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
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
26.1 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.65, Jaccard 0.52, H-bond role recall 0.17
Reason: no major geometry red flags detected
4 protein-contact clashes
5 intramolecular clashes
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.876 kcal/mol/HA)
✓ Good fit quality (FQ -8.36)
✓ Good H-bonds (4 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ High strain energy (26.1 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (7)
✗ Many internal clashes (10)
Score
-25.392
kcal/mol
LE
-0.876
kcal/mol/HA
Fit Quality
-8.36
FQ (Leeson)
HAC
29
heavy atoms
MW
401
Da
LogP
2.59
cLogP
Final rank
1.3243
rank score
Inter norm
-0.972
normalised
Contacts
15
H-bonds 5
Interaction summary
HBD 1
HBA 3
HY 6
PI 3
CLASH 5
Interaction summary
HBD 1
HBA 3
HY 6
PI 3
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
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 | 11 | Native recall | 0.65 |
| Jaccard | 0.52 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| HB same residue+role | 1 | HB role recall | 0.17 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 129 | 1.3243080058459407 | -0.971899 | -25.3925 | 5 | 15 | 11 | 0.65 | 0.17 | - | no | Current |
| 146 | 2.038497674388139 | -0.915901 | -20.5087 | 2 | 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
-25.392kcal/mol
Ligand efficiency (LE)
-0.8756kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.358
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
401.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.59
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
1.80kcal/mol
Minimised FF energy
-24.34kcal/mol
SASA & burial
✓ computed
SASA (unbound)
628.2Ų
Total solvent-accessible surface area of free ligand
BSA total
537.9Ų
Buried surface area upon binding
BSA apolar
480.0Ų
Hydrophobic contacts buried
BSA polar
57.9Ų
Polar contacts buried
Fraction buried
85.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
89.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1699.4Ų
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
1047.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)