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
34.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.26, Jaccard 0.18, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.000 kcal/mol/HA)
✓ Good fit quality (FQ -10.00)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (87%)
✗ Very high strain energy (34.7 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Many internal clashes (25)
Score
-33.993
kcal/mol
LE
-1.000
kcal/mol/HA
Fit Quality
-10.00
FQ (Leeson)
HAC
34
heavy atoms
MW
476
Da
LogP
3.33
cLogP
Interaction summary
HB 6
HY 23
PI 1
CLASH 2
Interaction summary
HB 6
HY 23
PI 1
CLASH 2
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 2.393 | Score | -33.993 |
|---|---|---|---|
| Inter norm | -0.945 | Intra norm | -0.055 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 6 |
| Artifact reason | geometry warning; 25 clashes; 4 protein contact clashes; high strain Δ 34.7 | ||
| Residues |
ARG287
ASP327
CYS52
CYS57
GLY56
ILE199
LEU334
LYS60
LYS61
MET333
NDP800
PHE182
PHE203
PHE367
PRO336
SER178
THR335
THR51
VAL55
| ||
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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 552 | 1.6576278380815919 | -0.656537 | -23.089 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 512 | 2.392663923194533 | -0.94457 | -33.9929 | 6 | 19 | 7 | 0.26 | 0.20 | - | no | Current |
| 570 | 3.1556443484883 | -0.748134 | -25.0111 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 536 | 3.3681136230714483 | -0.85907 | -28.691 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 539 | 3.4526540395330247 | -0.737126 | -23.0241 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 561 | 4.097305358856439 | -0.729279 | -25.6304 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 5.624928820907552 | -0.774059 | -26.3588 | 6 | 11 | 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
-33.993kcal/mol
Ligand efficiency (LE)
-0.9998kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.004
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
475.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.33
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
166.33kcal/mol
Minimised FF energy
131.64kcal/mol
SASA & burial
✓ computed
SASA (unbound)
688.1Ų
Total solvent-accessible surface area of free ligand
BSA total
617.3Ų
Buried surface area upon binding
BSA apolar
539.4Ų
Hydrophobic contacts buried
BSA polar
77.8Ų
Polar contacts buried
Fraction buried
89.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3194.1Ų
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
1467.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)