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
29.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.81, Jaccard 0.68, H-bond role recall 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.787 kcal/mol/HA)
✓ Good fit quality (FQ -7.59)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ High strain energy (29.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-23.612
kcal/mol
LE
-0.787
kcal/mol/HA
Fit Quality
-7.59
FQ (Leeson)
HAC
30
heavy atoms
MW
422
Da
LogP
3.37
cLogP
Interaction summary
HB 10
HY 8
PI 1
CLASH 2
Interaction summary
HB 10
HY 8
PI 1
CLASH 2
| Final rank | 3.011 | Score | -23.612 |
|---|---|---|---|
| Inter norm | -0.913 | Intra norm | 0.125 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 10 |
| Artifact reason | geometry warning; 15 clashes; 1 protein clash; moderate strain Δ 29.1 | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
TYR97
ARG116
ARG46
CYS72
GLY73
GLY77
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 | 13 | Native recall | 0.81 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 7 | Strict recall | 0.58 |
| HB same residue+role | 5 | HB role recall | 0.50 |
| HB same residue | 6 | HB residue recall | 0.60 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 401 | 1.3317583642642152 | -1.04731 | -26.642 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 432 | 1.6486052609835815 | -0.867169 | -23.2983 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 406 | 3.0108297546293987 | -0.912563 | -23.612 | 10 | 16 | 13 | 0.81 | 0.50 | - | no | Current |
| 426 | 4.039179568641927 | -1.12108 | -30.4478 | 6 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 490 | 4.085038280417157 | -0.853857 | -20.5979 | 3 | 18 | 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
-23.612kcal/mol
Ligand efficiency (LE)
-0.7871kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.592
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
422.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.37
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
29.09kcal/mol
Minimised FF energy
0.03kcal/mol
SASA & burial
✓ computed
SASA (unbound)
646.2Ų
Total solvent-accessible surface area of free ligand
BSA total
489.6Ų
Buried surface area upon binding
BSA apolar
365.4Ų
Hydrophobic contacts buried
BSA polar
124.3Ų
Polar contacts buried
Fraction buried
75.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2180.6Ų
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
774.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)