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 mixed
SASA done
Strain ΔE
17.2 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.40, Jaccard 0.30, H-bond role recall 0.00
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.095 kcal/mol/HA)
✓ Good fit quality (FQ -9.66)
✓ Good H-bonds (3 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (63%)
✗ Moderate strain (17.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-25.173
kcal/mol
LE
-1.095
kcal/mol/HA
Fit Quality
-9.66
FQ (Leeson)
HAC
23
heavy atoms
MW
340
Da
LogP
3.44
cLogP
Interaction summary
HB 3
HY 8
PI 0
CLASH 4
Interaction summary
HB 3
HY 8
PI 0
CLASH 4
| Final rank | 2.181 | Score | -25.173 |
|---|---|---|---|
| Inter norm | -1.065 | Intra norm | -0.030 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 3 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash | ||
| Residues |
ALA334
ARG337
ASP243
ASP385
GLU384
LEU339
MET386
PHE383
THR241
VAL335
VAL336
| ||
Protein summary
398 residues
| Protein target | T14 | Atoms | 6140 |
|---|---|---|---|
| Residues | 398 | Chains | 1 |
| Residue summary | VAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170 | ||
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:ORX602
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1NJJ | Contacts | 15 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG22
ARG242
ARG337
ARG342
ASP243
ASP385
GLN341
GLU384
LEU25
LEU339
LEU382
PRO340
PRO344
SER282
THR241
| ||
| Current overlap | 6 | Native recall | 0.40 |
| Jaccard | 0.30 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 1 | HB residue recall | 0.20 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 517 | 0.42060271769283386 | -1.01265 | -25.7013 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 507 | 1.3740988223350297 | -1.21271 | -31.4004 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 518 | 2.1812899757260524 | -1.06483 | -25.1728 | 3 | 11 | 6 | 0.40 | 0.00 | - | no | Current |
| 521 | 3.387400045559614 | -1.22342 | -30.5321 | 11 | 13 | 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
-25.173kcal/mol
Ligand efficiency (LE)
-1.0945kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.660
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
340.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.44
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
29.31kcal/mol
Minimised FF energy
12.10kcal/mol
SASA & burial
✓ computed
SASA (unbound)
542.8Ų
Total solvent-accessible surface area of free ligand
BSA total
415.1Ų
Buried surface area upon binding
BSA apolar
262.4Ų
Hydrophobic contacts buried
BSA polar
152.6Ų
Polar contacts buried
Fraction buried
76.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
63.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2338.6Ų
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
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1395.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)