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
11.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.75, Jaccard 0.63, H-bond role recall 0.40
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
39% of hydrophobic surface appears solvent-exposed (7/18 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 (-1.102 kcal/mol/HA)
✓ Good fit quality (FQ -10.28)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ Moderate strain (11.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-29.747
kcal/mol
LE
-1.102
kcal/mol/HA
Fit Quality
-10.28
FQ (Leeson)
HAC
27
heavy atoms
MW
420
Da
LogP
4.26
cLogP
Interaction summary
HB 10
HY 6
PI 3
CLASH 4
⚠ Exposure 38%
Interaction summary
HB 10
HY 6
PI 3
CLASH 4
⚠ Exposure 38%
Partial hydrophobic solvent exposure
39% of hydrophobic surface appears solvent-exposed (7/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 18
Buried (contacted) 11
Exposed 7
LogP 4.26
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.467 | Score | -29.747 |
|---|---|---|---|
| Inter norm | -1.182 | Intra norm | 0.081 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 10 |
| Artifact reason | geometry warning; 10 clashes; 2 protein clashes | ||
| Residues |
ARG140
ARG144
HIS105
HIS141
MET101
TYR97
ARG116
ARG46
ASP13
CYS72
GLY73
HIS14
ILE15
SER74
TYR49
| ||
Protein summary
302 residues
| Protein target | T12 | Atoms | 4598 |
|---|---|---|---|
| Residues | 302 | Chains | 2 |
| Residue summary | ARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:CSD72
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXS | Contacts | 16 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
SER74
TYR49
| ||
| Current overlap | 12 | Native recall | 0.75 |
| Jaccard | 0.63 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| HB same residue | 4 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 353 | 1.1309772480652507 | -0.909194 | -24.5341 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 396 | 1.6564984240851197 | -0.828175 | -30.0044 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 320 | 3.128678427280238 | -1.21241 | -29.8201 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 352 | 3.4666152745243677 | -1.18227 | -29.7471 | 10 | 15 | 12 | 0.75 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.747kcal/mol
Ligand efficiency (LE)
-1.1017kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.279
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
419.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.26
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
41.52kcal/mol
Minimised FF energy
29.73kcal/mol
SASA & burial
✓ computed
SASA (unbound)
656.5Ų
Total solvent-accessible surface area of free ligand
BSA total
440.3Ų
Buried surface area upon binding
BSA apolar
293.8Ų
Hydrophobic contacts buried
BSA polar
146.4Ų
Polar contacts buried
Fraction buried
67.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2115.6Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
828.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)