name ='r-adenosine'
symbol ='RA'

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

bonds = [Bond(sugar.O_5, phosphate.P), Bond(base.N_9, 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:        0.0394,
                sugar.H_1:        0.2007,
                base.N_9:        -0.0251,
                base.C_8:         0.2006,
                base.H_8:         0.1553,
                base.N_7:        -0.6073,
                base.C_5:         0.0515,
                base.C_6:         0.7009,
                base.N_6:        -0.9019,
                base.H_61:        0.4115,
                base.H_62:        0.4115,
                base.N_1:        -0.7615,
                base.C_2:         0.5875,
                base.H_2:         0.0473,
                base.N_3:        -0.6997,
                base.C_4:         0.3053,
                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,
                }
