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 strong
SASA done
Strain ΔE
6.6 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.47, H-bond role recall 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
3 intramolecular clashes
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (6.6 kcal/mol)
✓ Excellent LE (-1.431 kcal/mol/HA)
✓ Good fit quality (FQ -12.63)
✓ Good H-bonds (4 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-32.925
kcal/mol
LE
-1.431
kcal/mol/HA
Fit Quality
-12.63
FQ (Leeson)
HAC
23
heavy atoms
MW
305
Da
LogP
2.61
cLogP
Interaction summary
HB 4
HY 9
PI 2
CLASH 3
⚠ Exposure 35%
Interaction summary
HB 4
HY 9
PI 2
CLASH 3
⚠ Exposure 35%
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
Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 11
Exposed 6
LogP 2.61
H-bonds 4
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 1.276 | Score | -32.925 |
|---|---|---|---|
| Inter norm | -1.440 | Intra norm | 0.009 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 4 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; 1 severe cofactor-context clash | ||
| Residues |
ARG17
ASP181
GLY225
LEU188
LEU226
LYS16
NDP302
PHE113
TYR194
VAL230
ARG287
| ||
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 | 0.47 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 3 | HB role recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 103 | 1.2757744230391386 | -1.44048 | -32.9251 | 4 | 11 | 9 | 0.53 | 0.50 | - | no | Current |
| 97 | 2.943116397207334 | -1.22625 | -28.5339 | 11 | 15 | 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
-32.925kcal/mol
Ligand efficiency (LE)
-1.4315kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.634
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
305.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.61
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
6.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-3.09kcal/mol
Minimised FF energy
-9.71kcal/mol
SASA & burial
✓ computed
SASA (unbound)
570.0Ų
Total solvent-accessible surface area of free ligand
BSA total
495.8Ų
Buried surface area upon binding
BSA apolar
391.9Ų
Hydrophobic contacts buried
BSA polar
103.9Ų
Polar contacts buried
Fraction buried
87.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1590.3Ų
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
1052.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)