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 (-0.584 kcal/mol/HA)
✓ Good fit quality (FQ -5.98)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (40.9 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-21.611
kcal/mol
LE
-0.584
kcal/mol/HA
Fit Quality
-5.98
FQ (Leeson)
HAC
37
heavy atoms
MW
505
Da
LogP
2.13
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 40.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 1
Clashes 11
Severe clashes 1
| Final rank | 57.69257254357571 | Score | -21.6112 |
|---|---|---|---|
| Inter norm | -0.680225 | Intra norm | 0.0961376 |
| Top1000 | no | Excluded | yes |
| Contacts | 20 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 18 clashes; 1 protein clash | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:SER44;A:THR180;A:THR83;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49;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 | 16 | Native recall | 0.80 |
| Jaccard | 0.67 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.43 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 989 | 5.261315824560532 | -0.603714 | -16.1038 | 1 | 17 | 17 | 0.85 | 0.20 | - | no | Open |
| 986 | 5.770786952505254 | -0.684306 | -25.006 | 2 | 17 | 13 | 0.65 | 0.20 | - | no | Open |
| 982 | 6.831590296114315 | -0.631332 | -18.448 | 4 | 18 | 16 | 0.80 | 0.60 | - | no | Open |
| 999 | 8.21488777819133 | -0.691017 | -24.8564 | 2 | 20 | 14 | 0.70 | 0.20 | - | no | Open |
| 991 | 56.21558111624506 | -0.581631 | -21.5097 | 1 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 983 | 56.846023674689064 | -0.638341 | -15.8179 | 5 | 19 | 15 | 0.75 | 0.20 | - | no | Open |
| 985 | 56.90596655947617 | -0.616499 | -22.3388 | 1 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 992 | 57.12859200363561 | -0.667155 | -17.3578 | 2 | 17 | 14 | 0.70 | 0.20 | - | no | Open |
| 984 | 57.270324363866195 | -0.650453 | -21.9053 | 1 | 18 | 15 | 0.75 | 0.00 | - | no | Open |
| 1003 | 6.600791438983622 | -0.600972 | -24.8567 | 1 | 18 | 13 | 0.65 | 0.20 | - | yes | Open |
| 998 | 6.9864891900382 | -0.591297 | -19.3211 | 4 | 20 | 17 | 0.85 | 0.40 | - | yes | Open |
| 1004 | 56.51092702391629 | -0.655942 | -12.1454 | 2 | 14 | 14 | 0.70 | 0.20 | - | yes | Open |
| 997 | 57.303856470185664 | -0.62455 | -14.3072 | 4 | 18 | 17 | 0.85 | 0.60 | - | yes | Open |
| 993 | 57.37627785960962 | -0.636806 | -17.6957 | 0 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 987 | 57.53904655944858 | -0.633541 | -17.3119 | 1 | 13 | 10 | 0.50 | 0.00 | - | yes | Open |
| 990 | 57.69257254357571 | -0.680225 | -21.6112 | 3 | 20 | 16 | 0.80 | 0.40 | - | yes | Current |
| 996 | 57.96121863548281 | -0.642077 | -23.7322 | 2 | 14 | 13 | 0.65 | 0.20 | - | yes | Open |
| 994 | 58.22001385851653 | -0.678188 | -12.7809 | 1 | 21 | 17 | 0.85 | 0.20 | - | yes | Open |
| 981 | 59.37981478411859 | -0.677603 | -16.5586 | 2 | 19 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1001 | 59.40316350507955 | -0.636404 | -18.9482 | 1 | 20 | 16 | 0.80 | 0.20 | - | yes | Open |
| 988 | 59.95131573285785 | -0.613441 | -16.5014 | 1 | 21 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1000 | 60.513634966021684 | -0.684577 | -24.4245 | 2 | 18 | 12 | 0.60 | 0.20 | - | yes | Open |
| 995 | 62.1130761271655 | -0.642347 | -15.1306 | 1 | 20 | 17 | 0.85 | 0.20 | - | yes | Open |
| 1002 | 62.79162620982332 | -0.748739 | -22.3876 | 1 | 20 | 16 | 0.80 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.611kcal/mol
Ligand efficiency (LE)
-0.5841kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.980
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
504.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.13
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
145.01kcal/mol
Minimised FF energy
104.07kcal/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.