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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
82.9 kcal/mol
Protein clashes
0
Internal clashes
12
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.00
Reason: 12 internal clashes, strain 82.9 kcal/mol
strain ΔE 82.9 kcal/mol
12 intramolecular clashes
65% of hydrophobic surface is solvent-exposed (11/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.603 kcal/mol/HA)
✓ Good fit quality (FQ -5.82)
✓ Strong H-bond network (6 bonds)
✗ Extreme strain energy (82.9 kcal/mol)
✗ Poor burial (40% SASA buried)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-18.083
kcal/mol
LE
-0.603
kcal/mol/HA
Fit Quality
-5.82
FQ (Leeson)
HAC
30
heavy atoms
MW
440
Da
LogP
-0.85
cLogP
Final rank
3.7739
rank score
Inter norm
-0.734
normalised
Contacts
7
H-bonds 7
Interaction summary
HBD 3
HBA 3
HY 1
PI 1
CLASH 0
Interaction summary
HBD 3
HBA 3
HY 1
PI 1
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
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 | 5 | Native recall | 0.62 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 596 | 2.3252128428059002 | -1.13727 | -26.7529 | 10 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 630 | 3.1472053235268254 | -1.23245 | -33.5359 | 14 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 611 | 3.7738766762258784 | -0.734441 | -18.0833 | 7 | 7 | 5 | 0.62 | 0.00 | - | no | Current |
| 621 | 4.08861341711193 | -0.995124 | -23.7831 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 609 | 4.296899294431502 | -1.03684 | -25.0444 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 625 | 4.996400449539082 | -0.832977 | -22.274 | 10 | 10 | 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
-18.083kcal/mol
Ligand efficiency (LE)
-0.6028kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.815
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
440.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.85
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
82.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
113.18kcal/mol
Minimised FF energy
30.29kcal/mol
SASA & burial
✓ computed
SASA (unbound)
611.7Ų
Total solvent-accessible surface area of free ligand
BSA total
242.4Ų
Buried surface area upon binding
BSA apolar
137.8Ų
Hydrophobic contacts buried
BSA polar
104.6Ų
Polar contacts buried
Fraction buried
39.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
56.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2918.7Ų
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
1521.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)