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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.631 kcal/mol/HA)
✓ Good fit quality (FQ -6.15)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (20.7 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-19.567
kcal/mol
LE
-0.631
kcal/mol/HA
Fit Quality
-6.15
FQ (Leeson)
HAC
31
heavy atoms
MW
418
Da
LogP
4.87
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 20.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 2
Clashes 8
Severe clashes 2
| Final rank | 7.3055911202914725 | Score | -19.567 |
|---|---|---|---|
| Inter norm | -0.766235 | Intra norm | 0.135042 |
| Top1000 | no | Excluded | yes |
| Contacts | 15 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 11 clashes; 2 protein clashes; high strain Δ 20.4 | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:TRP47;A:VAL30;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 | 0.46 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.29 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2318 | 3.7498126433897983 | -0.445906 | -14.0398 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2314 | 4.903602217539733 | -0.471288 | -13.819 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2926 | 5.050290277552064 | -0.780424 | -23.428 | 2 | 16 | 15 | 0.75 | 0.20 | - | no | Open |
| 1927 | 5.812364335987131 | -0.814342 | -18.5892 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2928 | 6.0087334834110955 | -0.872379 | -26.2939 | 3 | 15 | 14 | 0.70 | 0.20 | - | no | Open |
| 3530 | 6.242144360334889 | -0.611806 | -11.6939 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2927 | 7.135802005149123 | -0.767871 | -20.0067 | 3 | 12 | 8 | 0.40 | 0.20 | - | no | Open |
| 2924 | 6.680144113084564 | -0.812473 | -17.0124 | 3 | 17 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2315 | 6.739646464992269 | -0.654749 | -14.765 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2317 | 6.7424712747569515 | -0.623508 | -21.481 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1929 | 6.8877552827131145 | -0.878421 | -24.8415 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1931 | 6.9177130815049335 | -0.920408 | -24.642 | 8 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1932 | 7.156305748004392 | -0.954865 | -29.5324 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2930 | 7.3055911202914725 | -0.766235 | -19.567 | 3 | 15 | 11 | 0.55 | 0.20 | - | yes | Current |
| 2319 | 7.528517069305413 | -0.632325 | -19.9429 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2313 | 7.5660059879386 | -0.661724 | -16.3802 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1930 | 7.93947950000679 | -0.846942 | -22.4682 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3533 | 7.967332316574096 | -0.595274 | -19.1116 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3534 | 8.133908196080094 | -0.570585 | -14.0134 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2925 | 8.748629818732718 | -0.93585 | -28.936 | 8 | 15 | 11 | 0.55 | 0.20 | - | yes | Open |
| 3532 | 9.030017257594768 | -0.545694 | -20.2107 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1928 | 9.381220953795175 | -1.03988 | -27.8253 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2316 | 9.608711404720706 | -0.56533 | -16.6624 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3535 | 9.933575358023363 | -0.529944 | -15.1005 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2929 | 10.367062029597765 | -0.860888 | -21.5023 | 7 | 14 | 11 | 0.55 | 0.20 | - | yes | Open |
| 2312 | 10.605473160217507 | -0.557339 | -10.3993 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3531 | 11.866163427723698 | -0.719043 | -21.4262 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2931 | 12.465157202117519 | -0.794618 | -23.7437 | 7 | 14 | 12 | 0.60 | 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
-19.567kcal/mol
Ligand efficiency (LE)
-0.6312kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.149
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
418.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.87
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
100.00kcal/mol
Minimised FF energy
79.34kcal/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.