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
9.9 kcal/mol
Protein clashes
2
Internal clashes
1
Native overlap
contact recall 0.26, Jaccard 0.18, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.278 kcal/mol/HA)
✓ Good fit quality (FQ -11.62)
✓ Good H-bonds (4 bonds)
✓ Deep burial (95% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Moderate strain (9.9 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Internal clashes (8)
Score
-31.942
kcal/mol
LE
-1.278
kcal/mol/HA
Fit Quality
-11.62
FQ (Leeson)
HAC
25
heavy atoms
MW
364
Da
LogP
5.35
cLogP
Interaction summary
HB 4
HY 24
PI 1
CLASH 1
Interaction summary
HB 4
HY 24
PI 1
CLASH 1
| Final rank | 0.133 | Score | -31.942 |
|---|---|---|---|
| Inter norm | -1.243 | Intra norm | -0.035 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 4 |
| Artifact reason | geometry warning; 8 clashes; 2 protein contact clashes; 1 cofactor-context clash | ||
| Residues |
ALA365
ARG287
ASP327
CYS52
CYS57
GLY56
ILE199
LEU334
LYS60
NDP800
PHE182
PHE203
PHE367
PRO336
SER178
SER364
THR335
THR51
VAL55
| ||
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
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 | 7 | Native recall | 0.26 |
| Jaccard | 0.18 | 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 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 638 | 0.1332537097269928 | -1.24291 | -31.9417 | 4 | 19 | 7 | 0.26 | 0.00 | - | no | Current |
| 631 | 1.5936328964263133 | -1.07005 | -25.9196 | 5 | 10 | 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
-31.942kcal/mol
Ligand efficiency (LE)
-1.2777kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.615
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
363.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.35
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
23.07kcal/mol
Minimised FF energy
13.20kcal/mol
SASA & burial
✓ computed
SASA (unbound)
622.0Ų
Total solvent-accessible surface area of free ligand
BSA total
589.0Ų
Buried surface area upon binding
BSA apolar
487.8Ų
Hydrophobic contacts buried
BSA polar
101.2Ų
Polar contacts buried
Fraction buried
94.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3103.8Ų
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
1481.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)