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. Author manuscript; available in PMC: 2014 Nov 1.
Published in final edited form as: J Mol Model. 2013 Oct 2;19(11):5075–5087. doi: 10.1007/s00894-013-1990-x

Table 5.

New bonded interaction parameters assigned for the acylphosphate moiety in 4

Bonds Atom Types Reqa KR
P1-O8 PG1-OG305 1.78 170
C9-O10 CG2O2-OG305 1.34 230
Bond Angles Atom Types Θeqb KΘ RUB KUB
P1-O8-C9 PG1-OG305- CG2O2 121.5 70
O2-P1-O8 OG2P1-PG1-OG305 103.0 60
O3-P1-O8 OG303-PG1-OG305 90.8 60
O7-P1-O8 OG2P1-PG1-OG305 103.0 60
O8-C9-O10 OG305- CG2O2- OG2D1 118.0 70 2.26 160
O10-C9-C11 OG305- CG2O2- CG331 104.0 30 2.33 5
Dihedral Angles Atom Types Kφc n δ
P1-O8-C9-O10 PG1-OG305-CG2O2-OG2D1 1.30 1 180
P1-O8-C9-O10 PG1-OG305-CG2O2-OG2D1 2.60 2 180
P1-O8-C9-C11 PG1-OG305-CG2O2-CG331 3.80 1 180
P1-O8-C9-C11 PG1-OG305-CG2O2-CG331 1.60 2 180
O2-P1-O8-C9 OG2P1-PG1-OG305-CG2O2 0.10 3 0
O3-P1-O8-C9 OG303-PG1-OG305-CG2O2 0.10 2 180
O3-P1-O8-C9 OG303-PG1-OG305-CG2O2 0.10 3 0
C4-O3-P1-O8 CG331-OG303-PG1-OG305 1.47 2 0
C4-O3-P1-O8 CG331-OG303-PG1-OG305 0.70 3 0
Improper Torsion Atom Types Kφd Φo
O8-O10-C11-C9 OG305-OG2D1-CG331-CG2O2 56 0
a

Req, reference bond distance (Å) and KR, force constant (kcal/mol/Å2).

b

Θeq, reference bond angle (°) and KΘ, force constant (kcal/mol/rad2).

c

Kφ, torsional potential (kcal/mol), n and δ, periodicity and phase offset (°) of the torsion, respectively.

d

Kφ, improper dihedral potential (kcal/mol/rad2) and Φo, reference improper dihedral angle (°).