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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.028 kcal/mol/HA)
✓ Good fit quality (FQ -9.47)
✓ Strong H-bond network (8 bonds)
✗ Very high strain energy (26.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-26.722
kcal/mol
LE
-1.028
kcal/mol/HA
Fit Quality
-9.47
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 26.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 24
π–π 2
Clashes 5
Severe clashes 0
| Final rank | 4.4601038974391924 | Score | -26.722 |
|---|---|---|---|
| Inter norm | -0.999455 | Intra norm | -0.0283138 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 8 |
| Artifact reason | geometry warning; 14 clashes; 5 protein contact clashes; high strain Δ 27.5 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:GLY157;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE55;A:PHE56;A:PHE91;A:THR180;A:TYR162;A:TYR178;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 | 16 | Native recall | 0.80 |
| Jaccard | 0.70 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 486 | 2.569525141618116 | -1.31932 | -35.1131 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 487 | 2.5706233481366123 | -1.21244 | -32.7468 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 485 | 2.6063318911184816 | -1.15151 | -31.3019 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 482 | 2.746560948394498 | -1.24922 | -33.3657 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 483 | 3.0881037770074276 | -1.16846 | -31.7187 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 515 | 3.1059336830861044 | -1.03863 | -26.8521 | 8 | 19 | 16 | 0.80 | 0.80 | - | no | Open |
| 520 | 3.3538301153175993 | -1.08354 | -31.3099 | 4 | 15 | 12 | 0.60 | 0.20 | - | no | Open |
| 516 | 3.356499595837022 | -1.01808 | -26.9593 | 8 | 18 | 13 | 0.65 | 0.80 | - | no | Open |
| 484 | 3.4584880697646083 | -1.20344 | -32.1171 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 471 | 3.831713010045734 | -0.79224 | -20.5914 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 658 | 3.9501692319057424 | -0.985528 | -25.2336 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 517 | 4.064825162545956 | -1.07948 | -31.1184 | 6 | 17 | 13 | 0.65 | 0.80 | - | no | Open |
| 519 | 4.251722486273004 | -1.105 | -31.8661 | 7 | 17 | 13 | 0.65 | 0.80 | - | no | Open |
| 518 | 4.4601038974391924 | -0.999455 | -26.722 | 8 | 19 | 16 | 0.80 | 0.80 | - | no | Current |
| 468 | 4.636093622647474 | -0.769462 | -22.2181 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 625 | 4.803546563768789 | -0.803217 | -21.7247 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 472 | 5.396863692971612 | -0.903161 | -25.3504 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 626 | 5.419036919500527 | -0.806911 | -21.6887 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 578 | 5.678253723502912 | -0.820976 | -21.4741 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 659 | 5.111686360577248 | -0.945538 | -24.3472 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 470 | 5.9141819054849005 | -0.771259 | -22.3003 | 4 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 467 | 5.94005831272731 | -0.751539 | -21.2439 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 579 | 6.556874896407342 | -0.8562 | -22.5503 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 624 | 7.0886128301442595 | -0.70565 | -21.0809 | 4 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 623 | 7.34512433450863 | -0.72924 | -20.2579 | 4 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 469 | 8.234825837583921 | -0.726875 | -18.3807 | 2 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 576 | 8.723183317896952 | -0.739238 | -19.674 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 577 | 9.658071359179605 | -0.757797 | -20.8286 | 6 | 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
-26.722kcal/mol
Ligand efficiency (LE)
-1.0278kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.469
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)
26.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-112.78kcal/mol
Minimised FF energy
-139.68kcal/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.