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
37.2 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.26, Jaccard 0.18, H-bond role recall 0.40
Reason: no major geometry red flags detected
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.393 kcal/mol/HA)
✓ Good fit quality (FQ -12.48)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (91% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Very high strain energy (37.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-33.436
kcal/mol
LE
-1.393
kcal/mol/HA
Fit Quality
-12.48
FQ (Leeson)
HAC
24
heavy atoms
MW
327
Da
LogP
1.78
cLogP
Interaction summary
HB 10
HY 14
PI 0
CLASH 1
Interaction summary
HB 10
HY 14
PI 0
CLASH 1
| Final rank | 3.557 | Score | -33.436 |
|---|---|---|---|
| Inter norm | -1.423 | Intra norm | 0.030 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 10 |
| Artifact reason | geometry warning; 11 clashes; 3 protein clashes; 1 cofactor-context clash; high strain Δ 37.2 | ||
| Residues |
ALA363
ALA365
CYS57
GLU202
GLY56
ILE199
LEU334
LYS60
NDP800
PHE182
PHE203
PHE367
PRO336
SER178
SER364
THR335
THR51
VAL55
| ||
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 | 0.18 | RMSD | - |
| HB strict | 2 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 221 | 2.0077812066392657 | -1.17383 | -28.7197 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 241 | 2.3528098974898835 | -0.863335 | -23.523 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 240 | 3.2412632912082957 | -1.01964 | -23.5904 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 210 | 3.449396824714685 | -1.26484 | -27.6814 | 14 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 257 | 3.5567855665101447 | -1.42321 | -33.4356 | 10 | 18 | 7 | 0.26 | 0.40 | - | no | Current |
| 150 | 4.302305108254698 | -1.30222 | -27.4863 | 14 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 267 | 4.3230268269514776 | -0.796912 | -19.6092 | 9 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 162 | 4.726542041013789 | -1.23245 | -28.9868 | 12 | 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
-33.436kcal/mol
Ligand efficiency (LE)
-1.3932kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.485
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
327.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.78
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
105.64kcal/mol
Minimised FF energy
68.43kcal/mol
SASA & burial
✓ computed
SASA (unbound)
563.1Ų
Total solvent-accessible surface area of free ligand
BSA total
512.6Ų
Buried surface area upon binding
BSA apolar
387.6Ų
Hydrophobic contacts buried
BSA polar
125.0Ų
Polar contacts buried
Fraction buried
91.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3013.8Ų
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
1484.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)