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 (-0.622 kcal/mol/HA)
✓ Good fit quality (FQ -6.22)
✗ Very high strain energy (31.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-21.154
kcal/mol
LE
-0.622
kcal/mol/HA
Fit Quality
-6.22
FQ (Leeson)
HAC
34
heavy atoms
MW
462
Da
LogP
2.80
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 31.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 0
Clashes 6
Severe clashes 1
| Final rank | 6.373871250571508 | Score | -21.1536 |
|---|---|---|---|
| Inter norm | -0.678999 | Intra norm | 0.0568354 |
| Top1000 | no | Excluded | yes |
| Contacts | 21 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 14 clashes; 1 protein clash; high strain Δ 28.5 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:THR180;A:THR83;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 | 17 | Native recall | 0.85 |
| Jaccard | 0.71 | 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: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
No π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1176 | 3.402864701018557 | -0.663813 | -18.2776 | 0 | 19 | 16 | 0.80 | 0.00 | - | no | Open |
| 1263 | 3.9990604149423805 | -0.711846 | -22.53 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1260 | 4.4753230285021495 | -0.712311 | -22.4158 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1264 | 5.159523238865605 | -0.662175 | -20.6769 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1204 | 5.477112655515728 | -0.691578 | -22.6745 | 1 | 18 | 13 | 0.65 | 0.20 | - | no | Open |
| 1184 | 5.541202272118075 | -0.659492 | -17.8819 | 0 | 17 | 13 | 0.65 | 0.00 | - | no | Open |
| 1177 | 5.566946121226586 | -0.751676 | -23.4419 | 2 | 18 | 16 | 0.80 | 0.20 | - | no | Open |
| 1199 | 5.631111653167176 | -0.625717 | -20.0399 | 1 | 16 | 11 | 0.55 | 0.20 | - | no | Open |
| 1190 | 5.678718160062305 | -0.713346 | -18.3026 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1198 | 6.254957794951255 | -0.778277 | -25.0414 | 1 | 22 | 18 | 0.90 | 0.20 | - | no | Open |
| 1188 | 6.325771420887529 | -0.587341 | -16.9229 | 0 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 1178 | 6.36188162765554 | -0.659512 | -12.7139 | 2 | 20 | 18 | 0.90 | 0.20 | - | no | Open |
| 1191 | 6.56750148961188 | -0.668599 | -18.9567 | 1 | 16 | 15 | 0.75 | 0.20 | - | no | Open |
| 1175 | 6.794888250722963 | -0.748457 | -20.9639 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1257 | 53.872438886812105 | -0.582816 | -18.3348 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1183 | 54.341520696096715 | -0.652059 | -19.5408 | 0 | 20 | 17 | 0.85 | 0.00 | - | no | Open |
| 1182 | 54.41382869599642 | -0.640632 | -21.134 | 0 | 20 | 17 | 0.85 | 0.00 | - | no | Open |
| 1258 | 54.490932092442215 | -0.680854 | -18.9453 | 0 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 1185 | 54.53606804760635 | -0.579419 | -15.016 | 2 | 11 | 9 | 0.45 | 0.00 | - | no | Open |
| 1181 | 54.67552439964703 | -0.663086 | -20.4531 | 0 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1180 | 55.078895244555575 | -0.714419 | -18.4452 | 0 | 15 | 13 | 0.65 | 0.00 | - | no | Open |
| 1179 | 55.569919695452114 | -0.548479 | -14.7052 | 1 | 16 | 15 | 0.75 | 0.00 | - | no | Open |
| 1201 | 6.106456679136357 | -0.635301 | -21.5905 | 0 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1200 | 6.373871250571508 | -0.678999 | -21.1536 | 1 | 21 | 17 | 0.85 | 0.00 | - | yes | Current |
| 1202 | 6.8209671570146355 | -0.697339 | -21.9246 | 0 | 16 | 11 | 0.55 | 0.00 | - | yes | Open |
| 1173 | 7.527546456074216 | -0.599193 | -23.0442 | 1 | 17 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1192 | 55.18249394600299 | -0.676298 | -19.0891 | 0 | 18 | 14 | 0.70 | 0.00 | - | yes | Open |
| 1262 | 55.442316641919334 | -0.676484 | -19.3769 | 1 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1187 | 55.72764713393109 | -0.582275 | -17.3587 | 1 | 17 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1197 | 56.31646235955749 | -0.703132 | -22.4177 | 0 | 22 | 18 | 0.90 | 0.00 | - | yes | Open |
| 1259 | 56.358462552788836 | -0.687859 | -22.5573 | 1 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1189 | 56.372576900626385 | -0.734814 | -22.0573 | 0 | 22 | 18 | 0.90 | 0.00 | - | yes | Open |
| 1193 | 56.79629875755536 | -0.612258 | -16.3708 | 2 | 14 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1196 | 56.89139187650238 | -0.769657 | -24.7178 | 0 | 18 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1261 | 57.14118150611999 | -0.671137 | -19.4895 | 0 | 23 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1203 | 57.36959418637549 | -0.739535 | -19.4651 | 1 | 20 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1174 | 57.40147018454787 | -0.730569 | -18.7216 | 1 | 18 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1194 | 58.223153835087224 | -0.642037 | -18.5372 | 1 | 19 | 15 | 0.75 | 0.20 | - | yes | Open |
| 1195 | 58.37196833807934 | -0.587214 | -14.7791 | 1 | 14 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1186 | 58.786068888430485 | -0.615115 | -19.4548 | 3 | 17 | 17 | 0.85 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.154kcal/mol
Ligand efficiency (LE)
-0.6222kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.225
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
461.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.80
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
164.26kcal/mol
Minimised FF energy
133.00kcal/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.