Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
py3Dmol interaction viewer
Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.146 kcal/mol/HA)
✓ Good fit quality (FQ -10.56)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (22.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-29.793
kcal/mol
LE
-1.146
kcal/mol/HA
Fit Quality
-10.56
FQ (Leeson)
HAC
26
heavy atoms
MW
435
Da
LogP
1.98
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 22.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 2
Clashes 8
Severe clashes 0
| Final rank | 4.7378066503832645 | Score | -29.7929 |
|---|---|---|---|
| Inter norm | -1.02205 | Intra norm | -0.123829 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 5 |
| Artifact reason | geometry warning; 10 clashes; 8 protein contact clashes; high strain Δ 28.6 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:TRP47;A:TYR162;A:VAL30;A:VAL31;A:VAL49 | ||
Protein summary
225 residues
| Protein target | T03 | Atoms | 3428 |
|---|---|---|---|
| Residues | 225 | Chains | 2 |
| Residue summary | LEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 20 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 9 |
| IFP residues | A:ALA32; A:ARG97; A:ASP52; A:ILE45; A:LEU94; A:LYS57; A:MET53; A:NDP301; A:PHE56; A:PHE91; A:PRO88; A:SER86; A:THR180; A:THR54; A:THR83; A:TYR162; A:VAL156; A:VAL30; A:VAL31; A:VAL87 | ||
| Current overlap | 11 | Native recall | 0.55 |
| Jaccard | 0.48 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.14 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
Hydrogen bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
Hydrophobic contacts
Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | Contacts | Native overlap | Native recall | HB role recall | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1799 | 2.5922308644237972 | -0.780292 | -22.9845 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 1816 | 2.603480252575096 | -0.611382 | -19.2858 | 4 | 7 | 0 | 0.00 | 0.00 | - | no | Open |
| 1504 | 2.6483393734638616 | -0.758669 | -18.8477 | 4 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 1795 | 2.8350199019054796 | -0.698548 | -18.7249 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 2475 | 2.8661637288361153 | -0.806505 | -25.0379 | 4 | 14 | 11 | 0.55 | 0.20 | - | no | Open |
| 1819 | 3.0340660301047606 | -0.697383 | -18.3322 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 1811 | 3.1460435951815557 | -0.545522 | -18.3066 | 3 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 1806 | 3.16035949801967 | -0.755747 | -20.6176 | 2 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 1814 | 3.163003562266033 | -0.679727 | -19.8031 | 4 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 1800 | 3.1962539644626737 | -0.8999 | -20.3371 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 1798 | 3.2776509231744653 | -0.849533 | -18.3222 | 5 | 7 | 0 | 0.00 | 0.00 | - | no | Open |
| 1820 | 3.571482587469795 | -0.734911 | -20.2249 | 4 | 7 | 0 | 0.00 | 0.00 | - | no | Open |
| 2481 | 3.6289010323440296 | -0.978195 | -25.5632 | 5 | 17 | 14 | 0.70 | 0.40 | - | no | Open |
| 1793 | 3.7415228207725946 | -0.720579 | -19.0601 | 6 | 7 | 0 | 0.00 | 0.00 | - | no | Open |
| 1810 | 3.8625868901999505 | -0.664312 | -19.4435 | 1 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 2466 | 3.924381890382917 | -0.859117 | -24.8272 | 2 | 14 | 13 | 0.65 | 0.20 | - | no | Open |
| 1496 | 3.946963605441815 | -0.779582 | -23.0111 | 0 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 1817 | 3.990603366604166 | -0.536827 | -12.7992 | 3 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 1342 | 4.081924481810327 | -0.83554 | -24.9778 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1805 | 4.1488996958990505 | -0.6834 | -18.5561 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1796 | 4.246571254077585 | -0.616735 | -17.0657 | 4 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 1803 | 4.273935458433773 | -0.699993 | -19.3964 | 3 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 1493 | 4.3528929329029085 | -0.664404 | -19.4056 | 2 | 14 | 1 | 0.05 | 0.00 | - | no | Open |
| 1815 | 4.356773776409487 | -0.512668 | -15.826 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1501 | 4.445314450310059 | -0.803064 | -20.6884 | 4 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 1790 | 4.555044669390025 | -0.666275 | -16.3589 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2472 | 4.701909556172778 | -0.912968 | -23.2195 | 5 | 17 | 13 | 0.65 | 0.20 | - | no | Open |
| 2483 | 4.7378066503832645 | -1.02205 | -29.7929 | 5 | 14 | 11 | 0.55 | 0.20 | - | no | Current |
| 2471 | 4.751750324838275 | -0.987555 | -28.6064 | 5 | 15 | 12 | 0.60 | 0.20 | - | no | Open |
| 2480 | 4.78053552197285 | -1.0247 | -24.3277 | 4 | 18 | 14 | 0.70 | 0.20 | - | no | Open |
| 2492 | 4.909566269653639 | -0.832421 | -20.3789 | 3 | 19 | 14 | 0.70 | 0.00 | - | no | Open |
| 2467 | 5.064017580738717 | -0.972904 | -24.3858 | 6 | 15 | 12 | 0.60 | 0.20 | - | no | Open |
| 1338 | 5.210504805240016 | -0.933631 | -24.891 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1346 | 5.338345235534365 | -1.03607 | -26.2983 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1812 | 5.5146272730461146 | -0.695639 | -19.7846 | 2 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 2479 | 6.24447274950162 | -0.922665 | -23.4314 | 5 | 14 | 11 | 0.55 | 0.20 | - | no | Open |
| 1794 | 53.18574462420246 | -0.806497 | -20.4234 | 4 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 1818 | 53.78060051861665 | -0.737239 | -12.4573 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2469 | 4.44130209848666 | -1.00431 | -28.0684 | 4 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2461 | 4.4826985288649555 | -0.944363 | -27.7116 | 4 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2468 | 4.797664700838881 | -0.879296 | -20.0855 | 5 | 15 | 12 | 0.60 | 0.00 | - | yes | Open |
| 1792 | 4.811171135268033 | -0.727264 | -22.1661 | 6 | 7 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1508 | 4.882120030453603 | -0.764392 | -15.7073 | 1 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1807 | 4.940047084519802 | -0.786585 | -21.0078 | 5 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2488 | 5.062188914900319 | -0.788068 | -19.9622 | 3 | 10 | 8 | 0.40 | 0.00 | - | yes | Open |
| 1494 | 5.283624847863544 | -1.07403 | -23.8557 | 3 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2473 | 5.324949288170533 | -0.96362 | -26.3553 | 4 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 1801 | 5.5297323466956225 | -0.700435 | -18.5597 | 3 | 7 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1482 | 5.565846865444336 | -1.08744 | -22.1946 | 5 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2491 | 6.058085661276846 | -0.869864 | -20.2598 | 4 | 13 | 12 | 0.60 | 0.20 | - | yes | Open |
| 1502 | 6.205885145849993 | -0.915362 | -14.8742 | 6 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1347 | 6.58322924330106 | -0.923045 | -17.4466 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2485 | 6.601722680693203 | -0.880582 | -23.4226 | 5 | 17 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1497 | 6.633352342053141 | -0.676911 | -19.8529 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2463 | 6.817674106399091 | -0.996398 | -24.3072 | 4 | 18 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1789 | 6.831248656765576 | -0.720647 | -18.8088 | 5 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1802 | 6.9132818198381765 | -0.675585 | -18.0802 | 2 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1490 | 7.13494367338626 | -1.02767 | -20.32 | 3 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1343 | 7.486706936115624 | -0.726098 | -22.3695 | 4 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1503 | 7.609254927596773 | -0.996267 | -25.5418 | 7 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1332 | 7.781370410541099 | -0.847049 | -20.7487 | 9 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1498 | 7.982440003327003 | -1.03708 | -24.1721 | 6 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1486 | 7.987265392929135 | -0.976887 | -19.6265 | 6 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1483 | 8.100976179447699 | -1.07442 | -26.5663 | 6 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1340 | 8.173434879952797 | -0.936691 | -23.9344 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1336 | 8.196218651936402 | -0.934806 | -27.691 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1491 | 8.228599107240216 | -1.06972 | -23.9399 | 5 | 20 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1334 | 8.28166205358735 | -1.11199 | -30.3653 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1489 | 8.383609270420267 | -0.750618 | -15.0353 | 4 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2478 | 8.403481544582682 | -0.908551 | -24.7629 | 6 | 18 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1510 | 8.509339805941794 | -1.00656 | -23.9884 | 8 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1506 | 8.73053024780878 | -0.982141 | -21.4866 | 6 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1339 | 9.202666425246257 | -0.73328 | -19.4444 | 5 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1344 | 9.216968788039097 | -0.761925 | -21.9149 | 10 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2487 | 9.286231530947587 | -0.954846 | -20.7454 | 4 | 11 | 10 | 0.50 | 0.20 | - | yes | Open |
| 2482 | 9.494787093542133 | -0.971915 | -23.0482 | 11 | 18 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1335 | 9.791915563468207 | -0.804006 | -22.0302 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1487 | 10.41091507614661 | -0.875762 | -19.6683 | 6 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2489 | 10.428291606528598 | -0.909505 | -16.1709 | 7 | 19 | 15 | 0.75 | 0.20 | - | yes | Open |
| 1500 | 10.454444076834635 | -0.968006 | -28.5188 | 4 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2476 | 10.578899336231943 | -0.81397 | -23.0646 | 5 | 10 | 9 | 0.45 | 0.20 | - | yes | Open |
| 1511 | 10.788139927352976 | -1.0594 | -28.5273 | 8 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1507 | 11.065406695465818 | -0.911728 | -18.213 | 6 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1485 | 11.098504588030917 | -0.735946 | -16.549 | 6 | 16 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1512 | 11.344997653195643 | -0.8579 | -17.0523 | 8 | 16 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2464 | 11.405663300468095 | -0.924867 | -20.8256 | 4 | 15 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1808 | 54.14083690107001 | -0.593083 | -17.6242 | 2 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1809 | 54.34863999048116 | -0.621934 | -19.9569 | 4 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1813 | 54.851575529517376 | -0.602433 | -14.8955 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1804 | 55.08157935022692 | -0.727933 | -20.0261 | 2 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1797 | 55.127849451594706 | -0.649909 | -19.1037 | 3 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2465 | 57.299787850902376 | -0.937112 | -21.0199 | 5 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2470 | 57.443717474471796 | -0.905282 | -19.7712 | 5 | 19 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2477 | 57.71029294998781 | -0.951973 | -17.8604 | 8 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 1337 | 57.9713398701685 | -0.952743 | -23.9014 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1791 | 58.03474584239798 | -0.666819 | -18.5553 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2484 | 58.06528728283529 | -0.873263 | -20.2556 | 4 | 14 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1492 | 58.29299645957875 | -0.865155 | -22.7147 | 4 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2486 | 59.02718145276851 | -0.711269 | -22.3498 | 7 | 18 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1341 | 59.06954163610186 | -0.924507 | -25.5914 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1505 | 59.32190856191966 | -0.752564 | -18.2694 | 4 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2474 | 59.405832096633326 | -0.851504 | -25.0991 | 7 | 20 | 15 | 0.75 | 0.20 | - | yes | Open |
| 1484 | 59.41865104266738 | -0.744262 | -19.6379 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1495 | 59.425251703250986 | -1.0439 | -28.188 | 8 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2490 | 59.57817497883951 | -0.817728 | -15.9528 | 4 | 9 | 7 | 0.35 | 0.00 | - | yes | Open |
| 2462 | 59.585670220165824 | -1.05369 | -22.2147 | 10 | 19 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1345 | 59.89869278745364 | -0.748086 | -9.06658 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1333 | 59.960702695526685 | -0.91337 | -24.6166 | 10 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1509 | 60.15688172678176 | -0.690121 | -14.3676 | 6 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1488 | 60.695398256170876 | -0.814783 | -19.0018 | 4 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1499 | 62.0321075300868 | -0.917723 | -23.6025 | 8 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1513 | 65.26262817334413 | -0.811581 | -13.6192 | 5 | 15 | 1 | 0.05 | 0.00 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.793kcal/mol
Ligand efficiency (LE)
-1.1459kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.557
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
435.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.98
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
112.11kcal/mol
Minimised FF energy
89.72kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate FreeSASA burial metrics without blocking the page.