Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
49.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.64, H-bond role recall 0.25
Reason: strain 49.4 kcal/mol
strain ΔE 49.4 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.613 kcal/mol/HA)
✓ Good fit quality (FQ -6.03)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Extreme strain energy (49.4 kcal/mol)
✗ No H-bonds detected
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Many internal clashes (10)
Score
-19.604
kcal/mol
LE
-0.613
kcal/mol/HA
Fit Quality
-6.03
FQ (Leeson)
HAC
32
heavy atoms
MW
472
Da
LogP
2.92
cLogP
Final rank
1.0399
rank score
Inter norm
-0.766
normalised
Contacts
20
H-bonds 2
Interaction summary
HB 0
PC 1
HY 11
PI 4
CLASH 3
Interaction summary
HB 0
PC 1
HY 11
PI 4
CLASH 3
HBD/HBA · H-bonds (geometric)
No hbd/hba · h-bonds (geometric) detected for this pose.
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: 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 | 0.64 | RMSD | - |
| HB strict | 1 | Strict recall | 0.20 |
| HB same residue+role | 1 | HB role recall | 0.25 |
| HB same residue | 1 | HB residue recall | 0.25 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 306 | 1.0399415523302338 | -0.766429 | -19.6042 | 2 | 20 | 16 | 0.76 | 0.25 | - | no | Current |
| 325 | 1.7622918572042872 | -0.72501 | -21.6638 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 339 | 1.8756034248014986 | -0.623323 | -14.0022 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 288 | 1.941314636855978 | -1.0223 | -32.8605 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 287 | 2.3052789623162595 | -0.860388 | -25.3677 | 5 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 391 | 3.0126089501724107 | -0.713197 | -22.3245 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 376 | 3.3532299697325993 | -0.830769 | -26.6969 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 306 | 3.4749873966025415 | -0.769904 | -23.8063 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 254 | 3.797851917357343 | -0.767932 | -25.5546 | 10 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 267 | 4.770866832306279 | -0.910892 | -28.0567 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 266 | 4.987550321084067 | -1.00253 | -26.5548 | 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
-19.604kcal/mol
Ligand efficiency (LE)
-0.6126kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.025
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
471.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.92
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
49.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-46.74kcal/mol
Minimised FF energy
-96.17kcal/mol
SASA & burial
✓ computed
SASA (unbound)
753.0Ų
Total solvent-accessible surface area of free ligand
BSA total
704.2Ų
Buried surface area upon binding
BSA apolar
515.0Ų
Hydrophobic contacts buried
BSA polar
189.1Ų
Polar contacts buried
Fraction buried
93.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1773.7Ų
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
597.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)