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 (-0.864 kcal/mol/HA)
✓ Good fit quality (FQ -8.34)
✓ Good H-bonds (4 bonds)
✗ High strain energy (10.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-25.922
kcal/mol
LE
-0.864
kcal/mol/HA
Fit Quality
-8.34
FQ (Leeson)
HAC
30
heavy atoms
MW
398
Da
LogP
3.86
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 10.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 23
π–π 2
Clashes 8
Severe clashes 1
| Final rank | 6.971189554398788 | Score | -25.9224 |
|---|---|---|---|
| Inter norm | -0.915938 | Intra norm | 0.0518564 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 17 clashes; 1 protein clash; moderate strain Δ 17.5 | ||
| Residues | A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO50;A:THR54;A:THR83;A:VAL156;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 | 12 | Native recall | 0.60 |
| Jaccard | 0.55 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1906 | 4.079634371228655 | -0.565681 | -19.4954 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1904 | 4.708431710135203 | -0.593572 | -18.3879 | 3 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 2552 | 5.837738885508001 | -0.84258 | -26.671 | 9 | 11 | 7 | 0.35 | 0.20 | - | no | Open |
| 1374 | 6.9491310065977725 | -1.21986 | -37.7354 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1553 | 7.366388362828268 | -0.629821 | -20.6491 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1549 | 8.450095171648368 | -0.721285 | -24.1068 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1900 | 6.1831904129384965 | -0.71915 | -21.2671 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2548 | 6.398582763603283 | -1.07455 | -32.5822 | 7 | 12 | 7 | 0.35 | 0.20 | - | yes | Open |
| 2553 | 6.594207675159006 | -0.943559 | -27.8785 | 4 | 14 | 12 | 0.60 | 0.40 | - | yes | Open |
| 2550 | 6.798936814767271 | -0.774692 | -22.9352 | 6 | 10 | 7 | 0.35 | 0.20 | - | yes | Open |
| 2549 | 6.971189554398788 | -0.915938 | -25.9224 | 4 | 14 | 12 | 0.60 | 0.40 | - | yes | Current |
| 1905 | 7.018537068616989 | -0.62468 | -21.7228 | 5 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2551 | 7.033853904040928 | -0.845777 | -26.335 | 4 | 15 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1903 | 7.414535980267811 | -0.629732 | -20.3929 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1901 | 7.816321035401791 | -0.673946 | -21.3884 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1548 | 8.866106778944213 | -0.923782 | -27.0501 | 11 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1554 | 9.058924025034537 | -0.757065 | -21.7722 | 11 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1902 | 9.330708255049892 | -0.712915 | -24.4361 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1907 | 9.607718702921597 | -0.633204 | -22.1142 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1547 | 9.80770316554089 | -0.668429 | -17.3057 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1552 | 10.005670834294907 | -0.777192 | -26.0641 | 9 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1550 | 10.24519874536975 | -1.07037 | -31.267 | 12 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1375 | 10.697110617251491 | -1.12097 | -37.0518 | 10 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1551 | 11.621956666465433 | -0.756254 | -18.4723 | 7 | 15 | 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
-25.922kcal/mol
Ligand efficiency (LE)
-0.8641kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.335
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
398.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.86
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
99.94kcal/mol
Minimised FF energy
89.37kcal/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.