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 (-0.562 kcal/mol/HA)
✓ Good fit quality (FQ -5.47)
✓ Strong H-bond network (8 bonds)
✗ High strain energy (12.5 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-17.408
kcal/mol
LE
-0.562
kcal/mol/HA
Fit Quality
-5.47
FQ (Leeson)
HAC
31
heavy atoms
MW
424
Da
LogP
3.89
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 12.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 21
π–π 3
Clashes 6
Severe clashes 0
| Final rank | 3.839088285027815 | Score | -17.4083 |
|---|---|---|---|
| Inter norm | -0.662661 | Intra norm | 0.101104 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 8 |
| Artifact reason | geometry warning; 12 clashes; 6 protein contact clashes; moderate strain Δ 16.2 | ||
| Residues | A:ARG17;A:ASP232;A:HIS241;A:LEU188;A:LEU226;A:LEU229;A:MET233;A:NDP302;A:PHE113;A:SER111;A:TYR191;A:TYR194;A:VAL230;D:ARG287 | ||
Protein summary
308 residues
| Protein target | T04 | Atoms | 4210 |
|---|---|---|---|
| Residues | 308 | Chains | 3 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 7PXX | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 8 |
| IFP residues | A:ARG17; A:ASP181; A:GLY225; A:HIS241; A:LEU188; A:LEU226; A:LEU229; A:LYS198; A:MET233; A:NDP302; A:PHE113; A:PRO115; A:SER111; A:SER112; A:SER227; A:TYR191; A:TYR194; A:VAL230; D:ARG287 | ||
| Current overlap | 13 | Native recall | 0.68 |
| Jaccard | 0.65 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 541 | 3.839088285027815 | -0.662661 | -17.4083 | 8 | 14 | 13 | 0.68 | 0.40 | - | no | Current |
| 2108 | 4.889108429564196 | -0.892143 | -20.6112 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2109 | 7.138682410262188 | -0.866866 | -21.6317 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 542 | 9.89773756711461 | -0.698348 | -13.7129 | 8 | 14 | 13 | 0.68 | 0.40 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-17.408kcal/mol
Ligand efficiency (LE)
-0.5616kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.471
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
423.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.89
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
51.29kcal/mol
Minimised FF energy
38.82kcal/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.