Electron density around NAD A 500 : |
Database ID | NAD (PDB) |
3-letter code | NAD |
CC(2mFo-DFc) | 0.9633 |
min(B-factor)‡ | 18.4 |
avg(B-factor)‡ | 21.9 |
max(B-factor)‡ | 25.7 |
min(occupancy)‡ | 1.00 |
max(occupancy)‡ | 1.00 |
‡ hydrogen atoms excluded | |
Mogul Analysis: | |
---|---|
'bad' bonds | 9/45 |
'bad' bond angles | 8/60 |
'unusual' dihedrals | 0/6 |
'bad' rings | 0/4 |
bonds rms Z | 3.044 |
angles rms Z | 3.054 |
Mogul bonds schematic | ||||||
atoms | actual in Å | Mogul mean in Å | difference in Å | Mogul σ in Å | Mogul # samples | Zscore |
---|---|---|---|---|---|---|
C2N-N1N | 1.397 | 1.344 | 0.053 | 0.006 | 10 | 9.44 |
C5B-C4B | 1.593 | 1.508 | 0.085 | 0.012 | 1182 | 7.03 |
C5A-N7A | 1.349 | 1.387 | -0.037 | 0.007 | 359 | 5.56 |
C6N-N1N | 1.389 | 1.347 | 0.043 | 0.008 | 44 | 5.54 |
C2A-N1A | 1.393 | 1.335 | 0.058 | 0.011 | 829 | 5.35 |
O7N-C7N | 1.362 | 1.239 | 0.123 | 0.025 | 568 | 4.96 |
C8A-N7A | 1.348 | 1.311 | 0.037 | 0.008 | 447 | 4.95 |
C6A-N1A | 1.397 | 1.350 | 0.047 | 0.010 | 239 | 4.86 |
C2A-N3A | 1.381 | 1.335 | 0.046 | 0.011 | 829 | 4.27 |
C2N-C3N | 1.407 | 1.381 | 0.026 | 0.007 | 79 | 3.44 |
O5D-C5D | 1.394 | 1.443 | -0.048 | 0.015 | 124 | 3.14 |
C5N-C4N | 1.412 | 1.384 | 0.028 | 0.010 | 2659 | 2.69 |
C4N-C3N | 1.424 | 1.391 | 0.033 | 0.013 | 4266 | 2.61 |
C4A-N9A | 1.354 | 1.374 | -0.020 | 0.008 | 181 | 2.55 |
C4A-N3A | 1.367 | 1.339 | 0.028 | 0.012 | 542 | 2.35 |
O5B-C5B | 1.407 | 1.443 | -0.035 | 0.015 | 124 | 2.29 |
C2D-C3D | 1.501 | 1.530 | -0.029 | 0.013 | 510 | 2.25 |
C2B-C3B | 1.502 | 1.530 | -0.029 | 0.013 | 510 | 2.21 |
C2B-C1B | 1.501 | 1.530 | -0.030 | 0.014 | 341 | 2.13 |
PA-O3 | 1.616 | 1.594 | 0.022 | 0.011 | 21 | 2.08 |
O2B-C2B | 1.400 | 1.423 | -0.024 | 0.013 | 3264 | 1.79 |
O4B-C4B | 1.424 | 1.444 | -0.020 | 0.011 | 1633 | 1.74 |
C5D-C4D | 1.528 | 1.508 | 0.020 | 0.012 | 1182 | 1.62 |
PN-O3 | 1.611 | 1.594 | 0.017 | 0.011 | 21 | 1.59 |
PN-O2N | 1.481 | 1.527 | -0.046 | 0.030 | 30 | 1.55 |
C5A-C4A | 1.403 | 1.388 | 0.016 | 0.011 | 332 | 1.40 |
O4B-C1B | 1.402 | 1.415 | -0.013 | 0.011 | 592 | 1.15 |
C5A-C6A | 1.397 | 1.408 | -0.011 | 0.010 | 166 | 1.15 |
C3B-C4B | 1.541 | 1.526 | 0.015 | 0.014 | 577 | 1.12 |
C1B-N9A | 1.472 | 1.459 | 0.012 | 0.012 | 78 | 1.07 |
C6N-C5N | 1.394 | 1.376 | 0.018 | 0.018 | 211 | 1.02 |
O2D-C2D | 1.412 | 1.423 | -0.012 | 0.013 | 3264 | 0.90 |
O4D-C1D | 1.415 | 1.404 | 0.011 | 0.012 | 17 | 0.89 |
C6A-N6A | 1.324 | 1.336 | -0.012 | 0.014 | 531 | 0.84 |
PA-O1A | 1.469 | 1.482 | -0.013 | 0.018 | 31 | 0.72 |
PA-O2A | 1.510 | 1.527 | -0.017 | 0.030 | 30 | 0.56 |
O4D-C4D | 1.449 | 1.444 | 0.005 | 0.011 | 1633 | 0.48 |
O3B-C3B | 1.429 | 1.423 | 0.006 | 0.013 | 3264 | 0.44 |
C8A-N9A | 1.371 | 1.370 | 0.002 | 0.008 | 190 | 0.22 |
C2D-C1D | 1.533 | 1.530 | 0.003 | 0.014 | 354 | 0.21 |
C7N-N7N | 1.324 | 1.327 | -0.004 | 0.021 | 568 | 0.18 |
PN-O1N | 1.479 | 1.482 | -0.003 | 0.018 | 31 | 0.14 |
C3D-C4D | 1.524 | 1.526 | -0.002 | 0.014 | 577 | 0.14 |
C3N-C7N | 1.499 | 1.501 | -0.002 | 0.016 | 409 | 0.11 |
O3D-C3D | 1.423 | 1.423 | -0.001 | 0.013 | 3264 | 0.05 |
Mogul angles schematic | ||||||
atoms | actual in ° | Mogul mean in ° | difference in ° | Mogul σ in ° | Mogul # samples | Zscore |
---|---|---|---|---|---|---|
C5A-N7A-C8A | 108.3 | 103.7 | 4.7 | 0.5 | 265 | 10.21 |
N3A-C2A-N1A | 120.0 | 128.8 | -8.9 | 0.9 | 329 | 10.06 |
N9A-C8A-N7A | 109.0 | 114.1 | -5.0 | 0.7 | 173 | 7.09 |
C3N-C7N-N7N | 124.2 | 117.9 | 6.4 | 1.0 | 373 | 6.70 |
C4A-C5A-N7A | 107.7 | 110.7 | -3.0 | 0.5 | 241 | 5.82 |
C5A-C4A-N3A | 122.8 | 126.8 | -4.0 | 0.7 | 212 | 5.63 |
C4B-O4B-C1B | 102.3 | 109.5 | -7.2 | 1.4 | 434 | 5.02 |
C4A-N9A-C8A | 107.7 | 105.7 | 2.0 | 0.5 | 150 | 4.17 |
C2A-N3A-C4A | 119.1 | 111.5 | 7.6 | 2.0 | 224 | 3.87 |
O4B-C1B-N9A | 113.1 | 108.4 | 4.7 | 1.3 | 66 | 3.62 |
C5A-C4A-N9A | 107.3 | 105.7 | 1.5 | 0.5 | 148 | 3.31 |
O7N-C7N-N7N | 118.7 | 122.8 | -4.0 | 1.3 | 516 | 3.16 |
O7N-C7N-C3N | 117.0 | 119.5 | -2.5 | 0.8 | 373 | 3.11 |
O4D-C1D-N1N | 110.5 | 108.4 | 2.1 | 0.7 | 16 | 2.90 |
C5A-C6A-N6A | 120.9 | 123.7 | -2.7 | 1.0 | 144 | 2.66 |
N3A-C4A-N9A | 129.9 | 127.1 | 2.9 | 1.2 | 126 | 2.48 |
C2A-N1A-C6A | 120.8 | 118.5 | 2.3 | 1.0 | 154 | 2.40 |
C4A-N9A-C1B | 122.8 | 127.0 | -4.2 | 1.8 | 67 | 2.36 |
C5A-C6A-N1A | 119.5 | 117.6 | 1.9 | 0.9 | 133 | 2.16 |
O2D-C2D-C1D | 116.7 | 110.6 | 6.1 | 2.8 | 336 | 2.15 |
C6A-C5A-N7A | 134.5 | 132.1 | 2.4 | 1.2 | 118 | 2.03 |
O4D-C1D-C2D | 104.9 | 107.0 | -2.1 | 1.1 | 17 | 1.98 |
C6N-N1N-C2N | 121.5 | 122.2 | -0.7 | 0.4 | 10 | 1.85 |
O5B-C5B-C4B | 104.8 | 109.1 | -4.3 | 2.3 | 84 | 1.85 |
O4B-C1B-C2B | 104.4 | 106.5 | -2.1 | 1.2 | 307 | 1.77 |
C3B-C2B-C1B | 99.4 | 101.5 | -2.1 | 1.2 | 273 | 1.77 |
C2D-C1D-N1N | 116.6 | 113.6 | 3.0 | 1.8 | 20 | 1.66 |
O2B-C2B-C3B | 116.2 | 111.9 | 4.2 | 2.6 | 938 | 1.61 |
PN-O3-PA | 127.9 | 132.5 | -4.6 | 3.0 | 21 | 1.53 |
O2B-C2B-C1B | 114.8 | 110.6 | 4.3 | 2.8 | 323 | 1.53 |
C3N-C2N-N1N | 119.4 | 120.1 | -0.7 | 0.5 | 24 | 1.47 |
C5B-C4B-C3B | 112.7 | 115.3 | -2.6 | 1.8 | 70 | 1.45 |
C1B-N9A-C8A | 129.5 | 126.8 | 2.8 | 1.9 | 65 | 1.45 |
C3D-C2D-C1D | 99.8 | 101.5 | -1.7 | 1.2 | 285 | 1.44 |
C6A-C5A-C4A | 117.9 | 117.0 | 0.9 | 0.7 | 127 | 1.34 |
O4B-C4B-C3B | 107.0 | 105.3 | 1.7 | 1.3 | 448 | 1.34 |
N6A-C6A-N1A | 119.6 | 118.2 | 1.4 | 1.2 | 214 | 1.15 |
O3-PN-O1N | 111.4 | 108.7 | 2.7 | 2.4 | 19 | 1.09 |
C6N-C5N-C4N | 119.1 | 119.9 | -0.8 | 0.7 | 149 | 1.08 |
C2D-C3D-C4D | 103.4 | 102.5 | 0.9 | 1.0 | 376 | 0.89 |
O3D-C3D-C4D | 109.1 | 111.0 | -1.9 | 2.6 | 541 | 0.72 |
O5D-C5D-C4D | 107.6 | 109.1 | -1.4 | 2.3 | 84 | 0.61 |
O3B-C3B-C2B | 113.5 | 111.9 | 1.6 | 2.6 | 938 | 0.60 |
C2B-C1B-N9A | 114.9 | 114.1 | 0.7 | 1.5 | 59 | 0.47 |
C2B-C3B-C4B | 102.9 | 102.5 | 0.4 | 1.0 | 376 | 0.45 |
C2N-C3N-C4N | 119.1 | 118.8 | 0.3 | 0.7 | 35 | 0.35 |
O3D-C3D-C2D | 112.8 | 111.9 | 0.8 | 2.6 | 938 | 0.31 |
C5N-C6N-N1N | 120.4 | 120.2 | 0.3 | 0.9 | 38 | 0.28 |
O4D-C4D-C5D | 109.1 | 109.6 | -0.4 | 1.5 | 204 | 0.28 |
C4D-O4D-C1D | 109.1 | 109.5 | -0.4 | 1.4 | 447 | 0.27 |
O2D-C2D-C3D | 112.6 | 111.9 | 0.6 | 2.6 | 938 | 0.24 |
O3B-C3B-C4B | 111.6 | 111.0 | 0.6 | 2.6 | 541 | 0.21 |
C5D-C4D-C3D | 114.9 | 115.3 | -0.3 | 1.8 | 70 | 0.19 |
C5N-C4N-C3N | 120.5 | 120.4 | 0.1 | 0.7 | 3664 | 0.18 |
O4B-C4B-C5B | 109.4 | 109.6 | -0.2 | 1.5 | 204 | 0.12 |
O4D-C4D-C3D | 105.4 | 105.3 | 0.2 | 1.3 | 448 | 0.12 |
O3-PA-O1A | 108.9 | 108.7 | 0.2 | 2.4 | 19 | 0.08 |
C4N-C3N-C7N | 120.9 | 120.7 | 0.1 | 2.4 | 598 | 0.06 |
C6N-N1N-C1D | 119.2 | 119.3 | -0.1 | 2.1 | 10 | 0.05 |
C2N-N1N-C1D | 119.3 | 119.3 | -0.0 | 2.1 | 10 | 0.02 |
Mogul dihedrals schematic | ||||
atoms | actual torsion angle in ° | Mogul histogram | Mogul # samples | classification or % Mogul population within ± 10° |
---|---|---|---|---|
…-C1B-N9A-… | common | |||
O4B-C1B-N9A-C8A | 61.0 | 64 | 14% | |
O4B-C1B-N9A-C4A | -120.6 | 68 | 18% | |
C2B-C1B-N9A-C4A | 119.7 | 66 | 18% | |
C2B-C1B-N9A-C8A | -58.7 | 63 | 14% | |
…-C3N-C7N-… | common | |||
C4N-C3N-C7N-O7N | -1.0 | 707 | 24% | |
C2N-C3N-C7N-N7N | -1.0 | 111 | 23% | |
C2N-C3N-C7N-O7N | 178.6 | 111 | 25% | |
C4N-C3N-C7N-N7N | 179.4 | 707 | 24% | |
…-C4B-C5B-… | rare | |||
C3B-C4B-C5B-O5B | -56.0 | 63 | 84% | |
O4B-C4B-C5B-O5B | -174.9 | 63 | 6% | |
…-C4D-C5D-… | rare | |||
C3D-C4D-C5D-O5D | 79.2 | 63 | 5% | |
O4D-C4D-C5D-O5D | -38.9 | 63 | 3% | |
…-C5B-O5B-… | common | |||
C4B-C5B-O5B-PA | 140.6 | 74 | 36% | |
…-C5D-O5D-… | common | |||
C4D-C5D-O5D-PN | 176.2 | 74 | 34% |
Mogul rings schematic | ||
atoms | Mogul # samples | Ring strangeness score‡ in ° |
---|---|---|
C4B-O4B-C1B-C2B-C3B | 191 | 2.8 |
C4D-O4D-C1D-C2D-C3D | 191 | 0.9 |
C5A-C6A-N1A-C2A-N3A-C4A | 184 | 0.1 |
N9A-C8A-N7A-C5A-C4A | 186 | 0.1 |
‡ 'ring strangeness score' is the RMS difference in torsion angles between the instance of the ring in the ligand in the model, and the nearest instance that mogul finds in the CSD.