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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
19.5 kcal/mol
Protein clashes
0
Internal clashes
5
Native overlap
contact recall 0.76, Jaccard 0.72, H-bond role recall 0.36
Reason: no major geometry red flags detected
5 intramolecular clashes
73% of hydrophobic surface is solvent-exposed (11/15 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.879 kcal/mol/HA)
✓ Good fit quality (FQ -7.88)
✓ Strong H-bond network (10 bonds)
✓ Good burial (64% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Moderate strain (19.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-21.097
kcal/mol
LE
-0.879
kcal/mol/HA
Fit Quality
-7.88
FQ (Leeson)
HAC
24
heavy atoms
MW
400
Da
LogP
4.39
cLogP
Interaction summary
HB 10
HY 4
PI 1
CLASH 0
⚠ Exposure 73%
Interaction summary
HB 10
HY 4
PI 1
CLASH 0
⚠ Exposure 73%
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
No clash · clashes detected for this pose.
Solvent-exposed hydrophobic surface — desolvation penalty likely
73% of hydrophobic surface is solvent-exposed (11/15 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 15
Buried (contacted) 4
Exposed 11
LogP 4.39
H-bonds 10
Exposed fragments:
thienyl (4/6 atoms exposed)thienyl (4/5 atoms exposed)thienyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 1.867 | Score | -21.097 |
|---|---|---|---|
| Inter norm | -1.034 | Intra norm | 0.155 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 10 |
| Artifact reason | geometry warning; 5 clashes; 1 protein clash | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
HIS105
HIS14
HIS141
SER46
THR74
TYR49
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
| Current overlap | 13 | Native recall | 0.76 |
| Jaccard | 0.72 | RMSD | - |
| HB strict | 6 | Strict recall | 0.46 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 5 | HB residue recall | 0.45 |
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 504 | -0.15004755271706952 | -1.26754 | -31.3979 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 552 | 0.5830570699899238 | -1.05964 | -23.3855 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 511 | 1.6745541816114429 | -1.31322 | -30.9498 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 522 | 1.8666992176791106 | -1.03361 | -21.0969 | 10 | 14 | 13 | 0.76 | 0.36 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.097kcal/mol
Ligand efficiency (LE)
-0.8790kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.878
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
399.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.39
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-11.48kcal/mol
Minimised FF energy
-30.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
587.1Ų
Total solvent-accessible surface area of free ligand
BSA total
377.5Ų
Buried surface area upon binding
BSA apolar
268.8Ų
Hydrophobic contacts buried
BSA polar
108.7Ų
Polar contacts buried
Fraction buried
64.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2176.7Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
658.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)