Detailed ligand analysis report on ANP A 502

ligand picture

Electron density around ANP A 502 :
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 ANP A 502 Statistics

Database ID ANP (PDB)
3-letter code ANP
CC(2mFo-DFc) 0.7959
min(B-factor)‡ 35.8
avg(B-factor)‡ 46.5
max(B-factor)‡ 56.1
min(occupancy)‡ 0.50
max(occupancy)‡ 0.50
‡ hydrogen atoms excluded

Mogul Analysis:
'bad' bonds 0/28
'bad' bond angles 0/33
'unusual' dihedrals 0/3
'bad' rings 0/3
bonds rms Z 0.249
angles rms Z 0.326

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Ligand Statistics Table

Restraints used

restraints for ANP (PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER) from cif dictionary ANP.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
'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
PA-O2A 1.511 1.527 -0.016 0.030 30 0.55
O4'-C4' 1.448 1.444 0.004 0.011 1633 0.40
C6-N1 1.354 1.350 0.004 0.010 239 0.39
C1'-N9 1.463 1.459 0.004 0.012 78 0.34
C2-N3 1.338 1.335 0.004 0.011 829 0.33
C4-N3 1.343 1.339 0.004 0.012 542 0.33
C2-N1 1.338 1.335 0.003 0.011 829 0.30
C8-N9 1.372 1.370 0.002 0.008 190 0.29
PG-N3B 1.637 1.631 0.006 0.022 23 0.28
C4-N9 1.372 1.374 -0.002 0.008 181 0.28
PA-O1A 1.477 1.482 -0.005 0.018 31 0.26
C5'-C4' 1.511 1.508 0.003 0.012 1182 0.25
C3'-C4' 1.529 1.526 0.003 0.014 577 0.22
C5-N7 1.385 1.387 -0.001 0.007 359 0.22
C6-N6 1.333 1.336 -0.003 0.014 531 0.20
PB-N3B 1.635 1.631 0.004 0.022 23 0.20
O3'-C3' 1.426 1.423 0.003 0.013 3264 0.19
O4'-C1' 1.417 1.415 0.002 0.011 592 0.14
PA-O3A 1.595 1.594 0.001 0.011 21 0.13
C5-C4 1.386 1.388 -0.001 0.011 332 0.13
C5-C6 1.409 1.408 0.001 0.010 166 0.11
PB-O1B 1.453 1.454 -0.001 0.009 68 0.11
C8-N7 1.312 1.311 0.001 0.008 447 0.11
C2'-C3' 1.531 1.530 0.001 0.013 510 0.07
O2'-C2' 1.423 1.423 -0.001 0.013 3264 0.06
C2'-C1' 1.529 1.530 -0.001 0.014 341 0.06
PG-O1G 1.454 1.454 -0.000 0.009 68 0.03
O5'-C5' 1.442 1.443 -0.000 0.015 124 0.02

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Ligand Mogul Analysis: Bonds

Mogul angle results

Mogul angles schematic
'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
O5'-C5'-C4' 111.1 109.1 2.0 2.3 84 0.87
O3'-C3'-C2' 113.7 111.9 1.7 2.6 938 0.66
O2'-C2'-C3' 113.6 111.9 1.7 2.6 938 0.65
C2'-C1'-N9 114.9 114.1 0.8 1.5 59 0.51
O4'-C4'-C5' 110.3 109.6 0.7 1.5 204 0.48
C4'-O4'-C1' 110.2 109.5 0.7 1.4 434 0.47
N3-C4-N9 127.5 127.1 0.5 1.2 126 0.41
O4'-C4'-C3' 105.8 105.3 0.5 1.3 448 0.39
C5'-C4'-C3' 114.7 115.3 -0.6 1.8 70 0.34
C5-C4-N3 126.6 126.8 -0.2 0.7 212 0.33
N6-C6-N1 118.6 118.2 0.4 1.2 214 0.30
C2-N1-C6 118.8 118.5 0.3 1.0 154 0.29
C3'-C2'-C1' 101.2 101.5 -0.3 1.2 273 0.29
O2'-C2'-C1' 111.4 110.6 0.8 2.8 323 0.28
O1B-PB-N3B 111.7 112.1 -0.4 1.7 15 0.24
C5-C4-N9 105.9 105.7 0.1 0.5 148 0.23
C1'-N9-C8 127.1 126.8 0.4 1.9 65 0.21
C2-N3-C4 111.1 111.5 -0.4 2.0 224 0.20
O4'-C1'-N9 108.6 108.4 0.2 1.3 66 0.18
C6-C5-N7 132.3 132.1 0.2 1.2 118 0.17
C5-N7-C8 103.7 103.7 0.0 0.5 265 0.10
C2'-C3'-C4' 102.6 102.5 0.1 1.0 376 0.10
C5-C6-N1 117.7 117.6 0.1 0.9 133 0.10
C4-N9-C8 105.7 105.7 -0.0 0.5 150 0.09
O4'-C1'-C2' 106.6 106.5 0.1 1.2 307 0.09
O3A-PA-O1A 108.9 108.7 0.2 2.4 19 0.07
N9-C8-N7 114.0 114.1 -0.1 0.7 173 0.07
C4-C5-N7 110.7 110.7 0.0 0.5 241 0.05
N3-C2-N1 128.8 128.8 -0.0 0.9 329 0.04
C4-N9-C1' 127.0 127.0 0.1 1.8 67 0.04
O3'-C3'-C4' 111.1 111.0 0.1 2.6 541 0.04
C5-C6-N6 123.6 123.7 -0.0 1.0 144 0.02
C6-C5-C4 117.0 117.0 -0.0 0.7 127 0.01

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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°
…-C1'-N9-… common
C2'-C1'-N9-C4 119.7 66 18%
O4'-C1'-N9-C8 54.0 64 16%
O4'-C1'-N9-C4 -121.0 68 18%
C2'-C1'-N9-C8 -65.3 63 17%
…-C4'-C5'-… rare
O4'-C4'-C5'-O5' 36.3 63 3%
C3'-C4'-C5'-O5' 155.5 63 2%
…-C5'-O5'-… common
C4'-C5'-O5'-PA -179.2 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 °
N9-C8-N7-C5-C4 186 0.0
C5-C6-N1-C2-N3-C4 184 0.1
C4'-O4'-C1'-C2'-C3' 191 0.5

‡ '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