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 high
Native mixed
SASA done
Strain ΔE
29.9 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.37, Jaccard 0.28, H-bond role recall 0.20
Reason: no major geometry red flags detected
41% of hydrophobic surface appears solvent-exposed (9/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.268 kcal/mol/HA)
✓ Good fit quality (FQ -12.11)
✓ Good H-bonds (5 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ High strain energy (29.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-36.777
kcal/mol
LE
-1.268
kcal/mol/HA
Fit Quality
-12.11
FQ (Leeson)
HAC
29
heavy atoms
MW
380
Da
LogP
3.75
cLogP
Final rank
2.0320
rank score
Inter norm
-1.266
normalised
Contacts
19
H-bonds 10
Interaction summary
HBD 2
HBA 3
PC 2
HY 5
PI 3
CLASH 1
Interaction summary
HBD 2
HBA 3
PC 2
HY 5
PI 3
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
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
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 10 | Native recall | 0.37 |
| Jaccard | 0.28 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 418 | 1.6519417124966898 | -1.13469 | -32.3302 | 9 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 399 | 1.8354677458848982 | -1.12292 | -25.9684 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 385 | 2.0319683187008457 | -1.26571 | -36.7774 | 10 | 19 | 10 | 0.37 | 0.20 | - | no | Current |
| 475 | 2.2594311359412096 | -1.03515 | -31.9582 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 428 | 2.5921100555360286 | -0.755558 | -24.5417 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 394 | 6.047368516924349 | -0.921961 | -23.0042 | 13 | 16 | 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
-36.777kcal/mol
Ligand efficiency (LE)
-1.2682kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.106
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
380.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.75
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
123.07kcal/mol
Minimised FF energy
93.15kcal/mol
SASA & burial
✓ computed
SASA (unbound)
642.9Ų
Total solvent-accessible surface area of free ligand
BSA total
548.8Ų
Buried surface area upon binding
BSA apolar
468.6Ų
Hydrophobic contacts buried
BSA polar
80.1Ų
Polar contacts buried
Fraction buried
85.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3133.2Ų
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
1493.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)