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) 0.9557
min(B-factor)‡ 28.7
avg(B-factor)‡ 36.1
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 0/4
'bad' rings 0/4
bonds rms Z 0.554
angles rms Z 1.028

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 1.718 1.734 -0.016 0.012 3693 1.34
C5-C4 1.392 1.377 0.015 0.013 125 1.09
C39-C38 1.375 1.388 -0.013 0.013 403 0.98
C2-N3 1.302 1.316 -0.014 0.015 17 0.95
C50-N51 1.354 1.341 0.012 0.013 434 0.95
C36-C5 1.484 1.478 0.006 0.007 10 0.88
C7-C6 1.532 1.514 0.018 0.023 243 0.78
C58-C57 1.528 1.516 0.012 0.018 1743 0.71
C50-N54 1.350 1.342 0.008 0.013 12 0.67
C59-C58 1.527 1.516 0.011 0.018 1743 0.62
C5-N1 1.398 1.389 0.008 0.014 79 0.59
C55-N54 1.466 1.458 0.008 0.013 47 0.59
C4-N3 1.377 1.385 -0.008 0.013 288 0.58
C56-C55 1.509 1.518 -0.008 0.015 793 0.55
C21-C20 1.520 1.512 0.008 0.014 29 0.55
C6-N1 1.472 1.467 0.005 0.012 575 0.42
C10-C7 1.492 1.509 -0.017 0.040 1023 0.42
C20-N19 1.474 1.467 0.007 0.018 139 0.42
C50-N49 1.345 1.340 0.004 0.011 146 0.39
C41-C35 1.396 1.391 0.005 0.013 4266 0.39
C17-C18 1.517 1.512 0.005 0.014 29 0.36
C40-C39 1.388 1.384 0.004 0.013 2673 0.31
C41-C40 1.385 1.382 0.003 0.010 4486 0.30
C18-N19 1.472 1.467 0.005 0.018 139 0.29
C60-C55 1.514 1.518 -0.004 0.015 793 0.26
C36-N51 1.343 1.341 0.002 0.007 892 0.24
C39-CL46 1.737 1.734 0.003 0.012 3693 0.23
C37-C38 1.383 1.381 0.002 0.009 2188 0.20
C48-N49 1.341 1.340 0.002 0.011 2774 0.17
C35-C4 1.479 1.478 0.002 0.010 913 0.16
C21-C16 1.532 1.531 0.001 0.014 1072 0.09
C17-C16 1.530 1.531 -0.001 0.014 1072 0.08
C47-C36 1.390 1.389 0.001 0.010 1673 0.08
C57-C56 1.526 1.525 0.001 0.013 1827 0.07
C59-C60 1.524 1.525 -0.001 0.013 1827 0.07
C47-C48 1.380 1.381 -0.001 0.011 2637 0.07
C37-C35 1.391 1.391 -0.000 0.009 1816 0.05
C2-N1 1.375 1.375 0.000 0.013 11 0.00

help? see BUSTER wiki Ligand Mogul Analysis: Bonds

Mogul angle results

Mogul angles schematic
'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
C5-C36-N51 118.5 115.8 2.7 1.0 10 2.62
C56-C55-N54 114.8 110.6 4.3 1.7 34 2.49
C60-C55-N54 114.4 110.6 3.8 1.7 34 2.24
N54-C50-N51 119.2 116.5 2.7 1.4 22 1.95
C35-C4-C5 132.1 130.0 2.0 1.3 92 1.54
C47-C36-C5 119.5 121.1 -1.6 1.1 10 1.45
C40-C39-CL46 120.2 118.4 1.9 1.3 2376 1.42
C35-C4-N3 117.3 119.3 -2.0 1.4 227 1.39
N54-C50-N49 114.6 116.5 -1.9 1.4 22 1.38
C47-C36-N51 122.0 123.0 -1.0 0.8 691 1.22
C39-C38-CL45 119.9 120.9 -1.0 0.8 728 1.16
C38-C39-CL46 120.0 120.9 -0.9 0.8 728 1.02
C4-C5-N1 104.5 105.4 -0.9 0.9 25 1.02
C6-N1-C2 125.6 127.1 -1.6 1.6 26 1.00
C59-C58-C57 111.8 110.9 0.9 1.0 1269 0.87
C6-N1-C5 127.8 126.6 1.2 1.4 14 0.86
C48-C47-C36 116.5 117.1 -0.6 0.7 16 0.86
C47-C48-N49 123.4 124.1 -0.7 0.9 427 0.81
C37-C38-C39 120.9 120.2 0.7 1.0 476 0.73
C20-N19-C18 111.4 110.5 0.9 1.3 60 0.67
C18-C17-C16 109.0 109.8 -0.9 1.5 90 0.59
N49-C50-N51 126.0 126.6 -0.5 1.0 20 0.57
C59-C60-C55 110.7 111.2 -0.5 0.8 586 0.57
C10-C7-C6 113.3 111.8 1.4 2.5 217 0.57
C58-C57-C56 111.8 111.3 0.5 1.0 1421 0.56
C41-C40-C39 119.8 120.2 -0.4 0.7 492 0.53
C37-C38-CL45 119.1 118.4 0.7 1.2 1948 0.53
C4-N3-C2 106.0 105.2 0.7 1.6 12 0.47
C36-N51-C50 116.3 116.7 -0.4 0.9 14 0.44
C37-C35-C4 120.5 119.9 0.6 1.4 31 0.43
C41-C35-C37 119.1 119.4 -0.3 0.9 2010 0.34
C40-C41-C35 120.6 120.8 -0.2 0.7 3513 0.33
C48-N49-C50 115.3 115.6 -0.2 0.7 106 0.32
C35-C37-C38 119.9 120.1 -0.2 0.7 61 0.23
C20-C21-C16 109.5 109.8 -0.3 1.5 90 0.21
C57-C56-C55 111.0 111.2 -0.2 0.8 586 0.21
C5-C4-N3 110.5 110.3 0.2 1.2 77 0.20
C21-C16-C17 109.3 109.5 -0.2 1.2 259 0.19
C41-C35-C4 120.4 120.7 -0.3 1.7 1605 0.19
C60-C55-C56 110.8 110.7 0.1 0.8 315 0.17
C7-C6-N1 112.6 112.5 0.2 1.9 33 0.10
C40-C39-C38 119.7 119.7 0.0 0.8 229 0.03
C58-C59-C60 111.3 111.3 0.0 1.0 1421 0.03

help? see BUSTER wiki 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°
…-C35-C4-… rare
C41-C35-C4-C5 -129.6 452 6%
C37-C35-C4-N3 -130.9 528 19%
C41-C35-C4-N3 46.6 528 16%
C37-C35-C4-C5 52.9 452 9%
…-C50-N54-… common
N51-C50-N54-C55 -7.8 22 45%
N49-C50-N54-C55 167.4 22 55%
…-C6-C7-… rare
N1-C6-C7-C10 32.4 196 1%
…-C6-N1-… common
C7-C6-N1-C5 -108.2 97 32%
C7-C6-N1-C2 71.6 49 43%

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 0.5
N1-C2-N3-C4-C5 58 0.1
C36-C47-C48-N49-C50-N51 41 0.7
C35-C37-C38-C39-C40-C41 246 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.


help? see BUSTER wiki Ligand Mogul Analysis: Rings

Mogul Run Conditions