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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
50.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.68, Jaccard 0.52, H-bond role recall 0.43
Reason: strain 50.8 kcal/mol
strain ΔE 50.8 kcal/mol
4 protein-contact clashes
4 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (8/21 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 (-0.767 kcal/mol/HA)
✓ Good fit quality (FQ -7.54)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Extreme strain energy (50.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-24.532
kcal/mol
LE
-0.767
kcal/mol/HA
Fit Quality
-7.54
FQ (Leeson)
HAC
32
heavy atoms
MW
456
Da
LogP
0.55
cLogP
Final rank
5.4202
rank score
Inter norm
-0.882
normalised
Contacts
19
H-bonds 11
Interaction summary
HBA 8
HY 4
PI 4
CLASH 4
Interaction summary
HBA 8
HY 4
PI 4
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 13 | Native recall | 0.68 |
| Jaccard | 0.52 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 66 | 1.3505982434811619 | -0.755698 | -17.641 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 650 | 1.6779348296445458 | -0.763793 | -24.7301 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 634 | 2.0657957641371216 | -0.809113 | -23.5291 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 141 | 3.3915646375584045 | -0.794759 | -23.1152 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 83 | 5.420150559491577 | -0.882408 | -24.5321 | 11 | 19 | 13 | 0.68 | 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
-24.532kcal/mol
Ligand efficiency (LE)
-0.7666kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.539
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
456.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.55
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
50.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
36.18kcal/mol
Minimised FF energy
-14.65kcal/mol
SASA & burial
✓ computed
SASA (unbound)
688.4Ų
Total solvent-accessible surface area of free ligand
BSA total
524.3Ų
Buried surface area upon binding
BSA apolar
344.1Ų
Hydrophobic contacts buried
BSA polar
180.1Ų
Polar contacts buried
Fraction buried
76.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2559.0Ų
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
1378.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)