PDB Chemical Component RPC

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 RPC

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP2 P 1.486 1.480
OP5 P2 1.599 1.480
OP6 P2 1.485 1.609
OP1 P 1.489 1.610
P O5' 1.581 1.610
C5' O5' 1.413 1.428
C5' C4' 1.498 1.531
P2 O3' 1.598 1.610
P2 OP4 1.486 1.610
C3' C4' 1.521 1.541
C3' O3' 1.422 1.429
C3' C2' 1.524 1.549
C4' O4' 1.456 1.437
C2' O2' 1.414 1.430
C2' C1' 1.526 1.550
O4' C1' 1.416 1.444
C1' N1 1.469 1.465
C6 N1 1.365 1.362
C6 C5 1.344 1.354
N1 C2 1.396 1.346
C5 C4 1.425 1.410
C2 O2 1.242 1.219
C2 N3 1.361 1.333
C4 N3 1.334 1.326
C4 N4 1.339 1.376
OP1 H1 0.950 0.967
C5' H2 1.100 1.090
C5' H3 1.100 1.090
C4' H4 1.100 1.090
C3' H5 1.100 1.090
C2' H6 1.100 1.089
O2' H7 0.951 0.968
C1' H8 1.100 1.090
C6 H9 1.079 1.081
C5 H10 1.080 1.079
N4 H11 1.000 0.970
N4 H12 1.000 0.969
OP4 H14 0.950 0.967
OP6 H15 0.950 0.967
P OP3   1.610
OP3 H17   0.967

Bond Angles for RPC

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP3   109.5
OP1 P O5' 108.2 109.5
OP1 P OP3   109.5
O5' P OP3   109.5
C5' C4' O4' 109.0 109.9
C4' C5' H2 109.1 109.4
C4' C5' H3 109.1 109.5
C5' C4' H4 109.2 109.8
P2 OP4 H14 109.5 114.0
C3' C4' O4' 106.2 107.3
C3' C4' H4 108.9 110.0
O3' C3' C2' 110.0 110.5
O3' C3' H5 112.9 110.5
C3' C2' O2' 115.0 110.8
C3' C2' C1' 101.1 102.1
C2' C3' H5 111.3 110.6
C3' C2' H6 108.9 110.9
C4' O4' C1' 109.4 107.0
O4' C4' H4 109.8 109.9
O2' C2' C1' 112.2 110.9
O2' C2' H6 110.4 110.8
C2' O2' H7 109.5 113.9
C2' C1' N1 114.6 110.6
C1' C2' H6 108.9 111.0
C2' C1' H8 108.5 110.6
O4' C1' N1 108.8 110.6
O4' C1' H8 110.0 110.7
C1' N1 C2 117.7 119.8
N1 C1' H8 109.2 110.6
C6 N1 C2 119.9 120.4
C6 C5 C4 118.0 118.9
C5 C6 H9 119.5 120.3
C6 C5 H10 121.0 120.6
N1 C2 O2 117.6 119.5
N1 C2 N3 119.8 121.0
C5 C4 N3 121.5 119.6
C5 C4 N4 120.2 120.2
C4 C5 H10 121.0 120.5
N4 C4 N3 118.3 120.2
C4 N4 H11 120.0 119.9
C4 N4 H12 120.0 120.0
H2 C5' H3 109.5 109.4
H11 N4 H12 120.0 120.0
P OP3 H17   114.1

Torsion Angles for RPC

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 OP3   120.0
O5' P OP2 OP3   240.0
OP2 P OP3 H17   60.0
OP5 P2 OP4 H14 0.0 180.0
OP6 P2 OP4 H14 126.8 60.0
OP2 P OP1 OP3   240.0
O5' P OP1 OP3   120.0
OP1 P OP3 H17   300.0
OP2 P O5' OP3   120.0
OP1 P O5' OP3   240.0
O5' P OP3 H17   180.0
C5' O5' P OP3   185.0
C3' C4' C5' O4' 118.2 117.9
C3' C4' C5' H4 238.1 238.9
C5' C4' O4' C1' 119.4 146.0
O4' C4' C5' H4 119.9 121.1
H2 C5' C4' H3 119.6 119.9
P2 O3' C3' H5 330.3 2.5
C5' C4' C3' O4' 240.2 240.6
C3' C4' C5' H2 17.4 64.3
C3' C4' C5' H3 257.8 304.3
C5' C4' C3' H4 122.1 121.0
C3' C4' O4' C1' 356.5 26.5
O4' C4' C3' H4 241.9 240.5
O3' C3' C4' O4' 270.0 239.3
O3' C3' C4' H4 28.1 358.8
O3' C3' C2' O2' 316.8 339.6
O3' C3' C2' C1' 77.9 97.8
C2' C3' O3' H5 124.9 122.7
O3' C3' C2' H6 192.4 216.1
C2' C3' C4' O4' 26.2 358.0
C2' C3' C4' H4 144.3 117.5
O3' C3' C2' H5 234.2 237.4
O2' C2' C3' C1' 238.9 241.8
O2' C2' C3' H6 124.4 123.6
C3' C2' O2' H7 135.6 180.0
C3' C2' C1' N1 156.4 155.5
C1' C2' C3' H6 245.5 241.7
C3' C2' C1' H8 278.7 278.4
O4' C4' C5' H2 259.1 306.4
O4' C4' C5' H3 139.5 186.5
C5' C4' O4' H4 240.4 239.0
C3' C4' O4' H4 117.6 119.6
C4' O4' C1' N1 215.5 201.4
C4' O4' C1' H8 95.9 78.5
C3' C2' O2' C1' 114.8 112.7
O2' C2' C3' H5 82.7 102.2
C3' C2' O2' H6 236.4 236.4
O2' C2' C1' N1 279.4 273.7
C1' C2' O2' H6 121.6 123.7
O2' C2' C1' H8 41.7 36.5
C3' C2' C1' O2' 237.0 241.9
C1' C2' C3' H5 203.7 220.4
C3' C2' C1' H6 114.5 118.3
C4' O4' C1' C2' 339.0 319.9
O2' C2' C1' H6 237.5 236.4
C1' C2' O2' H7 20.9 67.3
O4' C1' C2' N1 240.2 241.5
O4' C1' C2' H8 117.9 118.6
C2' C1' N1 C2 83.4 295.1
N1 C1' C2' H8 237.7 237.1
C1' O4' C4' H4 239.0 267.0
C2' C1' O4' N1 123.5 118.5
O4' C1' C2' H6 282.1 278.8
C2' C1' O4' H8 243.1 241.4
O4' C1' N1 C2 201.5 49.2
N1 C1' O4' H8 119.6 122.9
N1 C1' C2' H6 41.9 37.3
C2' C1' N1 H8 121.9 122.9
O4' C1' N1 H8 239.9 237.0
C6 N1 C1' C2 179.3 180.2
C1' N1 C2 O2 359.4 359.9
C1' N1 C2 N3 179.8 179.7
C1' N1 C6 C2 180.7 179.8
C6 N1 C1' H8 140.8 352.3
C6 N1 C2 O2 180.1 179.7
C6 N1 C2 N3 0.5 359.6
C5 C6 N1 C2 359.6 0.2
C6 C5 C4 N3 359.4 0.1
C6 C5 C4 N4 179.6 180.0
C4 C5 C6 H10 180.0 180.0
C2 N1 C1' H8 321.6 172.2
C4 C5 C6 H9 180.4 180.0
C6 C5 C4 H10 180.0 180.0
N4 C4 C5 N3 180.2 179.9
C5 C4 N4 H11 179.8 0.0
C5 C4 N4 H12 359.8 180.1
N1 C2 O2 N3 180.4 179.9
N1 C2 N3 O2 179.6 180.1
N1 C2 N3 C4 359.4 0.5
C5 C4 N3 N4 180.2 179.9
N3 C4 C5 H10 179.4 180.0
N3 C4 N4 H11 360.0 180.0
N3 C4 N4 H12 180.0 0.0
C5 C4 N4 N3 179.8 180.1
N4 C4 C5 H10 359.6 360.0
H11 N4 C4 H12 180.0 179.9
H1 OP1 P O5' 235.7 60.0
H1 OP1 P OP3   300.0
H2 C5' C4' O4' 259.1 306.4
C4' C5' H2 H3 240.6 240.0
H2 C5' C4' H4 139.2 185.4
H3 C5' C4' O4' 139.5 186.5
C4' C5' H3 H2 119.4 119.9
H3 C5' C4' H4 19.6 65.4
C5' C4' H4 O4' 119.4 121.0
H4 C4' C5' H2 139.2 185.4
H4 C4' C5' H3 19.6 65.4
C3' C4' H4 O4' 244.2 242.1
H4 C4' O4' C1' 239.0 267.0
H5 C3' C4' O4' 145.1 116.7
H5 C3' C4' H4 263.2 236.3
O3' C3' H5 C2' 124.2 122.7
H5 C3' C2' O2' 82.7 102.2
H5 C3' C2' C1' 203.7 220.4
H5 C3' C2' H6 318.3 338.7
C3' C2' H6 O2' 127.1 123.6
C3' C2' H6 C1' 250.7 247.2
H6 C2' C3' H5 318.3 338.7
O2' C2' H6 C1' 123.6 123.7
H6 C2' O2' H7 259.2 303.6
H6 C2' C1' N1 41.9 37.3
H6 C2' C1' H8 164.1 160.2
H7 O2' C2' C1' 20.9 67.3
H7 O2' C2' H6 259.2 303.6
C2' C1' H8 N1 234.5 237.1
H8 C1' C2' H6 164.1 160.2
O4' C1' H8 N1 119.4 122.9
H8 C1' N1 C2 321.6 172.2
H9 C6 N1 C2 179.6 180.2
H9 C6 C5 C4 180.4 180.0
H9 C6 C5 H10 0.5 0.1
C6 C5 H10 C4 180.0 179.9
H10 C5 C6 H9 0.5 0.1
H10 C5 C4 N3 179.4 180.0
H10 C5 C4 N4 359.6 360.0
H11 N4 C4 N3 360.0 180.0
C4 N4 H11 H12 180.0 180.1
H12 N4 C4 N3 180.0 0.0
C4 N4 H12 H11 180.0 179.9
OP1 P OP3 O5'   120.0