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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
25.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.68, Jaccard 0.54, H-bond role recall 0.43
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.084 kcal/mol/HA)
✓ Good fit quality (FQ -10.23)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ High strain energy (25.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-30.342
kcal/mol
LE
-1.084
kcal/mol/HA
Fit Quality
-10.23
FQ (Leeson)
HAC
28
heavy atoms
MW
395
Da
LogP
3.82
cLogP
Interaction summary
HB 9
HY 9
PI 3
CLASH 1
Interaction summary
HB 9
HY 9
PI 3
CLASH 1
| Final rank | 2.236 | Score | -30.342 |
|---|---|---|---|
| Inter norm | -0.978 | Intra norm | -0.106 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 9 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash; moderate strain Δ 25.5 | ||
| Residues |
ALA111
ALA67
ARG154
ARG277
ASP233
ASP88
GLU274
GLY235
GLY236
GLY237
GLY276
HIS197
LYS69
PHE196
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.54 | RMSD | - |
| HB strict | 4 | Strict recall | 0.44 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 121 | 0.6480317823511264 | -1.09263 | -30.7137 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 128 | 0.704294296580414 | -0.82137 | -25.8407 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 123 | 2.0763430321148384 | -0.882629 | -31.3156 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 146 | 2.1987026073112794 | -1.06308 | -36.4462 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 91 | 2.235709846232026 | -0.978118 | -30.3416 | 9 | 18 | 13 | 0.68 | 0.43 | - | no | Current |
| 102 | 2.3420725108936757 | -0.856611 | -30.5757 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 152 | 2.882361998789424 | -1.01322 | -36.5034 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 138 | 3.107716007599668 | -0.763711 | -30.2928 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 163 | 3.993422811367177 | -0.727878 | -30.4938 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 100 | 4.39388549559622 | -0.956566 | -34.2918 | 15 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 94 | 4.398591367272989 | -1.17212 | -40.5324 | 10 | 19 | 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
-30.342kcal/mol
Ligand efficiency (LE)
-1.0836kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.230
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
395.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.82
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-45.62kcal/mol
Minimised FF energy
-71.14kcal/mol
SASA & burial
✓ computed
SASA (unbound)
601.8Ų
Total solvent-accessible surface area of free ligand
BSA total
499.1Ų
Buried surface area upon binding
BSA apolar
343.4Ų
Hydrophobic contacts buried
BSA polar
155.7Ų
Polar contacts buried
Fraction buried
82.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2505.3Ų
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
1395.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)