Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
19.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.94, Jaccard 0.83, H-bond role recall 0.60
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.344 kcal/mol/HA)
✓ Good fit quality (FQ -11.46)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ Moderate strain (19.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-28.219
kcal/mol
LE
-1.344
kcal/mol/HA
Fit Quality
-11.46
FQ (Leeson)
HAC
21
heavy atoms
MW
326
Da
LogP
0.81
cLogP
Interaction summary
HB 11
HY 6
PI 4
CLASH 1
Interaction summary
HB 11
HY 6
PI 4
CLASH 1
| Final rank | 3.511 | Score | -28.219 |
|---|---|---|---|
| Inter norm | -1.433 | Intra norm | 0.090 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 11 |
| Artifact reason | geometry warning; 6 clashes; 3 protein clashes | ||
| Residues |
ALA102
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
ARG46
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
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 | 15 | Native recall | 0.94 |
| Jaccard | 0.83 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 6 | HB role recall | 0.60 |
| HB same residue | 7 | HB residue recall | 0.70 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 508 | 2.009788458540564 | -1.01822 | -20.5996 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 545 | 3.4732770804134097 | -1.18527 | -23.981 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 466 | 3.510541205591343 | -1.43344 | -28.2186 | 11 | 17 | 15 | 0.94 | 0.60 | - | no | Current |
| 482 | 3.5921666043258553 | -1.53996 | -31.7883 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 469 | 3.966350797122376 | -1.20182 | -23.6843 | 13 | 15 | 5 | 0.31 | 0.20 | - | no | Open |
| 474 | 4.003880070761457 | -1.66085 | -33.326 | 9 | 23 | 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
-28.219kcal/mol
Ligand efficiency (LE)
-1.3437kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.462
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
326.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.81
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-153.63kcal/mol
Minimised FF energy
-172.71kcal/mol
SASA & burial
✓ computed
SASA (unbound)
549.6Ų
Total solvent-accessible surface area of free ligand
BSA total
436.8Ų
Buried surface area upon binding
BSA apolar
270.4Ų
Hydrophobic contacts buried
BSA polar
166.4Ų
Polar contacts buried
Fraction buried
79.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
61.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2047.3Ų
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
787.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)