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 but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
14.1 kcal/mol
Protein clashes
0
Internal clashes
8
Native overlap
contact recall 0.54, Jaccard 0.35
Reason: 8 internal clashes
8 intramolecular clashes
55% of hydrophobic surface appears solvent-exposed (11/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.748 kcal/mol/HA)
✓ Good fit quality (FQ -6.80)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Moderate strain (14.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-18.703
kcal/mol
LE
-0.748
kcal/mol/HA
Fit Quality
-6.80
FQ (Leeson)
HAC
25
heavy atoms
MW
340
Da
LogP
3.91
cLogP
Final rank
2.6023
rank score
Inter norm
-0.939
normalised
Contacts
14
H-bonds 3
Interaction summary
HBD 2
HY 10
PI 1
CLASH 0
Interaction summary
HBD 2
HY 10
PI 1
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | 9IFF | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA209
ARG74
ASN208
GLY214
GLY215
GLY85
LEU73
LYS211
MET70
PHE83
PRO212
PRO213
VAL88
| ||
| Current overlap | 7 | Native recall | 0.54 |
| Jaccard | 0.35 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
489 residues
| Protein target | T15 | Atoms | 7420 |
|---|---|---|---|
| Residues | 489 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:204 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 66 | 0.8305093453479375 | -0.860099 | -15.002 | 6 | 19 | 0 | 0.00 | - | - | no | Open |
| 74 | 2.1373659912864653 | -0.970433 | -20.7683 | 6 | 16 | 0 | 0.00 | - | - | no | Open |
| 29 | 2.600107939307177 | -1.01846 | -24.5258 | 11 | 15 | 0 | 0.00 | - | - | no | Open |
| 65 | 2.6022736026417634 | -0.939392 | -18.7025 | 3 | 14 | 7 | 0.54 | - | - | no | Current |
| 54 | 3.0349276914671437 | -1.1562 | -26.1336 | 11 | 17 | 0 | 0.00 | - | - | no | Open |
| 43 | 3.222270151018671 | -1.10798 | -20.2889 | 10 | 16 | 0 | 0.00 | - | - | no | Open |
| 79 | 3.5206894931967216 | -1.022 | -18.8867 | 8 | 13 | 0 | 0.00 | - | - | no | Open |
| 90 | 3.7209462673393525 | -1.01938 | -22.3114 | 6 | 13 | 0 | 0.00 | - | - | no | Open |
| 64 | 4.14130884921673 | -1.0316 | -21.4621 | 9 | 18 | 0 | 0.00 | - | - | no | Open |
| 77 | 4.326743905642506 | -0.753896 | -17.6426 | 7 | 12 | 0 | 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
-18.703kcal/mol
Ligand efficiency (LE)
-0.7481kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.801
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
340.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.91
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
87.88kcal/mol
Minimised FF energy
73.73kcal/mol
SASA & burial
✓ computed
SASA (unbound)
613.0Ų
Total solvent-accessible surface area of free ligand
BSA total
497.3Ų
Buried surface area upon binding
BSA apolar
414.2Ų
Hydrophobic contacts buried
BSA polar
83.2Ų
Polar contacts buried
Fraction buried
81.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2965.8Ų
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
4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1523.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)