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
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
27.9 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.48, Jaccard 0.46, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
3 intramolecular clashes
62% of hydrophobic surface is solvent-exposed (16/26 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 (-0.818 kcal/mol/HA)
✓ Good fit quality (FQ -8.38)
✓ Good H-bonds (3 bonds)
✓ Deep burial (65% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ High strain energy (27.9 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Many internal clashes (16)
Score
-30.273
kcal/mol
LE
-0.818
kcal/mol/HA
Fit Quality
-8.38
FQ (Leeson)
HAC
37
heavy atoms
MW
552
Da
LogP
5.58
cLogP
Final rank
1.6967
rank score
Inter norm
-0.889
normalised
Contacts
14
H-bonds 3
Interaction summary
HBA 3
HY 2
PI 0
CLASH 3
Interaction summary
HBA 3
HY 2
PI 0
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
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 | 13 | Native recall | 0.48 |
| Jaccard | 0.46 | RMSD | - |
| HB strict | 1 | Strict recall | 0.08 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.25 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 17 | 1.696689240757872 | -0.88945 | -30.2726 | 3 | 14 | 13 | 0.48 | 0.20 | - | no | Current |
| 31 | 1.8181900263923123 | -0.842635 | -28.9563 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 34 | 1.9720018861540387 | -0.756542 | -20.7118 | 2 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 31 | 2.8261011475996827 | -0.748837 | -25.6083 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 30 | 2.8419970825468495 | -0.641834 | -17.5687 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 40 | 3.270248076072721 | -0.753324 | -24.4048 | 5 | 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
-30.273kcal/mol
Ligand efficiency (LE)
-0.8182kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.376
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
552.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.58
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
62.39kcal/mol
Minimised FF energy
34.49kcal/mol
SASA & burial
✓ computed
SASA (unbound)
792.3Ų
Total solvent-accessible surface area of free ligand
BSA total
516.0Ų
Buried surface area upon binding
BSA apolar
452.1Ų
Hydrophobic contacts buried
BSA polar
63.9Ų
Polar contacts buried
Fraction buried
65.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3093.6Ų
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
1618.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)