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 (-0.420 kcal/mol/HA)
✓ Good fit quality (FQ -3.92)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (25.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-11.344
kcal/mol
LE
-0.420
kcal/mol/HA
Fit Quality
-3.92
FQ (Leeson)
HAC
27
heavy atoms
MW
389
Da
LogP
1.65
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 25.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 21
π–π 1
Clashes 19
Severe clashes 5
| Final rank | 13.20656383768732 | Score | -11.3443 |
|---|---|---|---|
| Inter norm | -0.780294 | Intra norm | 0.360135 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 6 clashes; 5 protein clashes; high strain Δ 31.8 | ||
| Residues | A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:PRO93;A:SER44;A:SER86;A:VAL87 | ||
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1369 | 4.2067414667746466 | -0.981867 | -22.6681 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1819 | 4.7572323917008195 | -0.744168 | -24.2371 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 2437 | 5.147898269033301 | -1.06094 | -32.6346 | 3 | 14 | 13 | 0.65 | 0.40 | - | no | Open |
| 979 | 5.73744667772116 | -1.13132 | -30.8731 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1825 | 6.130601681038156 | -0.61434 | -21.0053 | 7 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 1823 | 5.035408152499395 | -0.678869 | -19.9772 | 5 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1822 | 5.5745355184588465 | -0.739879 | -17.8444 | 8 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1816 | 5.673900758652186 | -0.850416 | -19.456 | 12 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2442 | 6.0486424804734735 | -0.794932 | -19.5034 | 4 | 14 | 12 | 0.60 | 0.00 | - | yes | Open |
| 2436 | 6.127180061691416 | -0.940266 | -24.6331 | 3 | 16 | 14 | 0.70 | 0.00 | - | yes | Open |
| 2434 | 6.130982708603371 | -0.829458 | -17.1175 | 4 | 15 | 13 | 0.65 | 0.00 | - | yes | Open |
| 1820 | 6.173831864554822 | -0.657543 | -13.7134 | 8 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 983 | 6.319641516149942 | -0.996616 | -25.4921 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2443 | 6.464614519025771 | -0.969669 | -32.2107 | 8 | 12 | 11 | 0.55 | 0.40 | - | yes | Open |
| 1817 | 6.549370517071881 | -0.789605 | -19.8353 | 8 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1824 | 6.699420394745864 | -0.514093 | -17.8951 | 4 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1818 | 6.783012465613875 | -0.649106 | -21.28 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1376 | 7.113811811465945 | -0.959319 | -23.7154 | 10 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1372 | 7.211360022403535 | -0.89247 | -24.2441 | 8 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1368 | 7.3063578494846135 | -0.979595 | -20.8298 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1821 | 7.420027589188007 | -0.594101 | -14.529 | 6 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2435 | 7.433017776140588 | -0.987052 | -20.1565 | 5 | 17 | 16 | 0.80 | 0.60 | - | yes | Open |
| 1377 | 7.682433258561182 | -0.97278 | -26.5689 | 12 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 981 | 7.76045287915965 | -0.901826 | -23.0267 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1370 | 7.7814666906879495 | -0.986431 | -27.245 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1371 | 8.762274222805406 | -0.955723 | -25.8073 | 11 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1375 | 9.068434884376416 | -1.01379 | -23.0943 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2439 | 9.143238928302978 | -0.917732 | -24.6649 | 6 | 12 | 9 | 0.45 | 0.20 | - | yes | Open |
| 2441 | 9.68307304315479 | -0.956771 | -26.8399 | 5 | 16 | 14 | 0.70 | 0.40 | - | yes | Open |
| 2438 | 9.901200860898207 | -0.809611 | -19.3279 | 3 | 13 | 9 | 0.45 | 0.20 | - | yes | Open |
| 985 | 10.020070098757985 | -1.18816 | -36.955 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 977 | 11.177438893279382 | -1.28056 | -31.9367 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 984 | 11.19428606701474 | -1.02116 | -31.9133 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1373 | 11.403952809413063 | -1.03551 | -21.5961 | 9 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1374 | 11.46718422832834 | -0.827428 | -17.3766 | 11 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 980 | 12.965540698242858 | -1.15396 | -25.8128 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2440 | 13.20656383768732 | -0.780294 | -11.3443 | 3 | 14 | 11 | 0.55 | 0.20 | - | yes | Current |
| 976 | 14.05385730983681 | -1.27503 | -27.6545 | 6 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 978 | 15.182778967909266 | -1.0563 | -29.3728 | 9 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 982 | 15.325270646122474 | -0.955161 | -20.4247 | 6 | 19 | 0 | 0.00 | 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
-11.344kcal/mol
Ligand efficiency (LE)
-0.4202kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.920
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
389.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.65
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
21.43kcal/mol
Minimised FF energy
-3.99kcal/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.