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 mixed
SASA done
Strain ΔE
15.5 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.54, Jaccard 0.37
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.748 kcal/mol/HA)
✓ Good fit quality (FQ -6.60)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Moderate strain (15.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-17.211
kcal/mol
LE
-0.748
kcal/mol/HA
Fit Quality
-6.60
FQ (Leeson)
HAC
23
heavy atoms
MW
315
Da
LogP
1.60
cLogP
Interaction summary
HB 10
HY 24
PI 1
CLASH 4
Interaction summary
HB 10
HY 24
PI 1
CLASH 4
| Final rank | 2.465 | Score | -17.211 |
|---|---|---|---|
| Inter norm | -1.044 | Intra norm | 0.296 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 10 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash | ||
| Residues |
ALA77
ARG74
ASN208
ASN245
ASP71
GLU82
GLY85
LEU73
MET70
PHE83
SER76
TRP81
VAL88
| ||
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 | ||
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 | 7 | Native recall | 0.54 |
| Jaccard | 0.37 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 623 | -0.21493581621955696 | -1.3166 | -29.3146 | 4 | 16 | 0 | 0.00 | - | - | no | Open |
| 636 | 1.9065028710157321 | -0.990453 | -18.7513 | 5 | 15 | 0 | 0.00 | - | - | no | Open |
| 638 | 2.078718061437694 | -1.03904 | -19.278 | 6 | 14 | 0 | 0.00 | - | - | no | Open |
| 640 | 2.4645938733667183 | -1.04408 | -17.2106 | 10 | 13 | 7 | 0.54 | - | - | no | Current |
| 629 | 3.425746121157447 | -1.25604 | -25.7731 | 12 | 17 | 0 | 0.00 | - | - | no | Open |
| 625 | 3.6012935560196184 | -1.2648 | -22.3059 | 11 | 17 | 0 | 0.00 | - | - | no | Open |
| 648 | 4.1058842412556915 | -1.39928 | -29.419 | 12 | 18 | 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
-17.211kcal/mol
Ligand efficiency (LE)
-0.7483kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.604
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
315.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.60
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.49kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
84.44kcal/mol
Minimised FF energy
68.95kcal/mol
SASA & burial
✓ computed
SASA (unbound)
575.9Ų
Total solvent-accessible surface area of free ligand
BSA total
427.3Ų
Buried surface area upon binding
BSA apolar
316.2Ų
Hydrophobic contacts buried
BSA polar
111.1Ų
Polar contacts buried
Fraction buried
74.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2928.9Ų
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
1527.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)