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
34.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.60, Jaccard 0.41, H-bond role recall 0.60
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.818 kcal/mol/HA)
✓ Good fit quality (FQ -7.72)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Very high strain energy (34.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-22.904
kcal/mol
LE
-0.818
kcal/mol/HA
Fit Quality
-7.72
FQ (Leeson)
HAC
28
heavy atoms
MW
400
Da
LogP
1.38
cLogP
Interaction summary
HB 7
HY 22
PI 0
CLASH 1
Interaction summary
HB 7
HY 22
PI 0
CLASH 1
| Final rank | 4.555 | Score | -22.904 |
|---|---|---|---|
| Inter norm | -0.848 | Intra norm | 0.030 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 7 |
| Artifact reason | geometry warning; 12 clashes; 3 protein clashes; high strain Δ 34.8 | ||
| Residues |
ARG22
ARG342
ASN20
CYS26
GLN341
GLU343
GLU348
GLU384
LEU25
LEU339
LEU350
LEU382
PRO340
PRO344
PRO373
THR21
| ||
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 | 9 | Native recall | 0.60 |
| Jaccard | 0.41 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 530 | 1.6436894146790064 | -0.946279 | -23.4375 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 518 | 1.9309945238469914 | -1.23855 | -31.6367 | 6 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 548 | 2.2032501877030084 | -1.03621 | -28.9942 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 511 | 2.51524262721069 | -1.03912 | -27.2258 | 6 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 558 | 4.027810809821197 | -0.809508 | -25.1543 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 525 | 4.149815159392695 | -0.740682 | -21.2369 | 6 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 515 | 4.5554762834061915 | -0.848421 | -22.9041 | 7 | 16 | 9 | 0.60 | 0.60 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.904kcal/mol
Ligand efficiency (LE)
-0.8180kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.722
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
400.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.38
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-103.55kcal/mol
Minimised FF energy
-138.42kcal/mol
SASA & burial
✓ computed
SASA (unbound)
665.5Ų
Total solvent-accessible surface area of free ligand
BSA total
541.5Ų
Buried surface area upon binding
BSA apolar
419.3Ų
Hydrophobic contacts buried
BSA polar
122.2Ų
Polar contacts buried
Fraction buried
81.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2475.7Ų
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
1353.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)