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 medium
Native strong
SASA done
Strain ΔE
10.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 0.67, H-bond role recall 0.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.695 kcal/mol/HA)
✓ Good fit quality (FQ -6.56)
✓ Good H-bonds (5 bonds)
✓ Good burial (56% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ Moderate strain (10.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-19.456
kcal/mol
LE
-0.695
kcal/mol/HA
Fit Quality
-6.56
FQ (Leeson)
HAC
28
heavy atoms
MW
369
Da
LogP
2.86
cLogP
Interaction summary
HB 5
HY 14
PI 2
CLASH 3
Interaction summary
HB 5
HY 14
PI 2
CLASH 3
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 | 2.069 | Score | -19.456 |
|---|---|---|---|
| Inter norm | -0.726 | Intra norm | 0.031 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 5 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash | ||
| Residues |
ARG472
ASN402
GLU467
LEU399
MET393
MET471
PHE396
PRO398
SER394
SER395
SER470
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 | 8 | Native recall | 1.00 |
| Jaccard | 0.67 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 39 | 0.2926143135980963 | -1.11467 | -31.7234 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 69 | 0.9875579684309523 | -0.781677 | -18.8622 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 37 | 1.026816980381705 | -0.901056 | -26.2142 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 66 | 1.5219351344448833 | -1.19323 | -33.0077 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 64 | 2.068825905927844 | -0.72591 | -19.4561 | 5 | 12 | 8 | 1.00 | 0.00 | - | no | Current |
| 35 | 2.8077876146014913 | -1.10435 | -25.9593 | 7 | 18 | 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
-19.456kcal/mol
Ligand efficiency (LE)
-0.6949kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.560
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
369.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.86
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
32.73kcal/mol
Minimised FF energy
21.95kcal/mol
SASA & burial
✓ computed
SASA (unbound)
649.1Ų
Total solvent-accessible surface area of free ligand
BSA total
361.6Ų
Buried surface area upon binding
BSA apolar
320.2Ų
Hydrophobic contacts buried
BSA polar
41.3Ų
Polar contacts buried
Fraction buried
55.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3077.5Ų
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
1534.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)