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
23.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.76, Jaccard 0.72, H-bond role recall 0.27
Reason: no major geometry red flags detected
1 protein-contact clashes
65% of hydrophobic surface is solvent-exposed (11/17 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 (-0.920 kcal/mol/HA)
✓ Good fit quality (FQ -8.25)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ High strain energy (23.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-22.083
kcal/mol
LE
-0.920
kcal/mol/HA
Fit Quality
-8.25
FQ (Leeson)
HAC
24
heavy atoms
MW
340
Da
LogP
3.34
cLogP
Interaction summary
HB 10
HY 1
PI 1
CLASH 1
⚠ Exposure 64%
Interaction summary
HB 10
HY 1
PI 1
CLASH 1
⚠ Exposure 64%
Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (11/17 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 17
Buried (contacted) 6
Exposed 11
LogP 3.34
H-bonds 10
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (4/5 atoms exposed)phenyl (5/5 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 2.063 | Score | -22.083 |
|---|---|---|---|
| Inter norm | -1.064 | Intra norm | 0.144 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 10 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash; moderate strain Δ 23.7 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
HIS105
HIS14
HIS141
SER46
THR74
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: 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 | 5 | Strict recall | 0.38 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 5 | HB residue recall | 0.45 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 459 | 0.9834178066983842 | -1.01619 | -22.8206 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 489 | 1.3935518030020047 | -0.99865 | -20.7043 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 494 | 1.654975662962992 | -1.07605 | -28.4398 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 450 | 1.8221991932961779 | -0.948948 | -19.4208 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 432 | 2.0626620653116463 | -1.06385 | -22.0827 | 10 | 14 | 13 | 0.76 | 0.27 | - | no | Current |
| 415 | 2.2651134184818567 | -1.3172 | -31.1352 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 515 | 2.8696934123764937 | -0.963412 | -19.4317 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 406 | 3.633375166152976 | -1.19736 | -29.6559 | 6 | 14 | 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
-22.083kcal/mol
Ligand efficiency (LE)
-0.9201kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.246
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
340.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.34
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
77.52kcal/mol
Minimised FF energy
53.79kcal/mol
SASA & burial
✓ computed
SASA (unbound)
582.1Ų
Total solvent-accessible surface area of free ligand
BSA total
422.9Ų
Buried surface area upon binding
BSA apolar
358.2Ų
Hydrophobic contacts buried
BSA polar
64.7Ų
Polar contacts buried
Fraction buried
72.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2210.9Ų
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
651.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)