PDB Chemical Component 2D9

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 2D9

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C31 S28 1.796 1.814
C31 H311 1.100 1.090
C31 H312 1.100 1.090
C31 H313 1.100 1.089
S28 O29 1.501 1.420
S28 O30 1.518 1.421
S28 C25 1.848 1.763
C25 C26 1.413 1.383
C25 C24 1.401 1.382
C26 C27 1.423 1.382
C26 H26 1.080 1.080
C27 C19 1.412 1.382
C27 H27 1.080 1.080
C24 C23 1.410 1.382
C24 H24 1.080 1.080
C23 C19 1.396 1.382
C23 H23 1.080 1.080
C19 C18 1.569 1.508
C18 N15 1.512 1.469
C18 H181 1.100 1.090
C18 H182 1.100 1.090
N15 C16 1.494 1.468
N15 C14 1.502 1.468
C16 C17 1.538 1.529
C16 H161 1.100 1.090
C16 H162 1.100 1.090
C17 N12 1.466 1.468
C17 H171 1.100 1.090
C17 H172 1.100 1.090
C14 C13 1.562 1.530
C14 H141 1.100 1.090
C14 H142 1.100 1.090
C13 N12 1.479 1.468
C13 H131 1.100 1.090
C13 H132 1.100 1.090
N12 C3 1.416 1.405
C3 C2 1.315 1.400
C3 C4 1.459 1.382
C2 N1 1.342 1.309
C2 H2 1.080 1.080
N1 N5 1.250 1.400
N5 C4 1.333 1.368
N5 H5 1.000 0.970
C4 C6 1.426 1.478
C6 C7 1.379 1.395
C6 C11 1.399 1.401
C7 C8 1.406 1.380
C7 H7 1.080 1.080
C8 CL20 1.734 1.735
C8 C9 1.425 1.390
C9 O21 1.419 1.359
C9 C10 1.424 1.386
O21 H21 0.950 0.967
C10 C11 1.408 1.384
C10 H10 1.080 1.080
C11 O22 1.347 1.359
O22 H22 0.950 0.967

Bond Angles for 2D9

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
S28 C31 H311 109.5 109.5
S28 C31 H312 109.5 109.4
S28 C31 H313 109.5 109.4
C31 S28 O29 100.1 111.6
C31 S28 O30 103.1 111.6
C31 S28 C25 113.8 103.2
H311 C31 H312 109.5 109.4
H311 C31 H313 109.5 109.5
H312 C31 H313 109.4 109.5
O29 S28 O30 112.2 122.1
O29 S28 C25 110.9 102.8
O30 S28 C25 115.5 102.8
S28 C25 C26 125.5 120.0
S28 C25 C24 118.4 120.0
C26 C25 C24 116.1 120.0
C25 C26 C27 121.2 120.0
C25 C26 H26 119.4 120.0
C25 C24 C23 122.7 120.0
C25 C24 H24 118.6 120.0
C27 C26 H26 119.4 120.0
C26 C27 C19 121.8 120.0
C26 C27 H27 119.1 120.0
C19 C27 H27 119.1 120.0
C27 C19 C23 116.5 120.0
C27 C19 C18 124.5 120.0
C23 C24 H24 118.7 120.0
C24 C23 C19 121.7 120.0
C24 C23 H23 119.2 120.0
C19 C23 H23 119.2 120.0
C23 C19 C18 119.0 120.0
C19 C18 N15 118.0 109.5
C19 C18 H181 104.8 109.5
C19 C18 H182 106.8 109.4
N15 C18 H181 104.8 109.5
N15 C18 H182 106.7 109.5
C18 N15 C16 114.3 106.7
C18 N15 C14 111.1 106.7
H181 C18 H182 116.3 109.5
C16 N15 C14 115.5 106.9
N15 C16 C17 113.9 109.6
N15 C16 H161 107.0 109.5
N15 C16 H162 108.0 109.4
N15 C14 C13 115.4 109.6
N15 C14 H141 106.2 109.4
N15 C14 H142 107.5 109.5
C17 C16 H161 107.0 109.5
C17 C16 H162 108.0 109.4
C16 C17 N12 115.0 109.7
C16 C17 H171 106.4 109.4
C16 C17 H172 107.7 109.5
H161 C16 H162 113.0 109.4
N12 C17 H171 106.4 109.4
N12 C17 H172 107.6 109.5
C17 N12 C13 118.2 106.9
C17 N12 C3 121.3 106.7
H171 C17 H172 114.0 109.4
C13 C14 H141 106.2 109.5
C13 C14 H142 107.5 109.4
C14 C13 N12 112.0 109.6
C14 C13 H131 108.1 109.4
C14 C13 H132 108.6 109.4
H141 C14 H142 114.2 109.4
N12 C13 H131 108.1 109.5
N12 C13 H132 108.6 109.5
C13 N12 C3 120.4 106.7
H131 C13 H132 111.5 109.4
N12 C3 C2 119.1 126.2
N12 C3 C4 134.8 126.2
C2 C3 C4 106.1 107.5
C3 C2 N1 106.4 108.7
C3 C2 H2 126.8 125.6
C3 C4 N5 104.9 107.1
C3 C4 C6 129.3 126.5
N1 C2 H2 126.8 125.7
C2 N1 N5 113.5 108.9
N1 N5 C4 108.9 107.8
N1 N5 H5 125.5 126.1
C4 N5 H5 125.5 126.1
N5 C4 C6 125.8 126.5
C4 C6 C7 120.3 120.1
C4 C6 C11 122.7 120.1
C7 C6 C11 117.0 119.8
C6 C7 C8 121.8 120.0
C6 C7 H7 119.1 120.0
C6 C11 C10 122.8 119.8
C6 C11 O22 118.9 120.0
C8 C7 H7 119.1 120.0
C7 C8 CL20 116.7 120.0
C7 C8 C9 122.3 120.1
CL20 C8 C9 121.0 119.9
C8 C9 O21 122.6 119.8
C8 C9 C10 115.4 120.3
O21 C9 C10 122.1 119.9
C9 O21 H21 109.5 106.8
C9 C10 C11 120.8 120.1
C9 C10 H10 119.6 120.0
C11 C10 H10 119.6 119.9
C10 C11 O22 118.3 120.2
C11 O22 H22 109.5 106.8

Torsion Angles for 2D9

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
H311 C31 S28 H312 120.0 240.1
H311 C31 S28 H313 240.0 120.0
H312 C31 S28 H313 120.0 240.0
O29 S28 C31 O30 244.2 140.5
O29 S28 C31 C25 118.4 250.3
O30 S28 C31 C25 234.2 109.7
C31 S28 C25 C26 259.2 90.0
C31 S28 C25 C24 79.4 269.8
S28 C31 H311 H312 240.0 119.9
S28 C31 H311 H313 120.0 240.0
H311 C31 S28 O29 321.2 190.3
H311 C31 S28 O30 77.0 49.7
H311 C31 S28 C25 202.8 300.0
H312 C31 H311 H313 240.0 120.1
S28 C31 H312 H311 120.0 240.0
S28 C31 H312 H313 239.9 120.0
H312 C31 S28 O29 201.2 310.2
H312 C31 S28 O30 317.0 169.7
H312 C31 S28 C25 82.8 60.0
H311 C31 H312 H313 120.0 239.9
S28 C31 H313 H311 240.0 120.0
S28 C31 H313 H312 120.0 240.0
H313 C31 S28 O29 81.2 70.3
H313 C31 S28 O30 197.0 289.7
H313 C31 S28 C25 322.8 180.0
H311 C31 H313 H312 240.0 120.0
O29 S28 C31 H311 321.2 190.3
O29 S28 C31 H312 201.2 310.2
O29 S28 C31 H313 81.2 70.3
C31 S28 O29 O30 108.7 224.2
C31 S28 O29 C25 239.6 110.0
O30 S28 O29 C25 130.9 245.7
O29 S28 C25 C26 147.3 206.1
O29 S28 C25 C24 327.5 25.9
O30 S28 C31 H311 77.0 49.7
O30 S28 C31 H312 317.0 169.7
O30 S28 C31 H313 197.0 289.7
C31 S28 O30 O29 253.2 135.8
C31 S28 O30 C25 124.7 250.0
O29 S28 O30 C25 231.5 114.3
O30 S28 C25 C26 18.1 333.8
O30 S28 C25 C24 198.3 153.6
C25 S28 C31 H311 202.8 300.0
C25 S28 C31 H312 82.8 60.0
C25 S28 C31 H313 322.8 180.0
C31 S28 C25 O29 111.9 243.8
C31 S28 C25 O30 241.1 116.2
O29 S28 C25 O30 129.1 232.4
C26 C25 S28 C24 179.8 180.2
S28 C25 C26 C27 179.2 180.0
S28 C25 C26 H26 359.2 0.0
S28 C25 C24 C23 180.8 179.8
S28 C25 C24 H24 0.8 0.1
S28 C25 C26 C24 180.2 179.8
C26 C25 C24 C23 1.0 359.6
C26 C25 C24 H24 181.0 179.9
C27 C26 C25 H26 180.0 179.9
C25 C26 C27 C19 359.7 0.1
C25 C26 C27 H27 179.6 179.9
S28 C25 C24 C26 179.8 180.2
C24 C25 C26 C27 359.0 0.2
C24 C25 C26 H26 179.0 180.2
C23 C24 C25 H24 180.0 179.7
C25 C24 C23 C19 0.4 0.3
C25 C24 C23 H23 180.4 180.2
C27 C26 C25 C24 359.0 0.2
C25 C26 C27 H26 180.0 180.1
C19 C27 C26 H27 180.0 180.2
C26 C27 C19 C23 1.8 359.8
C26 C27 C19 C18 179.1 180.0
H26 C26 C25 C24 179.0 180.2
C25 C26 H26 C27 180.0 179.9
H26 C26 C27 C19 179.6 180.0
H26 C26 C27 H27 359.6 359.9
C19 C27 C26 H26 179.6 180.0
C26 C27 C19 H27 180.0 179.8
C24 C23 C19 C27 358.2 359.9
C27 C19 C23 H23 178.2 180.0
C23 C19 C27 C18 182.7 179.9
C27 C19 C18 N15 93.6 89.9
C27 C19 C18 H181 337.6 210.0
C27 C19 C18 H182 213.7 330.0
H27 C27 C26 H26 359.6 359.9
C26 C27 H27 C19 180.0 180.2
H27 C27 C19 C23 181.8 180.0
H27 C27 C19 C18 359.1 0.1
C25 C24 C23 H24 180.0 180.3
C27 C19 C23 C24 358.2 359.9
C19 C23 C24 H23 180.0 180.1
C24 C23 C19 C18 180.7 179.8
C25 C24 H24 C23 180.0 179.7
H24 C24 C23 C19 180.4 180.0
H24 C24 C23 H23 0.4 359.9
C23 C19 C27 H27 181.8 180.0
C27 C19 C23 C18 177.5 180.1
C19 C23 C24 H24 180.4 180.0
C24 C23 C19 H23 180.0 179.9
C23 C19 C18 N15 270.9 270.0
C23 C19 C18 H181 154.9 30.1
C23 C19 C18 H182 30.9 150.1
H23 C23 C24 H24 0.4 359.9
C24 C23 H23 C19 180.0 180.1
H23 C23 C19 C18 0.7 359.9
C18 C19 C27 H27 359.1 0.1
C27 C19 C18 C23 182.7 179.9
C18 C19 C23 H23 0.7 359.9
N15 C18 C19 H181 116.0 239.9
N15 C18 C19 H182 240.0 120.0
C19 C18 N15 C16 348.5 170.0
C19 C18 N15 C14 121.3 56.1
H181 C18 C19 H182 124.0 240.0
C19 C18 N15 H181 244.0 120.0
C19 C18 N15 H182 120.0 240.1
H181 C18 N15 H182 236.0 120.1
C16 N15 C18 C14 227.2 113.9
C18 N15 C16 C17 135.7 184.9
C18 N15 C16 H161 17.7 305.0
C18 N15 C16 H162 255.7 64.9
C18 N15 C14 C13 182.4 175.1
C18 N15 C14 H141 65.1 295.1
C18 N15 C14 H142 302.4 55.0
C19 C18 H181 N15 124.8 240.0
C19 C18 H181 H182 242.4 119.9
N15 C18 H181 H182 117.6 239.9
H181 C18 N15 C16 104.5 50.0
H181 C18 N15 C14 237.3 296.1
C19 C18 H182 N15 233.0 120.0
C19 C18 H182 H181 116.5 240.0
N15 C18 H182 H181 243.5 120.1
H182 C18 N15 C16 228.4 289.9
H182 C18 N15 C14 1.3 176.0
C16 N15 C18 H181 104.5 50.0
C16 N15 C18 H182 228.4 289.9
C18 N15 C16 C14 130.7 246.2
C16 N15 C14 C13 314.7 61.3
C16 N15 C14 H141 197.3 181.3
C16 N15 C14 H142 74.7 301.2
C17 C16 N15 H161 118.0 239.9
C17 C16 N15 H162 240.0 120.0
N15 C16 C17 N12 40.0 63.0
N15 C16 C17 H171 282.5 183.0
N15 C16 C17 H172 160.0 302.9
H161 C16 N15 H162 122.0 240.1
C14 N15 C18 H181 237.3 296.1
C14 N15 C18 H182 1.3 176.0
C18 N15 C14 C16 227.8 113.8
C14 N15 C16 C17 5.0 298.7
C14 N15 C16 H161 247.0 58.8
C14 N15 C16 H162 125.0 178.7
C13 C14 N15 H141 117.3 240.0
C13 C14 N15 H142 240.0 120.0
N15 C14 C13 N12 40.0 297.1
N15 C14 C13 H131 281.1 177.0
N15 C14 C13 H132 160.0 57.1
H141 C14 N15 H142 122.7 240.1
C17 C16 N15 C14 5.0 298.7
N15 C16 C17 H161 242.0 120.1
N15 C16 C17 H162 120.0 240.0
H161 C16 C17 H162 238.0 119.9
N12 C17 C16 H171 117.5 240.0
N12 C17 C16 H172 240.0 120.1
C16 C17 N12 C13 314.1 298.8
C16 C17 N12 C3 136.1 184.9
H171 C17 C16 H172 122.5 240.1
H161 C16 N15 C14 247.0 58.8
N15 C16 H161 C17 122.4 239.8
N15 C16 H161 H162 241.2 119.9
C17 C16 H161 H162 118.8 240.0
H161 C16 C17 N12 158.0 302.9
H161 C16 C17 H171 40.6 63.0
H161 C16 C17 H172 278.0 182.8
H162 C16 N15 C14 125.0 178.7
N15 C16 H162 C17 236.4 120.1
N15 C16 H162 H161 118.2 240.1
C17 C16 H162 H161 241.8 120.0
H162 C16 C17 N12 280.0 183.0
H162 C16 C17 H171 162.5 303.0
H162 C16 C17 H172 40.0 62.9
N12 C17 C16 H161 158.0 302.9
N12 C17 C16 H162 280.0 183.0
C16 C17 N12 H171 242.5 120.0
C16 C17 N12 H172 120.0 239.9
H171 C17 N12 H172 237.5 119.8
C14 C13 N12 C17 5.5 61.2
C17 N12 C13 H131 124.4 181.2
C17 N12 C13 H132 245.5 301.2
C13 N12 C17 C3 177.9 113.9
C17 N12 C3 C2 126.7 114.1
C17 N12 C3 C4 305.3 293.8
H171 C17 C16 H161 40.6 63.0
H171 C17 C16 H162 162.5 303.0
C16 C17 H171 N12 123.1 239.8
C16 C17 H171 H172 241.5 119.9
N12 C17 H171 H172 118.4 240.1
H171 C17 N12 C13 71.6 178.7
H171 C17 N12 C3 253.6 64.9
H172 C17 C16 H161 278.0 182.8
H172 C17 C16 H162 40.0 62.9
C16 C17 H172 N12 235.4 120.2
C16 C17 H172 H171 117.7 240.1
N12 C17 H172 H171 242.3 119.9
H172 C17 N12 C13 194.1 58.9
H172 C17 N12 C3 16.2 305.0
N15 C14 C13 H141 242.7 120.0
N15 C14 C13 H142 120.0 239.9
C17 N12 C13 C14 5.5 61.2
H141 C14 C13 H142 237.3 119.9
N12 C13 C14 H131 118.9 120.1
N12 C13 C14 H132 240.0 239.9
C14 C13 N12 C3 183.5 175.1
H131 C13 C14 H132 121.1 119.9
N15 C14 H141 C13 123.3 239.9
N15 C14 H141 H142 241.7 119.9
C13 C14 H141 H142 118.3 240.1
H141 C14 C13 N12 157.4 177.0
H141 C14 C13 H131 38.5 56.9
H141 C14 C13 H132 277.4 297.1
N15 C14 H142 C13 235.1 120.1
N15 C14 H142 H141 117.6 240.1
C13 C14 H142 H141 242.4 119.9
H142 C14 C13 N12 280.1 57.1
H142 C14 C13 H131 161.1 297.0
H142 C14 C13 H132 40.0 177.2
C13 N12 C17 H171 71.6 178.7
C13 N12 C17 H172 194.1 58.9
C17 N12 C13 C3 182.1 246.1
N12 C13 C14 H141 157.4 177.0
N12 C13 C14 H142 280.1 57.1
C14 C13 N12 H131 241.1 240.0
C14 C13 N12 H132 120.0 120.0
H131 C13 N12 H132 238.9 240.1
C13 N12 C3 C2 308.8 0.1
C13 N12 C3 C4 127.4 179.8
H131 C13 C14 H141 38.5 56.9
H131 C13 C14 H142 161.1 297.0
C14 C13 H131 N12 121.4 120.2
C14 C13 H131 H132 240.7 240.1
N12 C13 H131 H132 119.3 120.0
H131 C13 N12 C3 302.4 295.1
H132 C13 C14 H141 277.4 297.1
H132 C13 C14 H142 40.0 177.2
C14 C13 H132 N12 238.0 239.8
C14 C13 H132 H131 119.0 119.8
N12 C13 H132 H131 241.0 240.0
H132 C13 N12 C3 63.5 55.1
C3 N12 C17 H171 253.6 64.9
C3 N12 C17 H172 16.2 305.0
C17 N12 C3 C13 177.9 114.0
C3 N12 C13 H131 302.4 295.1
C3 N12 C13 H132 63.5 55.1
C2 C3 N12 C4 181.3 180.3
N12 C3 C2 N1 179.5 180.0
N12 C3 C2 H2 359.5 0.1
N12 C3 C4 N5 179.6 179.8
N12 C3 C4 C6 0.9 0.3
N12 C3 C2 C4 179.0 179.8
C2 C3 C4 N5 358.4 359.6
C2 C3 C4 C6 179.7 180.0
N1 C2 C3 H2 180.0 179.9
C3 C2 N1 N5 1.0 360.0
N12 C3 C4 C2 181.2 180.2
C4 C3 C2 N1 0.5 0.3
C4 C3 C2 H2 180.5 180.3
N1 N5 C4 C3 2.2 0.4
C3 C4 N5 H5 182.2 180.2
N5 C4 C3 C6 178.7 179.6
C3 C4 C6 C7 302.9 113.8
C3 C4 C6 C11 122.9 293.5
N1 C2 C3 C4 0.5 0.3
C3 C2 N1 H2 180.0 180.1
C2 N1 N5 C4 357.9 359.8
C2 N1 N5 H5 177.9 179.9
H2 C2 C3 C4 180.5 180.3
C3 C2 H2 N1 180.0 179.9
H2 C2 N1 N5 181.0 179.9
C3 C4 N5 N1 2.2 0.4
N5 N1 C2 H2 181.0 179.9
C4 N5 N1 H5 180.0 179.8
N1 N5 C4 C6 181.0 180.0
C3 C4 N5 C6 181.3 180.4
N1 N5 C4 H5 180.0 180.2
N5 C4 C6 C7 124.5 294.4
N5 C4 C6 C11 304.5 114.0
N1 N5 H5 C4 180.0 179.8
H5 N5 C4 C6 1.0 359.8
C3 C4 C6 N5 178.4 179.5
C6 C4 N5 H5 1.0 359.8
C7 C6 C4 C11 180.0 180.3
C4 C6 C7 C8 179.3 180.0
C4 C6 C7 H7 359.3 359.9
C4 C6 C11 C10 181.0 179.8
C4 C6 C11 O22 359.7 0.3
C4 C6 C7 C11 180.0 179.7
C7 C6 C11 C10 1.1 359.4
C7 C6 C11 O22 179.7 179.9
C8 C7 C6 H7 180.0 180.1
C6 C7 C8 CL20 179.4 179.9
C6 C7 C8 C9 359.2 359.9
C4 C6 C11 C7 180.0 180.3
C11 C6 C7 C8 359.2 0.3
C11 C6 C7 H7 179.2 180.2
C9 C10 C11 C6 0.2 0.5
C6 C11 C10 H10 180.2 180.3
C10 C11 C6 O22 181.4 179.5
C6 C11 O22 H22 31.4 274.4
C8 C7 C6 C11 359.2 0.3
C6 C7 C8 H7 180.0 179.9
CL20 C8 C7 C9 180.2 180.0
C7 C8 C9 O21 181.9 180.0
C7 C8 C9 C10 2.0 0.0
H7 C7 C6 C11 179.2 180.2
C6 C7 H7 C8 180.0 180.1
H7 C7 C8 CL20 359.4 0.1
H7 C7 C8 C9 179.2 180.1
CL20 C8 C7 H7 359.4 0.1
C7 C8 CL20 C9 179.8 180.0
CL20 C8 C9 O21 1.6 0.0
CL20 C8 C9 C10 181.7 180.0
C9 C8 C7 H7 179.2 180.1
C7 C8 C9 CL20 180.3 180.0
O21 C9 C8 C10 179.9 180.0
C8 C9 O21 H21 273.7 90.0
C8 C9 C10 C11 358.4 359.8
C8 C9 C10 H10 178.4 180.0
C8 C9 O21 C10 180.1 180.0
O21 C9 C10 C11 178.4 179.7
O21 C9 C10 H10 358.4 360.0
C6 C11 C10 C9 0.2 0.5
C8 C9 C10 O21 179.9 180.0
C10 C9 O21 H21 93.6 270.1
C11 C10 C9 H10 180.0 179.8
C9 C10 C11 O22 181.5 180.0
H21 O21 C9 C10 93.6 270.1
C6 C11 C10 O22 178.6 180.5
C9 C10 C11 H10 180.0 180.2
C10 C11 O22 H22 210.1 94.9
C9 C10 H10 C11 180.0 179.8
H10 C10 C11 O22 1.5 359.8
C6 C11 O22 C10 181.3 179.5
O22 C11 C10 H10 1.5 359.8