name ='r-cytosine'
symbol ='RC'

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

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:       0.0066,
                sugar.H_1:       0.2029,
                base.N_1:       -0.0484,
                base.C_6:        0.0053,
                base.H_6:        0.1958,
                base.C_5:       -0.5215,
                base.H_5:        0.1928,
                base.C_4:        0.8185,
                base.N_4:       -0.9530,
                base.H_41:       0.4234,
                base.H_42:       0.4234,
                base.N_3:       -0.7584,
                base.C_2:        0.7538,
                base.O_2:       -0.6252,
                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,
                }
