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 high
Native strong
SASA done
Strain ΔE
13.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.79, Jaccard 0.68, H-bond role recall 0.43
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.699 kcal/mol/HA)
✓ Good fit quality (FQ -13.62)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (13.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-30.581
kcal/mol
LE
-1.699
kcal/mol/HA
Fit Quality
-13.62
FQ (Leeson)
HAC
18
heavy atoms
MW
262
Da
LogP
1.95
cLogP
Interaction summary
HB 7
HY 8
PI 3
CLASH 2
Interaction summary
HB 7
HY 8
PI 3
CLASH 2
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 | 3.404 | Score | -30.581 |
|---|---|---|---|
| Inter norm | -1.826 | Intra norm | 0.127 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 7 |
| Artifact reason | geometry warning; 6 clashes; 3 protein clashes | ||
| Residues |
ALA111
ALA67
ARG154
ARG277
ASN112
ASP88
CYS70
GLU274
GLY236
GLY237
GLY276
HIS197
LYS69
PHE170
PHE238
PRO113
SER200
TYR389
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1F3T | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA111
ALA67
ARG154
ARG277
ASP332
ASP88
CYS70
GLU274
GLY236
GLY237
GLY276
HIS197
LYS69
PHE238
PRO275
SER200
TYR278
TYR331
TYR389
| ||
| Current overlap | 15 | Native recall | 0.79 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 5 | Strict recall | 0.56 |
| HB same residue+role | 3 | HB role recall | 0.43 |
| HB same residue | 4 | HB residue recall | 0.57 |
Protein summary
411 residues
| Protein target | T13 | Atoms | 6340 |
|---|---|---|---|
| Residues | 411 | Chains | 1 |
| Residue summary | VAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 479 | 2.6817679450667433 | -1.38535 | -24.4274 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 470 | 3.4035414826524377 | -1.82608 | -30.5807 | 7 | 18 | 15 | 0.79 | 0.43 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.581kcal/mol
Ligand efficiency (LE)
-1.6989kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.616
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
262.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.95
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-52.52kcal/mol
Minimised FF energy
-65.62kcal/mol
SASA & burial
✓ computed
SASA (unbound)
487.0Ų
Total solvent-accessible surface area of free ligand
BSA total
435.1Ų
Buried surface area upon binding
BSA apolar
332.0Ų
Hydrophobic contacts buried
BSA polar
103.2Ų
Polar contacts buried
Fraction buried
89.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2465.3Ų
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
3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1379.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)