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
26.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.94, Jaccard 0.89, H-bond role recall 0.73
Reason: no major geometry red flags detected
2 protein-contact clashes
83% of hydrophobic surface is solvent-exposed (19/23 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 (-0.791 kcal/mol/HA)
✓ Good fit quality (FQ -7.71)
✓ Strong H-bond network (12 bonds)
✓ Good burial (61% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ High strain energy (26.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-24.529
kcal/mol
LE
-0.791
kcal/mol/HA
Fit Quality
-7.71
FQ (Leeson)
HAC
31
heavy atoms
MW
456
Da
LogP
3.55
cLogP
Interaction summary
HB 12
HY 4
PI 0
CLASH 2
⚠ Exposure 82%
Interaction summary
HB 12
HY 4
PI 0
CLASH 2
⚠ Exposure 82%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Solvent-exposed hydrophobic surface — desolvation penalty likely
83% of hydrophobic surface is solvent-exposed (19/23 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 23
Buried (contacted) 4
Exposed 19
LogP 3.55
H-bonds 12
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 2.863 | Score | -24.529 |
|---|---|---|---|
| Inter norm | -0.765 | Intra norm | -0.026 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 12 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash; moderate strain Δ 25.9 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
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 | 16 | Native recall | 0.94 |
| Jaccard | 0.89 | RMSD | - |
| HB strict | 9 | Strict recall | 0.69 |
| HB same residue+role | 8 | HB role recall | 0.73 |
| HB same residue | 8 | HB residue recall | 0.73 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 425 | 0.9551242018102782 | -1.06722 | -33.4755 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 516 | 1.2768242680188926 | -0.846457 | -25.3115 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 434 | 2.462248084836765 | -0.70609 | -19.2858 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 402 | 2.8628267461029133 | -0.765245 | -24.5292 | 12 | 17 | 16 | 0.94 | 0.73 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.529kcal/mol
Ligand efficiency (LE)
-0.7913kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.709
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
455.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.55
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
52.10kcal/mol
Minimised FF energy
26.08kcal/mol
SASA & burial
✓ computed
SASA (unbound)
760.2Ų
Total solvent-accessible surface area of free ligand
BSA total
464.6Ų
Buried surface area upon binding
BSA apolar
325.5Ų
Hydrophobic contacts buried
BSA polar
139.0Ų
Polar contacts buried
Fraction buried
61.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2327.5Ų
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
704.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)