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
32.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.76, Jaccard 0.65, H-bond role recall 0.36
Reason: no major geometry red flags detected
1 protein-contact clashes
75% of hydrophobic surface is solvent-exposed (18/24 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 (-0.732 kcal/mol/HA)
✓ Good fit quality (FQ -7.19)
✓ Strong H-bond network (8 bonds)
✓ Good burial (64% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Very high strain energy (32.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-23.410
kcal/mol
LE
-0.732
kcal/mol/HA
Fit Quality
-7.19
FQ (Leeson)
HAC
32
heavy atoms
MW
456
Da
LogP
4.62
cLogP
Interaction summary
HB 8
HY 4
PI 1
CLASH 1
⚠ Exposure 75%
Interaction summary
HB 8
HY 4
PI 1
CLASH 1
⚠ Exposure 75%
Solvent-exposed hydrophobic surface — desolvation penalty likely
75% of hydrophobic surface is solvent-exposed (18/24 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 24
Buried (contacted) 6
Exposed 18
LogP 4.62
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 3.457 | Score | -23.410 |
|---|---|---|---|
| Inter norm | -0.814 | Intra norm | 0.082 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 8 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; high strain Δ 32.9 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
ASP44
CYS72
GLY73
HIS105
HIS14
HIS141
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 | 13 | Native recall | 0.76 |
| Jaccard | 0.65 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 435 | 0.810335944503407 | -1.00379 | -31.6549 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 458 | 2.1776711055970015 | -0.835379 | -25.4018 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 399 | 2.553696514850279 | -1.05214 | -33.4383 | 5 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 405 | 3.457171693765687 | -0.813551 | -23.41 | 8 | 16 | 13 | 0.76 | 0.36 | - | no | Current |
| 417 | 4.625661533511195 | -0.841732 | -28.7628 | 9 | 18 | 5 | 0.29 | 0.36 | - | no | Open |
| 440 | 4.772858685610839 | -0.989254 | -30.8756 | 8 | 22 | 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
-23.410kcal/mol
Ligand efficiency (LE)
-0.7316kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.194
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
455.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.62
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
59.03kcal/mol
Minimised FF energy
26.09kcal/mol
SASA & burial
✓ computed
SASA (unbound)
731.7Ų
Total solvent-accessible surface area of free ligand
BSA total
471.8Ų
Buried surface area upon binding
BSA apolar
406.9Ų
Hydrophobic contacts buried
BSA polar
64.9Ų
Polar contacts buried
Fraction buried
64.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2382.4Ų
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
693.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)