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
36.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.94, Jaccard 0.88, H-bond role recall 0.70
Reason: no major geometry red flags detected
1 protein-contact clashes
61% of hydrophobic surface is solvent-exposed (11/18 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 (-1.097 kcal/mol/HA)
✓ Good fit quality (FQ -10.23)
✓ Strong H-bond network (15 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ Very high strain energy (36.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-29.611
kcal/mol
LE
-1.097
kcal/mol/HA
Fit Quality
-10.23
FQ (Leeson)
HAC
27
heavy atoms
MW
415
Da
LogP
1.19
cLogP
Interaction summary
HB 15
HY 4
PI 1
CLASH 1
⚠ Exposure 61%
Interaction summary
HB 15
HY 4
PI 1
CLASH 1
⚠ Exposure 61%
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
61% of hydrophobic surface is solvent-exposed (11/18 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 18
Buried (contacted) 7
Exposed 11
LogP 1.19
H-bonds 15
Exposed fragments:
phenyl (5/5 atoms exposed)phenyl (5/5 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 3.817 | Score | -29.611 |
|---|---|---|---|
| Inter norm | -1.177 | Intra norm | 0.080 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 15 |
| Artifact reason | geometry warning; 8 clashes; 2 protein clashes; high strain Δ 36.3 | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
ARG46
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
SER74
TYR49
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXS | Contacts | 16 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
SER74
TYR49
| ||
| Current overlap | 15 | Native recall | 0.94 |
| Jaccard | 0.88 | RMSD | - |
| HB strict | 9 | Strict recall | 0.75 |
| HB same residue+role | 7 | HB role recall | 0.70 |
| HB same residue | 8 | HB residue recall | 0.80 |
Protein summary
302 residues
| Protein target | T12 | Atoms | 4598 |
|---|---|---|---|
| Residues | 302 | Chains | 2 |
| Residue summary | ARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:CSD72
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 616 | 3.147423451270175 | -0.969471 | -24.0552 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 597 | 3.816956584422617 | -1.17655 | -29.6107 | 15 | 16 | 15 | 0.94 | 0.70 | - | no | Current |
| 609 | 3.9524670316859187 | -0.834271 | -21.0301 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 603 | 4.47613555924801 | -1.03848 | -22.4069 | 16 | 17 | 5 | 0.31 | 0.20 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.611kcal/mol
Ligand efficiency (LE)
-1.0967kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.232
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
414.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.19
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-108.58kcal/mol
Minimised FF energy
-144.89kcal/mol
SASA & burial
✓ computed
SASA (unbound)
656.3Ų
Total solvent-accessible surface area of free ligand
BSA total
456.8Ų
Buried surface area upon binding
BSA apolar
281.7Ų
Hydrophobic contacts buried
BSA polar
175.1Ų
Polar contacts buried
Fraction buried
69.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
61.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2172.6Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
760.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)