Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
24.6 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.89, Jaccard 0.65, H-bond role recall 0.57
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.948 kcal/mol/HA)
✓ Good fit quality (FQ -8.62)
✓ Good H-bonds (5 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (94%)
✗ High strain energy (24.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-23.697
kcal/mol
LE
-0.948
kcal/mol/HA
Fit Quality
-8.62
FQ (Leeson)
HAC
25
heavy atoms
MW
340
Da
LogP
3.58
cLogP
Interaction summary
HB 5
HY 11
PI 3
CLASH 5
Interaction summary
HB 5
HY 11
PI 3
CLASH 5
| Final rank | 3.628 | Score | -23.697 |
|---|---|---|---|
| Inter norm | -1.162 | Intra norm | 0.214 |
| Top1000 | no | Excluded | no |
| Contacts | 24 | H-bonds | 5 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; moderate strain Δ 24.6 | ||
| Residues |
ALA111
ALA67
ARG154
ARG277
ASP233
ASP332
ASP88
GLU274
GLY199
GLY235
GLY236
GLY237
GLY276
HIS197
LYS69
PHE196
PHE238
PRO113
PRO275
SER195
SER200
THR132
TYR278
TYR389
| ||
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 | ||
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 | 17 | Native recall | 0.89 |
| Jaccard | 0.65 | RMSD | - |
| HB strict | 4 | Strict recall | 0.44 |
| HB same residue+role | 4 | HB role recall | 0.57 |
| HB same residue | 4 | HB residue recall | 0.57 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 68 | 1.4150472791634583 | -1.40486 | -32.9741 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 36 | 3.6278037511253904 | -1.1621 | -23.6974 | 5 | 24 | 17 | 0.89 | 0.57 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.697kcal/mol
Ligand efficiency (LE)
-0.9479kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.617
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
340.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.58
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
30.78kcal/mol
Minimised FF energy
6.18kcal/mol
SASA & burial
✓ computed
SASA (unbound)
653.0Ų
Total solvent-accessible surface area of free ligand
BSA total
561.7Ų
Buried surface area upon binding
BSA apolar
530.8Ų
Hydrophobic contacts buried
BSA polar
30.9Ų
Polar contacts buried
Fraction buried
86.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
94.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2708.4Ų
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
1375.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)