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 high
Native mixed
SASA done
Strain ΔE
21.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.54, Jaccard 0.37
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.906 kcal/mol/HA)
✓ Good fit quality (FQ -7.87)
✓ Good H-bonds (5 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ High strain energy (21.1 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Many internal clashes (11)
Score
-19.931
kcal/mol
LE
-0.906
kcal/mol/HA
Fit Quality
-7.87
FQ (Leeson)
HAC
22
heavy atoms
MW
296
Da
LogP
1.83
cLogP
Interaction summary
HB 5
HY 23
PI 1
CLASH 1
Interaction summary
HB 5
HY 23
PI 1
CLASH 1
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
| Final rank | 1.051 | Score | -19.931 |
|---|---|---|---|
| Inter norm | -1.091 | Intra norm | 0.156 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 5 |
| Artifact reason | geometry warning; 11 clashes; 5 protein contact clashes; moderate strain Δ 21.1 | ||
| Residues |
ALA209
ALA67
ALA90
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 | 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 | - |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 76 | -0.0376718823236489 | -1.61796 | -33.8305 | 6 | 17 | 0 | 0.00 | - | - | no | Open |
| 66 | 0.8351663788206477 | -1.68727 | -35.6949 | 6 | 17 | 0 | 0.00 | - | - | no | Open |
| 58 | 1.0514477632785009 | -1.09079 | -19.9306 | 5 | 13 | 7 | 0.54 | - | - | no | Current |
| 82 | 2.044959291095577 | -1.19069 | -21.9901 | 8 | 19 | 0 | 0.00 | - | - | no | Open |
| 75 | 2.0795113958424336 | -1.1709 | -25.4329 | 7 | 18 | 0 | 0.00 | - | - | no | Open |
| 58 | 2.41230841010167 | -1.22498 | -25.2812 | 10 | 19 | 0 | 0.00 | - | - | no | Open |
| 65 | 2.9117651005433762 | -1.22995 | -24.555 | 6 | 21 | 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
-19.931kcal/mol
Ligand efficiency (LE)
-0.9059kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.865
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
296.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.83
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-35.14kcal/mol
Minimised FF energy
-56.21kcal/mol
SASA & burial
✓ computed
SASA (unbound)
563.5Ų
Total solvent-accessible surface area of free ligand
BSA total
434.2Ų
Buried surface area upon binding
BSA apolar
385.2Ų
Hydrophobic contacts buried
BSA polar
49.0Ų
Polar contacts buried
Fraction buried
77.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3001.9Ų
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
1507.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)