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
33.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.89, H-bond role recall 0.55
Reason: no major geometry red flags detected
2 protein-contact clashes
72% of hydrophobic surface is solvent-exposed (23/32 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 (-0.707 kcal/mol/HA)
✓ Good fit quality (FQ -7.43)
✓ Strong H-bond network (13 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Very high strain energy (33.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-29.005
kcal/mol
LE
-0.707
kcal/mol/HA
Fit Quality
-7.43
FQ (Leeson)
HAC
41
heavy atoms
MW
560
Da
LogP
3.95
cLogP
Interaction summary
HB 13
HY 5
PI 2
CLASH 2
⚠ Exposure 71%
Interaction summary
HB 13
HY 5
PI 2
CLASH 2
⚠ Exposure 71%
Solvent-exposed hydrophobic surface — desolvation penalty likely
72% of hydrophobic surface is solvent-exposed (23/32 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 32
Buried (contacted) 9
Exposed 23
LogP 3.95
H-bonds 13
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (9 atoms exposed)
| Final rank | 4.648 | Score | -29.005 |
|---|---|---|---|
| Inter norm | -0.759 | Intra norm | 0.049 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 13 |
| Artifact reason | geometry warning; 16 clashes; 2 protein clashes; high strain Δ 31.8 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
SER46
THR45
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 | 17 | Native recall | 1.00 |
| Jaccard | 0.89 | RMSD | - |
| HB strict | 8 | Strict recall | 0.62 |
| HB same residue+role | 6 | HB role recall | 0.55 |
| HB same residue | 8 | HB residue recall | 0.73 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 248 | 1.6246835831422717 | -0.601813 | -18.4868 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 288 | 3.61104421216062 | -0.746466 | -24.3592 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 263 | 3.659223228327489 | -0.540403 | -20.4251 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 174 | 4.64758826859403 | -0.759112 | -29.0047 | 13 | 19 | 17 | 1.00 | 0.55 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.005kcal/mol
Ligand efficiency (LE)
-0.7074kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.433
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
41HA
Physicochemical properties
Molecular weight
559.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.95
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
115.50kcal/mol
Minimised FF energy
81.95kcal/mol
SASA & burial
✓ computed
SASA (unbound)
898.5Ų
Total solvent-accessible surface area of free ligand
BSA total
562.0Ų
Buried surface area upon binding
BSA apolar
453.2Ų
Hydrophobic contacts buried
BSA polar
108.8Ų
Polar contacts buried
Fraction buried
62.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2500.1Ų
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
700.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)