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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
24.7 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.77, Jaccard 0.53
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
43% of hydrophobic surface appears solvent-exposed (10/23 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 (-0.837 kcal/mol/HA)
✓ Good fit quality (FQ -8.15)
✓ Good H-bonds (4 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ High strain energy (24.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-25.939
kcal/mol
LE
-0.837
kcal/mol/HA
Fit Quality
-8.15
FQ (Leeson)
HAC
31
heavy atoms
MW
493
Da
LogP
4.44
cLogP
Interaction summary
HB 4
HY 24
PI 1
CLASH 5
⚠ Exposure 43%
Interaction summary
HB 4
HY 24
PI 1
CLASH 5
⚠ Exposure 43%
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
43% of hydrophobic surface appears solvent-exposed (10/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 23
Buried (contacted) 13
Exposed 10
LogP 4.44
H-bonds 4
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.995 | Score | -25.939 |
|---|---|---|---|
| Inter norm | -0.791 | Intra norm | -0.046 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 4 |
| Artifact reason | geometry warning; 14 clashes; 2 protein clashes; moderate strain Δ 24.7 | ||
| Residues |
ALA209
ALA67
ALA90
ASN208
GLY214
GLY215
GLY66
LEU73
LYS211
LYS89
MET70
PRO212
PRO213
TYR210
TYR69
VAL88
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| 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 | 10 | Native recall | 0.77 |
| Jaccard | 0.53 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 35 | 2.8828811325694805 | -0.793061 | -25.72 | 7 | 17 | 0 | 0.00 | - | - | no | Open |
| 99 | 2.951395967809543 | -0.753449 | -24.8488 | 4 | 13 | 0 | 0.00 | - | - | no | Open |
| 80 | 3.9952304875033002 | -0.791134 | -25.9386 | 4 | 16 | 10 | 0.77 | - | - | no | Current |
| 93 | 5.386905739411389 | -0.60838 | -19.6021 | 6 | 10 | 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
-25.939kcal/mol
Ligand efficiency (LE)
-0.8367kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.152
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
493.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.44
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
60.80kcal/mol
Minimised FF energy
36.12kcal/mol
SASA & burial
✓ computed
SASA (unbound)
707.5Ų
Total solvent-accessible surface area of free ligand
BSA total
531.2Ų
Buried surface area upon binding
BSA apolar
455.5Ų
Hydrophobic contacts buried
BSA polar
75.8Ų
Polar contacts buried
Fraction buried
75.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3031.2Ų
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
4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1563.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)