PDB Chemical Component LMD

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 LMD

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O4 C4 1.421 1.429
O6 C6 1.426 1.430
C5 C6 1.553 1.530
C5 C4 1.558 1.531
C5 O5 1.458 1.429
C4 C3 1.553 1.532
C3 O3 1.418 1.428
C3 C2 1.545 1.533
O5 C1 1.453 1.429
O2 C2 1.430 1.428
C2 C1 1.554 1.530
C1 O1 1.439 1.429
O1 CAP 1.445 1.430
OAU CAO 1.425 1.429
CAP CAO 1.557 1.532
CAP CAQ 1.564 1.531
CAR CAQ 1.560 1.530
CAR OAW 1.427 1.430
CAO CAN 1.539 1.532
CAQ OAV 1.456 1.429
CAN OAT 1.420 1.429
CAN CAM 1.543 1.531
OAV CAM 1.449 1.429
CAM OAS 1.440 1.429
OAS CAX 1.449 1.429
CAX CAY 1.546 1.531
CAY CAZ 1.549 1.530
CAZ CBA 1.551 1.531
CBA CBB 1.549 1.530
CBB CBC 1.551 1.531
CBC CBD 1.553 1.530
CBD CBE 1.553 1.531
CBE CBF 1.554 1.530
CBF CBG 1.542 1.531
CBG CBH 1.544 1.530
CBH CBI 1.538 1.531
CBI CBJ 1.538 1.529
CBJ CBK 1.540 1.530
CBK H1 1.100 1.091
CBK H2 1.100 1.090
CBK H3 1.100 1.090
CBJ H4 1.100 1.090
CBJ H5 1.100 1.089
CBI H6 1.100 1.090
CBI H7 1.100 1.091
CBH H8 1.100 1.090
CBH H9 1.100 1.090
CBG H10 1.100 1.090
CBG H11 1.100 1.090
CBF H12 1.099 1.090
CBF H13 1.100 1.090
CBE H14 1.100 1.089
CBE H15 1.101 1.090
CBD H16 1.100 1.090
CBD H17 1.100 1.090
CBC H18 1.100 1.089
CBC H19 1.100 1.090
CBB H20 1.100 1.089
CBB H21 1.100 1.090
CBA H22 1.100 1.090
CBA H23 1.100 1.090
CAZ H24 1.100 1.090
CAZ H25 1.100 1.090
CAY H26 1.100 1.090
CAY H27 1.100 1.090
CAX H28 1.100 1.090
CAX H29 1.100 1.089
CAM H30 1.100 1.090
CAN H31 1.100 1.090
OAT H32 0.950 0.967
CAO H33 1.100 1.090
OAU H34 0.949 0.967
CAQ H35 1.100 1.089
CAR H36 1.101 1.089
CAR H37 1.100 1.090
OAW H38 0.950 0.967
CAP H39 1.101 1.090
C1 H40 1.100 1.090
C5 H41 1.100 1.090
C6 H42 1.100 1.090
C6 H43 1.100 1.090
O6 H44 0.950 0.967
C4 H45 1.100 1.090
O4 H46 0.950 0.967
C3 H47 1.100 1.090
O3 H48 0.950 0.967
C2 H49 1.100 1.090
O2 H50 0.950 0.967

Bond Angles for LMD

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O4 C4 C3 108.8 109.5
O4 C4 H45 109.8 109.6
O6 C6 H42 109.1 109.4
O6 C6 H43 109.1 109.5
C6 C5 C4 113.5 109.5
C6 C5 H41 107.7 109.5
C5 C6 H42 109.1 109.5
C5 C6 H43 109.1 109.4
C5 C4 C3 108.0 109.2
C4 C5 H41 107.6 109.4
C5 C4 H45 108.0 109.5
C4 C3 O3 110.7 109.6
C4 C3 C2 107.4 109.0
C3 C4 H45 108.1 109.5
C4 C3 H47 108.6 109.5
O3 C3 C2 111.0 109.6
O3 C3 H47 110.4 109.6
C3 O3 H48 109.5 114.0
C2 C3 H47 108.7 109.6
C3 C2 H49 106.9 109.5
O5 C1 H40 106.4 109.5
O2 C2 H49 108.3 109.6
C2 C1 H40 105.3 109.5
O1 CAP H39 109.1 109.6
OAU CAO H33 110.3 109.5
CAP CAO H33 108.5 109.6
CAP CAQ H35 107.8 109.5
CAR CAQ H35 107.8 109.5
OAW CAR H36 108.7 109.4
OAW CAR H37 108.7 109.4
CAR OAW H38 109.5 114.0
CAO CAN H31 108.3 109.6
OAT CAN H31 109.9 109.5
CAN OAT H32 109.5 114.0
CAN CAM H30 103.9 109.5
OAV CAM H30 104.8 109.5
OAS CAX H28 109.4 109.5
OAS CAX H29 109.4 109.5
CAX CAY H26 108.6 109.4
CAX CAY H27 108.6 109.5
CAY CAZ H24 108.3 109.5
CAY CAZ H25 108.3 109.5
CAZ CBA H22 109.1 109.4
CAZ CBA H23 109.1 109.5
CBA CBB H20 108.3 109.5
CBA CBB H21 108.3 109.5
CBB CBC H18 109.2 109.5
CBB CBC H19 109.2 109.5
CBC CBD H16 108.4 109.5
CBC CBD H17 108.4 109.5
CBD CBE H14 108.8 109.5
CBD CBE H15 108.7 109.5
CBE CBF H12 109.0 109.5
CBE CBF H13 109.0 109.5
CBF CBG H10 108.7 109.4
CBF CBG H11 108.8 109.5
CBG CBH H8 109.2 109.5
CBG CBH H9 109.2 109.5
CBH CBI H6 109.8 109.5
CBH CBI H7 109.8 109.5
CBI CBJ H4 109.7 109.5
CBI CBJ H5 109.7 109.5
CBJ CBK H1 109.5 109.5
CBJ CBK H2 109.5 109.5
CBJ CBK H3 109.5 109.5
H1 CBK H2 109.5 109.5
H1 CBK H3 109.5 109.5
H2 CBK H3 109.5 109.5
H4 CBJ H5 109.5 109.4
H6 CBI H7 109.5 109.5
H8 CBH H9 109.5 109.5
H10 CBG H11 109.5 109.5
H12 CBF H13 109.5 109.5
H14 CBE H15 109.5 109.5
H16 CBD H17 109.5 109.5
H18 CBC H19 109.5 109.5
H20 CBB H21 109.5 109.5
H22 CBA H23 109.5 109.5
H24 CAZ H25 109.5 109.5
H26 CAY H27 109.5 109.5
H28 CAX H29 109.5 109.5
H36 CAR H37 109.4 109.5
H42 C6 H43 109.5 109.5

Torsion Angles for LMD

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C5 C4 O4 C3 120.6 119.7
O4 C4 C5 H41 311.6 302.4
C5 C4 O4 H45 238.7 239.9
O4 C4 C3 O3 318.4 296.8
O4 C4 C3 C2 197.1 176.9
C3 C4 O4 H45 118.1 120.1
O4 C4 C3 H47 79.8 57.0
O6 C6 C5 C4 196.8 185.0
O6 C6 C5 H41 315.7 305.0
C5 C6 O6 H42 239.8 120.0
C5 C6 O6 H43 120.2 240.0
H42 C6 O6 H43 240.4 120.0
O6 C6 C5 H42 120.2 240.0
O6 C6 C5 H43 239.8 120.0
C6 C5 C4 C3 191.6 182.4
C4 C5 C6 H41 241.0 240.0
C6 C5 C4 H45 308.2 302.3
H42 C6 C5 H43 119.6 240.0
O4 C4 C5 C3 239.0 240.1
O4 C4 C5 H45 122.3 120.2
C6 C5 C4 H41 119.0 120.0
C4 C5 C6 H42 76.6 305.0
C4 C5 C6 H43 317.0 65.1
C5 C4 C3 O3 194.2 176.8
C5 C4 C3 C2 72.9 56.9
C3 C4 C5 H45 243.3 240.1
C5 C4 C3 H47 315.6 297.0
C5 O5 C1 H40 305.4 178.9
O4 C4 C3 H45 240.8 239.9
C3 C4 C5 H41 72.6 62.4
C5 C4 C3 H45 116.6 119.9
O3 C3 C4 C2 121.3 119.9
O3 C3 C4 H47 238.6 239.8
C4 C3 O3 H48 180.0 180.0
C2 C3 C4 H47 117.3 119.9
C4 C3 C2 H49 82.8 62.9
C4 C3 O3 C2 240.8 240.4
O3 C3 C4 H45 77.6 56.9
C4 C3 O3 H47 120.3 120.2
C2 C3 O3 H47 239.4 239.8
O3 C3 C2 H49 321.6 303.1
C4 C3 C2 O3 121.2 119.9
C2 C3 C4 H45 316.3 297.0
C4 C3 C2 H47 242.7 240.1
O3 C3 C2 H47 121.6 120.2
C2 C3 O3 H48 299.1 299.6
O2 C2 C3 H49 118.7 120.2
C3 C2 C1 H40 85.7 177.6
C2 C1 O5 H40 115.9 120.0
O2 C2 C3 H47 318.8 303.0
C3 C2 O2 H49 242.1 239.9
O2 C2 C1 H40 211.3 297.5
O5 C1 C2 H40 243.5 240.0
C1 O1 CAP H39 285.1 324.7
O1 CAP CAO H33 46.1 57.0
O1 CAP CAQ H35 313.5 302.4
CAP CAO OAU H33 120.3 120.3
OAU CAO CAN H31 304.7 303.0
OAU CAO CAP H33 238.6 239.7
CAP CAO CAN H31 65.9 63.0
CAQ CAP CAO H33 284.5 297.2
CAR CAQ CAP H35 118.0 120.1
CAP CAQ CAR H35 242.0 239.9
OAW CAR CAQ H35 305.8 304.3
H36 CAR OAW H37 119.1 120.0
OAT CAN CAO H31 118.2 120.1
CAO CAN OAT H32 180.0 179.6
CAO CAN CAM H30 307.5 297.6
CAQ OAV CAM H30 50.0 58.8
CAO CAN OAT H31 242.8 239.8
OAT CAN CAM H30 66.9 57.5
OAV CAM CAN H30 111.2 120.0
CAN CAM OAV H30 249.5 240.0
CAM OAS CAX H28 14.6 60.1
CAM OAS CAX H29 134.5 300.0
OAS CAX CAY H26 318.6 60.0
OAS CAX CAY H27 77.6 300.0
H28 CAX OAS H29 240.1 120.0
CAX CAY CAZ H24 194.0 60.0
CAX CAY CAZ H25 312.7 300.0
H26 CAY CAX H27 241.0 120.0
CAY CAZ CBA H22 317.8 60.1
CAY CAZ CBA H23 77.4 300.0
H24 CAZ CAY H25 241.3 120.0
CAZ CBA CBB H20 350.7 60.1
CAZ CBA CBB H21 109.4 300.0
H22 CBA CAZ H23 240.4 120.0
CBA CBB CBC H18 294.2 60.1
CBA CBB CBC H19 53.9 300.0
H20 CBB CBA H21 241.4 120.1
CBB CBC CBD H16 270.4 60.0
CBB CBC CBD H17 29.1 299.9
H18 CBC CBB H19 240.3 120.1
CBC CBD CBE H14 283.7 60.0
CBC CBD CBE H15 42.8 300.0
H16 CBD CBC H17 241.3 120.1
CBD CBE CBF H12 293.6 60.0
CBD CBE CBF H13 53.1 300.0
H14 CBE CBD H15 240.9 120.1
CBE CBF CBG H10 255.1 60.1
CBE CBF CBG H11 14.2 300.0
H12 CBF CBE H13 240.6 120.0
CBF CBG CBH H8 236.2 60.0
CBF CBG CBH H9 355.9 300.0
H10 CBG CBF H11 240.9 120.0
CBG CBH CBI H6 304.2 60.0
CBG CBH CBI H7 64.6 300.0
H8 CBH CBG H9 240.4 120.0
CBH CBI CBJ H4 341.6 60.0
CBH CBI CBJ H5 101.9 300.0
H6 CBI CBH H7 239.6 120.0
CBI CBJ CBK H1 180.0 300.0
CBI CBJ CBK H2 300.0 60.0
CBI CBJ CBK H3 60.0 180.0
H4 CBJ CBI H5 239.7 120.0
H1 CBK CBJ H2 240.0 240.0
H1 CBK CBJ H3 120.0 120.0
H2 CBK CBJ H3 240.0 240.0
CBJ CBK H1 H2 120.0 120.0
CBJ CBK H1 H3 240.0 240.0
H2 CBK H1 H3 120.0 120.0
CBJ CBK H2 H1 240.0 240.0
CBJ CBK H2 H3 120.0 120.0
H1 CBK H2 H3 240.0 240.0
CBJ CBK H3 H1 120.0 120.0
CBJ CBK H3 H2 240.0 240.0
H1 CBK H3 H2 120.0 120.0
CBI CBJ H4 H5 120.4 239.9
H4 CBJ CBK H1 60.2 60.0
H4 CBJ CBK H2 180.2 180.0
H4 CBJ CBK H3 300.2 300.0
CBI CBJ H5 H4 239.6 120.0
H5 CBJ CBK H1 299.9 179.9
H5 CBJ CBK H2 59.9 299.9
H5 CBJ CBK H3 179.9 59.9
CBH CBI H6 H7 120.6 240.0
H6 CBI CBJ H4 221.8 180.0
H6 CBI CBJ H5 342.1 60.0
CBH CBI H7 H6 239.4 120.0
H7 CBI CBJ H4 101.4 300.0
H7 CBI CBJ H5 221.7 180.0
CBG CBH H8 H9 119.4 240.0
H8 CBH CBI H6 184.0 180.0
H8 CBH CBI H7 304.5 60.0
CBG CBH H9 H8 240.6 120.0
H9 CBH CBI H6 64.4 300.0
H9 CBH CBI H7 184.8 180.0
CBF CBG H10 H11 118.7 240.0
H10 CBG CBH H8 115.8 179.9
H10 CBG CBH H9 235.5 59.9
CBF CBG H11 H10 241.3 120.0
H11 CBG CBH H8 356.7 300.0
H11 CBG CBH H9 116.3 180.0
CBE CBF H12 H13 119.1 240.0
H12 CBF CBG H10 134.8 180.0
H12 CBF CBG H11 253.9 60.0
CBE CBF H13 H12 240.9 120.0
H13 CBF CBG H10 15.4 300.0
H13 CBF CBG H11 134.5 180.0
CBD CBE H14 H15 118.7 240.0
H14 CBE CBF H12 173.2 180.0
H14 CBE CBF H13 292.6 59.9
CBD CBE H15 H14 241.3 120.0
H15 CBE CBF H12 54.0 300.0
H15 CBE CBF H13 173.5 180.0
CBC CBD H16 H17 118.1 239.9
H16 CBD CBE H14 163.0 180.0
H16 CBD CBE H15 282.2 60.0
CBC CBD H17 H16 241.9 120.1
H17 CBD CBE H14 44.3 300.0
H17 CBD CBE H15 163.4 180.0
CBB CBC H18 H19 119.5 240.0
H18 CBC CBD H16 150.2 180.0
H18 CBC CBD H17 269.0 59.9
CBB CBC H19 H18 240.5 120.0
H19 CBC CBD H16 30.6 300.0
H19 CBC CBD H17 149.3 180.0
CBA CBB H20 H21 117.9 239.9
H20 CBB CBC H18 173.5 180.0
H20 CBB CBC H19 293.2 59.9
CBA CBB H21 H20 242.1 120.1
H21 CBB CBC H18 54.8 300.0
H21 CBB CBC H19 174.5 180.0
CAZ CBA H22 H23 119.4 240.0
H22 CBA CBB H20 230.5 180.0
H22 CBA CBB H21 349.2 59.9
CAZ CBA H23 H22 240.6 120.0
H23 CBA CBB H20 110.9 300.1
H23 CBA CBB H21 229.5 180.0
CAY CAZ H24 H25 118.0 240.0
H24 CAZ CBA H22 197.2 180.0
H24 CAZ CBA H23 316.8 60.0
CAY CAZ H25 H24 242.1 120.0
H25 CAZ CBA H22 78.5 300.0
H25 CAZ CBA H23 198.1 180.0
CAX CAY H26 H27 118.4 240.0
H26 CAY CAZ H24 73.5 180.0
H26 CAY CAZ H25 192.2 60.0
CAX CAY H27 H26 241.6 120.0
H27 CAY CAZ H24 314.6 300.0
H27 CAY CAZ H25 73.3 180.0
OAS CAX H28 H29 119.9 239.9
H28 CAX CAY H26 198.6 180.0
H28 CAX CAY H27 317.5 60.0
OAS CAX H29 H28 240.1 120.0
H29 CAX CAY H26 78.6 300.0
H29 CAX CAY H27 197.6 180.0
H31 CAN OAT H32 297.2 299.8
H31 CAN CAM H30 188.9 177.6
H32 OAT CAN H31 297.2 299.8
H33 CAO CAN H31 185.9 182.8
H34 OAU CAO H33 59.7 60.2
H36 CAR CAQ H35 66.3 64.2
OAW CAR H36 H37 241.4 240.1
H36 CAR OAW H38 59.5 60.0
H37 CAR CAQ H35 185.3 184.3
OAW CAR H37 H36 118.6 119.9
H37 CAR OAW H38 300.5 300.0
H38 OAW CAR H36 59.5 60.0
H38 OAW CAR H37 300.5 300.0
H39 CAP CAO H33 165.8 177.2
H39 CAP CAQ H35 196.0 182.2
C6 C5 H41 C4 237.4 240.0
H41 C5 C6 H42 195.5 65.0
H41 C5 C6 H43 76.0 185.0
H41 C5 C4 C3 72.6 62.4
H41 C5 C4 H45 189.3 182.3
O6 C6 H42 H43 119.3 240.0
H42 C6 C5 C4 76.6 305.0
H42 C6 C5 H41 195.5 65.0
C5 C6 H42 H43 240.7 120.0
O6 C6 H43 H42 240.7 120.0
H43 C6 C5 C4 317.0 65.1
H43 C6 C5 H41 76.0 185.0
C5 C6 H43 H42 119.3 240.0
H44 O6 C6 H42 300.2 60.1
H44 O6 C6 H43 59.7 300.0
O4 C4 H45 C3 118.6 120.1
C5 C4 H45 C3 243.4 240.3
H45 C4 C5 H41 189.3 182.3
H45 C4 C3 O3 77.6 56.9
H45 C4 C3 C2 316.3 297.0
H45 C4 C3 H47 199.0 177.1
H46 O4 C4 C3 59.4 60.3
H46 O4 C4 H45 301.3 300.2
C4 C3 H47 O3 238.4 239.8
C4 C3 H47 C2 116.5 119.6
H47 C3 C4 H45 199.0 177.1
O3 C3 H47 C2 238.0 239.8
H47 C3 O3 H48 59.7 59.8
H47 C3 C2 H49 200.0 182.8
H48 O3 C3 C2 299.1 299.6
H48 O3 C3 H47 59.7 59.8
H49 C2 C3 H47 200.0 182.8
H49 C2 C1 H40 330.8 57.7
H50 O2 C2 H49 297.9 300.1