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
16.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.30, Jaccard 0.23, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.511 kcal/mol/HA)
✓ Good fit quality (FQ -13.12)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (60%)
✗ Moderate strain (16.3 kcal/mol)
✗ Geometry warnings
Score
-33.239
kcal/mol
LE
-1.511
kcal/mol/HA
Fit Quality
-13.12
FQ (Leeson)
HAC
22
heavy atoms
MW
333
Da
LogP
2.74
cLogP
Interaction summary
HB 6
HY 11
PI 0
CLASH 1
Interaction summary
HB 6
HY 11
PI 0
CLASH 1
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 1.480 | Score | -33.239 |
|---|---|---|---|
| Inter norm | -1.453 | Intra norm | -0.057 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 6 |
| Artifact reason | geometry warning; 3 clashes; 2 protein clashes | ||
| Residues |
ALA365
ARG287
ASP327
CYS57
GLY56
ILE199
LEU334
LYS60
MET333
NDP800
PHE367
PRO336
SER162
SER364
THR335
THR51
| ||
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 | 0.23 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 377 | 1.203407316066101 | -1.44123 | -29.4257 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 364 | 1.4803074616739718 | -1.45342 | -33.2394 | 6 | 16 | 8 | 0.30 | 0.00 | - | no | Current |
| 429 | 1.546574384664465 | -0.993888 | -21.6201 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 409 | 2.0041694598625175 | -1.07628 | -20.4611 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 389 | 2.5970311124973797 | -1.1137 | -24.5546 | 5 | 15 | 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
-33.239kcal/mol
Ligand efficiency (LE)
-1.5109kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.117
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
333.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.74
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
27.67kcal/mol
Minimised FF energy
11.36kcal/mol
SASA & burial
✓ computed
SASA (unbound)
551.2Ų
Total solvent-accessible surface area of free ligand
BSA total
508.4Ų
Buried surface area upon binding
BSA apolar
306.6Ų
Hydrophobic contacts buried
BSA polar
201.8Ų
Polar contacts buried
Fraction buried
92.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
60.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2929.1Ų
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
1472.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)