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
37.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.94, Jaccard 0.94, H-bond role recall 0.70
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.772 kcal/mol/HA)
✓ Good fit quality (FQ -7.37)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Very high strain energy (37.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-22.400
kcal/mol
LE
-0.772
kcal/mol/HA
Fit Quality
-7.37
FQ (Leeson)
HAC
29
heavy atoms
MW
391
Da
LogP
3.16
cLogP
Interaction summary
HB 10
HY 5
PI 3
CLASH 2
Interaction summary
HB 10
HY 5
PI 3
CLASH 2
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
| Final rank | 3.455 | Score | -22.400 |
|---|---|---|---|
| Inter norm | -1.036 | Intra norm | 0.264 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 10 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 37.4 | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
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 | 0.94 | RMSD | - |
| HB strict | 8 | Strict recall | 0.67 |
| HB same residue+role | 7 | HB role recall | 0.70 |
| HB same residue | 7 | HB residue recall | 0.70 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 371 | 0.6766080884637871 | -0.850212 | -23.5297 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 456 | 1.3298642730659846 | -0.876871 | -20.7915 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 371 | 1.6592905543340895 | -1.1365 | -32.2539 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 321 | 2.4630441993751795 | -0.956144 | -26.0216 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 382 | 2.4869569999026053 | -0.980507 | -24.896 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 317 | 3.15422312242859 | -1.11678 | -29.9725 | 9 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 390 | 3.359899098482382 | -0.766488 | -19.917 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 348 | 3.455414740609191 | -1.03631 | -22.4 | 10 | 15 | 15 | 0.94 | 0.70 | - | no | Current |
| 482 | 3.675347513604983 | -0.805846 | -18.1081 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 420 | 3.9699373391131556 | -0.795492 | -16.2866 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 325 | 4.385363427863706 | -0.85659 | -21.0096 | 11 | 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
-22.400kcal/mol
Ligand efficiency (LE)
-0.7724kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.373
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
391.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.16
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
101.01kcal/mol
Minimised FF energy
63.63kcal/mol
SASA & burial
✓ computed
SASA (unbound)
659.6Ų
Total solvent-accessible surface area of free ligand
BSA total
444.8Ų
Buried surface area upon binding
BSA apolar
346.4Ų
Hydrophobic contacts buried
BSA polar
98.4Ų
Polar contacts buried
Fraction buried
67.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2160.7Ų
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
830.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)