Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
41.7 kcal/mol
Protein clashes
1
Internal clashes
5
Native overlap
contact recall 0.44, Jaccard 0.38, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
5 intramolecular clashes
60% of hydrophobic surface is solvent-exposed (15/25 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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.836 kcal/mol/HA)
✓ Good fit quality (FQ -8.55)
✓ Good H-bonds (5 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Extreme strain energy (41.7 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Many internal clashes (18)
Score
-30.916
kcal/mol
LE
-0.836
kcal/mol/HA
Fit Quality
-8.55
FQ (Leeson)
HAC
37
heavy atoms
MW
496
Da
LogP
3.70
cLogP
Final rank
1.9627
rank score
Inter norm
-0.856
normalised
Contacts
17
H-bonds 7
Interaction summary
HBD 2
HBA 3
HY 5
PI 2
CLASH 5
Interaction summary
HBD 2
HBA 3
HY 5
PI 2
CLASH 5
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 | 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 | 12 | Native recall | 0.44 |
| Jaccard | 0.38 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 316 | 1.8123558888823286 | -0.914971 | -21.5319 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 297 | 1.9627077011111906 | -0.856269 | -30.9159 | 7 | 17 | 12 | 0.44 | 0.20 | - | no | Current |
| 418 | 2.3141715410362105 | -0.726701 | -18.6058 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 355 | 2.726833739982142 | -0.713638 | -21.039 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 424 | 3.1850901586862492 | -0.660276 | -18.3491 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 343 | 3.3671400095098463 | -0.659786 | -18.405 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 403 | 3.4226305072552163 | -0.802117 | -22.9256 | 6 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 341 | 3.944633688462524 | -0.82259 | -30.6165 | 13 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 361 | 4.005889507463297 | -0.627719 | -10.5556 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 297 | 5.174209118778855 | -0.756161 | -20.4707 | 15 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 461 | 5.260205083426885 | -0.657307 | -17.5204 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 390 | 5.533655050515578 | -0.807189 | -28.3864 | 11 | 22 | 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
-30.916kcal/mol
Ligand efficiency (LE)
-0.8356kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.554
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
496.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.70
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
41.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
139.67kcal/mol
Minimised FF energy
97.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
757.5Ų
Total solvent-accessible surface area of free ligand
BSA total
630.2Ų
Buried surface area upon binding
BSA apolar
460.1Ų
Hydrophobic contacts buried
BSA polar
170.1Ų
Polar contacts buried
Fraction buried
83.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3097.2Ų
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
4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1524.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)