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
29.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.81, Jaccard 0.68, H-bond role recall 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
43% of hydrophobic surface appears solvent-exposed (9/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.934 kcal/mol/HA)
✓ Good fit quality (FQ -9.19)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ High strain energy (29.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-29.896
kcal/mol
LE
-0.934
kcal/mol/HA
Fit Quality
-9.19
FQ (Leeson)
HAC
32
heavy atoms
MW
506
Da
LogP
5.68
cLogP
Final rank
3.0258
rank score
Inter norm
-0.881
normalised
Contacts
16
H-bonds 13
Interaction summary
HBA 8
HY 4
PI 4
CLASH 2
Interaction summary
HBA 8
HY 4
PI 4
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
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: permissive.
| 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 | 0.68 | RMSD | - |
| HB strict | 7 | Strict recall | 0.58 |
| HB same residue+role | 5 | HB role recall | 0.50 |
| HB same residue | 6 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 561 | 0.991444987448605 | -1.05881 | -32.8775 | 4 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 576 | 1.3467598950311672 | -0.895269 | -27.8686 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 579 | 2.2751673109175004 | -0.983458 | -43.7544 | 8 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 566 | 3.0258276638234807 | -0.881178 | -29.8958 | 13 | 16 | 13 | 0.81 | 0.50 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.896kcal/mol
Ligand efficiency (LE)
-0.9342kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.187
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
506.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.68
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
57.60kcal/mol
Minimised FF energy
28.49kcal/mol
SASA & burial
✓ computed
SASA (unbound)
686.2Ų
Total solvent-accessible surface area of free ligand
BSA total
498.1Ų
Buried surface area upon binding
BSA apolar
355.8Ų
Hydrophobic contacts buried
BSA polar
142.3Ų
Polar contacts buried
Fraction buried
72.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2157.7Ų
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
830.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)