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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
30.2 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.84, Jaccard 0.62, H-bond role recall 0.57
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.973 kcal/mol/HA)
✓ Good fit quality (FQ -9.19)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Very high strain energy (30.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-27.251
kcal/mol
LE
-0.973
kcal/mol/HA
Fit Quality
-9.19
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.07
cLogP
Interaction summary
HB 8
HY 8
PI 4
CLASH 6
Interaction summary
HB 8
HY 8
PI 4
CLASH 6
| Final rank | 3.145 | Score | -27.251 |
|---|---|---|---|
| Inter norm | -1.024 | Intra norm | 0.051 |
| Top1000 | no | Excluded | no |
| Contacts | 23 | H-bonds | 8 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash; high strain Δ 30.2 | ||
| Residues |
ALA111
ALA67
ARG154
ARG277
ASP332
ASP88
GLU274
GLY199
GLY235
GLY236
GLY237
GLY276
HIS197
HIS333
LYS69
PHE196
PRO113
PRO275
SER195
SER200
THR132
TYR331
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 | 16 | Native recall | 0.84 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 5 | Strict recall | 0.56 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 349 | 0.7278409086070636 | -0.881455 | -21.5148 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 311 | 1.3229509224018154 | -1.16017 | -29.6884 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 334 | 1.51730203346956 | -0.851135 | -24.9989 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 335 | 1.7260732089299 | -0.999198 | -26.3291 | 6 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 403 | 1.7481430375200544 | -0.991243 | -27.3069 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 347 | 2.3447902198011827 | -0.753436 | -19.3121 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 389 | 2.786111419208295 | -1.0956 | -28.7016 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 289 | 3.0086401503696756 | -1.24814 | -30.9089 | 9 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 301 | 3.1451083125642456 | -1.02377 | -27.2511 | 8 | 23 | 16 | 0.84 | 0.57 | - | no | Current |
| 357 | 3.2475516904388395 | -0.897972 | -24.0584 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 377 | 3.304488419434868 | -0.914277 | -26.47 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 379 | 3.3253823915120413 | -1.07446 | -31.7967 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 414 | 3.598164167482077 | -0.922403 | -23.4985 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 332 | 3.624289409705216 | -0.937648 | -25.3511 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 330 | 4.212597954691834 | -0.897031 | -24.2894 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 451 | 4.456710646262987 | -0.898418 | -22.7057 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 324 | 5.157273396991818 | -1.11879 | -29.0355 | 13 | 26 | 0 | 0.00 | 0.00 | - | no | Open |
| 284 | 5.171548217517241 | -0.94018 | -23.463 | 14 | 15 | 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
-27.251kcal/mol
Ligand efficiency (LE)
-0.9733kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.188
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.07
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-79.16kcal/mol
Minimised FF energy
-109.38kcal/mol
SASA & burial
✓ computed
SASA (unbound)
674.0Ų
Total solvent-accessible surface area of free ligand
BSA total
564.6Ų
Buried surface area upon binding
BSA apolar
413.6Ų
Hydrophobic contacts buried
BSA polar
151.0Ų
Polar contacts buried
Fraction buried
83.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2574.2Ų
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
1387.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)