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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
14.7 kcal/mol
Protein clashes
0
Internal clashes
10
Native overlap
contact recall 0.88, Jaccard 0.83, H-bond role recall 0.27
Reason: 10 internal clashes
10 intramolecular clashes
60% of hydrophobic surface is solvent-exposed (12/20 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.007 kcal/mol/HA)
✓ Good fit quality (FQ -9.40)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Moderate strain (14.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-27.200
kcal/mol
LE
-1.007
kcal/mol/HA
Fit Quality
-9.40
FQ (Leeson)
HAC
27
heavy atoms
MW
415
Da
LogP
5.34
cLogP
Interaction summary
HB 7
HY 6
PI 2
CLASH 0
⚠ Exposure 60%
Interaction summary
HB 7
HY 6
PI 2
CLASH 0
⚠ Exposure 60%
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
60% of hydrophobic surface is solvent-exposed (12/20 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 20
Buried (contacted) 8
Exposed 12
LogP 5.34
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.106 | Score | -27.200 |
|---|---|---|---|
| Inter norm | -1.018 | Intra norm | 0.010 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 7 |
| Artifact reason | geometry warning; 10 clashes; 2 protein clashes | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY77
HIS105
HIS14
HIS141
LEU101
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 | 15 | Native recall | 0.88 |
| Jaccard | 0.83 | RMSD | - |
| HB strict | 3 | Strict recall | 0.23 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 4 | HB residue recall | 0.36 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 569 | 0.5131596875696631 | -1.1201 | -30.2913 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 578 | 0.6110929766522484 | -1.15007 | -30.0985 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 572 | 2.276295995643403 | -1.07847 | -29.4348 | 7 | 11 | 4 | 0.24 | 0.18 | - | no | Open |
| 578 | 2.3195254778524115 | -1.02963 | -28.1488 | 3 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 575 | 3.1058572745469006 | -1.01781 | -27.1998 | 7 | 16 | 15 | 0.88 | 0.27 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.200kcal/mol
Ligand efficiency (LE)
-1.0074kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.399
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
415.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.34
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
57.54kcal/mol
Minimised FF energy
42.83kcal/mol
SASA & burial
✓ computed
SASA (unbound)
636.6Ų
Total solvent-accessible surface area of free ligand
BSA total
440.0Ų
Buried surface area upon binding
BSA apolar
371.4Ų
Hydrophobic contacts buried
BSA polar
68.6Ų
Polar contacts buried
Fraction buried
69.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2291.5Ų
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
689.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)