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 medium
Native strong
SASA done
Strain ΔE
15.4 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.67, Jaccard 0.56, H-bond role recall 0.00
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.597 kcal/mol/HA)
✓ Good fit quality (FQ -5.93)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ Moderate strain (15.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-19.713
kcal/mol
LE
-0.597
kcal/mol/HA
Fit Quality
-5.93
FQ (Leeson)
HAC
33
heavy atoms
MW
451
Da
LogP
6.36
cLogP
Interaction summary
HB 1
HY 24
PI 4
CLASH 5
Interaction summary
HB 1
HY 24
PI 4
CLASH 5
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 | 3.789 | Score | -19.713 |
|---|---|---|---|
| Inter norm | -0.758 | Intra norm | 0.046 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 1 |
| Artifact reason | geometry warning; 16 clashes; 2 protein clashes | ||
| Residues |
ALA34
ARG100
ARG59
GLN56
ILE160
ILE47
LEU90
LEU97
MET55
NDP301
PHE58
PHE94
PRO91
SER98
THR86
TYR166
VAL32
VAL33
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 8RHT | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA34
ASP54
HIS182
ILE160
ILE47
LEU90
LEU97
MET55
NDP301
PHE233
PHE58
PHE94
PRO91
SER89
THR184
THR86
TRP49
TYR166
TYR57
VAL32
VAL33
| ||
| Current overlap | 14 | Native recall | 0.67 |
| Jaccard | 0.56 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
223 residues
| Protein target | T06 | Atoms | 3452 |
|---|---|---|---|
| Residues | 223 | Chains | 1 |
| Residue summary | ARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74 | ||
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:NDP301
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 634 | 0.7703295841755433 | -1.01228 | -30.485 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 619 | 0.9227104539675254 | -0.988832 | -29.8563 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 635 | 0.9872537622581262 | -0.909874 | -26.5051 | 1 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 624 | 1.3874062123717454 | -0.912299 | -28.609 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 623 | 2.5042832255124376 | -0.78944 | -24.6851 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 641 | 2.575160669811322 | -0.729551 | -19.9056 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 624 | 3.143187244987514 | -0.689014 | -19.0993 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 637 | 3.1469015228773753 | -0.653269 | -16.8113 | 4 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 623 | 3.788589440580992 | -0.75815 | -19.7132 | 1 | 18 | 14 | 0.67 | 0.00 | - | no | Current |
| 633 | 4.551784139291988 | -0.853444 | -26.9236 | 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
-19.713kcal/mol
Ligand efficiency (LE)
-0.5974kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.927
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
450.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.36
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
129.37kcal/mol
Minimised FF energy
113.94kcal/mol
SASA & burial
✓ computed
SASA (unbound)
732.6Ų
Total solvent-accessible surface area of free ligand
BSA total
671.6Ų
Buried surface area upon binding
BSA apolar
597.2Ų
Hydrophobic contacts buried
BSA polar
74.4Ų
Polar contacts buried
Fraction buried
91.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1880.9Ų
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
1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
586.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)