name ='d-thymine_3ter'
symbol ='DT3'

phosphate = Group('na_phosphate')
sugar = Group('desoxyribose_3ter')
base = Group('thymine')

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

chain_links = [phosphate.P, None]

amber_charge = {phosphate.P: 1.1659,
                phosphate.O_1: -0.7761,
                phosphate.O_2: -0.7761,
                sugar.O_5: -0.4954,
                sugar.C_5: -0.0069,
                sugar.H_51: 0.0754,
                sugar.H_52: 0.0754,
                sugar.C_4: 0.1629,
                sugar.H_4: 0.1176,
                sugar.O_4: -0.3691,
                sugar.C_1: 0.0680,
                sugar.H_1: 0.1804,
                base.N_1: -0.0239,
                base.C_6: -0.2209,
                base.H_6: 0.2607,
                base.C_5: 0.0025,
                base.C_7: -0.2269,
                base.H_71: 0.0770,
                base.H_72: 0.0770,
                base.H_73: 0.0770,
                base.C_4: 0.5194,
                base.O_4: -0.5563,
                base.N_3: -0.4340,
                base.H_3: 0.3420,
                base.C_2: 0.5677,
                base.O_2: -0.5881,
                sugar.C_3: 0.0713,
                sugar.H_3: 0.0985,
                sugar.C_2: -0.0854,
                sugar.H_21: 0.0718,
                sugar.H_22: 0.0718,
                sugar.O_3: -0.6549,
                sugar.H_3_terminal: 0.4396,
                }
