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 (-1.184 kcal/mol/HA)
✓ Good fit quality (FQ -9.91)
✓ Strong H-bond network (11 bonds)
✗ High strain energy (14.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.688
kcal/mol
LE
-1.184
kcal/mol/HA
Fit Quality
-9.91
FQ (Leeson)
HAC
20
heavy atoms
MW
296
Da
LogP
-0.68
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 14.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 11
Hydrophobic 24
π–π 2
Clashes 8
Severe clashes 0
| Final rank | 4.335538708389735 | Score | -23.6878 |
|---|---|---|---|
| Inter norm | -1.28094 | Intra norm | 0.0965517 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 11 |
| Artifact reason | geometry warning; 7 clashes; 8 protein contact clashes; high strain Δ 35.8 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:GLY157;A:ILE45;A:MET53;A:NDP301;A:PHE56;A:THR180;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;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 | 5 | Strict recall | 0.71 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 822 | 1.7651825253178435 | -1.54473 | -29.5498 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 804 | 1.7814656416736707 | -1.54385 | -29.6147 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1101 | 2.451736318244695 | -1.22209 | -22.957 | 10 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 1099 | 2.751730486354672 | -1.2615 | -23.9145 | 11 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 770 | 2.912457314165155 | -1.0945 | -22.0785 | 5 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 824 | 2.9572062989000787 | -1.58614 | -29.0417 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2973 | 2.958631931911466 | -1.35838 | -25.6607 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 724 | 2.958792498600509 | -1.19931 | -21.6886 | 10 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 2954 | 2.981482915776274 | -1.32647 | -25.5936 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2818 | 3.073606886422904 | -1.1316 | -21.8999 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2200 | 3.1894039718698437 | -1.40229 | -26.0771 | 9 | 15 | 10 | 0.50 | 0.80 | - | no | Open |
| 2838 | 3.209712360742235 | -1.16054 | -20.1799 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 785 | 3.371986881492304 | -1.44392 | -27.8137 | 14 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 772 | 3.4610727815057416 | -1.20072 | -21.8379 | 10 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 823 | 3.513058973892604 | -1.45659 | -26.4354 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2817 | 3.5148101262244955 | -1.34198 | -25.4179 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 806 | 3.5200046885906664 | -1.57638 | -29.017 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 725 | 3.657543007624825 | -1.18038 | -21.8508 | 6 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 2816 | 3.7496605103873684 | -1.22427 | -23.475 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2976 | 3.8993722559434802 | -0.996862 | -21.3146 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2955 | 3.9047540819396707 | -1.32016 | -24.533 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 805 | 4.233728072955784 | -1.3742 | -25.5985 | 11 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2209 | 4.335538708389735 | -1.28094 | -23.6878 | 11 | 15 | 11 | 0.55 | 0.80 | - | no | Current |
| 2837 | 4.471999308101291 | -1.29246 | -24.4616 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2819 | 4.509559112160315 | -1.18635 | -22.4397 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1100 | 4.532198986214107 | -1.30203 | -24.5606 | 9 | 15 | 1 | 0.05 | 0.00 | - | no | Open |
| 825 | 4.551399586390781 | -1.38019 | -25.7894 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 723 | 4.221287024700854 | -1.11783 | -21.1668 | 9 | 16 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2975 | 5.043363479944811 | -0.979852 | -17.9419 | 7 | 11 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2956 | 5.1289243130459905 | -1.06611 | -20.5302 | 11 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2836 | 5.189952954981379 | -1.25436 | -24.4355 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2839 | 5.2281491444919235 | -1.20309 | -22.6846 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 771 | 5.269168263680848 | -1.19091 | -21.9458 | 6 | 20 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2201 | 5.412711748212557 | -1.4146 | -26.5109 | 10 | 14 | 10 | 0.50 | 0.80 | - | yes | Open |
| 773 | 5.470576026124684 | -1.17562 | -21.6957 | 6 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 722 | 7.11719285334885 | -1.08093 | -21.2818 | 6 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2957 | 7.95279810263039 | -1.24603 | -22.8766 | 9 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2974 | 8.479483345283569 | -1.00809 | -19.2111 | 10 | 9 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2199 | 8.507687583879294 | -1.17628 | -21.9315 | 8 | 11 | 7 | 0.35 | 0.20 | - | yes | Open |
| 784 | 9.42692754453209 | -1.37134 | -26.8779 | 13 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 782 | 9.542291570199374 | -1.33149 | -26.616 | 13 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2210 | 9.96613238288551 | -1.21135 | -22.4258 | 8 | 9 | 6 | 0.30 | 0.20 | - | yes | Open |
| 2211 | 10.220336031702155 | -1.22577 | -23.9789 | 9 | 9 | 6 | 0.30 | 0.20 | - | yes | Open |
| 783 | 10.98940917383317 | -1.35565 | -26.1193 | 13 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 807 | 13.168104140684166 | -1.46486 | -27.2197 | 8 | 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
-23.688kcal/mol
Ligand efficiency (LE)
-1.1844kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.911
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
296.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.68
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-6.14kcal/mol
Minimised FF energy
-20.20kcal/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.