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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
29.5 kcal/mol
Protein clashes
0
Internal clashes
13
Native overlap
contact recall 0.60, Jaccard 0.36, H-bond role recall 0.40
Reason: 13 internal clashes
13 intramolecular clashes
60% of hydrophobic surface is solvent-exposed (15/25 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.653 kcal/mol/HA)
✓ Good fit quality (FQ -6.48)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ High strain energy (29.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-21.554
kcal/mol
LE
-0.653
kcal/mol/HA
Fit Quality
-6.48
FQ (Leeson)
HAC
33
heavy atoms
MW
460
Da
LogP
5.10
cLogP
Interaction summary
HB 6
HY 9
PI 0
CLASH 0
⚠ Exposure 60%
Interaction summary
HB 6
HY 9
PI 0
CLASH 0
⚠ Exposure 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
No clash · clashes detected for this pose.
Solvent-exposed hydrophobic surface — desolvation penalty likely
60% of hydrophobic surface is solvent-exposed (15/25 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 25
Buried (contacted) 10
Exposed 15
LogP 5.1
H-bonds 6
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.649 | Score | -21.554 |
|---|---|---|---|
| Inter norm | -0.725 | Intra norm | 0.065 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 6 |
| Artifact reason | geometry warning; 13 clashes; 2 protein clashes; moderate strain Δ 29.3 | ||
| Residues |
ARG22
ARG242
ARG342
ARG50
ASN20
ASP44
ASP47
CYS26
GLN341
GLU343
GLU384
LEU25
LEU382
PRO340
SER282
SER410
THR21
THR285
VAL408
| ||
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 | 0.36 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 620 | 0.9124878828115518 | -0.742763 | -23.1308 | 0 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 616 | 1.5903297613763936 | -0.695296 | -20.3004 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 617 | 1.6999776302048877 | -0.781972 | -26.1696 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 606 | 2.1579267805035065 | -0.935582 | -30.0151 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 619 | 2.321598553519423 | -0.843726 | -27.1331 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 611 | 2.3721997365242466 | -0.744991 | -19.006 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 632 | 2.5845937659195366 | -0.808096 | -24.1504 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 628 | 3.0667722052197655 | -0.693175 | -22.2941 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 615 | 3.648743788972634 | -0.72495 | -21.5538 | 6 | 19 | 9 | 0.60 | 0.40 | - | no | Current |
| 629 | 4.069678458429272 | -0.67542 | -22.0358 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 630 | 4.138721914791422 | -0.806706 | -25.3439 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 616 | 5.015225112007658 | -0.909212 | -28.7073 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 641 | 5.605204418092712 | -1.11254 | -33.8589 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 631 | 5.82846986775583 | -0.854024 | -26.3807 | 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
-21.554kcal/mol
Ligand efficiency (LE)
-0.6531kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.480
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
459.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.10
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
37.09kcal/mol
Minimised FF energy
7.60kcal/mol
SASA & burial
✓ computed
SASA (unbound)
738.1Ų
Total solvent-accessible surface area of free ligand
BSA total
571.6Ų
Buried surface area upon binding
BSA apolar
472.7Ų
Hydrophobic contacts buried
BSA polar
98.9Ų
Polar contacts buried
Fraction buried
77.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2569.9Ų
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
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1387.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)