Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
16.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.22, Jaccard 0.16, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.407 kcal/mol/HA)
✓ Good fit quality (FQ -12.00)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (98% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Moderate strain (16.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-29.538
kcal/mol
LE
-1.407
kcal/mol/HA
Fit Quality
-12.00
FQ (Leeson)
HAC
21
heavy atoms
MW
281
Da
LogP
2.60
cLogP
Final rank
2.3420
rank score
Inter norm
-1.533
normalised
Contacts
16
H-bonds 12
Interaction summary
HBD 3
HBA 5
HY 6
PI 2
CLASH 2
Interaction summary
HBD 3
HBA 5
HY 6
PI 2
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.
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 | 6 | Native recall | 0.22 |
| Jaccard | 0.16 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 258 | 2.3420135660914787 | -1.53302 | -29.5379 | 12 | 16 | 6 | 0.22 | 0.20 | - | no | Current |
| 154 | 2.400779548921348 | -1.32061 | -21.2342 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 164 | 2.6797035114445573 | -1.42417 | -25.8283 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 212 | 2.7518602202948346 | -1.26901 | -22.4487 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 242 | 3.682208440401173 | -1.2496 | -20.6703 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 152 | 4.565359075204383 | -1.34456 | -22.3208 | 11 | 18 | 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
-29.538kcal/mol
Ligand efficiency (LE)
-1.4066kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.998
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
281.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.60
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
44.08kcal/mol
Minimised FF energy
27.58kcal/mol
SASA & burial
✓ computed
SASA (unbound)
505.7Ų
Total solvent-accessible surface area of free ligand
BSA total
494.0Ų
Buried surface area upon binding
BSA apolar
389.7Ų
Hydrophobic contacts buried
BSA polar
104.2Ų
Polar contacts buried
Fraction buried
97.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2994.2Ų
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
1471.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)