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 mixed
SASA done
Strain ΔE
13.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.47, Jaccard 0.35, H-bond role recall 0.40
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.613 kcal/mol/HA)
✓ Good fit quality (FQ -5.91)
✓ Good H-bonds (4 bonds)
✓ Good burial (63% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (13.8 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
✗ Many internal clashes (12)
Score
-18.375
kcal/mol
LE
-0.613
kcal/mol/HA
Fit Quality
-5.91
FQ (Leeson)
HAC
30
heavy atoms
MW
434
Da
LogP
6.35
cLogP
Interaction summary
HB 4
HY 3
PI 0
CLASH 3
Interaction summary
HB 4
HY 3
PI 0
CLASH 3
| Final rank | 1.589 | Score | -18.375 |
|---|---|---|---|
| Inter norm | -0.730 | Intra norm | 0.117 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 4 |
| Artifact reason | geometry warning; 12 clashes; 6 protein contact clashes | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
GLU384
LEU339
LYS247
PHE383
PRO245
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 | 7 | Native recall | 0.47 |
| Jaccard | 0.35 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 605 | 1.1894692655876875 | -0.870835 | -21.2116 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 606 | 1.588714246084261 | -0.729519 | -18.3746 | 4 | 12 | 7 | 0.47 | 0.40 | - | no | Current |
| 610 | 2.454646317139425 | -0.964063 | -22.7193 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 614 | 2.8001036483619997 | -1.04803 | -29.3647 | 4 | 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
-18.375kcal/mol
Ligand efficiency (LE)
-0.6125kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.908
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
434.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.35
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
42.66kcal/mol
Minimised FF energy
28.84kcal/mol
SASA & burial
✓ computed
SASA (unbound)
693.1Ų
Total solvent-accessible surface area of free ligand
BSA total
438.1Ų
Buried surface area upon binding
BSA apolar
358.9Ų
Hydrophobic contacts buried
BSA polar
79.3Ų
Polar contacts buried
Fraction buried
63.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2429.0Ų
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
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1500.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)