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) 0.7893
min(B-factor)‡ 37.9
avg(B-factor)‡ 46.3
max(B-factor)‡ 53.4
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 0.252
angles rms Z 0.338

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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
C8-N9 1.373 1.370 0.004 0.008 190 0.48
C5-N7 1.384 1.387 -0.003 0.007 359 0.44
C6-N1 1.354 1.350 0.004 0.010 239 0.43
PA-O2A 1.516 1.527 -0.012 0.030 30 0.39
O4'-C4' 1.448 1.444 0.004 0.011 1633 0.39
C2-N1 1.339 1.335 0.004 0.011 829 0.37
C2-N3 1.338 1.335 0.004 0.011 829 0.36
PA-O1A 1.475 1.482 -0.006 0.018 31 0.34
PG-N3B 1.637 1.631 0.006 0.022 23 0.28
PB-N3B 1.637 1.631 0.006 0.022 23 0.28
C4-N3 1.342 1.339 0.003 0.012 542 0.26
C6-N6 1.333 1.336 -0.003 0.014 531 0.23
C4-N9 1.376 1.374 0.002 0.008 181 0.22
C3'-C4' 1.528 1.526 0.003 0.014 577 0.20
O4'-C1' 1.417 1.415 0.002 0.011 592 0.19
C5'-C4' 1.510 1.508 0.002 0.012 1182 0.16
C8-N7 1.310 1.311 -0.001 0.008 447 0.12
O5'-C5' 1.441 1.443 -0.002 0.015 124 0.11
C1'-N9 1.460 1.459 0.001 0.012 78 0.09
PG-O1G 1.455 1.454 0.001 0.009 68 0.09
PA-O3A 1.593 1.594 -0.001 0.011 21 0.07
C5-C4 1.387 1.388 -0.001 0.011 332 0.06
C5-C6 1.409 1.408 0.001 0.010 166 0.06
PB-O1B 1.453 1.454 -0.001 0.009 68 0.06
O3'-C3' 1.424 1.423 0.001 0.013 3264 0.06
C2'-C1' 1.530 1.530 -0.001 0.014 341 0.04
C2'-C3' 1.531 1.530 0.001 0.013 510 0.04
O2'-C2' 1.423 1.423 -0.000 0.013 3264 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' 110.5 109.1 1.5 2.3 84 0.65
O3'-C3'-C2' 113.6 111.9 1.6 2.6 938 0.63
O2'-C2'-C3' 113.6 111.9 1.6 2.6 938 0.62
C4-N9-C8 105.4 105.7 -0.3 0.5 150 0.60
C2'-C1'-N9 115.0 114.1 0.9 1.5 59 0.58
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
C5'-C4'-C3' 114.5 115.3 -0.8 1.8 70 0.46
O4'-C4'-C3' 105.7 105.3 0.5 1.3 448 0.38
O1B-PB-N3B 111.5 112.1 -0.6 1.7 15 0.37
C1'-N9-C8 127.4 126.8 0.7 1.9 65 0.35
C6-C5-C4 116.8 117.0 -0.2 0.7 127 0.30
C2-N3-C4 110.9 111.5 -0.6 2.0 224 0.29
C3'-C2'-C1' 101.2 101.5 -0.3 1.2 273 0.29
O2'-C2'-C1' 111.3 110.6 0.8 2.8 323 0.27
C6-C5-N7 132.4 132.1 0.3 1.2 118 0.27
O4'-C1'-N9 108.7 108.4 0.3 1.3 66 0.25
N3-C4-N9 127.3 127.1 0.3 1.2 126 0.24
C5-C6-N1 117.8 117.6 0.2 0.9 133 0.22
C2-N1-C6 118.7 118.5 0.2 1.0 154 0.20
C4-C5-N7 110.8 110.7 0.1 0.5 241 0.19
N9-C8-N7 114.2 114.1 0.1 0.7 173 0.18
C5-N7-C8 103.8 103.7 0.1 0.5 265 0.17
N6-C6-N1 118.4 118.2 0.2 1.2 214 0.16
O3'-C3'-C4' 110.6 111.0 -0.4 2.6 541 0.15
O3A-PA-O1A 109.0 108.7 0.3 2.4 19 0.13
C5-C4-N9 105.8 105.7 0.1 0.5 148 0.12
N3-C2-N1 128.9 128.8 0.1 0.9 329 0.07
C2'-C3'-C4' 102.5 102.5 0.1 1.0 376 0.06
O4'-C1'-C2' 106.5 106.5 0.1 1.2 307 0.05
C4-N9-C1' 127.0 127.0 0.1 1.8 67 0.03
C5-C6-N6 123.7 123.7 0.0 1.0 144 0.03
C5-C4-N3 126.9 126.8 0.0 0.7 212 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°
…-C1'-N9-… common
C2'-C1'-N9-C4 119.5 66 18%
O4'-C1'-N9-C8 54.2 64 16%
O4'-C1'-N9-C4 -121.2 68 18%
C2'-C1'-N9-C8 -65.2 63 17%
…-C4'-C5'-… rare
O4'-C4'-C5'-O5' 36.4 63 3%
C3'-C4'-C5'-O5' 155.4 63 2%
…-C5'-O5'-… common
C4'-C5'-O5'-PA 179.8 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 0.2
C4'-O4'-C1'-C2'-C3' 191 0.4

‡ '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