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
24.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.46, Jaccard 0.32
Reason: no major geometry red flags detected
2 protein-contact clashes
48% of hydrophobic surface appears solvent-exposed (13/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.603 kcal/mol/HA)
✓ Good fit quality (FQ -5.99)
✓ Strong H-bond network (7 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ High strain energy (24.7 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (10)
✗ Many internal clashes (15)
Score
-19.906
kcal/mol
LE
-0.603
kcal/mol/HA
Fit Quality
-5.99
FQ (Leeson)
HAC
33
heavy atoms
MW
451
Da
LogP
6.36
cLogP
Interaction summary
HB 7
HY 18
PI 0
CLASH 2
⚠ Exposure 48%
Interaction summary
HB 7
HY 18
PI 0
CLASH 2
⚠ Exposure 48%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Partial hydrophobic solvent exposure
48% of hydrophobic surface appears solvent-exposed (13/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 27
Buried (contacted) 14
Exposed 13
LogP 6.36
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 2.575 | Score | -19.906 |
|---|---|---|---|
| Inter norm | -0.730 | Intra norm | 0.126 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 7 |
| Artifact reason | geometry warning; 15 clashes; 10 protein contact clashes; moderate strain Δ 24.7 | ||
| Residues |
ALA209
ALA90
GLY214
GLY215
GLY246
LYS211
LYS216
LYS89
PRO187
PRO212
PRO213
TYR210
| ||
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 | 6 | Native recall | 0.46 |
| Jaccard | 0.32 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 634 | 0.7703295841755433 | -1.01228 | -30.485 | 3 | 17 | 0 | 0.00 | - | - | no | Open |
| 619 | 0.9227104539675254 | -0.988832 | -29.8563 | 3 | 18 | 0 | 0.00 | - | - | no | Open |
| 635 | 0.9872537622581262 | -0.909874 | -26.5051 | 1 | 17 | 0 | 0.00 | - | - | no | Open |
| 624 | 1.3874062123717454 | -0.912299 | -28.609 | 1 | 18 | 0 | 0.00 | - | - | no | Open |
| 623 | 2.5042832255124376 | -0.78944 | -24.6851 | 3 | 17 | 0 | 0.00 | - | - | no | Open |
| 641 | 2.575160669811322 | -0.729551 | -19.9056 | 7 | 12 | 6 | 0.46 | - | - | no | Current |
| 624 | 3.143187244987514 | -0.689014 | -19.0993 | 3 | 12 | 0 | 0.00 | - | - | no | Open |
| 637 | 3.1469015228773753 | -0.653269 | -16.8113 | 4 | 9 | 0 | 0.00 | - | - | no | Open |
| 623 | 3.788589440580992 | -0.75815 | -19.7132 | 1 | 18 | 0 | 0.00 | - | - | no | Open |
| 633 | 4.551784139291988 | -0.853444 | -26.9236 | 7 | 19 | 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
-19.906kcal/mol
Ligand efficiency (LE)
-0.6032kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.985
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
450.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.36
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
137.98kcal/mol
Minimised FF energy
113.24kcal/mol
SASA & burial
✓ computed
SASA (unbound)
738.5Ų
Total solvent-accessible surface area of free ligand
BSA total
457.8Ų
Buried surface area upon binding
BSA apolar
381.8Ų
Hydrophobic contacts buried
BSA polar
76.0Ų
Polar contacts buried
Fraction buried
62.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3089.5Ų
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
1565.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)