Detailed ligand analysis report on 880 A 501

ligand picture

Electron density around 880 A 501 :
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 880 A 501 Statistics

Database ID 880 (PDB)
3-letter code 880
CC(2mFo-DFc) 0.9615
min(B-factor)‡ 30.0
avg(B-factor)‡ 35.6
max(B-factor)‡ 44.2
min(occupancy)‡ 1.00
max(occupancy)‡ 1.00
‡ hydrogen atoms excluded

Mogul Analysis:
'bad' bonds 0/38
'bad' bond angles 0/43
'unusual' dihedrals 1/4
'bad' rings 0/4
bonds rms Z 0.585
angles rms Z 0.724

help? see BUSTER wiki
Ligand Statistics Table

Restraints used

restraints for 880 (CYCLOHEXYL-_4-_5-_3,4-DICHLOROPHENYL_-2-PIPERIDIN-4-YL-3-PROPYL-3H-IMIDAZOL-4-YL_-PYRIMIDIN-2-YL_AMINE) from cif dictionary 880.grade_PDB_ligand.cif; generated by GRADE_PDB_LIGAND 1.2.9 (pre-release) (June 15 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
C38-CL45 1.719 1.734 -0.014 0.012 3693 1.23
C7-C6 1.542 1.514 0.028 0.023 243 1.20
C36-C5 1.486 1.478 0.008 0.007 10 1.13
C58-C57 1.535 1.516 0.019 0.018 1743 1.08
C50-N51 1.354 1.341 0.013 0.013 434 0.98
C2-N3 1.303 1.316 -0.013 0.015 17 0.88
C39-C38 1.378 1.388 -0.011 0.013 403 0.82
C17-C18 1.524 1.512 0.011 0.014 29 0.80
C59-C58 1.528 1.516 0.012 0.018 1743 0.68
C21-C20 1.521 1.512 0.009 0.014 29 0.65
C5-C4 1.386 1.377 0.009 0.013 125 0.64
C20-N19 1.476 1.467 0.010 0.018 139 0.56
C50-N49 1.346 1.340 0.006 0.011 146 0.53
C4-N3 1.378 1.385 -0.007 0.013 288 0.53
C41-C40 1.387 1.382 0.005 0.010 4486 0.51
C6-N1 1.473 1.467 0.006 0.012 575 0.50
C5-N1 1.396 1.389 0.007 0.014 79 0.49
C47-C48 1.386 1.381 0.006 0.011 2637 0.49
C40-C39 1.390 1.384 0.006 0.013 2673 0.46
C41-C35 1.396 1.391 0.006 0.013 4266 0.44
C50-N54 1.347 1.342 0.005 0.013 12 0.43
C56-C55 1.524 1.518 0.006 0.015 793 0.41
C21-C16 1.537 1.531 0.006 0.014 1072 0.39
C18-N19 1.472 1.467 0.006 0.018 139 0.33
C57-C56 1.529 1.525 0.004 0.013 1827 0.29
C10-C7 1.497 1.509 -0.011 0.040 1023 0.29
C37-C38 1.379 1.381 -0.002 0.009 2188 0.23
C17-C16 1.534 1.531 0.003 0.014 1072 0.22
C59-C60 1.527 1.525 0.002 0.013 1827 0.18
C39-CL46 1.736 1.734 0.002 0.012 3693 0.18
C60-C55 1.520 1.518 0.002 0.015 793 0.14
C48-N49 1.341 1.340 0.001 0.011 2774 0.13
C55-N54 1.459 1.458 0.001 0.013 47 0.11
C2-N1 1.374 1.375 -0.001 0.013 11 0.08
C35-C4 1.477 1.478 -0.001 0.010 913 0.08
C36-N51 1.340 1.341 -0.001 0.007 892 0.08
C37-C35 1.391 1.391 -0.000 0.009 1816 0.05
C47-C36 1.388 1.389 -0.001 0.010 1673 0.05

help? see BUSTER wiki
Ligand Mogul Analysis: Bonds

Mogul angle results

Mogul angles schematic
'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
C10-C7-C6 117.3 111.8 5.4 2.5 217 2.16
C40-C39-CL46 120.3 118.4 2.0 1.3 2376 1.47
C35-C4-C5 131.8 130.0 1.8 1.3 92 1.35
C35-C4-N3 117.5 119.3 -1.8 1.4 227 1.27
C39-C38-CL45 119.9 120.9 -1.0 0.8 728 1.14
C6-N1-C5 128.2 126.6 1.5 1.4 14 1.09
C6-N1-C2 125.5 127.1 -1.7 1.6 26 1.06
C47-C36-N51 122.2 123.0 -0.8 0.8 691 1.01
C48-C47-C36 116.4 117.1 -0.7 0.7 16 1.01
C38-C39-CL46 120.1 120.9 -0.7 0.8 728 0.87
C37-C38-C39 121.0 120.2 0.8 1.0 476 0.85
C7-C6-N1 114.0 112.5 1.5 1.9 33 0.81
C47-C48-N49 123.4 124.1 -0.7 0.9 427 0.79
C4-C5-N1 104.8 105.4 -0.6 0.9 25 0.72
C60-C55-C56 110.1 110.7 -0.5 0.8 315 0.65
C60-C55-N54 109.5 110.6 -1.0 1.7 34 0.60
C41-C40-C39 119.7 120.2 -0.4 0.7 492 0.55
N54-C50-N51 117.2 116.5 0.7 1.4 22 0.50
N49-C50-N51 126.1 126.6 -0.5 1.0 20 0.48
C47-C36-C5 121.6 121.1 0.5 1.1 10 0.44
C37-C35-C4 120.5 119.9 0.6 1.4 31 0.43
C40-C41-C35 120.5 120.8 -0.3 0.7 3513 0.41
C37-C38-CL45 118.9 118.4 0.5 1.2 1948 0.39
C41-C35-C37 119.0 119.4 -0.3 0.9 2010 0.35
C5-C36-N51 116.2 115.8 0.4 1.0 10 0.35
C48-N49-C50 115.3 115.6 -0.3 0.7 106 0.34
C56-C55-N54 111.1 110.6 0.5 1.7 34 0.31
C4-N3-C2 105.7 105.2 0.5 1.6 12 0.31
C57-C56-C55 110.9 111.2 -0.2 0.8 586 0.31
C36-N51-C50 116.4 116.7 -0.3 0.9 14 0.31
C59-C60-C55 110.9 111.2 -0.2 0.8 586 0.28
C18-C17-C16 109.4 109.8 -0.4 1.5 90 0.27
C5-C4-N3 110.6 110.3 0.3 1.2 77 0.27
C58-C57-C56 111.5 111.3 0.2 1.0 1421 0.25
C40-C39-C38 119.6 119.7 -0.1 0.8 229 0.18
C41-C35-C4 120.4 120.7 -0.3 1.7 1605 0.16
C20-C21-C16 109.7 109.8 -0.2 1.5 90 0.10
C35-C37-C38 120.0 120.1 -0.1 0.7 61 0.08
C58-C59-C60 111.2 111.3 -0.0 1.0 1421 0.05
C59-C58-C57 110.9 110.9 0.0 1.0 1269 0.03
C21-C16-C17 109.5 109.5 -0.0 1.2 259 0.03
C20-N19-C18 110.5 110.5 -0.0 1.3 60 0.01
N54-C50-N49 116.5 116.5 0.0 1.4 22 0.01

help? see BUSTER wiki
Ligand Mogul Analysis: Angles

Mogul dihedral results

Mogul dihedrals schematic
'unusual' → violet (some torsion angles have < 0.5% of population within ± 10 °)
'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°
…-C35-C4-… rare
C41-C35-C4-C5 -128.3 452 6%
C37-C35-C4-N3 -131.5 528 19%
C41-C35-C4-N3 47.8 528 16%
C37-C35-C4-C5 52.3 452 9%
…-C50-N54-… common
N51-C50-N54-C55 1.7 22 45%
N49-C50-N54-C55 176.7 22 55%
…-C6-C7-… unusual
N1-C6-C7-C10 4.6 196 0%
…-C6-N1-… common
C7-C6-N1-C5 -103.0 97 41%
C7-C6-N1-C2 78.0 49 63%

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 °
C55-C56-C57-C58-C59-C60 148 0.3
N1-C2-N3-C4-C5 58 0.0
C36-C47-C48-N49-C50-N51 41 0.5
C35-C37-C38-C39-C40-C41 246 0.3

‡ '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