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
15.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.81, Jaccard 0.77, 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 (-1.173 kcal/mol/HA)
✓ Good fit quality (FQ -10.19)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Moderate strain (15.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-25.817
kcal/mol
LE
-1.173
kcal/mol/HA
Fit Quality
-10.19
FQ (Leeson)
HAC
22
heavy atoms
MW
302
Da
LogP
1.99
cLogP
Interaction summary
HB 9
HY 14
PI 2
CLASH 3
Interaction summary
HB 9
HY 14
PI 2
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 | 2.995 | Score | -25.817 |
|---|---|---|---|
| Inter norm | -1.249 | Intra norm | 0.076 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 9 |
| Artifact reason | geometry warning; 8 clashes; 2 protein clashes; 1 cofactor-context clash | ||
| Residues |
ALA10
ASP22
GLU31
GLY117
GLY21
ILE61
ILE8
LEU23
NAP201
PHE32
PHE35
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 | 17 | Native recall | 0.81 |
| Jaccard | 0.77 | 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 | T01 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 559 | 0.7198418180090042 | -0.933488 | -20.4818 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 525 | 2.4172194168614993 | -1.48041 | -32.0363 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 512 | 2.545937422647049 | -1.61802 | -34.0323 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 567 | 2.9952729829901434 | -1.24945 | -25.8165 | 9 | 18 | 17 | 0.81 | 0.40 | - | no | Current |
| 524 | 3.422947619134114 | -1.36673 | -26.6001 | 13 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 550 | 3.750956682432338 | -1.21808 | -25.8403 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 582 | 4.472569139535506 | -1.15982 | -25.4195 | 9 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 529 | 4.491059808940537 | -1.52163 | -29.8977 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 541 | 5.152210004952779 | -1.44518 | -30.0794 | 11 | 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
-25.817kcal/mol
Ligand efficiency (LE)
-1.1735kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.188
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
302.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.99
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
91.46kcal/mol
Minimised FF energy
75.55kcal/mol
SASA & burial
✓ computed
SASA (unbound)
497.8Ų
Total solvent-accessible surface area of free ligand
BSA total
462.6Ų
Buried surface area upon binding
BSA apolar
300.1Ų
Hydrophobic contacts buried
BSA polar
162.4Ų
Polar contacts buried
Fraction buried
92.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1376.6Ų
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
1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
627.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)