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 high
Native strong
SASA done
Strain ΔE
21.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.74, Jaccard 0.52, H-bond role recall 0.43
Reason: no major geometry red flags detected
2 protein-contact clashes
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.884 kcal/mol/HA)
✓ Good fit quality (FQ -8.15)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ High strain energy (21.4 kcal/mol)
✗ Geometry warnings
Score
-22.990
kcal/mol
LE
-0.884
kcal/mol/HA
Fit Quality
-8.15
FQ (Leeson)
HAC
26
heavy atoms
MW
376
Da
LogP
-2.91
cLogP
Interaction summary
HB 9
HY 5
PI 2
CLASH 2
⚠ Exposure 35%
Interaction summary
HB 9
HY 5
PI 2
CLASH 2
⚠ Exposure 35%
Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 11
Exposed 6
LogP -2.91
H-bonds 9
Exposed fragments:
phenyl (3/5 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 1.817 | Score | -22.990 |
|---|---|---|---|
| Inter norm | -1.055 | Intra norm | 0.171 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 9 |
| Artifact reason | geometry warning; 4 clashes; 1 protein clash; moderate strain Δ 21.4 | ||
| Residues |
ALA111
ALA67
ARG154
ARG277
ASP233
ASP332
ASP88
GLU274
GLY199
GLY235
GLY236
GLY237
GLY276
HIS197
HIS333
LYS69
PHE196
PRO113
SER195
SER200
THR132
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 | 14 | Native recall | 0.74 |
| Jaccard | 0.52 | RMSD | - |
| HB strict | 2 | Strict recall | 0.22 |
| HB same residue+role | 3 | HB role recall | 0.43 |
| HB same residue | 3 | HB residue recall | 0.43 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 124 | 1.4877473814898854 | -0.950138 | -21.24 | 5 | 21 | 1 | 0.05 | 0.00 | - | no | Open |
| 92 | 1.603037398703956 | -0.921814 | -22.1713 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 80 | 1.8166958470318022 | -1.05527 | -22.9902 | 9 | 22 | 14 | 0.74 | 0.43 | - | no | Current |
| 110 | 1.985015103021289 | -0.998783 | -18.1972 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 143 | 2.4259511102747977 | -1.18883 | -26.4653 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 115 | 2.775094337228209 | -0.851435 | -20.1478 | 6 | 11 | 0 | 0.00 | 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
-22.990kcal/mol
Ligand efficiency (LE)
-0.8842kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.147
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
375.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-2.91
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-171.15kcal/mol
Minimised FF energy
-192.54kcal/mol
SASA & burial
✓ computed
SASA (unbound)
692.5Ų
Total solvent-accessible surface area of free ligand
BSA total
564.2Ų
Buried surface area upon binding
BSA apolar
499.8Ų
Hydrophobic contacts buried
BSA polar
64.4Ų
Polar contacts buried
Fraction buried
81.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2680.3Ų
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
1380.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)