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 high
Native strong
SASA done
Strain ΔE
27.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.60, Jaccard 0.43, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.827 kcal/mol/HA)
✓ Good fit quality (FQ -8.06)
✓ Good H-bonds (3 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ High strain energy (27.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-25.648
kcal/mol
LE
-0.827
kcal/mol/HA
Fit Quality
-8.06
FQ (Leeson)
HAC
31
heavy atoms
MW
500
Da
LogP
5.50
cLogP
Interaction summary
HB 3
HY 24
PI 0
CLASH 2
Interaction summary
HB 3
HY 24
PI 0
CLASH 2
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
| Final rank | 3.358 | Score | -25.648 |
|---|---|---|---|
| Inter norm | -0.814 | Intra norm | -0.014 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 3 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; moderate strain Δ 27.6 | ||
| Residues |
ARG22
ARG342
ASN20
CYS26
GLN341
GLU343
GLU384
LEU25
LEU339
LEU382
PRO340
PRO344
PRO373
THR21
THR285
| ||
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 | 0.43 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 572 | 0.5870117947832066 | -1.10765 | -37.5989 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 583 | 0.8823549273857154 | -0.910836 | -30.2227 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 592 | 1.310495564240597 | -0.754262 | -27.3292 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 611 | 1.7798849023795245 | -0.802683 | -26.2147 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 594 | 1.9412230667148331 | -0.877204 | -32.0703 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 584 | 2.0822003114507757 | -0.856641 | -25.7246 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 583 | 2.606119674997513 | -0.894636 | -26.6402 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 600 | 2.62217074979796 | -0.689693 | -24.6956 | 3 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 575 | 3.3580502961066707 | -0.8137 | -25.6478 | 3 | 15 | 9 | 0.60 | 0.40 | - | no | Current |
| 595 | 3.5009994029016003 | -0.774293 | -24.4273 | 4 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 587 | 3.744243536944524 | -0.642671 | -23.6962 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 600 | 3.987159201366124 | -1.08362 | -33.2245 | 13 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 591 | 6.027892840267617 | -0.912188 | -27.1412 | 8 | 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
-25.648kcal/mol
Ligand efficiency (LE)
-0.8273kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.060
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
500.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.50
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
15.21kcal/mol
Minimised FF energy
-12.36kcal/mol
SASA & burial
✓ computed
SASA (unbound)
759.8Ų
Total solvent-accessible surface area of free ligand
BSA total
578.4Ų
Buried surface area upon binding
BSA apolar
486.6Ų
Hydrophobic contacts buried
BSA polar
91.8Ų
Polar contacts buried
Fraction buried
76.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2598.3Ų
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
1371.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)