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 medium
Native strong
SASA done
Strain ΔE
15.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.90, Jaccard 0.86, H-bond role recall 0.40
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.046 kcal/mol/HA)
✓ Good fit quality (FQ -9.51)
✓ Good H-bonds (3 bonds)
✓ Deep burial (95% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (15.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-26.144
kcal/mol
LE
-1.046
kcal/mol/HA
Fit Quality
-9.51
FQ (Leeson)
HAC
25
heavy atoms
MW
326
Da
LogP
2.77
cLogP
Interaction summary
HB 3
HY 24
PI 1
CLASH 3
Interaction summary
HB 3
HY 24
PI 1
CLASH 3
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
| Final rank | 2.073 | Score | -26.144 |
|---|---|---|---|
| Inter norm | -1.093 | Intra norm | 0.048 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 3 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash; 1 cofactor-context clash | ||
| Residues |
ALA10
ASN65
ASP22
GLU31
GLY117
GLY21
ILE61
ILE8
LEU23
NAP201
PHE32
PHE35
PRO62
SER60
THR137
THR57
TYR122
TYR34
VAL116
VAL9
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 5SD8 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA10
ASN65
ASP22
GLN36
GLU31
GLY117
GLY21
ILE61
ILE8
LEU23
LEU68
NAP201
PHE32
PHE35
PRO62
SER60
THR137
THR57
TYR122
VAL116
VAL9
| ||
| Current overlap | 19 | Native recall | 0.90 |
| Jaccard | 0.86 | RMSD | - |
| HB strict | 2 | Strict recall | 0.40 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
Protein summary
200 residues
| Protein target | T02 | Atoms | 3128 |
|---|---|---|---|
| Residues | 200 | Chains | 2 |
| Residue summary | LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91 | ||
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:NAP201
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 676 | -0.2008936714302171 | -1.43465 | -34.8564 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 660 | 0.46007232838639606 | -1.02491 | -26.2027 | 4 | 18 | 17 | 0.81 | 0.40 | - | no | Open |
| 678 | 0.8796915712031312 | -1.01561 | -23.9951 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 665 | 1.228388032666358 | -1.2817 | -29.3257 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 660 | 1.7403331477794532 | -0.965961 | -23.8553 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 661 | 2.0730042543206704 | -1.0933 | -26.1437 | 3 | 20 | 19 | 0.90 | 0.40 | - | no | Current |
| 678 | 2.096965528731848 | -1.2124 | -29.932 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 672 | 2.4180673824662544 | -1.14541 | -28.0703 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 671 | 2.4771333975395495 | -0.992363 | -24.8643 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 679 | 2.5572498642857204 | -1.22014 | -29.4993 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 667 | 2.6594168436889833 | -1.12471 | -25.0382 | 7 | 19 | 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
-26.144kcal/mol
Ligand efficiency (LE)
-1.0457kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.507
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
326.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.77
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
67.58kcal/mol
Minimised FF energy
51.97kcal/mol
SASA & burial
✓ computed
SASA (unbound)
570.0Ų
Total solvent-accessible surface area of free ligand
BSA total
540.6Ų
Buried surface area upon binding
BSA apolar
412.5Ų
Hydrophobic contacts buried
BSA polar
128.1Ų
Polar contacts buried
Fraction buried
94.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1494.1Ų
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
1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
624.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)