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
38.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.82, Jaccard 0.78, H-bond role recall 0.36
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
62% of hydrophobic surface is solvent-exposed (10/16 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 (-1.348 kcal/mol/HA)
✓ Good fit quality (FQ -12.08)
✓ Strong H-bond network (14 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Very high strain energy (38.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-32.345
kcal/mol
LE
-1.348
kcal/mol/HA
Fit Quality
-12.08
FQ (Leeson)
HAC
24
heavy atoms
MW
326
Da
LogP
2.38
cLogP
Interaction summary
HB 14
HY 6
PI 1
CLASH 3
⚠ Exposure 62%
Interaction summary
HB 14
HY 6
PI 1
CLASH 3
⚠ Exposure 62%
Solvent-exposed hydrophobic surface — desolvation penalty likely
62% of hydrophobic surface is solvent-exposed (10/16 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 16
Buried (contacted) 6
Exposed 10
LogP 2.38
H-bonds 14
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 2.650 | Score | -32.345 |
|---|---|---|---|
| Inter norm | -1.045 | Intra norm | -0.303 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 14 |
| Artifact reason | geometry warning; 10 clashes; 1 protein clash; high strain Δ 38.6 | ||
| 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 | 6 | Strict recall | 0.46 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 597 | 0.067938204709174 | -1.37122 | -32.4902 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 622 | 1.1959443571032502 | -1.0687 | -29.4649 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 592 | 1.5173985335030495 | -1.19629 | -37.5817 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 606 | 2.321576433442885 | -1.38185 | -36.0151 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 610 | 2.649542773492627 | -1.04458 | -32.3454 | 14 | 15 | 14 | 0.82 | 0.36 | - | no | Current |
| 621 | 3.945865475066838 | -1.05056 | -15.0057 | 11 | 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
-32.345kcal/mol
Ligand efficiency (LE)
-1.3477kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.078
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
326.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.38
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
183.11kcal/mol
Minimised FF energy
144.47kcal/mol
SASA & burial
✓ computed
SASA (unbound)
591.0Ų
Total solvent-accessible surface area of free ligand
BSA total
432.9Ų
Buried surface area upon binding
BSA apolar
337.6Ų
Hydrophobic contacts buried
BSA polar
95.4Ų
Polar contacts buried
Fraction buried
73.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2228.5Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
669.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)