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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
107.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.30, Jaccard 0.20, H-bond role recall 0.40
Reason: strain 107.8 kcal/mol
strain ΔE 107.8 kcal/mol
1 protein-contact clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.747 kcal/mol/HA)
✓ Good fit quality (FQ -7.47)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (90% SASA buried)
✗ Extreme strain energy (107.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-25.381
kcal/mol
LE
-0.747
kcal/mol/HA
Fit Quality
-7.47
FQ (Leeson)
HAC
34
heavy atoms
MW
512
Da
LogP
0.84
cLogP
Final rank
3.5602
rank score
Inter norm
-0.922
normalised
Contacts
22
H-bonds 11
Interaction summary
HBD 2
HBA 4
PC 1
HY 6
PI 1
CLASH 1
Interaction summary
HBD 2
HBA 4
PC 1
HY 6
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: 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 | 8 | Native recall | 0.30 |
| Jaccard | 0.20 | RMSD | - |
| HB strict | 3 | Strict recall | 0.25 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 352 | 2.6591088902554145 | -0.663334 | -20.9923 | 12 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 294 | 2.8169198974226206 | -0.763427 | -26.2094 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 279 | 2.9386173620887566 | -0.824993 | -29.3038 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 276 | 3.5602412451860346 | -0.921957 | -25.3809 | 11 | 22 | 8 | 0.30 | 0.40 | - | no | Current |
| 397 | 4.2664490731645195 | -0.737645 | -24.1163 | 16 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 258 | 5.655842000188189 | -0.696138 | -14.4763 | 16 | 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
-25.381kcal/mol
Ligand efficiency (LE)
-0.7465kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.469
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
512.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.84
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
107.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-82.33kcal/mol
Minimised FF energy
-190.08kcal/mol
SASA & burial
✓ computed
SASA (unbound)
698.1Ų
Total solvent-accessible surface area of free ligand
BSA total
631.9Ų
Buried surface area upon binding
BSA apolar
336.7Ų
Hydrophobic contacts buried
BSA polar
295.2Ų
Polar contacts buried
Fraction buried
90.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
53.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2984.2Ų
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
1462.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)