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
27.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.71, Jaccard 0.67, H-bond role recall 0.45
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
71% of hydrophobic surface is solvent-exposed (12/17 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.402 kcal/mol/HA)
✓ Good fit quality (FQ -12.17)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ High strain energy (27.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-30.838
kcal/mol
LE
-1.402
kcal/mol/HA
Fit Quality
-12.17
FQ (Leeson)
HAC
22
heavy atoms
MW
291
Da
LogP
3.28
cLogP
Interaction summary
HB 9
HY 3
PI 1
CLASH 3
⚠ Exposure 70%
Interaction summary
HB 9
HY 3
PI 1
CLASH 3
⚠ Exposure 70%
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
71% of hydrophobic surface is solvent-exposed (12/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 17
Buried (contacted) 5
Exposed 12
LogP 3.28
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 4.201 | Score | -30.838 |
|---|---|---|---|
| Inter norm | -1.175 | Intra norm | -0.227 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 9 |
| Artifact reason | geometry warning; 13 clashes; 2 protein clashes; moderate strain Δ 27.4 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
CYS72
GLY73
HIS105
HIS14
HIS141
SER46
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 | 12 | Native recall | 0.71 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 5 | Strict recall | 0.38 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
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
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.838kcal/mol
Ligand efficiency (LE)
-1.4017kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.170
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
291.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.28
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
94.52kcal/mol
Minimised FF energy
67.15kcal/mol
SASA & burial
✓ computed
SASA (unbound)
527.5Ų
Total solvent-accessible surface area of free ligand
BSA total
377.3Ų
Buried surface area upon binding
BSA apolar
287.7Ų
Hydrophobic contacts buried
BSA polar
89.6Ų
Polar contacts buried
Fraction buried
71.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2173.1Ų
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
682.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)