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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
32.9 kcal/mol
Protein clashes
8
Internal clashes
8
Native overlap
contact recall 0.82, Jaccard 0.78, H-bond role recall 0.55
Reason: 8 internal clashes
8 protein-contact clashes
8 intramolecular clashes
61% of hydrophobic surface is solvent-exposed (11/18 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 (-0.606 kcal/mol/HA)
✓ Good fit quality (FQ -5.79)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Very high strain energy (32.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-17.580
kcal/mol
LE
-0.606
kcal/mol/HA
Fit Quality
-5.79
FQ (Leeson)
HAC
29
heavy atoms
MW
416
Da
LogP
3.52
cLogP
Interaction summary
HB 9
HY 4
PI 2
CLASH 8
⚠ Exposure 61%
Interaction summary
HB 9
HY 4
PI 2
CLASH 8
⚠ Exposure 61%
Solvent-exposed hydrophobic surface — desolvation penalty likely
61% of hydrophobic surface is solvent-exposed (11/18 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 18
Buried (contacted) 7
Exposed 11
LogP 3.52
H-bonds 9
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 3.454 | Score | -17.580 |
|---|---|---|---|
| Inter norm | -0.831 | Intra norm | 0.224 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 9 |
| Artifact reason | geometry warning; 10 clashes; 1 protein clash; high strain Δ 32.9 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY77
HIS105
HIS14
HIS141
SER46
THR74
TYR49
| ||
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 | ||
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 | 14 | Native recall | 0.82 |
| Jaccard | 0.78 | RMSD | - |
| HB strict | 7 | Strict recall | 0.54 |
| HB same residue+role | 6 | HB role recall | 0.55 |
| HB same residue | 6 | HB residue recall | 0.55 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 105 | 1.463807451337273 | -0.86103 | -17.64 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 103 | 2.179240911546821 | -1.10688 | -23.9826 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 136 | 2.2833906419122694 | -0.977102 | -15.2062 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 106 | 3.0781322210493935 | -0.755485 | -20.4458 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 93 | 3.099851131733896 | -0.881887 | -24.0642 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 133 | 3.156262945020302 | -0.667012 | -12.8472 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 58 | 3.454106868880225 | -0.830529 | -17.5797 | 9 | 15 | 14 | 0.82 | 0.55 | - | no | Current |
| 78 | 4.754243717183497 | -1.05201 | -29.1107 | 10 | 21 | 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
-17.580kcal/mol
Ligand efficiency (LE)
-0.6062kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.787
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
416.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.52
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-41.47kcal/mol
Minimised FF energy
-74.36kcal/mol
SASA & burial
✓ computed
SASA (unbound)
649.5Ų
Total solvent-accessible surface area of free ligand
BSA total
438.1Ų
Buried surface area upon binding
BSA apolar
311.8Ų
Hydrophobic contacts buried
BSA polar
126.3Ų
Polar contacts buried
Fraction buried
67.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2204.9Ų
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
715.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)