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
28.2 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.37, Jaccard 0.33, H-bond role recall 0.60
Reason: no major geometry red flags detected
1 protein-contact clashes
3 intramolecular clashes
96% of hydrophobic surface is solvent-exposed (22/23 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 (-0.836 kcal/mol/HA)
✓ Good fit quality (FQ -8.43)
✓ Strong H-bond network (10 bonds)
✓ Good burial (63% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ High strain energy (28.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-29.244
kcal/mol
LE
-0.836
kcal/mol/HA
Fit Quality
-8.43
FQ (Leeson)
HAC
35
heavy atoms
MW
480
Da
LogP
-0.01
cLogP
Final rank
2.3885
rank score
Inter norm
-0.915
normalised
Contacts
13
H-bonds 13
Interaction summary
HBD 2
HBA 8
HY 2
PI 0
CLASH 3
Interaction summary
HBD 2
HBA 8
HY 2
PI 0
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | 2WOV | Contacts | 27 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA284
ALA365
ARG222
ARG228
ARG287
ASN223
ASN254
GLN165
GLU202
GLY195
GLY196
GLY197
GLY286
ILE199
ILE285
LEU227
LEU334
LYS60
MET333
NDP800
PHE198
PHE367
PRO167
SER200
TYR221
VAL194
VAL366
| ||
| Current overlap | 10 | Native recall | 0.37 |
| Jaccard | 0.33 | RMSD | - |
| HB strict | 4 | Strict recall | 0.33 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 2 | HB residue recall | 0.50 |
Protein summary
493 residues
| Protein target | T19 | Atoms | 7541 |
|---|---|---|---|
| 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:330; TYR:294; ASP:264; 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
C:NDP800
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 16 | 0.9318185768716343 | -1.30717 | -37.5358 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 8 | 2.388499099499413 | -0.914871 | -29.2444 | 13 | 13 | 10 | 0.37 | 0.60 | - | no | Current |
| 13 | 2.5152482222802455 | -1.00556 | -32.4774 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 16 | 3.282337965943439 | -1.05297 | -33.6719 | 13 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 7 | 3.3491516125816614 | -0.614311 | -21.785 | 9 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 15 | 4.881715648797068 | -0.997797 | -30.3693 | 11 | 18 | 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
-29.244kcal/mol
Ligand efficiency (LE)
-0.8356kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.428
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
479.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.01
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
37.62kcal/mol
Minimised FF energy
9.45kcal/mol
SASA & burial
✓ computed
SASA (unbound)
787.8Ų
Total solvent-accessible surface area of free ligand
BSA total
496.5Ų
Buried surface area upon binding
BSA apolar
357.6Ų
Hydrophobic contacts buried
BSA polar
138.9Ų
Polar contacts buried
Fraction buried
63.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3135.7Ų
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
4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1532.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)