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
23.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.94, Jaccard 0.94, H-bond role recall 0.50
Reason: no major geometry red flags detected
1 protein-contact clashes
53% of hydrophobic surface appears solvent-exposed (10/19 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 (-1.086 kcal/mol/HA)
✓ Good fit quality (FQ -10.00)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ High strain energy (23.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-28.228
kcal/mol
LE
-1.086
kcal/mol/HA
Fit Quality
-10.00
FQ (Leeson)
HAC
26
heavy atoms
MW
366
Da
LogP
4.37
cLogP
Final rank
4.5147
rank score
Inter norm
-1.170
normalised
Contacts
15
H-bonds 12
Interaction summary
HBD 1
HBA 7
HY 3
PI 4
CLASH 1
Interaction summary
HBD 1
HBA 7
HY 3
PI 4
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
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 | 15 | Native recall | 0.94 |
| Jaccard | 0.94 | RMSD | - |
| HB strict | 7 | Strict recall | 0.58 |
| HB same residue+role | 5 | HB role recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 566 | 1.241895999707433 | -0.864578 | -18.0317 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 538 | 2.3367169218121906 | -1.146 | -18.8322 | 13 | 17 | 5 | 0.31 | 0.30 | - | no | Open |
| 544 | 3.9129939104118683 | -1.0791 | -22.6874 | 12 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 532 | 4.5147354506759125 | -1.17 | -28.2284 | 12 | 15 | 15 | 0.94 | 0.50 | - | no | Current |
| 562 | 5.044498045614265 | -0.930602 | -23.1365 | 13 | 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
-28.228kcal/mol
Ligand efficiency (LE)
-1.0857kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.003
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
366.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.37
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
69.80kcal/mol
Minimised FF energy
45.87kcal/mol
SASA & burial
✓ computed
SASA (unbound)
607.4Ų
Total solvent-accessible surface area of free ligand
BSA total
413.1Ų
Buried surface area upon binding
BSA apolar
283.9Ų
Hydrophobic contacts buried
BSA polar
129.1Ų
Polar contacts buried
Fraction buried
68.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2132.2Ų
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
776.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)