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
22.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.81, Jaccard 0.65, H-bond role recall 0.30
Reason: no major geometry red flags detected
1 protein-contact clashes
64% of hydrophobic surface is solvent-exposed (16/25 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 (-0.837 kcal/mol/HA)
✓ Good fit quality (FQ -8.30)
✓ Strong H-bond network (6 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ High strain energy (22.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-27.623
kcal/mol
LE
-0.837
kcal/mol/HA
Fit Quality
-8.30
FQ (Leeson)
HAC
33
heavy atoms
MW
475
Da
LogP
4.89
cLogP
Final rank
2.3636
rank score
Inter norm
-0.897
normalised
Contacts
17
H-bonds 10
Interaction summary
HBD 1
HBA 5
HY 4
PI 4
CLASH 1
Interaction summary
HBD 1
HBA 5
HY 4
PI 4
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 13 | Native recall | 0.81 |
| Jaccard | 0.65 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| HB same residue+role | 3 | HB role recall | 0.30 |
| HB same residue | 4 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 495 | 0.7636299668614087 | -0.944298 | -31.6224 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 547 | 1.3092080501017846 | -0.748973 | -24.4712 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 568 | 2.1136660153511535 | -0.774735 | -23.372 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 508 | 2.363635055852463 | -0.896611 | -27.6232 | 10 | 17 | 13 | 0.81 | 0.30 | - | no | Current |
| 506 | 2.512933131032401 | -0.972941 | -29.8517 | 9 | 26 | 0 | 0.00 | 0.00 | - | no | Open |
| 547 | 2.7275152541986074 | -0.63594 | -20.531 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 3.647484580817899 | -0.738297 | -22.9327 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 517 | 3.7491718068183464 | -0.73996 | -23.338 | 12 | 20 | 5 | 0.31 | 0.30 | - | no | Open |
| 555 | 4.578227095484919 | -0.730577 | -20.9774 | 4 | 14 | 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
-27.623kcal/mol
Ligand efficiency (LE)
-0.8371kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.305
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
474.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.89
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.30kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
91.52kcal/mol
Minimised FF energy
69.22kcal/mol
SASA & burial
✓ computed
SASA (unbound)
801.5Ų
Total solvent-accessible surface area of free ligand
BSA total
493.9Ų
Buried surface area upon binding
BSA apolar
326.3Ų
Hydrophobic contacts buried
BSA polar
167.6Ų
Polar contacts buried
Fraction buried
61.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2275.8Ų
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
801.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)