PDB Chemical Component XCY

The following tables include covalent bond distance, bond angle and torsion angle values for the experimental model and ideal geometries stored in the definition for this chemical component.

Bond Distances for XCY

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP3 1.480 1.617
P OP2 1.480 1.617
P O5' 1.595 1.618
P OP1   1.501
OP3 HOP3 0.950 0.981
OP2 HOP2 0.950 0.980
O5' C5' 1.422 1.418
N1 C6 1.364 1.384
N1 C2 1.407 1.417
N1 C1' 1.471 1.434
C6 C5 1.340 1.332
C6 H6 1.103 1.085
C2 O2 1.245 1.232
C2 N3 1.357 1.384
N3 C4 1.332 1.307
C4 N4 1.344 1.376
C4 C5 1.430 1.485
N4 CH 1.478 1.431
N4 HN4 1.020 0.988
C5 H5 1.103 1.082
NZ CB 1.501 1.441
NZ HNZ1 1.020 1.006
NZ HNZ2 1.021 1.006
CB CG 1.513 1.491
CB HB1 1.115 1.099
CB HB2 1.115 1.099
CG CD1 1.434 1.395
CG CD2 1.426 1.395
CD1 CE1 1.438 1.395
CD1 HD1 1.103 1.087
CE1 CZ 1.432 1.390
CE1 HE1 1.103 1.087
CD2 CE2 1.441 1.395
CD2 HD2 1.103 1.087
CE2 CZ 1.418 1.389
CE2 HE2 1.103 1.087
CZ CH 1.525 1.502
CH HH1 1.115 1.096
CH HH2 1.115 1.095
C2' C1' 1.513 1.520
C2' C3' 1.518 1.512
C2' H2' 1.115 1.097
C2' H2'' 1.115 1.094
C5' C4' 1.507 1.524
C5' H5' 1.115 1.093
C5' H5'' 1.115 1.093
C4' O4' 1.445 1.441
C4' C3' 1.523 1.521
C4' H4' 1.115 1.094
O4' C1' 1.416 1.435
C1' H1' 1.115 1.094
C3' O3' 1.421 1.426
C3' H3' 1.115 1.093
O3' HO3' 0.950 0.974

Bond Angles for XCY

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP3 P OP2 119.6 103.3
OP3 P O5' 109.5 103.7
OP3 P OP1   115.3
P OP3 HOP3 119.6 118.9
OP2 P O5' 107.2 102.9
OP2 P OP1   115.0
P OP2 HOP2 119.5 119.0
O5' P OP1   115.0
P O5' C5' 120.9 118.5
O5' C5' C4' 109.8 108.9
O5' C5' H5' 112.0 109.0
O5' C5' H5'' 112.1 109.0
C6 N1 C2 120.2 119.5
C6 N1 C1' 120.8 118.7
N1 C6 C5 121.0 122.7
N1 C6 H6 120.4 116.2
C2 N1 C1' 119.0 121.9
N1 C2 O2 119.1 121.1
N1 C2 N3 119.3 118.7
N1 C1' C2' 115.2 112.8
N1 C1' O4' 107.6 109.3
N1 C1' H1' 105.6 107.8
C5 C6 H6 118.6 121.2
C6 C5 C4 117.7 116.4
C6 C5 H5 118.0 123.1
O2 C2 N3 121.6 120.2
C2 N3 C4 119.9 121.1
N3 C4 N4 118.3 120.1
N3 C4 C5 121.9 121.7
N4 C4 C5 119.8 118.2
C4 N4 CH 134.6 120.3
C4 N4 HN4 103.6 116.3
C4 C5 H5 124.2 120.6
CH N4 HN4 103.5 123.4
N4 CH CZ 110.8 112.0
N4 CH HH1 111.7 107.9
N4 CH HH2 111.7 107.8
CB NZ HNZ1 110.1 119.0
CB NZ HNZ2 115.3 119.1
NZ CB CG 115.3 112.4
NZ CB HB1 110.1 107.5
NZ CB HB2 110.1 107.4
HNZ1 NZ HNZ2 110.1 120.5
CG CB HB1 110.1 111.1
CG CB HB2 110.1 111.5
CB CG CD1 121.3 120.0
CB CG CD2 120.4 120.1
HB1 CB HB2 100.2 106.8
CD1 CG CD2 118.2 119.9
CG CD1 CE1 120.5 120.0
CG CD1 HD1 119.6 120.5
CG CD2 CE2 120.8 120.1
CG CD2 HD2 119.1 120.5
CE1 CD1 HD1 119.9 119.5
CD1 CE1 CZ 121.2 119.6
CD1 CE1 HE1 119.6 119.5
CZ CE1 HE1 119.2 120.9
CE1 CZ CE2 118.0 120.7
CE1 CZ CH 121.6 119.6
CE2 CD2 HD2 120.1 119.5
CD2 CE2 CZ 121.3 119.6
CD2 CE2 HE2 120.2 119.5
CZ CE2 HE2 118.5 120.9
CE2 CZ CH 120.4 119.6
CZ CH HH1 111.7 110.6
CZ CH HH2 111.7 111.0
HH1 CH HH2 98.7 107.3
C1' C2' C3' 101.7 102.5
C1' C2' H2' 115.2 110.5
C1' C2' H2'' 115.2 111.7
C2' C1' O4' 105.2 107.3
C2' C1' H1' 108.0 111.5
C3' C2' H2' 115.1 109.7
C3' C2' H2'' 115.1 114.1
C2' C3' C4' 102.9 103.1
C2' C3' O3' 112.0 109.6
C2' C3' H3' 112.1 113.2
H2' C2' H2'' 95.3 108.3
C4' C5' H5' 112.1 110.3
C4' C5' H5'' 112.1 110.3
C5' C4' O4' 109.4 107.9
C5' C4' C3' 113.1 112.9
C5' C4' H4' 105.9 109.4
H5' C5' H5'' 98.3 109.3
O4' C4' C3' 105.8 106.3
O4' C4' H4' 113.2 107.9
C4' O4' C1' 110.2 109.2
C3' C4' H4' 109.6 112.2
C4' C3' O3' 109.4 109.9
C4' C3' H3' 114.6 113.5
O4' C1' H1' 115.5 107.9
O3' C3' H3' 106.0 107.4
C3' O3' HO3' 112.0 107.2

Torsion Angles for XCY

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP3 O5' 124.2 107.1
OP2 P OP3 OP1   233.7
OP3 P OP2 HOP2 180.0 78.5
O5' P OP3 OP1   126.6
OP3 P O5' C5' 320.3 53.2
OP3 P OP2 O5' 234.7 252.3
OP3 P OP2 OP1   126.5
OP2 P OP3 HOP3 180.0 282.5
O5' P OP2 OP1   234.2
OP2 P O5' C5' 189.2 305.8
OP3 P O5' OP2 131.1 107.4
OP3 P O5' OP1   233.2
O5' P OP3 HOP3 55.8 175.4
OP2 P O5' OP1   125.8
O5' P OP2 HOP2 305.3 186.2
P O5' C5' C4' 202.0 180.0
P O5' C5' H5' 76.8 300.3
P O5' C5' H5'' 327.3 59.6
OP3 P OP1 OP2   239.9
OP3 P OP1 O5'   120.7
OP1 P OP3 HOP3   48.8
OP2 P OP1 O5'   240.7
OP1 P OP2 HOP2   312.0
OP1 P O5' C5'   180.0
HOP3 OP3 P OP2 180.0 282.5
HOP3 OP3 P O5' 55.8 175.4
HOP3 OP3 P OP1   48.8
HOP2 OP2 P O5' 305.3 186.2
HOP2 OP2 P OP1   312.0
C5' O5' P OP1   180.0
C4' C5' O5' H5' 125.2 239.6
C4' C5' O5' H5'' 234.7 120.4
O5' C5' C4' O4' 290.6 62.4
O5' C5' C4' C3' 48.2 179.5
O5' C5' C4' H4' 168.2 305.3
H5' C5' O5' H5'' 109.5 240.8
C2 N1 C6 C1' 179.6 180.0
C6 N1 C2 O2 180.5 179.9
C6 N1 C2 N3 0.3 0.0
C6 N1 C1' C2' 291.6 273.6
C6 N1 C1' O4' 48.6 32.9
C6 N1 C1' H1' 172.6 150.0
C5 C6 N1 H6 180.0 180.1
N1 C6 C5 C4 359.4 360.0
N1 C6 C5 H5 179.4 180.0
C6 N1 C2 C1' 180.4 180.0
C2 N1 C6 C5 360.0 0.0
C2 N1 C6 H6 180.0 180.0
C2 N1 C1' C2' 112.1 93.6
C2 N1 C1' O4' 229.1 212.9
C2 N1 C1' H1' 353.0 330.0
O2 C2 N1 N3 180.2 179.9
N1 C2 N3 C4 359.9 359.9
C6 N1 C1' C2 179.6 180.0
C1' N1 C6 C5 180.4 180.0
C1' N1 C6 H6 0.5 360.0
C1' N1 C2 O2 0.1 359.9
C1' N1 C2 N3 179.9 180.0
N1 C1' C2' C3' 154.4 147.3
N1 C1' C2' H2' 29.2 30.5
N1 C1' C2' H2'' 279.7 269.9
C2' C1' N1 O4' 243.0 240.7
C2' C1' N1 H1' 119.1 123.6
C4' O4' C1' N1 213.9 228.4
O4' C1' N1 H1' 236.1 242.9
C5 C6 N1 C2 360.0 0.0
C5 C6 N1 C1' 180.4 180.0
N1 C6 C5 H6 180.0 179.9
N3 C4 C5 C6 0.8 0.0
N4 C4 C5 C6 181.1 180.0
C4 C5 C6 H5 180.0 180.0
H6 C6 N1 C2 180.0 180.0
H6 C6 N1 C1' 0.5 360.0
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 C4 179.4 180.0
H6 C6 C5 H5 359.4 0.0
O2 C2 N1 C1' 0.1 359.9
N1 C2 O2 N3 179.8 180.1
O2 C2 N3 C4 179.8 180.1
N3 C2 N1 C1' 179.9 180.0
N1 C2 N3 O2 180.2 179.9
C2 N3 C4 N4 179.2 180.1
C2 N3 C4 C5 359.5 0.0
C6 C5 C4 N3 0.8 0.0
N4 C4 N3 C5 179.7 180.0
N3 C4 N4 CH 348.7 360.0
N3 C4 N4 HN4 223.4 180.0
N3 C4 C5 H5 180.8 180.0
C6 C5 C4 N4 181.1 180.0
N3 C4 N4 C5 180.3 180.0
N4 C4 C5 H5 1.1 360.0
CH N4 C4 HN4 125.3 180.0
C4 N4 CH CZ 190.9 182.0
C4 N4 CH HH1 65.7 60.0
C4 N4 CH HH2 316.2 304.4
C4 C5 C6 H6 179.4 180.0
C6 C5 C4 H5 180.0 180.0
N3 C4 C5 N4 179.7 180.0
C5 C4 N4 CH 168.4 180.0
C5 C4 N4 HN4 43.1 360.0
CH N4 C4 C5 168.4 180.0
C4 N4 CH HN4 234.7 180.0
CE1 CZ CH N4 269.3 90.0
CE2 CZ CH N4 88.1 270.1
CZ CH N4 HH1 125.3 122.0
CZ CH N4 HH2 234.7 237.6
HH1 CH N4 HH2 109.5 115.6
HN4 N4 C4 C5 43.1 360.0
C4 N4 HN4 CH 143.3 180.0
HN4 N4 CH CZ 316.2 2.0
HN4 N4 CH HH1 191.0 240.0
HN4 N4 CH HH2 81.5 124.4
H5 C5 C6 H6 359.4 0.0
C6 C5 H5 C4 180.0 180.0
HNZ1 NZ CB HNZ2 234.8 166.6
CG CB NZ HB1 125.2 122.5
CG CB NZ HB2 234.7 237.1
NZ CB CG CD1 15.6 90.0
NZ CB CG CD2 195.6 270.0
HB1 CB NZ HB2 109.5 114.6
CB NZ HNZ1 HNZ2 128.2 193.6
HNZ1 NZ CB CG 54.8 182.4
HNZ1 NZ CB HB1 289.5 59.9
HNZ1 NZ CB HB2 180.0 305.3
CB NZ HNZ2 HNZ1 234.8 166.4
HNZ2 NZ CB CG 180.0 15.8
HNZ2 NZ CB HB1 54.8 253.3
HNZ2 NZ CB HB2 305.3 138.8
CG CB NZ HNZ1 54.8 182.4
CG CB NZ HNZ2 180.0 15.8
NZ CB CG HB1 234.7 239.6
NZ CB CG HB2 125.2 120.6
HB1 CB CG HB2 250.5 241.0
CD1 CG CB CD2 180.1 179.9
CB CG CD1 CE1 180.4 180.0
CB CG CD1 HD1 0.4 0.1
CB CG CD2 CE2 179.7 179.9
CB CG CD2 HD2 359.7 359.9
HB1 CB NZ HNZ1 289.5 59.9
HB1 CB NZ HNZ2 54.8 253.3
NZ CB HB1 CG 128.2 123.3
NZ CB HB1 HB2 244.1 245.0
CG CB HB1 HB2 115.9 121.8
HB1 CB CG CD1 140.9 210.4
HB1 CB CG CD2 320.8 30.5
HB2 CB NZ HNZ1 180.0 305.3
HB2 CB NZ HNZ2 305.3 138.8
NZ CB HB2 CG 231.8 236.5
NZ CB HB2 HB1 115.9 115.0
CG CB HB2 HB1 244.1 238.5
HB2 CB CG CD1 250.4 329.4
HB2 CB CG CD2 70.3 149.5
CD1 CG CB HB1 140.9 210.4
CD1 CG CB HB2 250.4 329.4
CB CG CD1 CD2 179.9 180.1
CD1 CG CD2 CE2 359.6 0.0
CD1 CG CD2 HD2 179.6 180.0
CE1 CD1 CG HD1 180.0 179.9
CG CD1 CE1 CZ 359.8 0.0
CG CD1 CE1 HE1 179.8 180.0
CD2 CG CB HB1 320.8 30.5
CD2 CG CB HB2 70.3 149.5
CB CG CD2 CD1 180.1 179.9
CD2 CG CD1 CE1 0.5 359.9
CD2 CG CD1 HD1 180.4 180.0
CE2 CD2 CG HD2 180.0 180.0
CG CD2 CE2 CZ 0.0 0.0
CG CD2 CE2 HE2 180.0 180.0
CE1 CD1 CG CD2 0.5 359.9
CG CD1 CE1 HD1 180.0 180.1
CZ CE1 CD1 HE1 180.0 180.0
CD1 CE1 CZ CE2 359.8 0.0
CD1 CE1 CZ CH 178.7 180.1
HD1 CD1 CG CD2 180.4 180.0
CG CD1 HD1 CE1 180.0 179.9
HD1 CD1 CE1 CZ 179.8 180.0
HD1 CD1 CE1 HE1 359.8 359.9
N4 CH CZ CE1 269.3 90.0
CZ CE1 CD1 HD1 179.8 180.0
CD1 CE1 CZ HE1 180.0 180.0
CD2 CE2 CZ CE1 0.2 360.0
CE1 CZ CE2 HE2 180.2 180.0
CE2 CZ CE1 CH 181.1 180.0
CE1 CZ CH HH1 34.5 210.4
CE1 CZ CH HH2 144.0 329.4
HE1 CE1 CD1 HD1 359.8 359.9
CD1 CE1 HE1 CZ 180.0 180.0
HE1 CE1 CZ CE2 179.8 180.0
HE1 CE1 CZ CH 358.7 0.1
CG CD2 CE2 HD2 180.0 180.0
CE1 CZ CE2 CD2 0.2 360.0
CZ CE2 CD2 HE2 180.0 180.1
CD2 CE2 CZ CH 181.3 179.9
CG CD2 HD2 CE2 180.0 180.0
HD2 CD2 CE2 CZ 180.1 180.0
HD2 CD2 CE2 HE2 0.0 360.0
N4 CH CZ CE2 88.1 270.1
CE2 CZ CE1 HE1 179.8 180.0
CE1 CZ CE2 CH 178.9 180.0
CZ CE2 CD2 HD2 180.1 180.0
CD2 CE2 CZ HE2 180.0 179.9
CE2 CZ CH HH1 213.4 30.5
CE2 CZ CH HH2 322.8 149.5
HE2 CE2 CD2 HD2 0.0 360.0
CD2 CE2 HE2 CZ 180.0 180.1
HE2 CE2 CZ CH 1.3 360.0
CZ CH N4 HN4 316.2 2.0
N4 CH CZ HH1 234.7 239.6
N4 CH CZ HH2 125.3 120.6
CH CZ CE1 HE1 358.7 0.1
CE1 CZ CH CE2 181.1 180.0
CH CZ CE2 HE2 1.3 360.0
HH1 CH CZ HH2 250.5 241.0
HH1 CH N4 HN4 191.0 240.0
N4 CH HH1 CZ 124.7 122.8
N4 CH HH1 HH2 242.4 244.1
CZ CH HH1 HH2 117.6 121.2
HH2 CH N4 HN4 81.5 124.4
N4 CH HH2 CZ 235.2 237.0
N4 CH HH2 HH1 117.6 116.0
CZ CH HH2 HH1 242.4 239.0
N1 C1' C2' O4' 118.3 120.4
N1 C1' C2' H1' 242.2 238.4
C3' C2' C1' H2' 125.2 116.8
C3' C2' C1' H2'' 234.8 237.4
C1' C2' C3' C4' 324.8 326.6
C1' C2' C3' O3' 82.2 83.6
C1' C2' C3' H3' 201.1 203.6
H2' C2' C1' H2'' 109.5 120.6
C4' O4' C1' C2' 337.2 351.0
O4' C1' C2' H1' 123.9 118.0
C1' C2' C3' H2' 234.7 242.6
C1' C2' C3' H2'' 125.3 120.9
C3' C2' C1' O4' 36.1 26.8
C3' C2' C1' H1' 272.2 268.8
H2' C2' C3' H2'' 250.5 238.3
C5' C4' C3' C2' 263.0 271.1
O4' C4' C3' C2' 22.7 29.2
C2' C3' C4' H4' 145.1 146.9
C4' C3' C2' O3' 242.6 243.0
C4' C3' C2' H3' 123.7 123.1
O3' C3' C2' H3' 241.1 240.1
C2' C3' O3' HO3' 180.0 119.3
C1' C2' H2' C3' 118.0 112.3
C1' C2' H2' H2'' 239.0 237.4
H2' C2' C1' O4' 270.8 270.0
H2' C2' C1' H1' 147.0 152.0
C3' C2' H2' H2'' 121.0 125.1
H2' C2' C3' C4' 90.0 84.1
H2' C2' C3' O3' 207.4 201.1
H2' C2' C3' H3' 326.4 321.0
C1' C2' H2'' C3' 242.1 244.3
C1' C2' H2'' H2' 121.1 121.9
H2'' C2' C1' O4' 161.3 149.4
H2'' C2' C1' H1' 37.4 31.4
C3' C2' H2'' H2' 239.0 237.6
H2'' C2' C3' C4' 199.5 205.7
H2'' C2' C3' O3' 316.9 322.7
H2'' C2' C3' H3' 75.8 82.6
O5' C5' C4' H5' 234.8 119.6
O5' C5' C4' H5'' 125.3 240.4
C2' C3' C4' C5' 263.0 271.1
H5' C5' C4' H5'' 250.5 120.9
O4' C4' C5' C3' 242.4 242.8
O4' C4' C5' H4' 122.4 117.1
C5' C4' O4' C1' 122.0 108.6
C3' C4' C5' H4' 240.0 234.3
C5' C4' C3' O3' 143.8 154.3
C5' C4' C3' H3' 25.0 34.0
O5' C5' H5' C4' 124.0 240.5
O5' C5' H5' H5'' 242.0 119.0
C4' C5' H5' H5'' 118.0 238.5
H5' C5' C4' O4' 55.8 302.8
H5' C5' C4' C3' 173.5 60.0
H5' C5' C4' H4' 293.5 185.7
O5' C5' H5'' C4' 236.0 119.5
O5' C5' H5'' H5' 118.0 241.0
C4' C5' H5'' H5' 242.0 121.4
H5'' C5' C4' O4' 165.3 181.9
H5'' C5' C4' C3' 282.9 299.1
H5'' C5' C4' H4' 43.0 64.9
N1 C1' O4' C4' 213.9 228.4
C2' C1' O4' C4' 337.2 351.0
C2' C3' C4' O4' 22.7 29.2
O4' C4' C5' H5' 55.8 302.8
O4' C4' C5' H5'' 165.3 181.9
C5' C4' O4' C3' 122.1 121.4
C5' C4' O4' H4' 242.1 241.9
C3' C4' O4' H4' 120.0 120.5
O4' C4' C3' O3' 263.5 272.4
O4' C4' C3' H3' 144.7 152.1
C4' O4' C1' H1' 96.2 111.3
C4' C3' C2' H2' 90.0 84.1
C4' C3' C2' H2'' 199.5 205.7
C2' C3' C4' O3' 119.2 116.8
C2' C3' C4' H3' 238.0 237.1
C3' C4' C5' H5' 173.5 60.0
C3' C4' C5' H5'' 282.9 299.1
C5' C4' C3' O4' 240.2 241.9
C5' C4' C3' H4' 117.9 124.2
O4' C4' C3' H4' 237.7 242.3
C3' C4' O4' C1' 359.8 347.3
O3' C3' C4' H3' 118.8 120.3
C4' C3' O3' HO3' 293.5 232.0
H4' C4' C5' H5' 293.5 185.7
H4' C4' C5' H5'' 43.0 64.9
C5' C4' H4' O4' 119.9 117.1
C5' C4' H4' C3' 237.7 233.9
O4' C4' H4' C3' 117.8 116.8
H4' C4' O4' C1' 239.8 226.7
H4' C4' C3' O3' 25.9 30.1
H4' C4' C3' H3' 267.1 269.7
N1 C1' O4' C2' 236.7 237.3
N1 C1' O4' H1' 117.7 117.0
O4' C1' C2' C3' 36.1 26.8
O4' C1' C2' H2' 270.8 270.0
O4' C1' C2' H2'' 161.3 149.4
C2' C1' O4' H1' 241.0 239.7
C1' O4' C4' C3' 359.8 347.3
C1' O4' C4' H4' 239.8 226.7
N1 C1' H1' C2' 123.7 124.4
N1 C1' H1' O4' 241.2 242.1
H1' C1' C2' C3' 272.2 268.8
H1' C1' C2' H2' 147.0 152.0
H1' C1' C2' H2'' 37.4 31.4
C2' C1' H1' O4' 117.5 117.7
O3' C3' C2' H2' 207.4 201.1
O3' C3' C2' H2'' 316.9 322.7
C2' C3' O3' C4' 246.5 247.4
C2' C3' O3' H3' 122.5 123.4
O3' C3' C4' H4' 25.9 30.1
C4' C3' O3' H3' 236.0 236.0
H3' C3' C2' H2' 326.4 321.0
H3' C3' C2' H2'' 75.8 82.6
C2' C3' H3' C4' 116.8 117.1
C2' C3' H3' O3' 237.6 238.8
H3' C3' C4' H4' 267.1 269.7
C4' C3' H3' O3' 120.7 121.7
H3' C3' O3' HO3' 57.5 355.9
HO3' O3' C3' H3' 57.5 355.9