PDB Chemical Component 125

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 125

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.489 1.478
P OP2 1.482 1.610
P OP3 1.604 1.609
P O5' 1.590 1.610
OP2 HOP2 0.950 0.967
OP3 HOP3 0.950 0.966
O5' C5' 1.432 1.428
C5' C4' 1.507 1.530
C5' H5' 1.115 1.090
C5' H5'' 1.115 1.090
C4' O4' 1.451 1.443
C4' C3' 1.517 1.544
C4' H4' 1.115 1.090
O4' C1' 1.425 1.444
C3' O3' 1.409 1.429
C3' C2' 1.521 1.546
C3' H3' 1.115 1.090
O3' HO3' 0.949 0.967
C2' O2' 1.429 1.429
C2' C1' 1.531 1.544
C2' H2' 1.114 1.090
O2' CA' 1.419 1.428
C1' N1 1.484 1.464
C1' H1' 1.115 1.090
N1 C2 1.380 1.345
N1 C6 1.379 1.368
C2 O2 1.215 1.216
C2 N3 1.371 1.346
N3 C4 1.379 1.349
N3 H3 1.020 0.970
C4 O4 1.229 1.218
C4 C5 1.448 1.415
C5 C5M 1.497 1.507
C5 C6 1.343 1.350
C5M H71 1.115 1.090
C5M H72 1.115 1.090
C5M H73 1.115 1.090
C6 H6 1.103 1.080
CA' CB' 1.510 1.530
CA' HA'1 1.116 1.090
CA' HA'2 1.115 1.090
CB' FC' 1.392 1.398
CB' HB'1 1.116 1.090
CB' HB'2 1.115 1.090

Bond Angles for 125

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 119.7 109.5
OP1 P OP3 107.2 109.6
OP1 P O5' 107.3 109.4
OP2 P OP3 109.3 109.4
OP2 P O5' 109.0 109.4
P OP2 HOP2 119.7 106.8
OP3 P O5' 103.0 109.5
P OP3 HOP3 107.3 106.9
P O5' C5' 119.9 106.8
O5' C5' C4' 110.7 109.5
O5' C5' H5' 111.8 109.4
O5' C5' H5'' 111.7 109.4
C4' C5' H5' 111.7 109.5
C4' C5' H5'' 111.7 109.5
C5' C4' O4' 110.3 110.4
C5' C4' C3' 116.4 110.5
C5' C4' H4' 102.4 110.3
H5' C5' H5'' 98.6 109.4
O4' C4' C3' 103.7 104.8
O4' C4' H4' 115.4 110.4
C4' O4' C1' 109.5 105.3
C3' C4' H4' 109.2 110.4
C4' C3' O3' 113.3 110.6
C4' C3' C2' 102.4 104.1
C4' C3' H3' 112.6 110.5
O4' C1' C2' 107.3 104.9
O4' C1' N1 108.9 110.4
O4' C1' H1' 111.8 110.3
O3' C3' C2' 112.0 110.5
O3' C3' H3' 103.1 110.5
C3' O3' HO3' 113.3 106.8
C2' C3' H3' 113.9 110.5
C3' C2' O2' 106.9 110.5
C3' C2' C1' 100.9 104.0
C3' C2' H2' 115.9 110.5
O2' C2' C1' 108.2 110.8
O2' C2' H2' 109.5 110.4
C2' O2' CA' 117.0 106.9
C1' C2' H2' 114.7 110.4
C2' C1' N1 111.2 110.4
C2' C1' H1' 109.7 110.4
O2' CA' CB' 107.4 109.5
O2' CA' HA'1 113.0 109.4
O2' CA' HA'2 113.0 109.5
N1 C1' H1' 108.0 110.3
C1' N1 C2 117.9 119.7
C1' N1 C6 121.1 119.7
C2 N1 C6 120.9 120.6
N1 C2 O2 123.1 119.5
N1 C2 N3 114.9 120.9
N1 C6 C5 123.7 119.7
N1 C6 H6 119.6 120.2
O2 C2 N3 122.0 119.6
C2 N3 C4 127.2 120.3
C2 N3 H3 116.1 119.9
C4 N3 H3 116.7 119.9
N3 C4 O4 119.7 120.3
N3 C4 C5 115.2 119.4
O4 C4 C5 125.1 120.3
C4 C5 C5M 118.9 120.5
C4 C5 C6 118.0 119.1
C5M C5 C6 123.1 120.4
C5 C5M H71 118.9 109.4
C5 C5M H72 108.8 109.5
C5 C5M H73 108.8 109.4
C5 C6 H6 116.7 120.1
H71 C5M H72 108.9 109.5
H71 C5M H73 108.8 109.5
H72 C5M H73 101.2 109.5
CB' CA' HA'1 113.0 109.5
CB' CA' HA'2 113.0 109.5
CA' CB' FC' 111.0 109.4
CA' CB' HB'1 111.6 109.5
CA' CB' HB'2 111.6 109.5
HA'1 CA' HA'2 97.4 109.4
FC' CB' HB'1 111.7 109.4
FC' CB' HB'2 111.7 109.5
HB'1 CB' HB'2 98.7 109.5

Torsion Angles for 125

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 OP3 125.1 120.0
OP2 P OP1 O5' 235.2 240.0
OP1 P OP2 HOP2 180.0 300.0
OP3 P OP1 O5' 110.1 120.0
OP1 P OP3 HOP3 180.0 180.0
OP1 P O5' C5' 48.9 60.0
OP1 P OP2 OP3 235.9 239.9
OP1 P OP2 O5' 123.9 120.0
OP3 P OP2 O5' 248.0 240.0
OP2 P OP3 HOP3 48.8 60.0
OP2 P O5' C5' 179.9 180.0
OP1 P OP3 OP2 131.1 120.1
OP1 P OP3 O5' 247.0 240.0
OP2 P OP3 O5' 115.8 119.9
OP3 P OP2 HOP2 304.2 60.1
OP3 P O5' C5' 295.9 299.9
OP1 P O5' OP2 229.0 240.0
OP1 P O5' OP3 113.0 120.1
OP2 P O5' OP3 244.0 240.1
O5' P OP2 HOP2 56.1 180.0
O5' P OP3 HOP3 293.0 300.1
P O5' C5' C4' 175.2 180.0
P O5' C5' H5' 300.5 59.9
P O5' C5' H5'' 49.9 300.0
HOP2 OP2 P OP3 304.2 60.1
HOP2 OP2 P O5' 56.1 180.0
HOP3 OP3 P O5' 293.0 300.1
C4' C5' O5' H5' 234.7 120.1
C4' C5' O5' H5'' 125.3 240.0
O5' C5' C4' O4' 292.4 61.4
O5' C5' C4' C3' 50.1 176.9
O5' C5' C4' H4' 169.1 299.2
H5' C5' O5' H5'' 250.5 119.9
O5' C5' C4' H5' 125.3 240.0
O5' C5' C4' H5'' 234.7 120.0
H5' C5' C4' H5'' 109.4 240.0
O4' C4' C5' C3' 242.3 244.5
O4' C4' C5' H4' 123.3 122.2
C5' C4' O4' C1' 147.7 159.5
C3' C4' C5' H4' 241.0 237.7
C5' C4' C3' O3' 79.9 98.3
C5' C4' C3' C2' 200.7 217.0
C5' C4' C3' H3' 323.4 335.7
O5' C5' H5' C4' 235.3 120.1
O5' C5' H5' H5'' 117.6 240.1
C4' C5' H5' H5'' 242.4 120.0
H5' C5' C4' O4' 167.1 181.5
H5' C5' C4' C3' 284.8 296.9
H5' C5' C4' H4' 43.8 59.2
O5' C5' H5'' C4' 124.7 239.9
O5' C5' H5'' H5' 242.3 119.9
C4' C5' H5'' H5' 117.6 240.0
H5'' C5' C4' O4' 57.6 301.4
H5'' C5' C4' C3' 175.4 56.9
H5'' C5' C4' H4' 294.4 179.2
O4' C4' C5' H5' 167.1 181.5
O4' C4' C5' H5'' 57.6 301.4
C5' C4' O4' C3' 125.3 119.0
C5' C4' O4' H4' 244.6 237.8
C3' C4' O4' H4' 119.3 118.8
O4' C4' C3' O3' 201.2 217.2
O4' C4' C3' C2' 322.0 335.9
O4' C4' C3' H3' 84.7 94.6
C4' O4' C1' C2' 2.2 319.6
C4' O4' C1' N1 241.7 200.6
C4' O4' C1' H1' 122.5 78.5
C3' C4' C5' H5' 284.8 296.9
C3' C4' C5' H5'' 175.4 56.9
C5' C4' C3' O4' 238.7 241.1
C5' C4' C3' H4' 115.2 122.2
O4' C4' C3' H4' 236.5 241.1
C3' C4' O4' C1' 22.4 40.5
O3' C3' C4' C2' 239.2 241.3
O3' C3' C4' H3' 116.5 122.6
C4' C3' O3' HO3' 180.0 298.6
C2' C3' C4' H3' 237.3 241.3
C4' C3' C2' O2' 285.2 241.1
C4' C3' C2' C1' 38.2 0.1
C4' C3' C2' H2' 162.8 118.6
H4' C4' C5' H5' 43.8 59.2
H4' C4' C5' H5'' 294.4 179.2
C5' C4' H4' O4' 119.8 122.2
C5' C4' H4' C3' 236.1 237.6
O4' C4' H4' C3' 116.2 115.4
H4' C4' O4' C1' 263.1 281.6
H4' C4' C3' O3' 324.7 336.1
H4' C4' C3' C2' 85.5 94.8
H4' C4' C3' H3' 208.2 213.5
C1' O4' C4' C3' 22.4 40.5
C1' O4' C4' H4' 263.1 281.6
C3' C2' C1' O4' 334.4 23.8
O2' C2' C1' O4' 86.4 142.6
O4' C1' C2' H2' 209.0 265.3
C2' C1' O4' N1 120.5 119.0
C2' C1' O4' H1' 239.7 241.1
N1 C1' O4' H1' 119.2 122.2
O4' C1' N1 C2 207.0 57.1
O4' C1' N1 C6 27.6 237.1
O3' C3' C4' H4' 324.7 336.1
C4' C3' O3' C2' 115.2 114.7
C4' C3' O3' H3' 238.0 237.4
C2' C3' O3' H3' 122.8 122.7
O3' C3' C2' O2' 46.9 359.9
O3' C3' C2' C1' 159.9 118.9
O3' C3' C2' H2' 284.5 237.4
C2' C3' C4' H4' 85.5 94.8
C4' C3' C2' O3' 238.3 241.3
C4' C3' C2' H3' 121.8 118.6
O4' C1' C2' C3' 334.4 23.8
O3' C3' C2' H3' 243.5 237.4
C2' C3' O3' HO3' 64.8 183.9
O2' C2' C3' C1' 247.0 241.0
O2' C2' C3' H2' 122.4 122.5
C3' C2' O2' CA' 178.8 268.6
C1' C2' C3' H2' 235.4 241.5
C3' C2' C1' N1 93.4 142.8
C3' C2' C1' H1' 212.8 265.0
H3' C3' C4' H4' 208.2 213.5
C4' C3' H3' O3' 122.5 122.7
C4' C3' H3' C2' 244.0 245.4
O3' C3' H3' C2' 121.6 122.7
H3' C3' O3' HO3' 301.9 61.2
H3' C3' C2' O2' 163.4 122.5
H3' C3' C2' C1' 276.4 241.5
H3' C3' C2' H2' 41.0 360.0
HO3' O3' C3' C2' 64.8 183.9
HO3' O3' C3' H3' 301.9 61.2
O4' C1' C2' O2' 86.4 142.6
O2' C2' C3' H3' 163.4 122.5
C3' C2' O2' C1' 108.0 114.8
C3' C2' O2' H2' 233.7 237.4
C1' C2' O2' H2' 125.7 122.7
O2' C2' C1' N1 205.4 261.5
O2' C2' C1' H1' 324.8 23.8
C2' O2' CA' CB' 176.2 180.0
C2' O2' CA' HA'1 301.4 300.0
C2' O2' CA' HA'2 50.9 59.9
O4' C1' C2' N1 240.9 241.0
O4' C1' C2' H1' 121.6 118.8
C1' C2' C3' H3' 276.4 241.5
C3' C2' C1' O2' 248.0 241.2
C3' C2' C1' H2' 125.4 118.5
O2' C2' C1' H2' 237.4 237.3
C1' C2' O2' CA' 70.9 153.8
N1 C1' C2' H1' 240.7 237.8
C2' C1' N1 C2 89.0 301.5
C2' C1' N1 C6 269.6 121.5
H2' C2' C3' H3' 41.0 360.0
C3' C2' H2' O2' 121.0 122.6
C3' C2' H2' C1' 242.9 245.5
O2' C2' H2' C1' 121.9 122.9
H2' C2' O2' CA' 305.2 31.1
H2' C2' C1' N1 328.0 24.2
H2' C2' C1' H1' 87.4 146.4
CA' O2' C2' C1' 70.9 153.8
CA' O2' C2' H2' 305.2 31.1
CB' CA' O2' HA'1 234.8 240.0
CB' CA' O2' HA'2 125.3 120.0
O2' CA' CB' FC' 306.9 60.0
O2' CA' CB' HB'1 72.2 180.0
O2' CA' CB' HB'2 181.6 300.0
HA'1 CA' O2' HA'2 250.5 240.1
O4' C1' N1 C2' 118.1 115.6
O4' C1' N1 H1' 238.4 237.8
N1 C1' C2' H2' 328.0 24.2
C2' C1' N1 H1' 120.3 122.3
C2 N1 C1' C6 179.4 180.0
C1' N1 C2 O2 0.3 360.0
C1' N1 C2 N3 180.8 180.0
C1' N1 C6 C5 178.5 180.0
C1' N1 C6 H6 358.5 0.1
O4' C1' H1' C2' 241.1 244.5
O4' C1' H1' N1 119.8 122.2
H1' C1' C2' H2' 87.4 146.4
C2' C1' H1' N1 238.7 237.7
H1' C1' N1 C2 328.6 179.3
H1' C1' N1 C6 149.2 359.2
C2 N1 C1' H1' 328.6 179.3
C1' N1 C2 C6 180.6 180.0
C2 N1 C6 C5 359.2 359.9
C2 N1 C6 H6 179.2 180.0
O2 C2 N1 N3 179.5 180.0
N1 C2 N3 C4 0.5 359.8
N1 C2 N3 H3 180.5 179.9
C6 N1 C1' H1' 149.2 359.2
C1' N1 C6 C2 179.3 180.0
C6 N1 C2 O2 179.7 180.0
C6 N1 C2 N3 0.2 360.0
C4 C5 C6 N1 0.8 0.3
C5M C5 C6 N1 181.0 180.0
C5 C6 N1 H6 180.0 179.9
O2 C2 N1 C6 179.7 180.0
N1 C2 O2 N3 180.5 180.0
O2 C2 N3 C4 180.9 179.8
O2 C2 N3 H3 0.9 359.9
N3 C2 N1 C6 0.2 360.0
N1 C2 N3 O2 179.6 180.0
C4 N3 C2 H3 180.0 179.9
C2 N3 C4 O4 179.3 179.9
C2 N3 C4 C5 359.6 0.4
C2 N3 C4 H3 180.0 180.1
O4 C4 N3 C5 179.7 179.5
N3 C4 C5 C5M 179.6 179.9
N3 C4 C5 C6 359.8 359.5
C2 N3 H3 C4 180.0 179.9
H3 N3 C4 O4 359.3 359.8
H3 N3 C4 C5 179.6 180.3
O4 C4 N3 H3 359.3 359.8
N3 C4 O4 C5 180.3 180.5
O4 C4 C5 C5M 359.9 0.4
O4 C4 C5 C6 180.1 180.0
N1 C6 C5 C4 0.8 0.3
C5 C4 N3 H3 179.6 180.3
N3 C4 C5 O4 179.7 179.5
C5M C5 C4 C6 179.8 180.4
C4 C5 C5M H71 179.9 359.7
C4 C5 C5M H72 305.3 119.7
C4 C5 C5M H73 54.8 239.7
C4 C5 C6 H6 180.8 180.2
N1 C6 C5 C5M 181.0 180.0
C4 C5 C5M C6 180.2 179.6
C5M C5 C6 H6 1.0 359.8
H71 C5M C5 H72 234.6 240.0
H71 C5M C5 H73 125.2 120.0
H72 C5M C5 H73 250.5 240.0
N1 C6 C5 H6 180.0 180.1
C4 C5 C6 C5M 179.8 180.4
C6 C5 C5M H71 359.7 180.0
C6 C5 C5M H72 125.1 300.1
C6 C5 C5M H73 234.6 60.1
H71 C5M C5 C6 359.7 180.0
C5 C5M H71 H72 125.3 120.0
C5 C5M H71 H73 234.8 240.1
H72 C5M H71 H73 109.5 120.0
H72 C5M C5 C6 125.1 300.1
C5 C5M H72 H71 229.0 240.0
C5 C5M H72 H73 114.5 120.0
H71 C5M H72 H73 245.5 240.0
H73 C5M C5 C6 234.6 60.1
C5 C5M H73 H71 130.9 119.9
C5 C5M H73 H72 245.5 240.0
H71 C5M H73 H72 114.6 120.0
N1 C6 H6 C5 180.0 179.9
O2' CA' CB' HA'1 125.3 120.0
O2' CA' CB' HA'2 234.7 240.0
HA'1 CA' CB' HA'2 109.4 120.0
FC' CB' CA' HB'1 234.7 240.1
FC' CB' CA' HB'2 125.3 120.1
HB'1 CB' CA' HB'2 250.6 240.0
O2' CA' HA'1 CB' 237.9 240.0
O2' CA' HA'1 HA'2 119.0 119.9
CB' CA' HA'1 HA'2 241.1 240.0
HA'1 CA' CB' FC' 181.7 300.0
HA'1 CA' CB' HB'1 307.0 60.0
HA'1 CA' CB' HB'2 56.4 180.0
O2' CA' HA'2 CB' 122.2 120.0
O2' CA' HA'2 HA'1 241.0 240.1
CB' CA' HA'2 HA'1 118.9 120.0
HA'2 CA' CB' FC' 72.2 180.1
HA'2 CA' CB' HB'1 197.5 300.0
HA'2 CA' CB' HB'2 306.9 60.0
FC' CB' CA' HA'1 181.7 300.0
FC' CB' CA' HA'2 72.2 180.1
CA' CB' FC' HB'1 125.3 119.9
CA' CB' FC' HB'2 234.7 240.0
HB'1 CB' FC' HB'2 109.4 120.0
HB'1 CB' CA' HA'1 307.0 60.0
HB'1 CB' CA' HA'2 197.5 300.0
CA' CB' HB'1 FC' 235.1 240.1
CA' CB' HB'1 HB'2 117.5 120.0
FC' CB' HB'1 HB'2 242.4 239.9
HB'2 CB' CA' HA'1 56.4 180.0
HB'2 CB' CA' HA'2 306.9 60.0
CA' CB' HB'2 FC' 124.9 120.0
CA' CB' HB'2 HB'1 242.5 240.0
FC' CB' HB'2 HB'1 117.6 120.0