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 high
Native strong
SASA done
Strain ΔE
17.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.65, Jaccard 0.65, H-bond role recall 0.36
Reason: no major geometry red flags detected
1 protein-contact clashes
40% of hydrophobic surface appears solvent-exposed (8/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.850 kcal/mol/HA)
✓ Good fit quality (FQ -7.93)
✓ Strong H-bond network (12 bonds)
✓ Good burial (60% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Moderate strain (17.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-22.943
kcal/mol
LE
-0.850
kcal/mol/HA
Fit Quality
-7.93
FQ (Leeson)
HAC
27
heavy atoms
MW
377
Da
LogP
3.39
cLogP
Interaction summary
HB 12
HY 3
PI 2
CLASH 1
⚠ Exposure 40%
Interaction summary
HB 12
HY 3
PI 2
CLASH 1
⚠ Exposure 40%
Partial hydrophobic solvent exposure
40% of hydrophobic surface appears solvent-exposed (8/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20
Buried (contacted) 12
Exposed 8
LogP 3.39
H-bonds 12
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 3.267 | Score | -22.943 |
|---|---|---|---|
| Inter norm | -0.921 | Intra norm | 0.071 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 10 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASP13
CYS72
GLY73
HIS105
HIS14
HIS141
TYR49
| ||
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 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 11 | Native recall | 0.65 |
| Jaccard | 0.65 | RMSD | - |
| HB strict | 6 | Strict recall | 0.46 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
HB · H-bonds
Mode: permissive. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 378 | 0.45254100967401695 | -1.19369 | -33.2631 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 460 | 0.5753386101624237 | -0.979431 | -23.4038 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 445 | 0.9634963465238795 | -0.972905 | -25.4432 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 357 | 1.9316215269590413 | -0.873952 | -22.2228 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 359 | 2.8977259071513566 | -1.28181 | -35.089 | 6 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 461 | 3.049567594159186 | -0.847236 | -21.5065 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 337 | 3.266816838999127 | -0.920746 | -22.9429 | 10 | 11 | 11 | 0.65 | 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
-22.943kcal/mol
Ligand efficiency (LE)
-0.8497kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.928
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
377.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.39
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
52.14kcal/mol
Minimised FF energy
34.37kcal/mol
SASA & burial
✓ computed
SASA (unbound)
608.4Ų
Total solvent-accessible surface area of free ligand
BSA total
366.0Ų
Buried surface area upon binding
BSA apolar
303.7Ų
Hydrophobic contacts buried
BSA polar
62.3Ų
Polar contacts buried
Fraction buried
60.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2234.7Ų
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
698.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)