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
48.6 kcal/mol
Protein clashes
2
Internal clashes
12
Native overlap
contact recall 0.22, Jaccard 0.14, H-bond role recall 0.40
Reason: 12 internal clashes, strain 48.6 kcal/mol
strain ΔE 48.6 kcal/mol
2 protein-contact clashes
12 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.071 kcal/mol/HA)
✓ Good fit quality (FQ -10.22)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ Extreme strain energy (48.6 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (12)
Score
-31.063
kcal/mol
LE
-1.071
kcal/mol/HA
Fit Quality
-10.22
FQ (Leeson)
HAC
29
heavy atoms
MW
382
Da
LogP
3.61
cLogP
Final rank
0.7212
rank score
Inter norm
-1.087
normalised
Contacts
21
H-bonds 5
Interaction summary
HBA 2
HY 10
PI 2
CLASH 0
Interaction summary
HBA 2
HY 10
PI 2
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
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 | 6 | Native recall | 0.22 |
| Jaccard | 0.14 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 478 | 0.7211984913946701 | -1.08719 | -31.0629 | 5 | 21 | 6 | 0.22 | 0.40 | - | no | Current |
| 496 | 2.9255430322928193 | -0.955188 | -24.8733 | 7 | 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
-31.063kcal/mol
Ligand efficiency (LE)
-1.0711kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.225
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
382.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.61
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
48.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
94.21kcal/mol
Minimised FF energy
45.64kcal/mol
SASA & burial
✓ computed
SASA (unbound)
678.7Ų
Total solvent-accessible surface area of free ligand
BSA total
631.8Ų
Buried surface area upon binding
BSA apolar
566.1Ų
Hydrophobic contacts buried
BSA polar
65.8Ų
Polar contacts buried
Fraction buried
93.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
89.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3193.6Ų
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
1481.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)