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
68.3 kcal/mol
Protein clashes
10
Internal clashes
10
Native overlap
contact recall 0.74, Jaccard 0.52, H-bond role recall 0.57
Reason: 10 protein-contact clashes, 10 internal clashes, strain 68.3 kcal/mol
strain ΔE 68.3 kcal/mol
10 protein-contact clashes
10 intramolecular clashes
41% of hydrophobic surface appears solvent-exposed (7/17 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 (-0.758 kcal/mol/HA)
✓ Good fit quality (FQ -7.24)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Extreme strain energy (68.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-21.988
kcal/mol
LE
-0.758
kcal/mol/HA
Fit Quality
-7.24
FQ (Leeson)
HAC
29
heavy atoms
MW
434
Da
LogP
2.24
cLogP
Final rank
5.2367
rank score
Inter norm
-0.972
normalised
Contacts
22
H-bonds 11
Interaction summary
HBD 3
HBA 6
HY 2
PI 2
CLASH 10
Interaction summary
HBD 3
HBA 6
HY 2
PI 2
CLASH 10
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.
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: 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 | 5 | Strict recall | 0.56 |
| HB same residue+role | 4 | HB role recall | 0.57 |
| HB same residue | 5 | HB residue recall | 0.71 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 327 | 1.113016812929585 | -0.837606 | -23.8962 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 430 | 2.3252787033319144 | -0.938777 | -27.2792 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 360 | 2.515614498002701 | -1.00043 | -29.7334 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 401 | 3.832792503061684 | -0.889515 | -25.6391 | 11 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 277 | 3.8876534768210544 | -1.08809 | -28.9894 | 10 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 276 | 3.987457950263569 | -0.9943 | -24.6113 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 301 | 3.991224331337767 | -0.914304 | -27.8504 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 355 | 4.515890243073721 | -0.794133 | -23.2595 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 278 | 5.236654933239286 | -0.9719 | -21.9883 | 11 | 22 | 14 | 0.74 | 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
-21.988kcal/mol
Ligand efficiency (LE)
-0.7582kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.238
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
434.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.24
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
68.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
14.05kcal/mol
Minimised FF energy
-54.27kcal/mol
SASA & burial
✓ computed
SASA (unbound)
671.4Ų
Total solvent-accessible surface area of free ligand
BSA total
539.2Ų
Buried surface area upon binding
BSA apolar
390.7Ų
Hydrophobic contacts buried
BSA polar
148.6Ų
Polar contacts buried
Fraction buried
80.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2521.8Ų
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
1389.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)