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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
47.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.26, Jaccard 0.17, H-bond role recall 0.00
Reason: strain 47.7 kcal/mol
strain ΔE 47.7 kcal/mol
1 protein-contact clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.142 kcal/mol/HA)
✓ Good fit quality (FQ -10.65)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Extreme strain energy (47.7 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (11)
Score
-30.829
kcal/mol
LE
-1.142
kcal/mol/HA
Fit Quality
-10.65
FQ (Leeson)
HAC
27
heavy atoms
MW
406
Da
LogP
4.24
cLogP
Final rank
0.7332
rank score
Inter norm
-1.170
normalised
Contacts
20
H-bonds 5
Interaction summary
HBA 2
PC 1
HY 9
PI 3
CLASH 1
Interaction summary
HBA 2
PC 1
HY 9
PI 3
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.
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 | 7 | Native recall | 0.26 |
| Jaccard | 0.17 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 534 | 0.7331711787524858 | -1.16989 | -30.8294 | 5 | 20 | 7 | 0.26 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.829kcal/mol
Ligand efficiency (LE)
-1.1418kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.653
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
405.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.24
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
47.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
40.97kcal/mol
Minimised FF energy
-6.73kcal/mol
SASA & burial
✓ computed
SASA (unbound)
656.8Ų
Total solvent-accessible surface area of free ligand
BSA total
607.6Ų
Buried surface area upon binding
BSA apolar
484.3Ų
Hydrophobic contacts buried
BSA polar
123.3Ų
Polar contacts buried
Fraction buried
92.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3101.9Ų
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
1490.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)