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 medium
Native strong
SASA done
Strain ΔE
9.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.76, H-bond role recall 0.50
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.103 kcal/mol/HA)
✓ Good fit quality (FQ -9.23)
✓ Deep burial (98% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Moderate strain (9.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-22.062
kcal/mol
LE
-1.103
kcal/mol/HA
Fit Quality
-9.23
FQ (Leeson)
HAC
20
heavy atoms
MW
270
Da
LogP
2.58
cLogP
Final rank
1.6945
rank score
Inter norm
-1.215
normalised
Contacts
16
H-bonds 6
Interaction summary
HBD 2
HY 7
PI 2
CLASH 3
Interaction summary
HBD 2
HY 7
PI 2
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.
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 | 8RHT | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA34
ASP54
HIS182
ILE160
ILE47
LEU90
LEU97
MET55
NDP301
PHE233
PHE58
PHE94
PRO91
SER89
THR184
THR86
TRP49
TYR166
TYR57
VAL32
VAL33
| ||
| Current overlap | 16 | Native recall | 0.76 |
| Jaccard | 0.76 | RMSD | - |
| HB strict | 3 | Strict recall | 0.60 |
| HB same residue+role | 2 | HB role recall | 0.50 |
| HB same residue | 3 | HB residue recall | 0.75 |
Protein summary
223 residues
| Protein target | T06 | Atoms | 3452 |
|---|---|---|---|
| Residues | 223 | Chains | 1 |
| Residue summary | ARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74 | ||
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
A:NDP301
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 71 | -0.6425912787373339 | -1.5364 | -30.9434 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 69 | 1.694537518369985 | -1.21538 | -22.0621 | 6 | 16 | 16 | 0.76 | 0.50 | - | no | Current |
| 59 | 2.771198386423646 | -1.45638 | -28.5775 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 80 | 3.406183505862583 | -1.22511 | -24.0434 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 45 | 3.6208123248314377 | -1.33156 | -25.6337 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 75 | 4.1092730997855105 | -1.13353 | -20.6307 | 8 | 13 | 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
-22.062kcal/mol
Ligand efficiency (LE)
-1.1031kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.231
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
270.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.58
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
70.01kcal/mol
Minimised FF energy
60.54kcal/mol
SASA & burial
✓ computed
SASA (unbound)
471.7Ų
Total solvent-accessible surface area of free ligand
BSA total
464.5Ų
Buried surface area upon binding
BSA apolar
338.9Ų
Hydrophobic contacts buried
BSA polar
125.6Ų
Polar contacts buried
Fraction buried
98.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1549.8Ų
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
1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
602.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)