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 high
Native strong
SASA done
Strain ΔE
21.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.71, Jaccard 0.67, H-bond role recall 0.45
Reason: no major geometry red flags detected
2 protein-contact 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 (-0.809 kcal/mol/HA)
✓ Good fit quality (FQ -6.90)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ High strain energy (21.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-16.981
kcal/mol
LE
-0.809
kcal/mol/HA
Fit Quality
-6.90
FQ (Leeson)
HAC
21
heavy atoms
MW
277
Da
LogP
3.83
cLogP
Interaction summary
HB 10
HY 2
PI 2
CLASH 2
⚠ Exposure 62%
Interaction summary
HB 10
HY 2
PI 2
CLASH 2
⚠ Exposure 62%
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 (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 3.83
H-bonds 10
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 3.273 | Score | -16.981 |
|---|---|---|---|
| Inter norm | -1.147 | Intra norm | 0.339 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 10 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; moderate strain Δ 21.2 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
HIS105
HIS14
HIS141
SER46
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 | 7 | Strict recall | 0.54 |
| 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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 561 | 3.2726214109760745 | -1.14733 | -16.9807 | 10 | 13 | 12 | 0.71 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-16.981kcal/mol
Ligand efficiency (LE)
-0.8086kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.897
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
277.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.83
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
42.49kcal/mol
Minimised FF energy
21.27kcal/mol
SASA & burial
✓ computed
SASA (unbound)
504.3Ų
Total solvent-accessible surface area of free ligand
BSA total
353.2Ų
Buried surface area upon binding
BSA apolar
282.0Ų
Hydrophobic contacts buried
BSA polar
71.3Ų
Polar contacts buried
Fraction buried
70.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2156.6Ų
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
681.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)