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
Weak or marginal quality
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
23.5 kcal/mol
Protein clashes
3
Internal clashes
5
Native overlap
contact recall 0.53, Jaccard 0.41, H-bond role recall 0.33
Reason: no major geometry red flags detected
3 protein-contact clashes
5 intramolecular clashes
52% of hydrophobic surface appears solvent-exposed (11/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.094 kcal/mol/HA)
✓ Good fit quality (FQ -10.21)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ High strain energy (23.5 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Many internal clashes (14)
Score
-29.538
kcal/mol
LE
-1.094
kcal/mol/HA
Fit Quality
-10.21
FQ (Leeson)
HAC
27
heavy atoms
MW
375
Da
LogP
4.45
cLogP
Final rank
1.2635
rank score
Inter norm
-1.089
normalised
Contacts
14
H-bonds 5
Interaction summary
HBA 1
PC 1
HY 3
PI 2
CLASH 5
Interaction summary
HBA 1
PC 1
HY 3
PI 2
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.
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 | 0.41 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 621 | 0.7273040778789923 | -0.954499 | -26.3543 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 620 | 1.2634532461947954 | -1.08927 | -29.5379 | 5 | 14 | 9 | 0.53 | 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
-29.538kcal/mol
Ligand efficiency (LE)
-1.0940kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.207
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
375.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.45
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
50.44kcal/mol
Minimised FF energy
26.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
624.4Ų
Total solvent-accessible surface area of free ligand
BSA total
539.3Ų
Buried surface area upon binding
BSA apolar
443.9Ų
Hydrophobic contacts buried
BSA polar
95.4Ų
Polar contacts buried
Fraction buried
86.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1667.2Ų
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
1037.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)