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 (-1.059 kcal/mol/HA)
✓ Good fit quality (FQ -9.76)
✓ Good H-bonds (5 bonds)
✗ High strain energy (13.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-27.541
kcal/mol
LE
-1.059
kcal/mol/HA
Fit Quality
-9.76
FQ (Leeson)
HAC
26
heavy atoms
MW
349
Da
LogP
2.66
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 13.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 3
Clashes 6
Severe clashes 0
| Final rank | 3.699891532165524 | Score | -27.5408 |
|---|---|---|---|
| Inter norm | -0.996357 | Intra norm | -0.0629054 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | geometry warning; 13 clashes; 6 protein contact clashes; moderate strain Δ 14.4 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:GLY157;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:THR180;A:TYR162;A:VAL156;A:VAL30;A:VAL31;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 | 15 | Native recall | 0.75 |
| Jaccard | 0.71 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.57 |
| H-bond same residue+role | 4 | Role recall | 0.80 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 111 | 3.360779007337855 | -1.21674 | -32.028 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 110 | 3.442122624019677 | -1.21522 | -31.9059 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 93 | 3.699891532165524 | -0.996357 | -27.5408 | 5 | 16 | 15 | 0.75 | 0.80 | - | no | Current |
| 112 | 3.8145373961952544 | -1.09529 | -28.7447 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 92 | 3.894791390276917 | -1.09051 | -30.1724 | 6 | 17 | 13 | 0.65 | 0.80 | - | no | Open |
| 94 | 4.117158662979138 | -1.06014 | -24.3512 | 5 | 18 | 16 | 0.80 | 0.80 | - | no | Open |
| 79 | 4.323370650410053 | -0.760687 | -17.7451 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 115 | 4.537151348789815 | -0.97357 | -25.402 | 4 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 68 | 4.76876667974091 | -0.719336 | -20.7661 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 80 | 5.020995352586303 | -0.804207 | -18.2131 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 78 | 5.844625676418907 | -0.834551 | -20.0158 | 4 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 116 | 6.943216971288747 | -1.08568 | -25.0988 | 6 | 16 | 1 | 0.05 | 0.00 | - | yes | Open |
| 69 | 7.1954168182638885 | -0.812568 | -20.336 | 5 | 10 | 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
-27.541kcal/mol
Ligand efficiency (LE)
-1.0593kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.759
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
349.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.66
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-129.32kcal/mol
Minimised FF energy
-143.05kcal/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.