Computational Biology Journal

Research Article

Calculated Vibrational Properties of Ubisemiquinones

Table 1

Calculated bond lengths (in Å) and bond angles (in degrees) for all conformers in the gas phase and CCl₄. Calculated methoxy group dihedral angles and relative energies (in kcal/mol) for all conformers are also listed. The lowest energy conformer is set to zero and the energies of conformers relative to this zero are listed (kT at 298 K is ~0.59 kcal/mol). Bond lengths and angles for neutral in the Q_A binding site (PDB file: 1AIJ) and in the Q_B binding site (PDB file: 1AIG) are also listed.


	in gas phase				in CCl₄				Q_A	Q_B
	A	B	E	F	A	B	E	F

C₁O	1.273	1.273	1.273	1.273	1.274	1.274	1.273	1.273	1.234	1.227
C₄O	1.272	1.272	1.271	1.271	1.247	1.274	1.274	1.274	1.232	1.221
C₂C₃	1.380	1.380	1.379	1.379	1.380	1.379	1.378	1.379	1.404	1.379
C₅C₆	1.384	1.384	1.384	1.384	1.384	1.385	1.385	1.385	1.419	1.398
C₆–C₁₀–C₁₁	113.4	113.5	113.5	113.5	113.3	113.2	113.3	113.2	113.0	111.0
C₃–C₂–O–CH₃	−121.8	120.8	116.7	−117.3	−118.5	116.1	111.8	−113.6	−57.1	79.9
C₂–C₃–O–CH₃	122.4	−123.2	118.3	−119.0	118.2	−117.7	111.6	−113.6	109.5	−121.3
	0.537	0.646	0.106	0	0.450	0.387	0.002	0