PDB Chemical Component CN5

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 CN5

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O14 P 1.636 1.480
O12 P 1.601 1.610
P O11 1.703 1.610
P O13 1.664 1.610
O11 C1 1.473 1.428
O12 HO12 0.950 0.968
O13 CC 1.446 1.429
C2 C1 1.475 1.530
C1 H1 1.100 1.091
C1 H1A 1.100 1.090
C2 C3 1.509 1.530
C2 H2 1.100 1.090
C2 H2A 1.100 1.090
O31 C3 1.391 1.451
C3 H3 1.100 1.090
C3 H3A 1.100 1.091
O31 C31 1.374 1.343
C31 O32 1.227 1.208
C32 C31 1.560 1.507
C33 C32 1.559 1.530
C32 H32 1.100 1.091
C32 H32A 1.100 1.089
C33 C34 1.484 1.531
C33 H33 1.100 1.090
C33 H33A 1.100 1.090
C35 C34 1.547 1.530
C34 H34 1.100 1.091
C34 H34A 1.100 1.089
C35 C36 1.549 1.531
C35 H35 1.100 1.090
C35 H35A 1.099 1.090
C37 C36 1.570 1.530
C36 H36 1.100 1.091
C36 H36A 1.100 1.089
C37 C38 1.565 1.530
C37 H37 1.100 1.090
C37 H37A 1.100 1.090
C39 C38 1.564 1.530
C38 H38 1.100 1.091
C38 H38A 1.100 1.089
C39 C3A 1.551 1.531
C39 H39 1.100 1.090
C39 H39A 1.100 1.090
C3B C3A 1.550 1.530
C3A H3AA 1.100 1.091
C3A H3AB 1.100 1.089
C3C C3B 1.484 1.531
C3B H3B 1.100 1.090
C3B H3BA 1.100 1.090
C3D C3C 1.549 1.530
C3C H3C 1.099 1.091
C3C H3CA 1.100 1.089
C3E C3D 1.550 1.530
C3D H3D 1.100 1.090
C3D H3DA 1.100 1.090
C3F C3E 1.562 1.530
C3E H3E 1.100 1.091
C3E H3EA 1.100 1.090
C3F H3F 1.100 1.090
C3F H3FA 1.100 1.091
C3F H3FB 1.100 1.089
O3' P' 1.623 1.611
O1' P' 1.675 1.609
P' O2' 1.611 1.481
P' O4' 1.643 1.610
C1' O1' 1.449 1.429
CA O3' 1.311 1.429
O4' HO4' 0.950 0.966
C2' C1' 1.465 1.530
C1' H1' 1.100 1.090
C1' H1'A 1.100 1.090
C2' C3' 1.419 1.530
C2' H2' 1.100 1.090
C2' H2'A 1.100 1.090
O41 C3' 1.430 1.452
C3' H3' 1.100 1.090
C3' H3'A 1.100 1.091
C41 O41 1.403 1.342
O42 C41 1.264 1.208
C42 C41 1.562 1.508
C42 H42 1.100 1.090
C42 H42A 1.100 1.090
C42 H42B 1.100 1.090
CB CA 1.553 1.530
CA HA 1.100 1.090
CA HAA 1.100 1.089
OA CB 1.513 1.429
CC CB 1.599 1.530
CB HB 1.100 1.090
OA HOA 0.950 0.967
CC HC 1.100 1.090
CC HCA 1.100 1.090

Bond Angles for CN5

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O12 P O13 114.2 109.5
O11 P O13 104.5 109.5
P O11 C1 111.6 123.0
P O13 CC 137.4 123.0
O11 C1 H1 114.4 109.5
O11 C1 H1A 117.2 109.5
O13 CC CB 112.7 109.5
O13 CC HC 108.4 109.5
O13 CC HCA 107.7 109.4
C2 C1 H1 114.4 109.5
C2 C1 H1A 117.1 109.5
H1 C1 H1A 99.3 109.4
C3 C2 H2 110.7 109.4
C3 C2 H2A 111.5 109.5
C2 C3 H3 110.5 109.4
C2 C3 H3A 111.2 109.4
H2 C2 H2A 106.6 109.5
O31 C3 H3 110.5 109.5
O31 C3 H3A 111.2 109.5
H3 C3 H3A 107.1 109.5
O31 C31 O32 126.4 120.0
C33 C32 H32 105.3 109.5
C33 C32 H32A 102.3 109.5
H32 C32 H32A 120.4 109.5
C34 C33 H33 109.6 109.5
C34 C33 H33A 109.7 109.4
C33 C34 H34 107.5 109.5
C33 C34 H34A 106.2 109.5
H33 C33 H33A 109.2 109.5
C35 C34 H34 107.6 109.5
C35 C34 H34A 106.2 109.5
H34 C34 H34A 114.2 109.5
C36 C35 H35 104.6 109.5
C36 C35 H35A 101.0 109.4
C35 C36 H36 109.7 109.5
C35 C36 H36A 109.8 109.5
H35 C35 H35A 122.5 109.5
C37 C36 H36 109.7 109.5
C37 C36 H36A 109.9 109.5
H36 C36 H36A 108.9 109.5
C38 C37 H37 109.6 109.5
C38 C37 H37A 109.7 109.5
C37 C38 H38 107.4 109.5
C37 C38 H38A 106.0 109.5
H37 C37 H37A 109.2 109.5
C39 C38 H38 107.4 109.5
C39 C38 H38A 105.9 109.5
H38 C38 H38A 114.6 109.5
C3A C39 H39 107.4 109.4
C3A C39 H39A 105.9 109.4
C39 C3A H3AA 108.1 109.5
C39 C3A H3AB 107.1 109.5
H39 C39 H39A 114.7 109.5
C3B C3A H3AA 108.0 109.5
C3B C3A H3AB 107.1 109.5
H3AA C3A H3AB 112.9 109.5
C3C C3B H3B 107.4 109.5
C3C C3B H3BA 105.9 109.4
H3B C3B H3BA 114.6 109.5
C3D C3C H3C 107.4 109.5
C3D C3C H3CA 106.0 109.5
H3C C3C H3CA 114.5 109.5
C3E C3D H3D 104.7 109.5
C3E C3D H3DA 101.1 109.4
H3D C3D H3DA 122.4 109.5
C3F C3E H3E 108.1 109.5
C3F C3E H3EA 107.1 109.5
H3E C3E H3EA 112.8 109.4
H3F C3F H3FA 109.5 109.4
H3F C3F H3FB 109.4 109.5
H3FA C3F H3FB 109.5 109.5
O3' P' O4' 105.8 109.4
O1' P' O2' 103.7 109.5
O1' P' O4' 114.4 109.5
O2' P' O4' 112.4 109.5
P' O4' HO4' 109.5 114.0
C2' C1' H1' 103.0 109.5
C2' C1' H1'A 98.2 109.5
H1' C1' H1'A 127.7 109.5
C3' C2' H2' 113.6 109.5
C3' C2' H2'A 116.0 109.4
C2' C3' H3' 110.2 109.5
C2' C3' H3'A 110.8 109.4
H2' C2' H2'A 100.7 109.5
O41 C3' H3' 110.3 109.5
O41 C3' H3'A 110.7 109.4
H3' C3' H3'A 107.7 109.5
H42 C42 H42A 109.4 109.5
H42 C42 H42B 109.5 109.5
H42A C42 H42B 109.5 109.5
CB CA HA 108.0 109.4
CB CA HAA 106.9 109.5
HA CA HAA 113.2 109.5
OA CB HB 107.2 109.5
CC CB HB 110.4 109.5
HC CC HCA 112.0 109.5

Torsion Angles for CN5

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O14 P O11 C1 287.4 55.0
O14 P O13 CC 190.5 305.0
O11 P O12 O13 246.0 240.0
O12 P O11 C1 162.7 295.0
O12 P O13 CC 317.5 65.0
O12 P O11 O13 120.6 120.0
O11 P O13 CC 71.9 184.9
P O11 C1 H1 246.0 300.1
P O11 C1 H1A 1.7 60.0
O13 P O11 C1 42.1 175.0
P O13 CC CB 308.9 180.0
P O13 CC HC 68.9 300.1
P O13 CC HCA 190.3 60.0
C1 O11 P O13 42.1 175.0
C2 C1 O11 H1 240.0 240.0
C2 C1 O11 H1A 124.4 120.0
H1 C1 O11 H1A 244.4 240.0
HO12 O12 P O13 241.7 60.0
O13 CC CB HB 297.8 305.1
HC CC O13 HCA 238.6 240.1
O11 C1 C2 H1 120.0 120.1
O11 C1 C2 H1A 235.6 240.0
H1 C1 C2 H1A 115.6 119.9
O11 C1 H1 H1A 125.6 120.0
C2 C1 H1 H1A 234.4 240.0
O11 C1 H1A H1 236.3 240.0
C2 C1 H1A H1 123.7 120.0
C3 C2 C1 H1 99.2 59.9
C3 C2 C1 H1A 343.6 300.0
H2 C2 C3 H2A 118.6 120.0
O31 C3 C2 H3 240.0 240.0
O31 C3 C2 H3A 121.2 120.0
H3 C3 C2 H3A 241.2 240.0
H2 C2 C1 H1 219.2 179.9
H2 C2 C1 H1A 103.6 60.0
C3 C2 H2 H2A 238.5 240.0
H2 C2 C3 H3 180.0 180.0
H2 C2 C3 H3A 298.8 300.0
H2A C2 C1 H1 337.8 299.9
H2A C2 C1 H1A 222.2 180.0
C3 C2 H2A H2 121.0 120.0
H2A C2 C3 H3 61.4 60.0
H2A C2 C3 H3A 180.3 180.0
O31 C3 C2 H2 60.0 60.0
O31 C3 C2 H2A 301.4 300.0
C2 C3 O31 H3 120.0 120.0
C2 C3 O31 H3A 238.8 240.0
H3 C3 O31 H3A 118.8 120.0
H3 C3 C2 H2 180.0 180.0
H3 C3 C2 H2A 61.4 60.0
C2 C3 H3 H3A 121.3 120.0
O31 C3 H3 H3A 238.8 240.0
H3A C3 C2 H2 298.8 300.0
H3A C3 C2 H2A 180.3 180.0
C2 C3 H3A H3 239.2 240.0
O31 C3 H3A H3 120.9 120.0
C31 O31 C3 H3 59.9 60.0
C31 O31 C3 H3A 301.0 300.0
H32 C32 C33 H32A 126.7 120.0
C33 C32 H32 H32A 245.4 240.0
C33 C32 H32A H32 116.2 120.0
C34 C33 C32 H32 327.1 60.0
C34 C33 C32 H32A 200.4 300.0
H33 C33 C34 H33A 119.8 120.0
C35 C34 C33 H34 240.0 240.0
C35 C34 C33 H34A 117.4 120.0
H34 C34 C33 H34A 237.4 240.0
H33 C33 C32 H32 87.0 180.0
H33 C33 C32 H32A 320.4 60.0
C34 C33 H33 H33A 239.8 240.0
H33 C33 C34 H34 159.5 180.0
H33 C33 C34 H34A 282.1 300.0
H33A C33 C32 H32 206.9 300.1
H33A C33 C32 H32A 80.2 180.1
C34 C33 H33A H33 120.1 120.0
H33A C33 C34 H34 39.6 59.9
H33A C33 C34 H34A 162.3 180.0
C35 C34 C33 H33 39.5 60.0
C35 C34 C33 H33A 279.6 300.0
C33 C34 C35 H34 120.0 120.0
C33 C34 C35 H34A 242.7 240.0
H34 C34 C35 H34A 122.7 120.0
H34 C34 C33 H33 159.5 180.0
H34 C34 C33 H33A 39.6 59.9
C33 C34 H34 H34A 117.6 120.0
C35 C34 H34 H34A 242.4 240.0
H34A C34 C33 H33 282.1 300.0
H34A C34 C33 H33A 162.3 180.0
C33 C34 H34A H34 241.7 240.0
C35 C34 H34A H34 118.4 120.0
C36 C35 C34 H34 37.9 60.0
C36 C35 C34 H34A 275.2 300.0
H35 C35 C36 H35A 128.1 120.0
C37 C36 C35 H36 240.0 240.0
C37 C36 C35 H36A 120.3 120.0
H36 C36 C35 H36A 240.3 240.0
H35 C35 C34 H34 157.9 180.0
H35 C35 C34 H34A 35.2 60.0
C36 C35 H35 H35A 246.4 240.0
H35 C35 C36 H36 173.0 180.0
H35 C35 C36 H36A 292.7 300.0
H35A C35 C34 H34 286.0 300.1
H35A C35 C34 H34A 163.3 180.0
C36 C35 H35A H35 115.4 120.0
H35A C35 C36 H36 44.9 59.9
H35A C35 C36 H36A 164.6 180.0
C37 C36 C35 H35 53.0 60.0
C37 C36 C35 H35A 284.9 300.0
C35 C36 C37 H36 120.0 120.0
C35 C36 C37 H36A 239.7 240.0
H36 C36 C37 H36A 119.7 120.0
H36 C36 C35 H35 173.0 180.0
H36 C36 C35 H35A 44.9 59.9
C35 C36 H36 H36A 120.3 120.0
C37 C36 H36 H36A 239.7 240.0
H36A C36 C35 H35 292.7 300.0
H36A C36 C35 H35A 164.6 180.0
C35 C36 H36A H36 239.8 240.0
C37 C36 H36A H36 120.2 120.0
C38 C37 C36 H36 329.4 60.0
C38 C37 C36 H36A 209.7 300.0
H37 C37 C38 H37A 119.8 120.1
C39 C38 C37 H38 240.0 240.0
C39 C38 C37 H38A 117.1 120.0
H38 C38 C37 H38A 237.1 239.9
H37 C37 C36 H36 89.4 180.0
H37 C37 C36 H36A 329.7 60.0
C38 C37 H37 H37A 239.9 239.9
H37 C37 C38 H38 200.0 180.0
H37 C37 C38 H38A 322.9 300.0
H37A C37 C36 H36 209.2 300.0
H37A C37 C36 H36A 89.5 180.0
C38 C37 H37A H37 120.1 120.1
H37A C37 C38 H38 80.1 59.9
H37A C37 C38 H38A 203.0 180.0
C39 C38 C37 H37 80.0 60.0
C39 C38 C37 H37A 320.2 299.9
C37 C38 C39 H38 120.0 120.0
C37 C38 C39 H38A 242.9 240.0
H38 C38 C39 H38A 122.8 120.0
H38 C38 C37 H37 200.0 180.0
H38 C38 C37 H37A 80.1 59.9
C37 C38 H38 H38A 117.4 120.1
C39 C38 H38 H38A 242.6 240.0
H38A C38 C37 H37 322.9 300.0
H38A C38 C37 H37A 203.0 180.0
C37 C38 H38A H38 241.7 239.9
C39 C38 H38A H38 118.2 120.0
C3A C39 C38 H38 122.1 60.0
C3A C39 C38 H38A 359.3 300.0
H39 C39 C3A H39A 122.9 120.0
C3B C3A C39 H3AA 240.0 240.0
C3B C3A C39 H3AB 118.1 120.0
H3AA C3A C39 H3AB 238.1 240.0
H39 C39 C38 H38 242.1 180.0
H39 C39 C38 H38A 119.3 60.0
C3A C39 H39 H39A 242.6 240.0
H39 C39 C3A H3AA 89.6 180.0
H39 C39 C3A H3AB 211.5 300.0
H39A C39 C38 H38 5.1 300.1
H39A C39 C38 H38A 242.2 180.1
C3A C39 H39A H39 118.2 120.0
H39A C39 C3A H3AA 326.6 59.9
H39A C39 C3A H3AB 88.5 180.0
C3B C3A C39 H39 329.6 60.0
C3B C3A C39 H39A 206.6 300.0
C39 C3A C3B H3AA 120.0 120.0
C39 C3A C3B H3AB 241.9 240.0
H3AA C3A C3B H3AB 121.9 120.0
H3AA C3A C39 H39 89.6 180.0
H3AA C3A C39 H39A 326.6 59.9
C39 C3A H3AA H3AB 118.2 120.1
C3B C3A H3AA H3AB 241.8 240.0
H3AB C3A C39 H39 211.5 300.0
H3AB C3A C39 H39A 88.5 180.0
C39 C3A H3AB H3AA 241.2 240.0
C3B C3A H3AB H3AA 118.8 120.0
C3C C3B C3A H3AA 341.7 60.0
C3C C3B C3A H3AB 219.8 300.0
H3B C3B C3C H3BA 122.9 120.0
H3B C3B C3A H3AA 101.7 180.0
H3B C3B C3A H3AB 339.8 60.0
C3C C3B H3B H3BA 242.6 240.0
H3BA C3B C3A H3AA 224.6 300.1
H3BA C3B C3A H3AB 102.7 180.1
C3C C3B H3BA H3B 118.2 120.0
C3D C3C C3B H3B 126.2 60.0
C3D C3C C3B H3BA 3.3 300.0
H3C C3C C3D H3CA 122.9 120.0
H3C C3C C3B H3B 246.2 180.0
H3C C3C C3B H3BA 123.3 59.9
C3D C3C H3C H3CA 242.6 240.0
H3CA C3C C3B H3B 9.0 300.0
H3CA C3C C3B H3BA 246.2 180.0
C3D C3C H3CA H3C 118.3 120.0
C3E C3D C3C H3C 342.5 60.0
C3E C3D C3C H3CA 219.7 300.0
H3D C3D C3E H3DA 128.0 120.0
H3D C3D C3C H3C 102.5 180.0
H3D C3D C3C H3CA 339.6 60.0
C3E C3D H3D H3DA 246.3 240.0
H3DA C3D C3C H3C 230.5 300.1
H3DA C3D C3C H3CA 107.7 180.0
C3E C3D H3DA H3D 115.5 120.0
C3F C3E C3D H3D 36.6 60.0
C3F C3E C3D H3DA 268.6 300.0
H3E C3E C3F H3EA 121.8 119.9
H3E C3E C3D H3D 156.6 180.1
H3E C3E C3D H3DA 28.6 60.0
C3F C3E H3E H3EA 241.7 240.0
H3EA C3E C3D H3D 278.4 300.0
H3EA C3E C3D H3DA 150.4 179.9
C3F C3E H3EA H3E 118.8 120.0
H3F C3F C3E H3E 301.1 60.0
H3F C3F C3E H3EA 179.2 300.1
H3FA C3F H3F H3FB 120.0 120.0
H3FA C3F C3E H3E 61.1 180.0
H3FA C3F C3E H3EA 299.3 60.0
H3F C3F H3FA H3FB 240.0 240.0
H3FB C3F C3E H3E 181.1 299.9
H3FB C3F C3E H3EA 59.3 180.0
H3F C3F H3FB H3FA 120.0 120.0
O1' P' O3' O4' 237.9 240.0
O2' P' O3' O4' 124.1 120.0
O3' P' O4' HO4' 352.5 299.9
O3' P' O1' O4' 116.5 120.0
O2' P' O1' O4' 237.2 240.0
O1' P' O4' HO4' 109.4 59.9
O3' P' O2' O4' 239.5 240.0
O1' P' O2' O4' 124.1 120.1
O2' P' O4' HO4' 227.4 180.0
O1' P' O4' O2' 242.1 240.0
H1' C1' C2' H1'A 131.9 120.0
C2' C1' H1' H1'A 248.7 239.9
C2' C1' H1'A H1' 113.5 120.0
C3' C2' C1' H1' 102.4 60.0
C3' C2' C1' H1'A 330.5 300.0
H2' C2' C3' H2'A 116.1 120.0
O41 C3' C2' H3' 240.0 239.9
O41 C3' C2' H3'A 120.9 119.9
H3' C3' C2' H3'A 240.9 240.0
H2' C2' C1' H1' 222.5 180.0
H2' C2' C1' H1'A 90.5 60.0
C3' C2' H2' H2'A 235.2 240.0
H2' C2' C3' H3' 179.3 180.0
H2' C2' C3' H3'A 298.4 300.0
H2'A C2' C1' H1' 338.5 300.0
H2'A C2' C1' H1'A 206.6 180.0
C3' C2' H2'A H2' 123.1 120.0
H2'A C2' C3' H3' 63.2 60.0
H2'A C2' C3' H3'A 182.3 180.0
O41 C3' C2' H2' 59.3 59.9
O41 C3' C2' H2'A 303.2 299.9
C2' C3' O41 H3' 120.0 120.1
C2' C3' O41 H3'A 239.1 240.1
H3' C3' O41 H3'A 119.1 120.0
H3' C3' C2' H2' 179.3 180.0
H3' C3' C2' H2'A 63.2 60.0
C2' C3' H3' H3'A 120.9 120.0
O41 C3' H3' H3'A 239.1 240.0
H3'A C3' C2' H2' 298.4 300.0
H3'A C3' C2' H2'A 182.3 180.0
C2' C3' H3'A H3' 239.4 240.0
O41 C3' H3'A H3' 120.6 120.0
C41 O41 C3' H3' 333.5 60.0
C41 O41 C3' H3'A 214.4 300.0
H42A C42 H42 H42B 120.0 120.1
H42 C42 H42A H42B 240.0 239.9
H42 C42 H42B H42A 120.0 120.1
O13 CC CB CA 180.1 185.0
HA CA CB HAA 122.0 120.1
CB CA HA HAA 241.9 240.0
CB CA HAA HA 118.7 120.0
O13 CC CB OA 55.6 65.0
OA CB CA HA 146.2 175.0
OA CB CA HAA 24.2 54.9
CC CB OA HB 240.2 240.0
O13 CC CB HC 120.0 120.0
O13 CC CB HCA 241.4 240.1
CC CB CA HA 23.7 55.1
CC CB CA HAA 261.6 295.0
OA CB CC HB 117.8 120.0
HB CB CA HA 263.9 295.0
HB CB CA HAA 141.8 175.0
HOA OA CB HB 97.1 180.0
O13 CC HC CB 237.4 239.9
O13 CC HC HCA 118.7 119.9
HC CC CB HB 177.8 185.0
O13 CC HCA CB 121.8 120.0
O13 CC HCA HC 240.9 240.0
HCA CC CB HB 56.4 65.0