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 mixed
SASA done
Strain ΔE
18.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.909 kcal/mol/HA)
✓ Good fit quality (FQ -8.58)
✓ Good H-bonds (5 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Moderate strain (18.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-25.458
kcal/mol
LE
-0.909
kcal/mol/HA
Fit Quality
-8.58
FQ (Leeson)
HAC
28
heavy atoms
MW
417
Da
LogP
2.68
cLogP
Interaction summary
HB 5
HY 24
PI 3
CLASH 1
Interaction summary
HB 5
HY 24
PI 3
CLASH 1
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 | 2.215 | Score | -25.458 |
|---|---|---|---|
| Inter norm | -0.944 | Intra norm | 0.035 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 5 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash | ||
| Residues |
ALA10
ARG29
GLU31
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
PRO27
THR137
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 | 11 | Native recall | 0.52 |
| Jaccard | 0.44 | RMSD | - |
| HB strict | 1 | Strict recall | 0.20 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 621 | 1.4345497717291078 | -1.0318 | -28.9875 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 624 | 1.9005361944032626 | -0.963332 | -23.5994 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 633 | 2.034066149755648 | -0.997448 | -27.4985 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 614 | 2.1205691892069596 | -1.06766 | -31.8052 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 617 | 2.21543994317517 | -0.943733 | -25.4581 | 5 | 15 | 11 | 0.52 | 0.20 | - | no | Current |
| 636 | 2.2733624275643116 | -0.935816 | -24.4034 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 631 | 2.613527185358712 | -0.808865 | -21.8381 | 2 | 15 | 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
-25.458kcal/mol
Ligand efficiency (LE)
-0.9092kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.583
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
416.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.68
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
21.82kcal/mol
Minimised FF energy
3.86kcal/mol
SASA & burial
✓ computed
SASA (unbound)
640.8Ų
Total solvent-accessible surface area of free ligand
BSA total
545.9Ų
Buried surface area upon binding
BSA apolar
390.3Ų
Hydrophobic contacts buried
BSA polar
155.6Ų
Polar contacts buried
Fraction buried
85.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1553.0Ų
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
591.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)