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
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
17.4 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.76, Jaccard 0.72, H-bond role recall 0.45
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
60% of hydrophobic surface is solvent-exposed (15/25 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 (-0.674 kcal/mol/HA)
✓ Good fit quality (FQ -6.56)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (17.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-20.882
kcal/mol
LE
-0.674
kcal/mol/HA
Fit Quality
-6.56
FQ (Leeson)
HAC
31
heavy atoms
MW
423
Da
LogP
5.66
cLogP
Interaction summary
HB 13
HY 6
PI 2
CLASH 5
⚠ Exposure 60%
Interaction summary
HB 13
HY 6
PI 2
CLASH 5
⚠ 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
Solvent-exposed hydrophobic surface — desolvation penalty likely
60% of hydrophobic surface is solvent-exposed (15/25 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 25
Buried (contacted) 10
Exposed 15
LogP 5.66
H-bonds 13
Exposed fragments:
phenyl (3/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 4.357 | Score | -20.882 |
|---|---|---|---|
| Inter norm | -0.775 | Intra norm | 0.101 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 13 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
GLY73
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 | 13 | Native recall | 0.76 |
| Jaccard | 0.72 | RMSD | - |
| HB strict | 7 | Strict recall | 0.54 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 439 | 1.1628233344151113 | -0.906918 | -27.9879 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 1.2633865118385668 | -0.898731 | -27.8853 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 366 | 2.346994116576859 | -1.13989 | -35.9598 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 432 | 2.981404368719356 | -0.687014 | -21.8499 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 385 | 3.6381866787315404 | -0.739509 | -19.1107 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 422 | 3.724908937099832 | -0.82493 | -26.6656 | 8 | 13 | 1 | 0.06 | 0.00 | - | no | Open |
| 386 | 3.85148268722908 | -0.870285 | -26.6452 | 10 | 13 | 4 | 0.24 | 0.18 | - | no | Open |
| 393 | 4.116103612653292 | -0.926482 | -28.3794 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 376 | 4.356730612096464 | -0.774795 | -20.8823 | 13 | 14 | 13 | 0.76 | 0.45 | - | no | Current |
| 416 | 4.907697742604002 | -0.626708 | -19.1249 | 3 | 10 | 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
-20.882kcal/mol
Ligand efficiency (LE)
-0.6736kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.563
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
422.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.66
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
114.35kcal/mol
Minimised FF energy
96.94kcal/mol
SASA & burial
✓ computed
SASA (unbound)
717.0Ų
Total solvent-accessible surface area of free ligand
BSA total
477.2Ų
Buried surface area upon binding
BSA apolar
356.3Ų
Hydrophobic contacts buried
BSA polar
121.0Ų
Polar contacts buried
Fraction buried
66.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2310.0Ų
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
703.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)