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 (-1.086 kcal/mol/HA)
✓ Good fit quality (FQ -10.37)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (24.1 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-31.503
kcal/mol
LE
-1.086
kcal/mol/HA
Fit Quality
-10.37
FQ (Leeson)
HAC
29
heavy atoms
MW
432
Da
LogP
2.46
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 24.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 24
π–π 3
Clashes 17
Severe clashes 4
| Final rank | 12.509670080167565 | Score | -31.503 |
|---|---|---|---|
| Inter norm | -0.881243 | Intra norm | -0.205067 |
| Top1000 | no | Excluded | yes |
| Contacts | 15 | H-bonds | 7 |
| Artifact reason | excluded; geometry warning; 12 clashes; 4 protein clashes; high strain Δ 29.5 | ||
| Residues | A:ARG92;A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS90;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO93;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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 947 | 3.685796895602662 | -1.15115 | -30.8536 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 945 | 4.01589966986883 | -1.16385 | -39.1929 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1508 | 4.545654326349949 | -0.601787 | -23.7857 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 3053 | 4.6469712824838325 | -0.615403 | -18.6524 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2938 | 4.893433566307431 | -0.914081 | -26.2321 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 946 | 5.099464498447895 | -1.16396 | -39.3269 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2283 | 5.587246581638521 | -0.868032 | -23.4287 | 4 | 19 | 17 | 0.85 | 0.60 | - | no | Open |
| 1215 | 5.597812162690021 | -0.893438 | -24.523 | 5 | 21 | 1 | 0.05 | 0.00 | - | no | Open |
| 2939 | 5.91595891871275 | -0.7364 | -22.3903 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1166 | 5.9714898924218405 | -0.782661 | -21.9471 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1167 | 6.328841122786455 | -0.820539 | -23.1705 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1212 | 6.399801172572356 | -0.867267 | -31.1176 | 9 | 13 | 1 | 0.05 | 0.00 | - | no | Open |
| 2281 | 6.505309085875486 | -0.806459 | -25.853 | 4 | 15 | 13 | 0.65 | 0.20 | - | no | Open |
| 1056 | 6.757643329791728 | -0.913873 | -22.4923 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2278 | 7.089451804269929 | -0.922707 | -32.0998 | 4 | 20 | 18 | 0.90 | 0.20 | - | no | Open |
| 1510 | 6.278580802045207 | -0.668175 | -16.8338 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1054 | 6.892013669930548 | -0.954315 | -23.4905 | 12 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1509 | 7.008371354667256 | -0.695582 | -17.2833 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1507 | 7.438275695918752 | -0.644618 | -24.9097 | 4 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3052 | 7.663031767295704 | -0.84589 | -24.7448 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1053 | 7.723839908221002 | -0.918774 | -23.8187 | 8 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2282 | 7.75755817382527 | -0.990903 | -25.5451 | 4 | 19 | 17 | 0.85 | 0.20 | - | yes | Open |
| 1165 | 7.878558658148589 | -0.777158 | -21.8061 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1213 | 8.36934802716161 | -0.865914 | -22.5926 | 3 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2279 | 8.382404387946393 | -0.933107 | -27.3468 | 4 | 18 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1214 | 8.394175177881948 | -0.988746 | -29.6316 | 12 | 16 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1052 | 8.422637548759578 | -0.93638 | -33.6314 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2937 | 8.757853424058045 | -0.880444 | -26.2327 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1055 | 9.119079605330361 | -0.970755 | -26.4205 | 11 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1164 | 9.615793555772534 | -0.764226 | -27.7249 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1051 | 10.248109841291988 | -0.758542 | -28.9482 | 8 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2284 | 10.751445528226279 | -0.967121 | -26.3674 | 4 | 16 | 13 | 0.65 | 0.20 | - | yes | Open |
| 948 | 11.261270625310344 | -1.08614 | -27.3435 | 7 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2280 | 12.509670080167565 | -0.881243 | -31.503 | 7 | 15 | 11 | 0.55 | 0.20 | - | yes | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.503kcal/mol
Ligand efficiency (LE)
-1.0863kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.370
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
431.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.46
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.12kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-8.05kcal/mol
Minimised FF energy
-32.17kcal/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.