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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
25.6 kcal/mol
Protein clashes
2
Internal clashes
6
Native overlap
contact recall 0.71, Jaccard 0.60, H-bond role recall 0.33
Reason: 6 internal clashes
2 protein-contact clashes
6 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.882 kcal/mol/HA)
✓ Good fit quality (FQ -8.23)
✓ Good H-bonds (3 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ High strain energy (25.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-23.825
kcal/mol
LE
-0.882
kcal/mol/HA
Fit Quality
-8.23
FQ (Leeson)
HAC
27
heavy atoms
MW
376
Da
LogP
3.69
cLogP
Final rank
1.8806
rank score
Inter norm
-1.049
normalised
Contacts
15
H-bonds 5
Interaction summary
HBA 3
PC 1
HY 7
PI 2
CLASH 6
Interaction summary
HBA 3
PC 1
HY 7
PI 2
CLASH 6
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
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 | ligand | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 12 | Native recall | 0.71 |
| Jaccard | 0.60 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 3 | HB residue recall | 0.60 |
Protein summary
274 residues
| Protein target | T05 | Atoms | 4108 |
|---|---|---|---|
| Residues | 274 | Chains | 2 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
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:NDP302
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 645 | 1.8805825715907276 | -1.04875 | -23.8247 | 5 | 15 | 12 | 0.71 | 0.33 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.825kcal/mol
Ligand efficiency (LE)
-0.8824kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.232
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
376.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.69
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
90.77kcal/mol
Minimised FF energy
65.18kcal/mol
SASA & burial
✓ computed
SASA (unbound)
592.7Ų
Total solvent-accessible surface area of free ligand
BSA total
523.3Ų
Buried surface area upon binding
BSA apolar
443.0Ų
Hydrophobic contacts buried
BSA polar
80.3Ų
Polar contacts buried
Fraction buried
88.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1654.7Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1037.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)