Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
py3Dmol interaction viewer
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Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.852 kcal/mol/HA)
✓ Good fit quality (FQ -7.95)
✓ Strong H-bond network (10 bonds)
✗ Very high strain energy (36.5 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.000
kcal/mol
LE
-0.852
kcal/mol/HA
Fit Quality
-7.95
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.03
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 36.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 10
Hydrophobic 19
π–π 2
Clashes 9
Severe clashes 0
⚠ Hydrophobic exposure 35%
Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 11
Exposed 6
LogP 2.03
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 6.29149002761757 | Score | -22.9997 |
|---|---|---|---|
| Inter norm | -1.09247 | Intra norm | 0.24063 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 10 |
| Artifact reason | geometry warning; 15 clashes; 9 protein contact clashes; high strain Δ 37.2 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:GLY157;A:ILE182;A:ILE45;A:MET53;A:NDP301;A:PHE56;A:PRO88;A:SER44;A:SER86;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49;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 | 13 | Native recall | 0.65 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2901 | 4.028687280299404 | -0.907217 | -24.1632 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 705 | 4.617604670507904 | -0.951386 | -23.6661 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2171 | 4.648840547993053 | -1.06787 | -28.4955 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1666 | 4.878872415741254 | -0.651287 | -10.8375 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 1406 | 4.948872868174309 | -0.768893 | -22.5979 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1403 | 4.98975176952761 | -0.861395 | -21.0234 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1664 | 4.999869876932782 | -0.576576 | -14.9287 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 3028 | 5.152843824591004 | -0.699809 | -19.1047 | 7 | 13 | 1 | 0.05 | 0.00 | - | no | Open |
| 2249 | 5.213620208008555 | -0.980276 | -26.2785 | 3 | 13 | 9 | 0.45 | 0.40 | - | no | Open |
| 2174 | 5.5248637613734655 | -0.898447 | -24.1949 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1400 | 5.558795150490041 | -0.883685 | -21.8791 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1469 | 5.785709981021195 | -0.979613 | -23.342 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2172 | 5.931597822970552 | -1.00614 | -21.5639 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 3024 | 5.971905984331958 | -0.847654 | -21.8037 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1665 | 6.005391053677059 | -0.55793 | -13.5373 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1470 | 6.082552607164666 | -0.84061 | -23.1766 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1466 | 6.236697808622543 | -0.835401 | -22.907 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2248 | 6.2728203785403345 | -1.03595 | -29.1473 | 10 | 18 | 13 | 0.65 | 0.80 | - | no | Open |
| 2250 | 6.29149002761757 | -1.09247 | -22.9997 | 10 | 19 | 13 | 0.65 | 0.80 | - | no | Current |
| 888 | 6.8363901620857 | -0.894499 | -23.8358 | 5 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 1401 | 7.206793043580023 | -0.825058 | -19.0084 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 889 | 7.218383353034549 | -0.901999 | -22.8948 | 4 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 706 | 5.725854191870677 | -0.941668 | -27.2502 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1663 | 6.018127464569724 | -0.726074 | -21.0149 | 8 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3023 | 6.385110334286703 | -0.801457 | -21.4868 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 707 | 6.385421128421418 | -0.87677 | -21.8939 | 1 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2173 | 6.481130597725988 | -1.09005 | -30.4446 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2170 | 6.864203310544136 | -0.939835 | -28.2747 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1467 | 6.99810249456146 | -0.88496 | -24.6047 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 704 | 7.1793952206470415 | -0.920158 | -24.4753 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1662 | 7.296920009981743 | -0.89635 | -23.6694 | 9 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 708 | 7.378745441523422 | -0.923248 | -18.7419 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 710 | 7.698542524980535 | -0.870403 | -19.6666 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1402 | 8.006299573122549 | -0.796345 | -21.681 | 9 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1471 | 8.181359555602715 | -0.918956 | -24.6781 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3026 | 8.530125622083602 | -0.791049 | -16.0963 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1468 | 8.69668542876588 | -0.803708 | -20.2513 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3027 | 8.975609037195873 | -0.855223 | -23.6426 | 8 | 13 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1465 | 9.017645249922971 | -0.817497 | -22.9433 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1405 | 9.90881541648978 | -0.897658 | -24.7777 | 12 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2902 | 9.977921049614068 | -0.775712 | -19.7775 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 709 | 10.867351728814572 | -0.803687 | -22.6612 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1404 | 11.274322487740843 | -0.904232 | -20.3369 | 11 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3025 | 13.265796688558861 | -0.759357 | -21.7876 | 5 | 14 | 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
-23.000kcal/mol
Ligand efficiency (LE)
-0.8518kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.947
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.03
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.53kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
4.13kcal/mol
Minimised FF energy
-32.41kcal/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.