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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
15.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.30, Jaccard 0.21, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.258 kcal/mol/HA)
✓ Good fit quality (FQ -11.59)
✓ Good H-bonds (3 bonds)
✓ Deep burial (95% SASA buried)
✗ Moderate strain (15.4 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (6)
Score
-32.695
kcal/mol
LE
-1.258
kcal/mol/HA
Fit Quality
-11.59
FQ (Leeson)
HAC
26
heavy atoms
MW
349
Da
LogP
0.14
cLogP
Final rank
0.2316
rank score
Inter norm
-1.231
normalised
Contacts
20
H-bonds 10
Interaction summary
HBA 3
PC 1
HY 5
PI 0
CLASH 1
Interaction summary
HBA 3
PC 1
HY 5
PI 0
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.
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 | 8 | Native recall | 0.30 |
| Jaccard | 0.21 | RMSD | - |
| HB strict | 3 | Strict recall | 0.25 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 544 | 0.23158115016668995 | -1.23143 | -32.6948 | 10 | 20 | 8 | 0.30 | 0.40 | - | no | Current |
| 533 | 1.9279944703250649 | -1.07377 | -35.4971 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 557 | 2.135489178188233 | -0.737278 | -25.5446 | 11 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 543 | 3.378183793606937 | -1.06111 | -27.5432 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 563 | 4.787378041497767 | -1.01267 | -30.6833 | 16 | 17 | 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
-32.695kcal/mol
Ligand efficiency (LE)
-1.2575kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.586
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
349.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.14
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
160.25kcal/mol
Minimised FF energy
144.88kcal/mol
SASA & burial
✓ computed
SASA (unbound)
538.0Ų
Total solvent-accessible surface area of free ligand
BSA total
511.6Ų
Buried surface area upon binding
BSA apolar
259.7Ų
Hydrophobic contacts buried
BSA polar
251.9Ų
Polar contacts buried
Fraction buried
95.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
50.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2865.2Ų
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
1475.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)