PDB Chemical Component 4YM

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 4YM

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C01 C02 1.494 1.530
C02 O03 1.376 1.452
O03 C04 1.379 1.348
C04 O05 1.217 1.215
C04 C06 1.489 1.470
C06 C07 1.398 1.402
C06 C22 1.412 1.408
C07 N08 1.341 1.312
N08 C09 1.380 1.332
C09 N10 1.382 1.366
C09 C21 1.380 1.406
N10 N11 1.362 1.398
N11 C12 1.346 1.311
C12 C13 1.377 1.484
C12 C21 1.443 1.464
C13 C14 1.384 1.395
C13 C20 1.385 1.391
C14 C15 1.389 1.382
C15 C16 1.382 1.380
C16 C17 1.382 1.397
C17 C18 1.484 1.432
C17 C20 1.392 1.394
C18 N19 1.131 1.136
C21 C22 1.445 1.404
C22 N23 1.453 1.380
N23 C24 1.407 1.470
N23 C30 1.407 1.470
C24 C25 1.489 1.530
C25 O26 1.401 1.431
O26 C27 1.407 1.431
C27 C28 1.502 1.530
C27 C30 1.500 1.531
C28 N29 1.441 1.469
C01 H01 1.100 1.090
C01 H01A 1.100 1.091
C01 H01B 1.100 1.090
C02 H02 1.100 1.090
C02 H02A 1.100 1.090
C07 H07 1.080 1.080
N10 HN10 1.000 0.970
C14 H14 1.080 1.080
C15 H15 1.080 1.080
C16 H16 1.080 1.081
C20 H20 1.080 1.081
C24 H24 1.100 1.090
C24 H24A 1.100 1.090
C25 H25 1.100 1.090
C25 H25A 1.100 1.090
C27 H27 1.100 1.090
C28 H28 1.100 1.090
C28 H28A 1.100 1.090
N29 HN29 1.000 1.010
N29 HN2A 1.000 1.008
C30 H30 1.099 1.090
C30 H30A 1.100 1.091

Bond Angles for 4YM

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C01 C02 O03 118.1 109.4
C02 C01 H01 109.5 109.5
C02 C01 H01A 109.5 109.5
C02 C01 H01B 109.5 109.5
C01 C02 H02 107.3 109.5
C01 C02 H02A 107.3 109.5
C02 O03 C04 118.5 117.0
O03 C02 H02 107.3 109.5
O03 C02 H02A 107.3 109.5
O03 C04 O05 120.0 120.0
O03 C04 C06 118.3 120.0
O05 C04 C06 121.7 120.0
C04 C06 C07 115.7 120.5
C04 C06 C22 124.7 120.5
C07 C06 C22 119.6 118.9
C06 C07 N08 120.9 121.4
C06 C07 H07 119.5 119.3
C06 C22 C21 118.8 117.8
C06 C22 N23 120.0 121.1
C07 N08 C09 121.0 122.1
N08 C07 H07 119.5 119.3
N08 C09 N10 128.0 133.0
N08 C09 C21 121.9 120.3
N10 C09 C21 110.1 106.7
C09 N10 N11 108.2 109.5
C09 N10 HN10 125.9 125.2
C09 C21 C12 103.6 106.5
C09 C21 C22 117.8 119.4
N10 N11 C12 108.4 109.8
N11 N10 HN10 125.9 125.2
N11 C12 C13 123.5 126.3
N11 C12 C21 109.7 107.4
C13 C12 C21 126.7 126.3
C12 C13 C14 121.1 120.0
C12 C13 C20 119.4 120.1
C12 C21 C22 138.6 134.0
C14 C13 C20 119.5 119.9
C13 C14 C15 120.5 120.1
C13 C14 H14 119.7 120.0
C13 C20 C17 119.9 119.7
C13 C20 H20 120.0 120.1
C14 C15 C16 119.9 120.3
C15 C14 H14 119.7 119.9
C14 C15 H15 120.0 119.8
C15 C16 C17 119.7 120.1
C16 C15 H15 120.0 119.9
C15 C16 H16 120.2 119.9
C16 C17 C18 119.5 120.1
C16 C17 C20 120.4 119.8
C17 C16 H16 120.1 120.0
C18 C17 C20 120.1 120.1
C17 C18 N19 179.8 180.0
C17 C20 H20 120.1 120.1
C21 C22 N23 121.2 121.1
C22 N23 C24 109.3 111.0
C22 N23 C30 113.2 111.0
C24 N23 C30 113.2 110.7
N23 C24 C25 110.1 109.3
N23 C24 H24 109.3 109.5
N23 C24 H24A 109.3 109.5
N23 C30 C27 112.9 109.3
N23 C30 H30 108.6 109.6
N23 C30 H30A 108.6 109.5
C24 C25 O26 111.1 109.3
C25 C24 H24 109.3 109.5
C25 C24 H24A 109.3 109.5
C24 C25 H25 109.1 109.5
C24 C25 H25A 109.1 109.5
C25 O26 C27 114.3 113.7
O26 C25 H25 109.0 109.5
O26 C25 H25A 109.1 109.5
O26 C27 C28 110.4 109.5
O26 C27 C30 112.9 109.2
O26 C27 H27 108.6 109.5
C28 C27 C30 110.0 109.5
C27 C28 N29 109.3 109.5
C28 C27 H27 107.3 109.5
C27 C28 H28 109.5 109.5
C27 C28 H28A 109.5 109.5
C30 C27 H27 107.4 109.6
C27 C30 H30 108.6 109.5
C27 C30 H30A 108.6 109.5
N29 C28 H28 109.5 109.4
N29 C28 H28A 109.5 109.5
C28 N29 HN29 109.5 111.0
C28 N29 HN2A 109.5 111.0
H01 C01 H01A 109.4 109.4
H01 C01 H01B 109.4 109.5
H01A C01 H01B 109.5 109.4
H02 C02 H02A 109.5 109.5
H24 C24 H24A 109.5 109.5
H25 C25 H25A 109.5 109.5
H28 C28 H28A 109.5 109.4
HN29 N29 HN2A 109.5 111.0
H30 C30 H30A 109.5 109.5

Torsion Angles for 4YM

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C01 C02 O03 C04 140.1 180.0
O03 C02 C01 H02 238.8 240.0
O03 C02 C01 H02A 121.2 120.0
H01 C01 C02 H01A 240.0 240.0
H01 C01 C02 H01B 120.0 120.1
H01A C01 C02 H01B 240.0 240.0
H02 C02 C01 H02A 242.5 240.0
O03 C02 C01 H01 180.0 180.0
O03 C02 C01 H01A 300.0 300.0
O03 C02 C01 H01B 60.0 60.0
C01 C02 O03 H02 121.2 120.0
C01 C02 O03 H02A 238.8 240.0
C02 O03 C04 O05 59.8 0.0
C02 O03 C04 C06 242.3 180.0
H02 C02 O03 H02A 117.5 120.0
C04 O03 C02 H02 18.9 60.0
C04 O03 C02 H02A 261.4 300.0
O05 C04 O03 C06 177.5 180.0
O03 C04 C06 C07 37.9 320.9
O03 C04 C06 C22 218.4 140.6
O03 C04 O05 C06 182.6 180.0
O05 C04 C06 C07 220.4 140.9
O05 C04 C06 C22 40.9 320.6
O03 C04 C06 O05 177.5 180.0
C07 C06 C04 C22 179.6 180.3
C04 C06 C07 N08 180.1 180.0
C04 C06 C07 H07 0.1 359.9
C04 C06 C22 C21 180.3 179.7
C04 C06 C22 N23 359.1 360.0
C04 C06 C07 C22 180.4 179.7
C07 C06 C22 C21 0.8 359.4
C07 C06 C22 N23 179.5 179.7
C06 C07 N08 C09 359.9 359.9
N08 C07 C06 H07 180.0 180.1
C04 C06 C22 C07 179.5 180.3
C22 C06 C07 N08 359.7 0.4
C22 C06 C07 H07 179.7 180.3
C09 C21 C22 C06 359.2 0.5
C12 C21 C22 C06 180.2 180.2
C21 C22 C06 N23 181.3 179.7
C06 C22 N23 C24 285.0 315.3
C06 C22 N23 C30 52.3 78.9
N08 C07 C06 C22 359.7 0.4
C06 C07 N08 H07 180.0 179.9
C07 N08 C09 N10 180.0 180.0
C07 N08 C09 C21 0.1 0.0
C09 N08 C07 H07 179.9 180.0
N10 C09 N08 C21 179.9 180.0
N08 C09 N10 N11 180.1 180.0
N08 C09 N10 HN10 0.1 360.0
N08 C09 C21 C12 179.7 180.0
N08 C09 C21 C22 0.3 359.7
N08 C09 N10 C21 180.1 180.0
N10 C09 C21 C12 359.8 360.0
N10 C09 C21 C22 180.4 179.7
C09 N10 N11 C12 0.3 360.0
N11 N10 C09 HN10 180.0 180.1
C06 C22 C21 C09 359.2 0.5
N08 C09 C21 N10 179.9 180.0
C21 C09 N10 N11 360.0 0.0
C21 C09 N10 HN10 180.0 179.9
N11 C12 C21 C09 0.4 360.0
C13 C12 C21 C09 179.4 180.0
C12 C21 C09 C22 179.4 180.3
C09 C21 C22 N23 180.5 180.3
N11 N10 C09 C21 360.0 0.0
C09 N10 N11 HN10 180.0 179.9
N10 N11 C12 C13 180.6 180.0
N10 N11 C12 C21 359.6 0.0
C09 C21 C12 N11 0.4 360.0
C12 N11 N10 HN10 180.3 180.0
C13 C12 N11 C21 181.0 180.0
N11 C12 C13 C14 194.9 126.9
N11 C12 C13 C20 15.3 306.6
N11 C12 C21 C22 179.6 180.3
C09 C21 C12 C13 179.4 180.0
N11 C12 C13 C21 178.8 180.0
C13 C12 C21 C22 358.5 0.3
C14 C13 C12 C20 179.7 180.2
C12 C13 C14 C15 180.3 180.0
C12 C13 C14 H14 0.3 360.0
C12 C13 C20 C17 179.8 179.7
C12 C13 C20 H20 359.7 360.0
C06 C22 C21 C12 180.2 180.2
C09 C21 C12 C22 180.9 179.7
N11 C12 C21 C13 181.1 180.0
C21 C12 C13 C14 16.1 306.8
C21 C12 C13 C20 196.5 126.6
C12 C21 C22 N23 1.5 359.9
C14 C13 C12 C21 16.1 306.8
C12 C13 C14 C20 180.3 179.8
C14 C13 C20 C17 0.1 359.5
C14 C13 C20 H20 180.1 179.8
C13 C14 C15 C16 359.9 0.1
C15 C14 C13 H14 180.0 180.0
C13 C14 C15 H15 179.8 180.0
C20 C13 C12 C21 196.5 126.6
C12 C13 C20 C14 179.7 180.2
C20 C13 C14 C15 0.0 0.2
C20 C13 C14 H14 180.0 180.2
C16 C17 C20 C13 359.9 0.5
C18 C17 C20 C13 179.9 180.2
C17 C20 C13 H20 180.0 179.7
C15 C14 C13 C20 0.0 0.2
C13 C14 C15 H14 180.0 180.0
C14 C15 C16 C17 0.1 359.9
C16 C15 C14 H15 180.0 180.1
C14 C15 C16 H16 180.2 179.9
C16 C15 C14 H14 179.9 180.1
C14 C15 C16 H15 180.0 179.9
C15 C16 C17 C18 180.0 180.1
C15 C16 C17 C20 360.0 359.8
C17 C16 C15 H16 180.0 180.0
C13 C20 C17 C16 359.9 0.5
C17 C16 C15 H15 180.2 180.0
C15 C16 C17 H16 180.0 180.0
C18 C17 C16 C20 180.0 180.3
C16 C17 C18 N19 10.9 307.9
C16 C17 C20 H20 179.9 180.3
C13 C20 C17 C18 179.9 180.2
C16 C17 C18 C20 180.0 179.7
C18 C17 C16 H16 360.0 0.1
C18 C17 C20 H20 359.9 360.0
C13 C20 C17 H20 180.0 180.3
C16 C17 C20 C18 180.0 180.3
C20 C17 C16 H16 180.0 179.8
C20 C17 C18 N19 190.9 128.2
N19 C18 C17 C20 190.9 128.2
C06 C22 C21 N23 178.7 180.3
C09 C21 C22 C12 179.1 180.4
C21 C22 N23 C24 103.7 135.5
C21 C22 N23 C30 231.0 259.1
C06 C22 N23 C21 181.3 179.7
C24 N23 C22 C30 232.8 236.4
C22 N23 C24 C25 183.4 182.4
C22 N23 C24 H24 303.5 302.4
C22 N23 C24 H24A 63.3 62.4
C22 N23 C30 C27 184.3 177.6
C22 N23 C30 H30 304.8 297.6
C22 N23 C30 H30A 63.8 57.7
C22 N23 C24 C30 127.3 123.7
C24 N23 C30 C27 309.5 301.3
C24 N23 C30 H30 70.0 61.3
C24 N23 C30 H30A 189.0 181.4
N23 C24 C25 O26 303.1 303.1
C25 C24 N23 H24 239.9 240.0
C25 C24 N23 H24A 120.1 119.9
N23 C24 C25 H25 63.3 63.1
N23 C24 C25 H25A 182.8 183.2
H24 C24 N23 H24A 240.2 239.9
C22 N23 C30 C24 234.8 236.3
C30 N23 C24 C25 56.2 58.6
C30 N23 C24 H24 176.3 178.6
C30 N23 C24 H24A 296.1 298.7
O26 C27 C30 N23 44.9 56.9
C28 C27 C30 N23 281.1 297.0
N23 C30 C27 H27 164.6 176.9
C27 C30 N23 H30 239.5 240.0
C27 C30 N23 H30A 120.5 119.9
H30 C30 N23 H30A 241.0 239.9
C25 C24 N23 C30 56.2 58.6
N23 C24 C25 H24 120.1 120.0
N23 C24 C25 H24A 239.9 240.1
C24 C25 O26 C27 53.6 58.6
O26 C25 C24 H25 239.8 240.1
O26 C25 C24 H25A 120.3 119.9
H24 C24 C25 H24A 119.8 120.1
H25 C25 C24 H25A 240.5 239.9
O26 C25 C24 H24 183.0 183.2
O26 C25 C24 H24A 63.2 63.1
C24 C25 O26 H25 120.3 119.9
C24 C25 O26 H25A 239.7 240.1
C25 O26 C27 C28 76.1 61.3
C25 O26 C27 C30 312.6 301.4
C25 O26 C27 H27 193.6 181.4
H25 C25 O26 H25A 119.5 120.1
N23 C30 C27 O26 44.9 56.9
C27 O26 C25 H25 293.3 298.7
C27 O26 C25 H25A 173.8 178.6
C28 C27 O26 C30 123.6 119.9
O26 C27 C28 N29 192.8 66.2
C28 C27 O26 H27 242.6 239.9
O26 C27 C28 H28 312.8 186.2
O26 C27 C28 H28A 72.9 306.1
C30 C27 O26 H27 119.0 120.0
O26 C27 C30 H30 284.4 296.8
O26 C27 C30 H30A 165.4 176.8
N23 C30 C27 C28 281.1 297.0
O26 C27 C28 C30 234.8 240.3
O26 C27 C28 H27 118.2 120.1
C30 C27 C28 H27 243.4 239.8
C28 C27 C30 H30 160.6 177.0
C28 C27 C30 H30A 41.6 56.9
N29 C28 C27 H28 240.0 240.0
N29 C28 C27 H28A 120.0 120.1
C27 C28 N29 HN29 180.0 56.0
C27 C28 N29 HN2A 300.0 180.0
H28 C28 C27 H28A 239.9 240.1
N23 C30 C27 H30 120.5 120.0
N23 C30 C27 H30A 239.5 240.1
O26 C27 C30 C28 123.8 119.9
O26 C27 C30 H27 240.3 240.0
C30 C27 C28 N29 318.1 185.9
C28 C27 C30 H27 116.5 120.1
C30 C27 C28 H28 78.0 305.9
C30 C27 C28 H28A 198.1 65.8
H30 C30 C27 H30A 119.0 120.1
N29 C28 C27 C30 318.1 185.9
N29 C28 C27 H27 74.6 306.1
C27 C28 N29 H28 120.0 120.0
C27 C28 N29 H28A 240.0 239.9
H28 C28 N29 H28A 120.0 119.9
HN29 N29 C28 HN2A 240.0 236.0
H01 C01 C02 O03 180.0 180.0
C02 C01 H01 H01A 120.0 120.0
C02 C01 H01 H01B 240.0 239.9
H01 C01 C02 H02 301.2 300.0
H01 C01 C02 H02A 58.8 60.0
H01A C01 H01 H01B 120.0 120.0
H01A C01 C02 O03 300.0 300.0
C02 C01 H01A H01 240.0 240.0
C02 C01 H01A H01B 120.0 120.0
H01A C01 C02 H02 61.2 60.0
H01A C01 C02 H02A 178.7 180.0
H01 C01 H01A H01B 240.0 240.0
H01B C01 C02 O03 60.0 60.0
C02 C01 H01B H01 120.0 120.0
C02 C01 H01B H01A 240.0 240.0
H01B C01 C02 H02 181.3 180.0
H01B C01 C02 H02A 298.8 300.0
H01 C01 H01B H01A 120.0 119.9
C01 C02 H02 O03 232.2 240.0
H02 C02 C01 H01 301.2 300.0
H02 C02 C01 H01A 61.2 60.0
H02 C02 C01 H01B 181.3 180.0
C01 C02 H02 H02A 116.1 120.0
H02 C02 O03 C04 18.9 60.0
O03 C02 H02 H02A 243.9 240.0
C01 C02 H02A O03 127.8 120.0
H02A C02 C01 H01 58.8 60.0
H02A C02 C01 H01A 178.7 180.0
H02A C02 C01 H01B 298.8 300.0
C01 C02 H02A H02 243.9 240.0
H02A C02 O03 C04 261.4 300.0
O03 C02 H02A H02 116.1 120.0
H07 C07 C06 C22 179.7 180.3
C06 C07 H07 N08 180.0 180.1
H07 C07 N08 C09 179.9 180.0
HN10 N10 C09 C21 180.0 179.9
C09 N10 HN10 N11 180.0 180.1
HN10 N10 N11 C12 180.3 180.0
H14 C14 C13 C20 180.0 180.2
C13 C14 H14 C15 180.0 180.0
H14 C14 C15 C16 179.9 180.1
H14 C14 C15 H15 359.9 360.0
C14 C15 H15 C16 180.0 180.1
H15 C15 C14 H14 359.9 360.0
H15 C15 C16 C17 180.2 180.0
H15 C15 C16 H16 0.2 0.0
C15 C16 H16 C17 180.0 180.0
H16 C16 C15 H15 0.2 0.0
H16 C16 C17 C18 360.0 0.1
H16 C16 C17 C20 180.0 179.8
C13 C20 H20 C17 180.0 179.7
H24 C24 N23 C30 176.3 178.6
N23 C24 H24 C25 239.4 240.2
N23 C24 H24 H24A 119.7 120.1
H24 C24 C25 O26 183.0 183.2
C25 C24 H24 H24A 240.3 239.9
H24 C24 C25 H25 303.2 303.1
H24 C24 C25 H25A 62.7 63.2
H24A C24 N23 C30 296.1 298.7
N23 C24 H24A C25 120.6 119.8
N23 C24 H24A H24 240.3 239.9
H24A C24 C25 O26 63.2 63.1
C25 C24 H24A H24 119.7 120.1
H24A C24 C25 H25 183.4 183.0
H24A C24 C25 H25A 302.9 303.2
C24 C25 H25 O26 238.5 240.2
H25 C25 C24 H24 303.2 303.1
H25 C25 C24 H24A 183.4 183.0
C24 C25 H25 H25A 119.2 120.1
H25 C25 O26 C27 293.3 298.7
O26 C25 H25 H25A 240.8 239.9
C24 C25 H25A O26 121.5 119.8
H25A C25 C24 H24 62.7 63.2
H25A C25 C24 H24A 302.9 303.2
C24 C25 H25A H25 240.7 239.9
H25A C25 O26 C27 173.8 178.6
O26 C25 H25A H25 119.2 120.1
O26 C27 H27 C28 240.6 239.9
O26 C27 H27 C30 122.4 119.8
C28 C27 H27 C30 241.8 239.9
H27 C27 C28 N29 74.6 306.1
H27 C27 C28 H28 194.6 66.1
H27 C27 C28 H28A 314.7 186.0
H27 C27 C30 H30 44.1 56.8
H27 C27 C30 H30A 285.1 296.8
H28 C28 C27 C30 78.0 305.9
C27 C28 H28 N29 240.1 240.0
H28 C28 C27 H27 194.6 66.1
C27 C28 H28 H28A 120.1 120.0
N29 C28 H28 H28A 240.0 240.0
H28 C28 N29 HN29 60.0 296.0
H28 C28 N29 HN2A 180.0 60.0
H28A C28 C27 C30 198.1 65.8
C27 C28 H28A N29 119.8 120.1
H28A C28 C27 H27 314.7 186.0
C27 C28 H28A H28 239.9 240.0
N29 C28 H28A H28 120.1 119.9
H28A C28 N29 HN29 300.0 176.1
H28A C28 N29 HN2A 60.0 300.1
HN29 N29 C28 H28 60.0 296.0
HN29 N29 C28 H28A 300.0 176.1
C28 N29 HN29 HN2A 120.0 124.0
HN2A N29 C28 H28 180.0 60.0
HN2A N29 C28 H28A 60.0 300.1
C28 N29 HN2A HN29 240.0 236.0
N23 C30 H30 C27 236.9 240.2
N23 C30 H30 H30A 118.4 120.1
H30 C30 C27 H27 44.1 56.8
C27 C30 H30 H30A 241.6 239.9
N23 C30 H30A C27 123.1 119.8
N23 C30 H30A H30 241.5 239.9
H30A C30 C27 H27 285.1 296.8
C27 C30 H30A H30 118.4 120.1