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 medium
Native mixed
SASA done
Strain ΔE
9.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.33, Jaccard 0.29, H-bond role recall 0.20
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.341 kcal/mol/HA)
✓ Good fit quality (FQ -12.02)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Moderate strain (9.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-32.178
kcal/mol
LE
-1.341
kcal/mol/HA
Fit Quality
-12.02
FQ (Leeson)
HAC
24
heavy atoms
MW
409
Da
LogP
3.72
cLogP
Interaction summary
HB 7
HY 9
PI 0
CLASH 3
Interaction summary
HB 7
HY 9
PI 0
CLASH 3
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 1.654 | Score | -32.178 |
|---|---|---|---|
| Inter norm | -1.301 | Intra norm | -0.039 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 7 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; 3 severe cofactor-context clashes | ||
| Residues |
ARG228
ARG287
ASP330
GLY196
GLY197
LEU227
LEU332
LYS306
MET333
NDP800
PHE198
PHE230
TYR221
| ||
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 | 9 | Native recall | 0.33 |
| Jaccard | 0.29 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 437 | 1.0622373773057405 | -1.14598 | -24.2338 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 384 | 1.6543390194869305 | -1.30146 | -32.1781 | 7 | 13 | 9 | 0.33 | 0.20 | - | no | Current |
| 393 | 1.8894308683503533 | -1.45598 | -31.2552 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 417 | 2.420917382962812 | -1.29827 | -28.0042 | 14 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 427 | 2.9718852536009854 | -0.815124 | -17.3361 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 421 | 4.01819321477796 | -0.930807 | -22.6703 | 10 | 13 | 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
-32.178kcal/mol
Ligand efficiency (LE)
-1.3408kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.016
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
409.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.72
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
103.06kcal/mol
Minimised FF energy
93.66kcal/mol
SASA & burial
✓ computed
SASA (unbound)
617.5Ų
Total solvent-accessible surface area of free ligand
BSA total
491.9Ų
Buried surface area upon binding
BSA apolar
396.7Ų
Hydrophobic contacts buried
BSA polar
95.2Ų
Polar contacts buried
Fraction buried
79.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3010.0Ų
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
4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1541.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)