PDB Chemical Component QDM

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 QDM

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C2M N3Q 1.472 1.469
O4Q C4Q 1.422 1.429
C1M N3Q 1.490 1.469
N3Q C3Q 1.480 1.468
C4Q C3Q 1.544 1.532
C4Q C5Q 1.550 1.531
C3Q C2Q 1.539 1.532
C6Q C5Q 1.556 1.530
C5Q O5Q 1.388 1.430
C2Q O2Q 1.460 1.429
C2Q C1Q 1.531 1.531
O5Q C1Q 1.475 1.428
C1Q O3B 1.396 1.430
O3B PB 1.697 1.609
O2B PB 1.477 1.481
PB O1B 1.502 1.609
PB O3A 1.577 1.610
O3A PA 1.612 1.611
O2A PA 1.486 1.479
PA O1A 1.551 1.611
PA O5' 1.573 1.610
O5' C5' 1.423 1.429
O3' C3' 1.446 1.429
C4' C5' 1.509 1.530
C4' C3' 1.519 1.545
C4' O4' 1.434 1.444
C3' C2' 1.510 1.545
O4' C1' 1.412 1.444
C1' C2' 1.508 1.545
C1' N1 1.474 1.465
N1 C6 1.327 1.368
N1 C2 1.338 1.345
O2 C2 1.356 1.216
C6 C5 1.387 1.350
C2 N3 1.351 1.346
C5 C5M 1.503 1.507
C5 C4 1.385 1.416
N3 C4 1.359 1.349
C4 O4 1.351 1.217
O1A H1 0.950 0.967
O1B H2 0.950 0.967
C1Q H3 1.100 1.090
C2Q H4 1.100 1.090
O2Q H5 0.950 0.967
C3Q H6 1.100 1.090
C2M H8 1.100 1.091
C2M H9 1.100 1.090
C2M H10 1.100 1.089
C1M H11 1.101 1.091
C1M H12 1.100 1.091
C1M H13 1.100 1.090
C4Q H14 1.100 1.090
O4Q H15 0.949 0.967
C5Q H16 1.100 1.091
C6Q H17 1.100 1.090
C6Q H18 1.100 1.090
C6Q H19 1.100 1.090
C5' H20 1.100 1.090
C5' H21 1.100 1.090
C4' H22 1.100 1.091
C3' H23 1.100 1.090
O3' H24 0.950 0.967
C2' H25 1.100 1.090
C2' H26 1.100 1.090
C1' H27 1.100 1.090
C6 H28 1.080 1.080
C5M H29 1.100 1.090
C5M H30 1.100 1.089
C5M H31 1.100 1.090
N3 H32 1.000 0.971

Bond Angles for QDM

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O4Q C4Q C5Q 114.7 109.5
O4Q C4Q H14 109.0 109.6
N3Q C3Q H6 106.1 109.6
C4Q C3Q H6 105.4 109.5
C4Q C5Q O5Q 115.0 109.4
C5Q C4Q H14 107.4 109.5
C4Q C5Q H16 110.5 109.5
C3Q C2Q H4 108.1 109.6
C6Q C5Q O5Q 98.7 109.5
C6Q C5Q H16 110.4 109.5
O5Q C5Q H16 113.0 109.5
O2Q C2Q H4 109.1 109.5
C2Q O2Q H5 109.5 114.0
C2Q C1Q H3 110.1 109.4
O5Q C1Q H3 110.8 109.5
PB O1B H2 109.5 114.0
O3A PA O5' 101.7 109.5
O2A PA O1A 118.0 109.5
O2A PA O5' 111.6 109.5
O1A PA O5' 107.5 109.4
PA O1A H1 109.5 114.0
PA O5' C5' 126.3 123.0
O5' C5' H20 109.2 109.5
O5' C5' H21 109.2 109.5
O3' C3' C2' 111.3 110.5
O3' C3' H23 110.3 110.6
C4' C5' H20 109.3 109.5
C4' C5' H21 109.3 109.5
C3' C4' O4' 103.9 104.8
C4' C3' C2' 106.3 104.1
C3' C4' H22 111.0 110.4
C4' C3' H23 109.3 110.5
C4' O4' C1' 110.8 105.3
O4' C4' H22 112.3 110.4
C2' C3' H23 109.4 110.5
C3' C2' H25 111.8 110.5
C3' C2' H26 111.9 110.5
O4' C1' N1 107.3 110.4
O4' C1' H27 108.8 110.5
C1' C2' H25 111.9 110.5
C1' C2' H26 111.9 110.6
C1' N1 C6 118.7 119.7
C1' N1 C2 116.5 119.7
N1 C1' H27 108.0 110.3
C6 N1 C2 124.7 120.6
N1 C6 C5 114.1 119.7
N1 C6 H28 122.9 120.2
N1 C2 N3 124.0 120.9
C6 C5 C5M 117.9 120.5
C6 C5 C4 120.0 119.2
C5 C6 H28 123.0 120.2
C2 N3 H32 123.8 119.9
C5M C5 C4 122.1 120.4
C5 C5M H29 109.5 109.5
C5 C5M H30 109.5 109.5
C5 C5M H31 109.5 109.5
C5 C4 O4 124.3 120.4
H8 C2M H9 109.5 109.5
H8 C2M H10 109.4 109.5
H9 C2M H10 109.5 109.5
H11 C1M H12 109.4 109.5
H11 C1M H13 109.5 109.5
H12 C1M H13 109.5 109.5
H17 C6Q H18 109.5 109.5
H17 C6Q H19 109.5 109.5
H18 C6Q H19 109.4 109.5
H20 C5' H21 109.5 109.5
H25 C2' H26 109.5 110.5
H29 C5M H30 109.4 109.5
H29 C5M H31 109.5 109.5
H30 C5M H31 109.5 109.5

Torsion Angles for QDM

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C2M N3Q C3Q H6 312.9 192.5
O4Q C4Q C3Q H6 58.7 57.0
O4Q C4Q C5Q O5Q 177.6 182.5
C5Q C4Q O4Q H14 239.6 239.9
O4Q C4Q C5Q H16 307.0 302.5
C1M N3Q C3Q H6 188.8 316.4
C4Q C3Q N3Q H6 117.0 120.2
N3Q C3Q C2Q H4 298.4 303.0
N3Q C3Q C4Q H6 242.6 239.8
C4Q C3Q C2Q H4 70.0 62.9
O4Q C4Q C5Q H14 121.3 120.2
C5Q C4Q C3Q H6 292.8 297.1
C6Q C5Q C4Q O5Q 250.6 240.0
C6Q C5Q C4Q H16 121.2 120.0
O5Q C5Q C4Q H16 230.6 240.0
O2Q C2Q C3Q H4 117.9 120.2
C3Q C2Q O2Q H5 180.0 179.7
C3Q C2Q C1Q H3 178.9 177.6
C4Q C5Q C6Q O5Q 120.1 120.0
C6Q C5Q C4Q H14 306.9 302.3
C4Q C5Q C6Q H16 238.7 239.9
O5Q C5Q C6Q H16 118.6 120.0
O5Q C5Q C4Q H14 56.3 62.3
C4Q C5Q O5Q H16 128.2 120.0
C6Q C5Q O5Q H16 243.4 240.0
C5Q O5Q C1Q H3 174.9 178.9
C3Q C2Q O2Q H4 242.7 239.8
O2Q C2Q C1Q H3 300.0 297.5
O5Q C1Q C2Q H3 238.7 240.0
C2Q C1Q O5Q H3 120.9 120.0
O3B PB O1B H2 122.0 300.0
O2B PB O1B H2 0.0 180.0
PB O3A PA O5' 202.7 165.0
O2A PA O3A O5' 238.8 240.0
O1A PA O3A O5' 110.5 120.0
O3A PA O1A H1 126.9 300.0
O3A PA O5' C5' 56.6 185.0
O3A PA O2A O5' 115.7 120.0
O1A PA O2A O5' 234.8 240.0
O2A PA O1A H1 360.0 180.0
O2A PA O5' C5' 180.7 305.1
O3A PA O1A O5' 254.1 240.0
O2A PA O1A O5' 127.1 120.0
O1A PA O5' C5' 311.5 65.0
O2A PA O5' O1A 229.2 240.0
O5' PA O1A H1 232.8 60.0
PA O5' C5' H20 1.9 300.0
PA O5' C5' H21 121.6 60.0
C4' C5' O5' H20 239.9 240.0
C4' C5' O5' H21 120.1 120.0
H20 C5' O5' H21 240.3 240.0
O3' C3' C4' O4' 261.9 217.4
C4' C3' O3' C2' 117.6 114.6
O3' C3' C4' H22 22.8 336.3
C4' C3' O3' H23 239.3 237.3
C2' C3' O3' H23 121.7 122.7
O3' C3' C2' H25 205.4 237.2
O3' C3' C2' H26 328.7 359.8
O5' C5' C4' H20 120.1 120.0
O5' C5' C4' H21 239.9 240.0
H20 C5' C4' H21 119.8 120.0
O3' C3' C4' C2' 239.3 241.4
O3' C3' C4' H23 121.3 122.7
C3' C4' C5' H20 173.2 65.0
C3' C4' C5' H21 53.5 305.0
C3' C4' O4' C1' 358.1 40.5
O4' C4' C3' H22 239.1 241.1
C2' C3' C4' H23 242.0 241.3
C4' C3' C2' H25 85.6 118.6
C4' C3' C2' H26 208.9 241.2
O4' C4' C5' H20 60.4 309.6
O4' C4' C5' H21 300.6 189.6
O4' C4' C3' C2' 22.6 336.0
C3' C4' O4' H22 120.0 118.9
O4' C4' C3' H23 140.6 94.7
C4' O4' C1' N1 213.2 200.7
C4' O4' C1' H27 96.6 78.4
O3' C3' C2' H23 237.8 237.3
C2' C3' C4' O4' 22.6 336.0
C2' C3' C4' H22 143.5 94.9
C4' C3' C2' H23 118.0 118.7
C1' C2' C3' H25 241.6 241.4
C1' C2' C3' H26 118.4 118.8
H25 C2' C3' H26 236.8 237.4
C1' O4' C4' H22 238.1 281.6
O4' C1' C2' H25 273.6 265.4
O4' C1' C2' H26 150.3 142.7
O4' C1' N1 C6 35.9 230.4
O4' C1' N1 C2 218.4 50.1
N1 C1' O4' H27 116.6 122.3
C4' O4' C1' C2' 340.3 319.5
C1' C2' C3' H23 209.3 241.3
C3' C2' C1' H25 118.4 118.6
C3' C2' C1' H26 241.6 241.3
H25 C2' C1' H26 123.2 122.7
O4' C1' N1 H27 242.8 237.6
N1 C1' C2' H25 34.6 24.2
N1 C1' C2' H26 271.3 261.5
C6 N1 C1' C2 177.5 180.3
C1' N1 C6 C5 180.0 180.0
C1' N1 C6 H28 360.0 359.9
C1' N1 C2 N3 180.4 179.7
C1' N1 C6 C2 182.7 179.7
C6 N1 C1' H27 153.0 352.8
C6 N1 C2 N3 3.1 359.5
N1 C6 C5 C5M 182.9 180.0
N1 C6 C5 C4 3.7 360.0
C5 C6 N1 H28 180.0 180.1
C1' N1 C2 C6 177.3 180.3
C2 N1 C1' H27 335.5 172.5
C2 N1 C6 C5 357.3 0.3
C2 N1 C6 H28 177.3 180.2
N1 C2 N3 H32 176.2 180.3
O2 C2 N3 H32 358.2 0.0
C5 C6 N1 C2 357.3 0.3
N1 C6 C5 H28 180.0 179.9
C5M C5 C6 C4 179.2 180.1
C6 C5 C5M H29 180.0 90.0
C6 C5 C5M H30 300.0 210.0
C6 C5 C5M H31 60.0 330.0
C6 C5 C4 O4 178.1 180.0
C6 C5 C5M C4 180.8 179.9
C5M C5 C6 H28 2.9 0.1
C5M C5 C4 O4 358.9 360.0
H29 C5M C5 H30 240.0 240.0
H29 C5M C5 H31 120.0 120.0
H30 C5M C5 H31 240.0 240.0
C6 C5 C4 C5M 179.1 180.1
C4 C5 C6 H28 183.7 180.1
C4 C5 C5M H29 359.2 270.0
C4 C5 C5M H30 119.1 30.0
C4 C5 C5M H31 239.1 150.0
N1 C2 N3 C4 356.2 0.5
H1 O1A PA O5' 232.8 60.0
H4 C2Q O2Q H5 297.2 299.9
H4 C2Q C1Q H3 59.2 57.7
H5 O2Q C2Q H4 297.2 299.9
H6 C3Q C2Q H4 183.4 182.8
H9 C2M H8 H10 120.0 120.0
H8 C2M H9 H10 240.0 239.9
H8 C2M H10 H9 120.0 120.0
H12 C1M H11 H13 120.0 120.0
H11 C1M H12 H13 240.0 240.0
H11 C1M H13 H12 120.0 120.0
O4Q C4Q H14 C5Q 235.1 239.9
H14 C4Q C3Q H6 177.5 177.3
H14 C4Q C5Q O5Q 56.3 62.3
H14 C4Q C5Q H16 185.7 182.3
H15 O4Q C4Q C5Q 301.7 299.6
H15 O4Q C4Q H14 62.1 59.7
C4Q C5Q H16 O5Q 229.6 240.0
H16 C5Q C4Q H14 185.7 182.3
C6Q C5Q H16 O5Q 109.5 120.0
H17 C6Q C5Q O5Q 59.9 300.0
H17 C6Q C5Q H16 301.3 180.1
H18 C6Q H17 H19 120.0 120.1
H18 C6Q C5Q O5Q 179.9 60.0
H18 C6Q C5Q H16 61.3 300.0
H17 C6Q H18 H19 240.0 239.9
H19 C6Q C5Q O5Q 299.9 180.0
H19 C6Q C5Q H16 181.3 60.0
H17 C6Q H19 H18 120.0 120.1
O5' C5' H20 H21 119.6 120.0
C4' C5' H20 H21 240.4 240.0
O5' C5' H21 H20 240.4 240.0
C4' C5' H21 H20 119.6 120.0
H22 C4' C5' H20 297.7 187.3
H22 C4' C5' H21 177.9 67.3
C3' C4' H22 O4' 244.2 244.6
H22 C4' C3' C2' 143.5 94.9
H22 C4' C3' H23 261.5 213.6
H22 C4' O4' C1' 238.1 281.6
O3' C3' H23 C2' 122.8 122.7
H23 C3' C4' O4' 140.6 94.7
C4' C3' H23 C2' 243.9 245.3
H23 C3' C4' H22 261.5 213.6
H23 C3' C2' H25 327.7 360.0
H23 C3' C2' H26 90.9 122.5
H24 O3' C3' C2' 62.4 65.4
H24 O3' C3' H23 300.7 302.7
H25 C2' C3' H23 327.7 360.0
C3' C2' H25 H26 124.6 122.6
C1' C2' H25 H26 235.4 237.2
H26 C2' C3' H23 90.9 122.5
C3' C2' H26 H25 235.4 237.4
C1' C2' H26 H25 124.6 122.7
O4' C1' H27 N1 116.2 122.3
H27 C1' C2' H25 156.5 146.4
H27 C1' C2' H26 33.3 23.7
H27 C1' N1 C6 153.0 352.8
H27 C1' N1 C2 335.5 172.5
H28 C6 N1 C2 177.3 180.2
N1 C6 H28 C5 180.0 180.1
H28 C6 C5 C5M 2.9 0.1
H28 C6 C5 C4 183.7 180.1
H29 C5M C5 C4 359.2 270.0
C5 C5M H29 H30 120.0 120.0
C5 C5M H29 H31 240.0 240.0
H30 C5M H29 H31 120.0 120.0
H30 C5M C5 C4 119.1 30.0
C5 C5M H30 H29 240.0 240.0
C5 C5M H30 H31 120.0 120.0
H29 C5M H30 H31 240.0 240.0
H31 C5M C5 C4 239.1 150.0
C5 C5M H31 H29 120.1 120.0
C5 C5M H31 H30 240.0 240.0
H29 C5M H31 H30 119.9 120.0