Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
17.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.60, H-bond role recall 1.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.689 kcal/mol/HA)
✓ Good fit quality (FQ -6.35)
✓ Strong H-bond network (9 bonds)
✓ Good burial (45% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Moderate strain (17.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-17.919
kcal/mol
LE
-0.689
kcal/mol/HA
Fit Quality
-6.35
FQ (Leeson)
HAC
26
heavy atoms
MW
352
Da
LogP
0.38
cLogP
Interaction summary
HB 9
HY 9
PI 1
CLASH 1
Interaction summary
HB 9
HY 9
PI 1
CLASH 1
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 4.193 | Score | -17.919 |
|---|---|---|---|
| Inter norm | -0.751 | Intra norm | 0.062 |
| Top1000 | no | Excluded | no |
| Contacts | 8 | H-bonds | 9 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes | ||
| Residues |
ASN402
GLU467
LEU399
LYS407
PHE396
SER394
SER395
THR397
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASN402
GLU467
LEU399
PHE396
PRO398
SER394
SER470
THR397
| ||
| Current overlap | 6 | Native recall | 0.75 |
| Jaccard | 0.60 | RMSD | - |
| HB strict | 2 | Strict recall | 1.00 |
| HB same residue+role | 1 | HB role recall | 1.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
Protein summary
492 residues
| Protein target | T20 | Atoms | 7539 |
|---|---|---|---|
| Residues | 492 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 295 | 0.6848745770730704 | -0.992809 | -21.5063 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 236 | 1.380950836095837 | -1.01859 | -24.4746 | 3 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 295 | 1.8295021937022387 | -1.25182 | -24.5663 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 214 | 2.5703367368996966 | -1.33185 | -30.4746 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 291 | 4.193386414552068 | -0.751105 | -17.9194 | 9 | 8 | 6 | 0.75 | 1.00 | - | no | Current |
| 268 | 5.7271341078999916 | -0.794776 | -19.5866 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-17.919kcal/mol
Ligand efficiency (LE)
-0.6892kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.350
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
352.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.38
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
125.18kcal/mol
Minimised FF energy
107.82kcal/mol
SASA & burial
✓ computed
SASA (unbound)
626.5Ų
Total solvent-accessible surface area of free ligand
BSA total
280.0Ų
Buried surface area upon binding
BSA apolar
208.2Ų
Hydrophobic contacts buried
BSA polar
71.8Ų
Polar contacts buried
Fraction buried
44.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3043.8Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1512.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)