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)


help? see BUSTER wiki Ligand Electron Density Picture

Residue ANP A 502 Statistics

Database ID ANP (PDB)
3-letter code ANP
CC(2mFo-DFc) 0.8619
min(B-factor)‡ 22.9
avg(B-factor)‡ 33.6
max(B-factor)‡ 43.4
min(occupancy)‡ 0.66
max(occupancy)‡ 0.66
‡ 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 0.283
angles rms Z 0.298

help? see BUSTER wiki Ligand Statistics Table

Restraints used

restraints for ANP (PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER) from cif dictionary ANP.cif; buster common-compounds v 3.1 (07 Mar 2014); Generated by GRADE_PDB_LIGAND 1.2.9 (July 24 2014) using MOGUL 1.7(RC5), CSD as536be, 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
C3'-C4' 1.536 1.526 0.010 0.014 577 0.75
PG-N3B 1.646 1.631 0.015 0.022 23 0.67
C2-N3 1.339 1.335 0.005 0.011 829 0.46
C6-N1 1.354 1.350 0.004 0.010 239 0.39
C2'-C3' 1.535 1.530 0.005 0.013 510 0.36
C2-N1 1.338 1.335 0.004 0.011 829 0.34
C6-N6 1.331 1.336 -0.005 0.014 531 0.33
PA-O3A 1.597 1.594 0.003 0.011 21 0.27
PA-O2A 1.520 1.527 -0.008 0.030 30 0.26
C1'-N9 1.462 1.459 0.003 0.012 78 0.25
O3'-C3' 1.426 1.423 0.003 0.013 3264 0.24
O4'-C4' 1.446 1.444 0.003 0.011 1633 0.23
C2'-C1' 1.527 1.530 -0.003 0.014 341 0.20
C4-N9 1.373 1.374 -0.002 0.008 181 0.19
C4-N3 1.341 1.339 0.002 0.012 542 0.19
PA-O1A 1.478 1.482 -0.003 0.018 31 0.18
C5-N7 1.386 1.387 -0.001 0.007 359 0.16
O2'-C2' 1.425 1.423 0.001 0.013 3264 0.09
C5-C4 1.387 1.388 -0.001 0.011 332 0.06
O4'-C1' 1.415 1.415 -0.001 0.011 592 0.06
PG-O1G 1.454 1.454 0.000 0.009 68 0.05
PB-O1B 1.454 1.454 -0.000 0.009 68 0.04
C8-N7 1.311 1.311 -0.000 0.008 447 0.04
C5-C6 1.409 1.408 0.000 0.010 166 0.03
O5'-C5' 1.443 1.443 0.000 0.015 124 0.01
PB-N3B 1.631 1.631 0.000 0.022 23 0.01
C5'-C4' 1.508 1.508 -0.000 0.012 1182 0.01
C8-N9 1.370 1.370 0.000 0.008 190 0.00

help? see BUSTER wiki 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
O4'-C4'-C3' 106.5 105.3 1.3 1.3 448 0.99
C2'-C3'-C4' 103.0 102.5 0.6 1.0 376 0.57
N3-C4-N9 127.7 127.1 0.6 1.2 126 0.55
O2'-C2'-C3' 113.3 111.9 1.3 2.6 938 0.50
C2'-C1'-N9 114.9 114.1 0.8 1.5 59 0.50
C5'-C4'-C3' 115.9 115.3 0.6 1.8 70 0.36
C5-C4-N3 126.6 126.8 -0.2 0.7 212 0.34
O1B-PB-N3B 111.6 112.1 -0.5 1.7 15 0.31
O4'-C1'-C2' 106.2 106.5 -0.3 1.2 307 0.27
C4'-O4'-C1' 109.9 109.5 0.4 1.4 434 0.26
O3A-PA-O1A 108.1 108.7 -0.6 2.4 19 0.25
C2-N3-C4 111.0 111.5 -0.4 2.0 224 0.23
O3'-C3'-C4' 111.6 111.0 0.6 2.6 541 0.22
O3'-C3'-C2' 112.4 111.9 0.4 2.6 938 0.16
C5-C6-N1 117.7 117.6 0.1 0.9 133 0.15
C2-N1-C6 118.7 118.5 0.1 1.0 154 0.14
C3'-C2'-C1' 101.3 101.5 -0.2 1.2 273 0.14
C6-C5-N7 132.3 132.1 0.2 1.2 118 0.14
C5-C4-N9 105.7 105.7 -0.1 0.5 148 0.12
N6-C6-N1 118.3 118.2 0.1 1.2 214 0.11
N3-C2-N1 128.9 128.8 0.1 0.9 329 0.08
C4-C5-N7 110.7 110.7 0.0 0.5 241 0.08
O4'-C1'-N9 108.3 108.4 -0.1 1.3 66 0.07
O5'-C5'-C4' 109.2 109.1 0.2 2.3 84 0.07
C4-N9-C8 105.8 105.7 0.0 0.5 150 0.07
O4'-C4'-C5' 109.5 109.6 -0.1 1.5 204 0.06
O2'-C2'-C1' 110.4 110.6 -0.1 2.8 323 0.05
C1'-N9-C8 126.8 126.8 0.1 1.9 65 0.05
C4-N9-C1' 127.1 127.0 0.1 1.8 67 0.05
N9-C8-N7 114.1 114.1 0.0 0.7 173 0.05
C5-C6-N6 123.7 123.7 0.0 1.0 144 0.03
C5-N7-C8 103.7 103.7 -0.0 0.5 265 0.01
C6-C5-C4 117.0 117.0 0.0 0.7 127 0.01

help? see BUSTER wiki Ligand Mogul Analysis: Angles

Mogul dihedral results

Mogul dihedrals schematic
'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 139.5 66 14%
O4'-C1'-N9-C8 70.2 64 12%
O4'-C1'-N9-C4 -102.1 68 15%
C2'-C1'-N9-C8 -48.3 63 11%
…-C4'-C5'-… common
O4'-C4'-C5'-O5' -63.7 63 90%
C3'-C4'-C5'-O5' 56.8 63 84%
…-C5'-O5'-… common
C4'-C5'-O5'-PA 175.6 74 34%

help? see BUSTER wiki 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 0.3
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.


help? see BUSTER wiki Ligand Mogul Analysis: Rings

Mogul Run Conditions