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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
15.4 kcal/mol
Protein clashes
0
Internal clashes
10
Native overlap
contact recall 0.83, Jaccard 0.56
Reason: 10 internal clashes
10 intramolecular clashes
39% of hydrophobic surface appears solvent-exposed (9/23 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 (-0.734 kcal/mol/HA)
✓ Good fit quality (FQ -7.08)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ Moderate strain (15.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-22.015
kcal/mol
LE
-0.734
kcal/mol/HA
Fit Quality
-7.08
FQ (Leeson)
HAC
30
heavy atoms
MW
543
Da
LogP
6.80
cLogP
Final rank
2.7367
rank score
Inter norm
-0.778
normalised
Contacts
16
H-bonds 2
Interaction summary
HBD 2
HY 6
PI 1
CLASH 0
Interaction summary
HBD 2
HY 6
PI 1
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA90
ARG74
GLY85
LEU73
LYS89
MET70
PHE83
PRO212
PRO213
SER86
SER87
VAL88
| ||
| Current overlap | 10 | Native recall | 0.83 |
| Jaccard | 0.56 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
493 residues
| Protein target | T16 | Atoms | 7551 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221 | ||
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:FAD501
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 672 | 0.514679985666019 | -0.894442 | -23.4063 | 2 | 18 | 0 | 0.00 | - | - | no | Open |
| 678 | 0.8105169412196023 | -0.697208 | -16.6119 | 3 | 9 | 0 | 0.00 | - | - | no | Open |
| 674 | 2.040126377083499 | -0.900631 | -24.1106 | 3 | 19 | 0 | 0.00 | - | - | no | Open |
| 676 | 2.2112625099320904 | -0.894359 | -20.4876 | 4 | 14 | 0 | 0.00 | - | - | no | Open |
| 672 | 2.23237953245765 | -0.881443 | -23.9855 | 2 | 19 | 0 | 0.00 | - | - | no | Open |
| 674 | 2.7366679178174302 | -0.777686 | -22.0152 | 2 | 16 | 10 | 0.83 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.015kcal/mol
Ligand efficiency (LE)
-0.7338kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.079
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
543.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.80
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
42.52kcal/mol
Minimised FF energy
27.07kcal/mol
SASA & burial
✓ computed
SASA (unbound)
683.4Ų
Total solvent-accessible surface area of free ligand
BSA total
518.6Ų
Buried surface area upon binding
BSA apolar
468.0Ų
Hydrophobic contacts buried
BSA polar
50.7Ų
Polar contacts buried
Fraction buried
75.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3190.0Ų
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
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1501.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)