PDB Chemical Component 12A

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 12A

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP3 P 1.595 1.610
OP3 HOP3 0.951 0.967
P OP1 1.491 1.479
P OP2 1.484 1.610
P O5' 1.587 1.609
OP2 HOP2 0.949 0.967
O5' C5' 1.402 1.428
C5' C4' 1.498 1.529
C5' H5' 1.115 1.089
C5' H5'' 1.115 1.090
C4' O4' 1.445 1.444
C4' C3' 1.519 1.545
C4' H4' 1.115 1.090
O4' C1' 1.405 1.444
C3' O3' 1.421 1.429
C3' C2' 1.521 1.547
C3' H3' 1.115 1.090
O3' HO3' 0.950 0.967
C2' O2' 1.413 1.429
C2' C1' 1.526 1.544
C2' H2' 1.114 1.090
O2' HO2' 0.950 0.967
C1' N9 1.447 1.465
C1' H1' 1.115 1.089
N9 C8 1.362 1.364
N9 C4 1.365 1.372
C8 N7 1.304 1.300
C8 H8 1.104 1.080
N7 C5 1.382 1.356
C5 C6 1.378 1.404
C5 C4 1.375 1.405
C6 N6 1.314 1.388
C6 N1 1.341 1.327
N6 CC 1.316 1.347
N6 HN6 1.020 0.970
N1 C2 1.333 1.327
C2 N3 1.322 1.324
C2 S2 1.337 1.762
N3 C4 1.338 1.328
S2 C2M 1.824 1.811
C2M H2M1 1.114 1.090
C2M H2M2 1.115 1.091
C2M H2M3 1.115 1.090
CC OO 1.229 1.215
CC N 1.322 1.348
N CA 1.458 1.465
N H 1.020 0.970
CA C 1.544 1.506
CA CB 1.563 1.530
CA HA 1.116 1.089
C O 1.256 1.208
C OXT 1.255 1.342
OXT HXT 0.949 0.967
CB OG1 1.434 1.428
CB CG2 1.540 1.531
CB HB 1.115 1.090
OG1 HG1 0.949 0.967
CG2 HG21 1.114 1.090
CG2 HG22 1.115 1.090
CG2 HG23 1.114 1.089

Bond Angles for 12A

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
P OP3 HOP3 108.5 106.8
OP3 P OP1 108.5 109.4
OP3 P OP2 108.3 109.4
OP3 P O5' 102.6 109.5
OP1 P OP2 120.0 109.5
OP1 P O5' 107.5 109.5
OP2 P O5' 108.4 109.5
P OP2 HOP2 108.3 106.8
P O5' C5' 120.1 106.8
O5' C5' C4' 110.3 109.5
O5' C5' H5' 111.9 109.5
O5' C5' H5'' 111.9 109.4
C4' C5' H5' 111.9 109.6
C4' C5' H5'' 111.9 109.4
C5' C4' O4' 109.8 110.4
C5' C4' C3' 112.2 110.4
C5' C4' H4' 106.5 110.3
H5' C5' H5'' 98.5 109.4
O4' C4' C3' 106.5 104.8
O4' C4' H4' 112.2 110.5
C4' O4' C1' 109.3 105.3
C3' C4' H4' 109.8 110.3
C4' C3' O3' 106.7 110.5
C4' C3' C2' 102.7 104.1
C4' C3' H3' 116.5 110.5
O4' C1' C2' 106.5 104.9
O4' C1' N9 105.4 110.4
O4' C1' H1' 114.6 110.4
O3' C3' C2' 112.5 110.5
O3' C3' H3' 107.4 110.5
C3' O3' HO3' 106.7 106.8
C2' C3' H3' 111.1 110.6
C3' C2' O2' 113.3 110.5
C3' C2' C1' 100.7 104.0
C3' C2' H2' 112.9 110.5
O2' C2' C1' 109.6 110.8
O2' C2' H2' 104.4 110.4
C2' O2' HO2' 113.3 106.8
C1' C2' H2' 116.3 110.4
C2' C1' N9 111.6 110.4
C2' C1' H1' 108.8 110.4
N9 C1' H1' 109.9 110.3
C1' N9 C8 125.8 126.3
C1' N9 C4 128.1 126.3
C8 N9 C4 106.1 107.4
N9 C8 N7 113.8 110.0
N9 C8 H8 125.0 125.0
N9 C4 C5 105.6 106.0
N9 C4 N3 127.4 134.8
N7 C8 H8 121.2 125.0
C8 N7 C5 103.7 109.4
N7 C5 C6 132.0 134.5
N7 C5 C4 110.8 107.1
C6 C5 C4 117.2 118.3
C5 C6 N6 123.8 120.8
C5 C6 N1 117.9 118.6
C5 C4 N3 127.0 119.2
N6 C6 N1 118.3 120.7
C6 N6 CC 117.7 120.1
C6 N6 HN6 109.2 120.0
C6 N1 C2 118.7 121.2
CC N6 HN6 109.3 120.0
N6 CC OO 120.4 120.0
N6 CC N 118.2 120.0
N1 C2 N3 129.1 122.2
N1 C2 S2 117.8 118.9
N3 C2 S2 113.1 118.8
C2 N3 C4 110.2 120.5
C2 S2 C2M 102.4 100.0
S2 C2M H2M1 102.4 109.5
S2 C2M H2M2 114.8 109.5
S2 C2M H2M3 114.8 109.5
H2M1 C2M H2M2 114.9 109.4
H2M1 C2M H2M3 115.0 109.5
H2M2 C2M H2M3 95.6 109.5
OO CC N 121.5 120.0
CC N CA 120.6 120.0
CC N H 114.8 120.0
CA N H 124.6 120.0
N CA C 112.1 109.5
N CA CB 110.4 109.5
N CA HA 107.6 109.5
C CA CB 111.1 109.4
C CA HA 106.8 109.5
CA C O 117.1 120.0
CA C OXT 119.4 120.0
CB CA HA 108.7 109.5
CA CB OG1 109.7 109.5
CA CB CG2 111.0 109.4
CA CB HB 108.8 109.5
O C OXT 123.5 120.0
C OXT HXT 119.3 120.0
OG1 CB CG2 110.9 109.4
OG1 CB HB 108.8 109.5
CB OG1 HG1 109.7 106.8
CG2 CB HB 107.5 109.4
CB CG2 HG21 111.0 109.4
CB CG2 HG22 111.6 109.4
CB CG2 HG23 111.6 109.5
HG21 CG2 HG22 111.7 109.5
HG21 CG2 HG23 111.7 109.5
HG22 CG2 HG23 98.7 109.5

Torsion Angles for 12A

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP3 OP2 228.2 240.0
OP1 P OP3 O5' 113.6 120.0
OP2 P OP3 O5' 245.4 240.0
OP3 P OP2 HOP2 180.0 60.0
OP3 P O5' C5' 159.3 180.0
HOP3 OP3 P OP1 180.0 300.0
HOP3 OP3 P OP2 311.8 60.0
HOP3 OP3 P O5' 66.4 180.0
OP1 P OP3 HOP3 180.0 300.0
OP3 P OP1 OP2 125.2 120.0
OP3 P OP1 O5' 249.7 240.0
OP2 P OP1 O5' 124.4 120.0
OP1 P OP2 HOP2 305.3 180.0
OP1 P O5' C5' 45.0 60.0
OP2 P OP3 HOP3 311.8 60.0
OP3 P OP2 OP1 234.7 240.0
OP3 P OP2 O5' 110.7 120.0
OP1 P OP2 O5' 236.0 240.0
OP2 P O5' C5' 273.8 300.0
O5' P OP3 HOP3 66.4 180.0
OP3 P O5' OP1 114.3 120.0
OP3 P O5' OP2 245.5 240.0
OP1 P O5' OP2 131.2 120.1
O5' P OP2 HOP2 69.3 300.0
P O5' C5' C4' 166.1 180.1
P O5' C5' H5' 291.4 59.9
P O5' C5' H5'' 40.8 300.0
HOP2 OP2 P O5' 69.3 300.0
C4' C5' O5' H5' 234.7 120.2
C4' C5' O5' H5'' 125.3 240.1
O5' C5' C4' O4' 62.4 61.4
O5' C5' C4' C3' 180.5 176.9
O5' C5' C4' H4' 300.7 299.1
H5' C5' O5' H5'' 250.5 119.9
O5' C5' C4' H5' 125.2 239.9
O5' C5' C4' H5'' 234.8 119.9
H5' C5' C4' H5'' 109.5 240.0
O4' C4' C5' C3' 241.8 244.5
O4' C4' C5' H4' 121.7 122.3
C5' C4' O4' C1' 124.8 159.5
C3' C4' C5' H4' 239.8 237.8
C5' C4' C3' O3' 96.1 98.3
C5' C4' C3' C2' 214.6 217.0
C5' C4' C3' H3' 336.3 335.7
O5' C5' H5' C4' 235.7 120.1
O5' C5' H5' H5'' 117.8 240.0
C4' C5' H5' H5'' 242.1 119.9
H5' C5' C4' O4' 297.2 181.5
H5' C5' C4' C3' 55.3 297.0
H5' C5' C4' H4' 175.5 59.2
O5' C5' H5'' C4' 124.4 240.0
O5' C5' H5'' H5' 242.2 120.0
C4' C5' H5'' H5' 117.9 240.0
H5'' C5' C4' O4' 187.6 301.5
H5'' C5' C4' C3' 305.8 57.0
H5'' C5' C4' H4' 66.0 179.1
O4' C4' C5' H5' 297.2 181.5
O4' C4' C5' H5'' 187.6 301.5
C5' C4' O4' C3' 121.6 118.9
C5' C4' O4' H4' 241.8 237.8
C3' C4' O4' H4' 120.2 118.8
O4' C4' C3' O3' 216.2 217.3
O4' C4' C3' C2' 334.7 335.9
O4' C4' C3' H3' 96.4 94.6
C4' O4' C1' C2' 20.5 319.5
C4' O4' C1' N9 261.9 200.6
C4' O4' C1' H1' 140.9 78.4
C3' C4' C5' H5' 55.3 297.0
C3' C4' C5' H5'' 305.8 57.0
C5' C4' C3' O4' 239.9 241.1
C5' C4' C3' H4' 118.2 122.2
O4' C4' C3' H4' 238.3 241.1
C3' C4' O4' C1' 3.2 40.5
O3' C3' C4' C2' 241.5 241.3
O3' C3' C4' H3' 119.9 122.6
C4' C3' O3' HO3' 180.0 180.0
C2' C3' C4' H3' 238.3 241.3
C4' C3' C2' O2' 278.8 241.2
C4' C3' C2' C1' 35.8 0.1
C4' C3' C2' H2' 160.4 118.7
H4' C4' C5' H5' 175.5 59.2
H4' C4' C5' H5'' 66.0 179.1
C5' C4' H4' O4' 120.1 122.3
C5' C4' H4' C3' 238.3 237.7
O4' C4' H4' C3' 118.2 115.4
H4' C4' O4' C1' 243.0 281.7
H4' C4' C3' O3' 337.9 336.2
H4' C4' C3' C2' 96.4 94.8
H4' C4' C3' H3' 218.0 213.5
C1' O4' C4' C3' 3.2 40.5
C1' O4' C4' H4' 243.0 281.7
C3' C2' C1' O4' 324.6 23.9
O2' C2' C1' O4' 84.2 142.6
O4' C1' C2' H2' 202.3 265.2
C2' C1' O4' N9 118.7 118.9
C2' C1' O4' H1' 239.6 241.1
N9 C1' O4' H1' 121.0 122.2
O4' C1' N9 C8 2.3 27.1
O4' C1' N9 C4 182.3 207.0
O3' C3' C4' H4' 337.9 336.2
C4' C3' O3' C2' 111.8 114.6
C4' C3' O3' H3' 234.4 237.4
C2' C3' O3' H3' 122.6 122.7
O3' C3' C2' O2' 33.1 359.9
O3' C3' C2' C1' 150.1 118.8
O3' C3' C2' H2' 274.7 237.4
C2' C3' C4' H4' 96.4 94.8
C4' C3' C2' O3' 245.7 241.3
C4' C3' C2' H3' 125.2 118.7
O4' C1' C2' C3' 324.6 23.9
O3' C3' C2' H3' 239.6 237.3
C2' C3' O3' HO3' 68.1 65.4
O2' C2' C3' C1' 243.0 241.1
O2' C2' C3' H2' 118.4 122.5
C3' C2' O2' HO2' 179.9 298.6
C1' C2' C3' H2' 235.4 241.5
C3' C2' C1' N9 79.1 142.8
C3' C2' C1' H1' 200.6 264.9
H3' C3' C4' H4' 218.0 213.5
C4' C3' H3' O3' 119.5 122.7
C4' C3' H3' C2' 242.9 245.3
O3' C3' H3' C2' 123.4 122.7
H3' C3' O3' HO3' 305.6 302.7
H3' C3' C2' O2' 153.6 122.6
H3' C3' C2' C1' 270.5 241.5
H3' C3' C2' H2' 35.2 0.0
HO3' O3' C3' C2' 68.1 65.4
HO3' O3' C3' H3' 305.6 302.7
O4' C1' C2' O2' 84.2 142.6
O2' C2' C3' H3' 153.6 122.6
C3' C2' O2' C1' 111.6 114.7
C3' C2' O2' H2' 236.8 237.4
C1' C2' O2' H2' 125.2 122.7
O2' C2' C1' N9 198.8 261.5
O2' C2' C1' H1' 320.2 23.7
O4' C1' C2' N9 245.5 241.1
O4' C1' C2' H1' 124.0 118.9
C1' C2' C3' H3' 270.5 241.5
C3' C2' C1' O2' 240.4 241.3
C3' C2' C1' H2' 122.3 118.6
O2' C2' C1' H2' 241.9 237.4
C1' C2' O2' HO2' 68.3 183.8
N9 C1' C2' H1' 238.6 237.8
C2' C1' N9 C8 247.0 271.6
C2' C1' N9 C4 67.1 91.5
H2' C2' C3' H3' 35.2 0.0
C3' C2' H2' O2' 123.4 122.6
C3' C2' H2' C1' 244.4 245.5
O2' C2' H2' C1' 120.9 122.9
H2' C2' O2' HO2' 303.1 61.2
H2' C2' C1' N9 316.9 24.1
H2' C2' C1' H1' 78.3 146.3
HO2' O2' C2' C1' 68.3 183.8
HO2' O2' C2' H2' 303.1 61.2
O4' C1' N9 C2' 115.2 115.5
O4' C1' N9 H1' 236.0 237.7
N9 C1' C2' H2' 316.9 24.1
C2' C1' N9 H1' 120.8 122.2
C8 N9 C1' C4 179.9 180.0
C1' N9 C8 N7 180.3 180.0
C1' N9 C8 H8 0.3 360.0
C1' N9 C4 C5 179.6 180.0
C1' N9 C4 N3 359.9 0.4
O4' C1' H1' C2' 240.9 244.5
O4' C1' H1' N9 118.4 122.3
H1' C1' C2' H2' 78.3 146.3
C2' C1' H1' N9 237.6 237.7
H1' C1' N9 C8 126.3 149.3
H1' C1' N9 C4 306.3 329.3
C8 N9 C1' H1' 126.3 149.3
C1' N9 C8 C4 180.0 180.0
C8 N9 C4 C5 359.7 359.9
C8 N9 C4 N3 179.9 180.3
N7 C8 N9 H8 180.0 180.0
N9 C8 N7 C5 359.9 359.9
C4 N9 C1' H1' 306.3 329.3
C1' N9 C4 C8 180.0 180.0
C4 N9 C8 N7 0.2 0.1
C4 N9 C8 H8 180.2 180.0
N7 C5 C4 N9 0.3 0.0
C6 C5 C4 N9 180.4 180.0
C5 C4 N9 N3 179.8 179.6
C2 N3 C4 N9 179.5 180.1
N7 C8 N9 C4 0.2 0.1
N9 C8 N7 H8 180.0 180.0
C8 N7 C5 C6 179.7 180.1
C8 N7 C5 C4 359.8 0.0
H8 C8 N9 C4 180.2 180.0
N9 C8 H8 N7 180.0 180.1
H8 C8 N7 C5 180.0 180.0
N9 C4 C5 N7 0.3 0.0
C5 N7 C8 H8 180.0 180.0
C6 C5 N7 C4 179.9 180.0
N7 C5 C6 N6 358.3 359.9
N7 C5 C6 N1 179.5 180.0
N7 C5 C4 N3 180.1 179.7
N9 C4 C5 C6 180.4 180.0
N7 C5 C6 C4 180.1 180.0
C6 C5 C4 N3 0.2 359.7
N6 C6 C5 N1 178.8 179.9
C5 C6 N6 CC 216.4 180.0
C5 C6 N6 HN6 91.2 0.1
C5 C6 N1 C2 1.2 360.0
N9 C4 C5 N3 180.2 180.3
N7 C5 C4 C6 179.9 180.0
C4 C5 C6 N6 178.2 179.9
C4 C5 C6 N1 359.4 0.1
C2 N3 C4 C5 359.8 0.6
N6 C6 C5 C4 178.2 179.9
C5 C6 N6 N1 181.2 180.1
N6 C6 N1 C2 182.3 180.1
CC N6 C6 HN6 125.3 179.9
C6 N6 CC OO 359.6 0.1
C6 N6 CC N 179.7 180.0
N1 C6 C5 C4 359.4 0.1
C5 C6 N1 N6 178.9 179.9
N1 C6 N6 CC 35.2 359.9
N1 C6 N6 HN6 270.0 180.0
C6 N1 C2 N3 358.7 0.3
C6 N1 C2 S2 178.2 180.0
CC N6 C6 N1 35.2 359.9
C6 N6 CC HN6 234.7 180.1
OO CC N6 N 179.9 180.1
N6 CC N CA 180.0 180.0
N6 CC N H 0.0 0.1
HN6 N6 C6 N1 270.0 180.0
C6 N6 HN6 CC 130.0 179.9
HN6 N6 CC OO 124.9 180.0
HN6 N6 CC N 305.0 359.9
N3 C2 N1 S2 180.5 180.2
N1 C2 N3 C4 0.8 359.5
N1 C2 S2 C2M 17.0 360.0
N9 C4 N3 C2 179.5 180.1
C5 C4 N3 C2 359.8 0.6
N1 C2 N3 S2 179.5 179.8
N3 C2 S2 C2M 196.6 179.7
N1 C2 S2 N3 180.4 180.2
S2 C2 N3 C4 181.3 179.7
C2 S2 C2M H2M1 180.0 180.0
C2 S2 C2M H2M2 305.3 300.0
C2 S2 C2M H2M3 54.7 60.0
N9 C4 N3 C5 179.7 179.6
C4 N3 C2 S2 181.3 179.7
H2M1 C2M S2 H2M2 234.7 240.0
H2M1 C2M S2 H2M3 125.3 120.1
H2M2 C2M S2 H2M3 250.6 240.0
S2 C2M H2M1 H2M2 125.2 120.0
S2 C2M H2M1 H2M3 234.8 240.0
H2M2 C2M H2M1 H2M3 109.6 120.0
S2 C2M H2M2 H2M1 241.6 240.0
S2 C2M H2M2 H2M3 120.7 120.0
H2M1 C2M H2M2 H2M3 239.1 239.9
S2 C2M H2M3 H2M1 118.5 120.0
S2 C2M H2M3 H2M2 239.3 240.0
H2M1 C2M H2M3 H2M2 120.9 120.0
OO CC N6 HN6 124.9 180.0
N6 CC OO N 180.1 179.9
OO CC N CA 0.1 359.9
OO CC N H 180.1 179.9
N CC N6 HN6 305.0 359.9
N6 CC N OO 179.9 180.1
CA N CC H 180.0 180.0
CC N CA C 336.8 270.0
CC N CA CB 212.4 150.1
CC N CA HA 94.0 30.0
CC N CA H 180.0 180.0
C CA N CB 124.4 120.0
C CA N HA 242.9 240.0
N CA C O 103.8 150.0
N CA C OXT 285.8 330.1
CB CA N HA 118.4 120.0
N CA CB OG1 158.8 59.9
N CA CB CG2 35.8 300.0
N CA CB HB 277.7 180.0
CC N H CA 180.0 180.0
H N CA C 156.8 90.0
H N CA CB 32.4 330.1
H N CA HA 273.9 210.0
C CA N H 156.8 90.0
N CA C CB 236.0 240.0
N CA C HA 117.6 120.0
CB CA C HA 241.6 240.0
C CA CB OG1 33.8 299.9
C CA CB CG2 270.8 180.0
C CA CB HB 152.7 60.0
O C CA OXT 178.0 179.9
CA C OXT HXT 179.9 180.0
CB CA N H 32.4 330.1
N CA CB C 125.0 120.0
N CA CB HA 242.2 240.0
C CA CB HA 117.2 119.9
CB CA C O 227.8 270.0
CB CA C OXT 49.8 90.1
OG1 CB CA CG2 123.0 119.9
OG1 CB CA HB 241.0 239.9
CA CB OG1 HG1 180.0 300.1
CG2 CB CA HB 118.1 120.0
CA CB CG2 HG21 180.0 180.0
CA CB CG2 HG22 305.3 300.0
CA CB CG2 HG23 54.7 60.0
HA CA N H 273.9 210.0
N CA HA C 239.5 239.9
N CA HA CB 119.5 120.0
C CA HA CB 240.0 240.1
HA CA C O 346.2 30.0
HA CA C OXT 168.2 210.0
HA CA CB OG1 276.5 180.0
HA CA CB CG2 153.6 60.0
HA CA CB HB 35.5 300.0
O C CA CB 227.8 270.0
O C CA HA 346.2 30.0
CA C O OXT 182.1 180.1
O C OXT HXT 2.0 0.1
OXT C CA CB 49.8 90.1
OXT C CA HA 168.2 210.0
CA C OXT O 177.9 179.9
OG1 CB CA HA 276.5 180.0
CA CB OG1 CG2 237.0 240.0
CA CB OG1 HB 118.9 120.1
CG2 CB OG1 HB 241.9 240.1
OG1 CB CG2 HG21 57.7 60.0
OG1 CB CG2 HG22 183.1 180.0
OG1 CB CG2 HG23 292.4 300.0
CG2 CB CA HA 153.6 60.0
CA CB CG2 OG1 122.3 120.0
CA CB CG2 HB 241.2 240.0
OG1 CB CG2 HB 118.9 120.0
CG2 CB OG1 HG1 303.0 60.0
HG21 CG2 CB HG22 234.6 240.0
HG21 CG2 CB HG23 125.3 120.0
HG22 CG2 CB HG23 250.6 240.0
HB CB CA HA 35.5 300.0
CA CB HB OG1 240.5 239.9
CA CB HB CG2 120.3 120.0
OG1 CB HB CG2 239.8 240.1
HB CB OG1 HG1 61.1 180.0
HB CB CG2 HG21 298.8 300.0
HB CB CG2 HG22 64.2 60.0
HB CB CG2 HG23 173.5 180.1
HG1 OG1 CB CG2 303.0 60.0
HG1 OG1 CB HB 61.1 180.0
HG21 CG2 CB HB 298.8 300.0
CB CG2 HG21 HG22 125.3 119.9
CB CG2 HG21 HG23 234.7 240.0
HG22 CG2 HG21 HG23 109.4 120.1
HG22 CG2 CB HB 64.2 60.0
CB CG2 HG22 HG21 235.0 240.1
CB CG2 HG22 HG23 117.5 120.0
HG21 CG2 HG22 HG23 242.4 239.9
HG23 CG2 CB HB 173.5 180.1
CB CG2 HG23 HG21 124.9 119.9
CB CG2 HG23 HG22 242.5 240.0
HG21 CG2 HG23 HG22 117.6 120.1