Structure based on 5fkj

Ideal structure
Name: 1,3-bis[5(diethyl-o-nitrobenzylammonium)pentyl]-6-methyluracil
Formula: C37 H56 N6 O6
Weight: 680.877
SMILES: "CC[N+](CC)(CCCCCN1C(=CC(=O)N(CCCCC[N+](CC)(CC)Cc2ccccc2[N+]([O-])=O)C1=O)C)Cc3ccccc3[N+]([O-])=O"
Spacial conformation based on PDB 5fkj
RESIDUE   G0W    105
CONECT      C01    4 C02  H01  H01A H01B
CONECT      C02    4 C01  N03  H02  H02A
CONECT      N03    4 C02  C04  C06  C40 
CONECT      C04    4 N03  C05  H04  H04A
CONECT      C05    4 C04  H05  H05A H05B
CONECT      C06    4 N03  C07  H06  H06A
CONECT      C07    4 C06  C08  H07  H07A
CONECT      C08    4 C07  C09  H08  H08A
CONECT      C09    4 C08  C10  H09  H09A
CONECT      C10    4 C09  N11  H10  H10A
CONECT      N11    3 C10  C12  C38 
CONECT      C12    3 N11  C13  C14 
CONECT      C13    4 C12  H13  H13A H13B
CONECT      C14    3 C12  C15  H14 
CONECT      C15    3 C14  O16  N17 
CONECT      O16    1 C15 
CONECT      N17    3 C15  C18  C38 
CONECT      C18    4 N17  C19  H18  H18A
CONECT      C19    4 C18  C20  H19  H19A
CONECT      C20    4 C19  C21  H20  H20A
CONECT      C21    4 C20  C22  H21  H21A
CONECT      C22    4 C21  N23  H22  H22A
CONECT      N23    4 C22  C24  C26  C28 
CONECT      C24    4 N23  C25  H24  H24A
CONECT      C25    4 C24  H25  H25A H25B
CONECT      C26    4 N23  C27  H26  H26A
CONECT      C27    4 C26  H27  H27A H27B
CONECT      C28    4 N23  C29  H28  H28A
CONECT      C29    3 C28  C30  C34 
CONECT      C30    3 C29  C31  H30 
CONECT      C31    3 C30  C32  H31 
CONECT      C32    3 C31  C33  H32 
CONECT      C33    3 C32  C34  H33 
CONECT      C34    3 C29  C33  N35 
CONECT      N35    3 C34  O36  O37 
CONECT      O36    1 N35 
CONECT      O37    1 N35 
CONECT      C38    3 N11  N17  O39 
CONECT      O39    1 C38 
CONECT      C40    4 N03  C41  H40  H40A
CONECT      C41    3 C40  C42  C46 
CONECT      C42    3 C41  C43  H42 
CONECT      C43    3 C42  C44  H43 
CONECT      C44    3 C43  C45  H44 
CONECT      C45    3 C44  C46  H45 
CONECT      C46    3 C41  C45  N47 
CONECT      N47    3 C46  O48  O49 
CONECT      O48    1 N47 
CONECT      O49    1 N47 
CONECT      H01    1 C01 
CONECT      H01A   1 C01 
CONECT      H01B   1 C01 
CONECT      H02    1 C02 
CONECT      H02A   1 C02 
CONECT      H04    1 C04 
CONECT      H04A   1 C04 
CONECT      H05    1 C05 
CONECT      H05A   1 C05 
CONECT      H05B   1 C05 
CONECT      H06    1 C06 
CONECT      H06A   1 C06 
CONECT      H07    1 C07 
CONECT      H07A   1 C07 
CONECT      H08    1 C08 
CONECT      H08A   1 C08 
CONECT      H09    1 C09 
CONECT      H09A   1 C09 
CONECT      H10    1 C10 
CONECT      H10A   1 C10 
CONECT      H13    1 C13 
CONECT      H13A   1 C13 
CONECT      H13B   1 C13 
CONECT      H14    1 C14 
CONECT      H18    1 C18 
CONECT      H18A   1 C18 
CONECT      H19    1 C19 
CONECT      H19A   1 C19 
CONECT      H20    1 C20 
CONECT      H20A   1 C20 
CONECT      H21    1 C21 
CONECT      H21A   1 C21 
CONECT      H22    1 C22 
CONECT      H22A   1 C22 
CONECT      H24    1 C24 
CONECT      H24A   1 C24 
CONECT      H25    1 C25 
CONECT      H25A   1 C25 
CONECT      H25B   1 C25 
CONECT      H26    1 C26 
CONECT      H26A   1 C26 
CONECT      H27    1 C27 
CONECT      H27A   1 C27 
CONECT      H27B   1 C27 
CONECT      H28    1 C28 
CONECT      H28A   1 C28 
CONECT      H30    1 C30 
CONECT      H31    1 C31 
CONECT      H32    1 C32 
CONECT      H33    1 C33 
CONECT      H40    1 C40 
CONECT      H40A   1 C40 
CONECT      H42    1 C42 
CONECT      H43    1 C43 
CONECT      H44    1 C44 
CONECT      H45    1 C45 
HET    G0W            105
FORMUL      G0W    C37 H56 N6 O6 2+

uses Jmol, developed by the Jmol Development Team (color reference)
OCA© by Jaime Prilusky, 1996-2004,2006,2010,2014
Bioinformatics Unit
Weizmann Institute of Science