A.sdf
# res RMSD Fit DG ZeCo HB MET LIPO iHB DEC DEI ROT COVA HBw METw LIPOw iHBw DECw DEIw ROTw
1 xray 1.555 23.8391 -26.1833 -5.4800 2.5416 0.0000 126.2763 0.0000 0.0299 2.3144 1.0000 undef -8.4890 -0.0000 -14.7743 0.0000 0.0299 2.3144 2.5600
2 xray 1.253 23.8346 -26.5241 -5.4800 2.3656 0.0000 134.2125 0.0000 0.1752 2.5143 1.0000 undef -7.9012 -0.0000 -15.7029 0.0000 0.1752 2.5143 2.5600
3 xray 1.360 23.7303 -26.3598 -5.4800 2.2955 0.0000 134.8113 0.0000 0.0607 2.5688 1.0000 undef -7.6669 -0.0000 -15.7729 0.0000 0.0607 2.5688 2.5600
4 xray 1.703 23.7221 -26.5361 -5.4800 2.6230 0.0000 126.9684 0.0000 0.5871 2.2270 1.0000 undef -8.7608 -0.0000 -14.8553 0.0000 0.5871 2.2270 2.5600
5 xray 1.481 23.6889 -26.0893 -5.4800 2.4603 0.0000 127.7945 0.0000 0.0314 2.3690 1.0000 undef -8.2173 -0.0000 -14.9520 0.0000 0.0314 2.3690 2.5600
6 xray 1.209 23.5504 -26.2047 -5.4800 2.3339 0.0000 132.3885 0.0000 0.2927 2.3617 1.0000 undef -7.7953 -0.0000 -15.4895 0.0000 0.2927 2.3617 2.5600
7 xray 1.229 23.5180 -26.2463 -5.4800 2.2645 0.0000 134.7244 0.0000 0.2752 2.4531 1.0000 undef -7.5636 -0.0000 -15.7628 0.0000 0.2752 2.4531 2.5600
8 xray 1.326 23.4895 -26.1972 -5.4800 2.2882 0.0000 133.6306 0.0000 0.0299 2.6778 1.0000 undef -7.6424 -0.0000 -15.6348 0.0000 0.0299 2.6778 2.5600
9 xray 1.575 23.4750 -26.2926 -5.4800 2.4847 0.0000 128.8349 0.0000 0.3230 2.4946 1.0000 undef -8.2990 -0.0000 -15.0737 0.0000 0.3230 2.4946 2.5600
10 xray 1.228 23.4650 -26.1828 -5.4800 2.2593 0.0000 134.3320 0.0000 0.4286 2.2891 1.0000 undef -7.5459 -0.0000 -15.7168 0.0000 0.4286 2.2891 2.5600
11 xray 1.249 23.4091 -26.4963 -5.4800 2.2488 0.0000 137.3097 0.0000 0.5570 2.5301 1.0000 undef -7.5110 -0.0000 -16.0652 0.0000 0.5570 2.5301 2.5600
12 xray 1.302 23.3949 -25.8037 -5.4800 2.1141 0.0000 135.2357 0.0000 0.0852 2.3236 1.0000 undef -7.0612 -0.0000 -15.8226 0.0000 0.0852 2.3236 2.5600
13 xray 1.227 23.3783 -26.0745 -5.4800 2.1599 0.0000 136.2424 0.0000 0.0149 2.6813 1.0000 undef -7.2141 -0.0000 -15.9404 0.0000 0.0149 2.6813 2.5600
14 xray 1.435 23.3160 -25.8437 -5.4800 2.4079 0.0000 127.1902 0.0000 0.1502 2.3774 1.0000 undef -8.0424 -0.0000 -14.8813 0.0000 0.1502 2.3774 2.5600
15 xray 1.231 23.2437 -26.0960 -5.4800 2.2215 0.0000 134.6695 0.0000 0.2551 2.5972 1.0000 undef -7.4197 -0.0000 -15.7563 0.0000 0.2551 2.5972 2.5600
16 xray 1.259 23.0912 -25.7086 -5.4800 2.0882 0.0000 135.1617 0.0000 0.1493 2.4680 1.0000 undef -6.9746 -0.0000 -15.8139 0.0000 0.1493 2.4680 2.5600
17 xray 1.571 23.0906 -25.7695 -5.4800 2.3878 0.0000 127.1304 0.0000 0.0162 2.6626 1.0000 undef -7.9752 -0.0000 -14.8743 0.0000 0.0162 2.6626 2.5600
18 xray 1.421 23.0427 -25.9430 -5.4800 2.2678 0.0000 132.0391 0.0000 0.0324 2.8678 1.0000 undef -7.5744 -0.0000 -15.4486 0.0000 0.0324 2.8678 2.5600
19 xray 1.096 22.9913 -25.5926 -5.4800 1.9239 0.0000 138.8614 0.0000 0.1103 2.4910 1.0000 undef -6.4258 -0.0000 -16.2468 0.0000 0.1103 2.4910 2.5600
20 xray 1.493 22.9809 -25.6706 -5.4800 2.4162 0.0000 125.4741 0.0000 0.0285 2.6613 1.0000 undef -8.0701 -0.0000 -14.6805 0.0000 0.0285 2.6613 2.5600
21 xray 1.066 22.9357 -25.2608 -5.4800 2.1464 0.0000 129.6733 0.0000 0.0665 2.2587 1.0000 undef -7.1691 -0.0000 -15.1718 0.0000 0.0665 2.2587 2.5600
22 xray 1.115 22.8450 -25.3484 -5.4800 1.8388 0.0000 139.2024 0.0000 0.0618 2.4416 1.0000 undef -6.1417 -0.0000 -16.2867 0.0000 0.0618 2.4416 2.5600
23 xray 1.126 22.8183 -25.4256 -5.4800 2.0901 0.0000 132.6899 0.0000 0.0885 2.5189 1.0000 undef -6.9809 -0.0000 -15.5247 0.0000 0.0885 2.5189 2.5600
24 xray 1.108 22.7831 -25.6177 -5.4800 1.9195 0.0000 139.2032 0.0000 0.5347 2.3000 1.0000 undef -6.4110 -0.0000 -16.2868 0.0000 0.5347 2.3000 2.5600
25 xray 1.514 22.7200 -25.4137 -5.4800 2.1843 0.0000 129.8977 0.0000 0.0388 2.6549 1.0000 undef -7.2956 -0.0000 -15.1980 0.0000 0.0388 2.6549 2.5600
26 xray 0.968 22.3420 -24.9975 -5.4800 2.0339 0.0000 130.6339 0.0000 0.3029 2.3526 1.0000 undef -6.7933 -0.0000 -15.2842 0.0000 0.3029 2.3526 2.5600
27 xray 1.124 22.3079 -24.9635 -5.4800 2.0861 0.0000 128.8554 0.0000 0.0885 2.5672 1.0000 undef -6.9675 -0.0000 -15.0761 0.0000 0.0885 2.5672 2.5600
28 xray 1.262 22.1208 -26.5586 -5.4800 2.5258 0.0000 129.9344 0.0000 0.8524 3.5854 1.0000 undef -8.4362 -0.0000 -15.2023 0.0000 0.8524 3.5854 2.5600
29 xray 1.933 22.0860 -26.2746 -5.4800 2.3703 0.0000 131.9481 0.0000 2.1162 2.0725 1.0000 undef -7.9167 -0.0000 -15.4379 0.0000 2.1162 2.0725 2.5600
30 xray 1.997 22.0190 -25.8988 -5.4800 2.4079 0.0000 127.6629 0.0000 1.7797 2.1001 1.0000 undef -8.0422 -0.0000 -14.9366 0.0000 1.7797 2.1001 2.5600
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