name ='r-uracil'
symbol ='RU'

phosphate = Group('na_phosphate')
sugar = Group('ribose')
base = Group('uracil')

bonds = [Bond(sugar.O_5, phosphate.P), Bond(base.N_1, sugar.C_1), ]

chain_links = [phosphate.P, sugar.O_3]

amber_charge = {phosphate.P:     1.1662,
                phosphate.O_1:  -0.7760,
                phosphate.O_2:  -0.7760,
                sugar.O_5:      -0.4989,
                sugar.C_5:       0.0558,
                sugar.H_51:      0.0679,
                sugar.H_52:      0.0679,
                sugar.C_4:       0.1065,
                sugar.H_4:       0.1174,
                sugar.O_4:      -0.3548,
                sugar.C_1:       0.0674,
                sugar.H_1:       0.1824,
                base.N_1:        0.0418,
                base.C_6:       -0.1126,
                base.H_6:        0.2188,
                base.C_5:       -0.3635,
                base.H_5:        0.1811,
                base.C_4:        0.5952,
                base.O_4:       -0.5761,
                base.N_3:       -0.3549,
                base.H_3:        0.3154,
                base.C_2:        0.4687,
                base.O_2:       -0.5477,
                sugar.C_3:       0.2022,
                sugar.H_3:       0.0615,
                sugar.C_2:       0.0670,
                sugar.H_21:      0.0972,
                sugar.O_2:      -0.6139,
                sugar.H_O2:      0.4186,
                sugar.O_3:      -0.5246,
                }
