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 mixed
SASA done
Strain ΔE
8.0 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.53, Jaccard 0.45, H-bond role recall 0.33
Reason: no major geometry red flags detected
2 protein-contact clashes
4 intramolecular clashes
61% of hydrophobic surface is solvent-exposed (11/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.308 kcal/mol/HA)
✓ Good fit quality (FQ -11.73)
✓ Good H-bonds (3 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (8.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-31.402
kcal/mol
LE
-1.308
kcal/mol/HA
Fit Quality
-11.73
FQ (Leeson)
HAC
24
heavy atoms
MW
319
Da
LogP
2.54
cLogP
Final rank
1.5191
rank score
Inter norm
-1.333
normalised
Contacts
12
H-bonds 4
Interaction summary
HBD 1
HBA 2
PC 1
HY 2
PI 2
CLASH 4
Interaction summary
HBD 1
HBA 2
PC 1
HY 2
PI 2
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
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: strict.
| 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 | 9 | Native recall | 0.53 |
| Jaccard | 0.45 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 123 | 0.1451304685743686 | -0.97239 | -17.5241 | 0 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 432 | 1.5191133026187429 | -1.33258 | -31.4017 | 4 | 12 | 9 | 0.53 | 0.33 | - | no | Current |
| 492 | 1.8540039960023957 | -0.91064 | -21.3878 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 490 | 2.0689198891758367 | -1.11677 | -20.0821 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 135 | 2.8257868822054713 | -0.950388 | -21.5698 | 5 | 11 | 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
-31.402kcal/mol
Ligand efficiency (LE)
-1.3084kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.726
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
319.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.54
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
8.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
18.43kcal/mol
Minimised FF energy
10.40kcal/mol
SASA & burial
✓ computed
SASA (unbound)
586.7Ų
Total solvent-accessible surface area of free ligand
BSA total
509.2Ų
Buried surface area upon binding
BSA apolar
406.6Ų
Hydrophobic contacts buried
BSA polar
102.7Ų
Polar contacts buried
Fraction buried
86.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1625.4Ų
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
1031.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)