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 (-0.779 kcal/mol/HA)
✓ Good fit quality (FQ -7.66)
✗ High strain energy (18.0 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-24.921
kcal/mol
LE
-0.779
kcal/mol/HA
Fit Quality
-7.66
FQ (Leeson)
HAC
32
heavy atoms
MW
422
Da
LogP
4.90
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 18.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 3
Clashes 7
Severe clashes 1
| Final rank | 6.737152572584959 | Score | -24.9207 |
|---|---|---|---|
| Inter norm | -0.80934 | Intra norm | 0.0305676 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 0 |
| Artifact reason | excluded; geometry warning; 18 clashes; 1 protein clash; moderate strain Δ 18.9 | ||
| 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:THR83;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: permissive.
| 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 | 18 | Native recall | 0.90 |
| Jaccard | 0.90 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
Hydrogen bonds
Mode: permissive. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 882 | 3.68015874069592 | -0.758599 | -23.1905 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 618 | 4.753718222757358 | -0.879782 | -27.9333 | 0 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 880 | 4.760586587214268 | -0.789752 | -25.2392 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 876 | 4.865720514621524 | -0.80982 | -25.2682 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 614 | 5.2705305231790405 | -0.881861 | -28.2029 | 0 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 806 | 5.387341035556807 | -0.80016 | -25.685 | 0 | 18 | 15 | 0.75 | 0.00 | - | no | Open |
| 878 | 5.717936949193543 | -0.823674 | -25.1139 | 0 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 610 | 5.896851545489233 | -0.88753 | -28.019 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 609 | 5.912714715887796 | -1.02151 | -29.0331 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 883 | 7.483230480035522 | -0.74954 | -21.634 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 611 | 7.781050852582138 | -1.01052 | -24.7664 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 613 | 8.164514631771638 | -0.879609 | -27.0241 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 615 | 5.871673633146488 | -1.02301 | -27.44 | 0 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 801 | 6.1364179169700765 | -0.774794 | -24.3976 | 0 | 14 | 11 | 0.55 | 0.00 | - | yes | Open |
| 881 | 6.176569636524991 | -0.838986 | -26.0928 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 873 | 6.2987060644719 | -0.84473 | -26.2076 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 877 | 6.460596193474383 | -0.823996 | -25.8147 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 803 | 6.696921226225941 | -0.778381 | -24.3934 | 0 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 802 | 6.737152572584959 | -0.80934 | -24.9207 | 0 | 18 | 18 | 0.90 | 0.00 | - | yes | Current |
| 800 | 6.828955810971412 | -0.797342 | -23.8658 | 0 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 620 | 6.890565349006715 | -0.992624 | -28.6432 | 0 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 807 | 6.924363385512182 | -0.789267 | -24.8433 | 0 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 798 | 7.197254895005341 | -0.83178 | -25.6924 | 0 | 16 | 16 | 0.80 | 0.00 | - | yes | Open |
| 617 | 7.25695253679321 | -0.943383 | -24.9559 | 0 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 874 | 7.455804747405748 | -0.790897 | -20.6835 | 0 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 797 | 7.481414084461965 | -0.82142 | -26.2502 | 0 | 21 | 17 | 0.85 | 0.00 | - | yes | Open |
| 805 | 7.9142323766242315 | -0.819836 | -26.4257 | 0 | 21 | 17 | 0.85 | 0.00 | - | yes | Open |
| 884 | 55.83634397036696 | -0.843594 | -26.1424 | 0 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 616 | 56.02875660341615 | -1.00343 | -28.9633 | 0 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 619 | 56.83784189917394 | -1.00164 | -26.3548 | 0 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 804 | 57.194339723439576 | -0.77967 | -23.1691 | 0 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 612 | 57.4222504101707 | -1.08289 | -32.3895 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 799 | 57.975958599277476 | -0.773564 | -19.6304 | 0 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 875 | 58.73167053078245 | -0.687968 | -20.6455 | 0 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 808 | 58.975628311942216 | -0.757633 | -22.2892 | 0 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 879 | 59.98350652153543 | -0.688332 | -19.289 | 0 | 19 | 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
-24.921kcal/mol
Ligand efficiency (LE)
-0.7788kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.658
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
421.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.90
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
106.36kcal/mol
Minimised FF energy
88.41kcal/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.