Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
34.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.94, Jaccard 0.94, H-bond role recall 0.55
Reason: no major geometry red flags detected
2 protein-contact clashes
62% of hydrophobic surface is solvent-exposed (8/13 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.428 kcal/mol/HA)
✓ Good fit quality (FQ -12.18)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (60%)
✗ Very high strain energy (34.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-29.992
kcal/mol
LE
-1.428
kcal/mol/HA
Fit Quality
-12.18
FQ (Leeson)
HAC
21
heavy atoms
MW
301
Da
LogP
1.68
cLogP
Interaction summary
HB 11
HY 4
PI 2
CLASH 2
⚠ Exposure 61%
Interaction summary
HB 11
HY 4
PI 2
CLASH 2
⚠ Exposure 61%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
62% of hydrophobic surface is solvent-exposed (8/13 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 13
Buried (contacted) 5
Exposed 8
LogP 1.68
H-bonds 11
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.829 | Score | -29.992 |
|---|---|---|---|
| Inter norm | -1.226 | Intra norm | -0.202 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 11 |
| Artifact reason | geometry warning; 5 clashes; 3 protein clashes; high strain Δ 34.0 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
THR74
TYR49
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
| Current overlap | 16 | Native recall | 0.94 |
| Jaccard | 0.94 | RMSD | - |
| HB strict | 7 | Strict recall | 0.54 |
| HB same residue+role | 6 | HB role recall | 0.55 |
| HB same residue | 7 | HB residue recall | 0.64 |
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 525 | -0.2542710995135058 | -1.21566 | -23.1584 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 532 | 0.5971717101617344 | -1.14756 | -19.4002 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 497 | 1.2324117898771396 | -1.43373 | -22.5907 | 12 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 515 | 1.4790178136390348 | -1.51283 | -28.374 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 515 | 3.4416681627078414 | -1.32144 | -34.3345 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 518 | 3.8294717471537094 | -1.22635 | -29.9924 | 11 | 16 | 16 | 0.94 | 0.55 | - | no | Current |
| 501 | 3.849075903106818 | -1.34917 | -33.7785 | 6 | 16 | 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
-29.992kcal/mol
Ligand efficiency (LE)
-1.4282kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.182
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
301.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.68
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
63.42kcal/mol
Minimised FF energy
29.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
523.4Ų
Total solvent-accessible surface area of free ligand
BSA total
394.1Ų
Buried surface area upon binding
BSA apolar
236.8Ų
Hydrophobic contacts buried
BSA polar
157.3Ų
Polar contacts buried
Fraction buried
75.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
60.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2105.6Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
667.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)