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
54.2 kcal/mol
Protein clashes
12
Internal clashes
12
Native overlap
contact recall 0.81, Jaccard 0.74, H-bond role recall 0.00
Reason: 12 protein-contact clashes, 12 internal clashes, strain 54.2 kcal/mol
strain ΔE 54.2 kcal/mol
12 protein-contact clashes
12 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.439 kcal/mol/HA)
✓ Good fit quality (FQ -4.35)
✓ Good H-bonds (3 bonds)
✓ Deep burial (96% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Extreme strain energy (54.2 kcal/mol)
✗ Geometry warnings
✗ Severe protein-contact clashes (13)
✗ Many internal clashes (13)
Score
-14.477
kcal/mol
LE
-0.439
kcal/mol/HA
Fit Quality
-4.35
FQ (Leeson)
HAC
33
heavy atoms
MW
494
Da
LogP
3.85
cLogP
Interaction summary
HB 3
HY 24
PI 2
CLASH 12
Interaction summary
HB 3
HY 24
PI 2
CLASH 12
| Final rank | 2.872 | Score | -14.477 |
|---|---|---|---|
| Inter norm | -0.686 | Intra norm | 0.234 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 3 |
| Artifact reason | geometry warning; 13 clashes; 13 protein contact clashes; 1 cofactor-context clash; high strain Δ 54.2 | ||
| Residues |
ALA34
ARG100
ARG59
ASP54
HIS182
ILE160
ILE47
LEU90
LEU97
MET55
NDP301
PHE58
PHE94
PRO91
THR184
TYR166
TYR57
VAL32
VAL33
| ||
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
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| 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 | 17 | Native recall | 0.81 |
| Jaccard | 0.74 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 460 | 0.6519554372013339 | -0.915239 | -35.1703 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 534 | 2.127728214395661 | -0.824251 | -28.5767 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 475 | 2.871927623588891 | -0.685703 | -14.4773 | 3 | 19 | 17 | 0.81 | 0.00 | - | no | Current |
| 489 | 2.8906447746620816 | -0.804653 | -27.0185 | 6 | 15 | 1 | 0.05 | 0.00 | - | no | Open |
| 519 | 3.3855222369474767 | -0.670185 | -21.9094 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 493 | 4.566432422981136 | -0.578552 | -20.134 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 491 | 4.603364842916196 | -0.786607 | -26.2787 | 3 | 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
-14.477kcal/mol
Ligand efficiency (LE)
-0.4387kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.353
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
494.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.85
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
54.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-0.34kcal/mol
Minimised FF energy
-54.55kcal/mol
SASA & burial
✓ computed
SASA (unbound)
737.3Ų
Total solvent-accessible surface area of free ligand
BSA total
707.5Ų
Buried surface area upon binding
BSA apolar
597.4Ų
Hydrophobic contacts buried
BSA polar
110.1Ų
Polar contacts buried
Fraction buried
96.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1859.9Ų
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
576.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)