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 strong
SASA done
Strain ΔE
61.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.37, Jaccard 0.36, H-bond role recall 0.60
Reason: strain 61.1 kcal/mol
strain ΔE 61.1 kcal/mol
2 protein-contact clashes
78% of hydrophobic surface is solvent-exposed (21/27 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.812 kcal/mol/HA)
✓ Good fit quality (FQ -8.25)
✓ Strong H-bond network (6 bonds)
✓ Good burial (56% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Extreme strain energy (61.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-29.218
kcal/mol
LE
-0.812
kcal/mol/HA
Fit Quality
-8.25
FQ (Leeson)
HAC
36
heavy atoms
MW
499
Da
LogP
1.32
cLogP
Final rank
3.2535
rank score
Inter norm
-0.958
normalised
Contacts
11
H-bonds 11
Interaction summary
HBD 2
HBA 4
HY 1
PI 0
CLASH 2
Interaction summary
HBD 2
HBA 4
HY 1
PI 0
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | 0.36 | RMSD | - |
| HB strict | 1 | Strict recall | 0.08 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 2 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 314 | 1.8403910590171513 | -0.854739 | -30.533 | 4 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 265 | 3.2535200232590507 | -0.957853 | -29.2182 | 11 | 11 | 10 | 0.37 | 0.60 | - | no | Current |
| 236 | 3.7004113748811287 | -0.679853 | -25.4528 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 273 | 3.8458234271104295 | -0.611894 | -16.691 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 276 | 3.866792565577019 | -0.639361 | -14.0366 | 8 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 196 | 4.975403539515579 | -0.770765 | -16.315 | 12 | 20 | 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
-29.218kcal/mol
Ligand efficiency (LE)
-0.8116kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.249
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
498.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.32
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
61.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
87.56kcal/mol
Minimised FF energy
26.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
861.3Ų
Total solvent-accessible surface area of free ligand
BSA total
481.2Ų
Buried surface area upon binding
BSA apolar
381.6Ų
Hydrophobic contacts buried
BSA polar
99.5Ų
Polar contacts buried
Fraction buried
55.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3243.9Ų
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
1542.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)