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 mixed
SASA done
Strain ΔE
31.6 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.26, Jaccard 0.19, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.550 kcal/mol/HA)
✓ Good fit quality (FQ -13.46)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Very high strain energy (31.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-34.096
kcal/mol
LE
-1.550
kcal/mol/HA
Fit Quality
-13.46
FQ (Leeson)
HAC
22
heavy atoms
MW
341
Da
LogP
1.09
cLogP
Interaction summary
HB 10
HY 12
PI 0
CLASH 3
Interaction summary
HB 10
HY 12
PI 0
CLASH 3
| Final rank | 1.948 | Score | -34.096 |
|---|---|---|---|
| Inter norm | -1.454 | Intra norm | -0.096 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 10 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash; 1 cofactor-context clash; high strain Δ 31.6 | ||
| Residues |
ARG287
ASP327
CYS52
CYS57
GLY56
ILE199
LEU334
LYS60
LYS61
MET333
NDP800
PHE367
PRO336
SER162
THR335
THR51
| ||
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
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 | 7 | Native recall | 0.26 |
| Jaccard | 0.19 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 290 | 1.2400918844836533 | -1.32566 | -31.3991 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 280 | 1.9479445650642564 | -1.4541 | -34.0963 | 10 | 16 | 7 | 0.26 | 0.20 | - | no | Current |
| 316 | 2.5592650100209733 | -1.17281 | -27.0734 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 351 | 3.2313434384288184 | -0.875523 | -24.1215 | 7 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 368 | 4.637274696060762 | -1.28123 | -30.212 | 11 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 364 | 4.759061949290954 | -1.02841 | -24.1546 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 268 | 4.912505546384761 | -1.13782 | -27.2844 | 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
-34.096kcal/mol
Ligand efficiency (LE)
-1.5498kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.456
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
341.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.09
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-49.05kcal/mol
Minimised FF energy
-80.64kcal/mol
SASA & burial
✓ computed
SASA (unbound)
563.9Ų
Total solvent-accessible surface area of free ligand
BSA total
498.8Ų
Buried surface area upon binding
BSA apolar
364.9Ų
Hydrophobic contacts buried
BSA polar
133.8Ų
Polar contacts buried
Fraction buried
88.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3009.5Ų
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
1465.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)