Detailed ligand analysis report on NAD A 500

ligand picture

Electron density around NAD A 500 :
2mFo-DFc (at 0.7 rmsd) in grey.
mFo-DFc (at 3 rmsd) in red (negative) and green (positive),
(picture produced with PyMOL)


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Ligand Electron Density Picture

Residue NAD A 500 Statistics

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

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Ligand Statistics Table

Restraints used

restraints for NAD (NICOTINAMIDE-ADENINE-DINUCLEOTIDE) from cif dictionary NAD.cif; buster common-compounds v 3.0, Generated by GRADE_PDB_LIGAND 1.2.9pre (June 16 2014) using MOGUL 1.6.1(DEV7), CSD as535be, with quantum mechanics RM1

Mogul bond results

Mogul bonds schematic
'bad' → purple (Z > 4)
'poor' → violet (2.5 < Z < 4)
'ok' → lime (1.5 < Z < 2.5)
'good' → green (Z < 1.5)
'unknown' → gray (Mogul does not find sufficient CSD equivalents).

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

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Ligand Mogul Analysis: Bonds

Mogul angle results

Mogul angles schematic
'bad' → purple (Z > 4)
'poor' → violet (2.5 < Z < 4)
'ok' → lime (1.5 < Z < 2.5)
'good' → green (Z < 1.5)
'unknown' → gray (Mogul does not find sufficient CSD equivalents).

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

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Ligand Mogul Analysis: Angles

Mogul dihedral results

Mogul dihedrals schematic
'rare' → lime (all torsion angles have > 0.5% of population within ± 10 °)
'common' → green (all torsion angles have > 10% of population within ± 10 °)
'unknown' → gray (Mogul does not find sufficient CSD equivalents).

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%

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Ligand Mogul Analysis: Dihedrals

Mogul ring results

Mogul rings schematic
'good' → green (ring strangeness score < 3 °)
'unknown' → gray (Mogul does not find sufficient CSD equivalents).

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.


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Ligand Mogul Analysis: Rings

Mogul Run Conditions