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) 0.9495
min(B-factor)‡ 30.2
avg(B-factor)‡ 35.5
max(B-factor)‡ 45.5
min(occupancy)‡ 1.00
max(occupancy)‡ 1.00
‡ hydrogen atoms excluded

Mogul Analysis:
'bad' bonds 11/38
'bad' bond angles 7/43
'unusual' dihedrals 2/4
'bad' rings 0/4
bonds rms Z 4.186
angles rms Z 3.033

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
'bad' → purple (Z > 4)
'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 Å		 Mogul
mean
in Å		 difference
in Å		 Mogul σ
in Å		 Mogul
# samples		 Zscore
C36-C5 1.555 1.478 0.078 0.007 10 10.49
C5-N1 1.520 1.389 0.131 0.014 79 9.07
C5-C4 1.493 1.377 0.116 0.013 125 8.72
C41-C40 1.466 1.382 0.083 0.010 4486 8.42
C21-C20 1.595 1.512 0.083 0.014 29 5.98
C40-C39 1.459 1.384 0.075 0.013 2673 5.62
C17-C18 1.585 1.512 0.072 0.014 29 5.23
C38-CL45 1.672 1.734 -0.061 0.012 3693 5.22
C60-C55 1.587 1.518 0.069 0.015 793 4.56
C4-N3 1.443 1.385 0.059 0.013 288 4.47
C21-C16 1.590 1.531 0.059 0.014 1072 4.06
C41-C35 1.441 1.391 0.050 0.013 4266 3.95
C47-C36 1.428 1.389 0.039 0.010 1673 3.93
C36-N51 1.367 1.341 0.026 0.007 892 3.79
C59-C60 1.571 1.525 0.046 0.013 1827 3.48
C2-N3 1.366 1.316 0.050 0.015 17 3.39
C47-C48 1.418 1.381 0.037 0.011 2637 3.27
C37-C35 1.420 1.391 0.029 0.009 1816 3.18
C17-C16 1.575 1.531 0.043 0.014 1072 3.00
C57-C56 1.559 1.525 0.034 0.013 1827 2.57
C6-N1 1.497 1.467 0.031 0.012 575 2.51
C48-N49 1.366 1.340 0.026 0.011 2774 2.44
C56-C55 1.550 1.518 0.032 0.015 793 2.14
C39-CL46 1.709 1.734 -0.025 0.012 3693 2.09
C37-C38 1.399 1.381 0.018 0.009 2188 1.88
C39-C38 1.412 1.388 0.023 0.013 403 1.79
C55-N54 1.435 1.458 -0.023 0.013 47 1.69
C59-C58 1.486 1.516 -0.030 0.018 1743 1.67
C20-N19 1.493 1.467 0.026 0.018 139 1.50
C7-C6 1.542 1.514 0.028 0.023 243 1.21
C50-N54 1.357 1.342 0.015 0.013 12 1.21
C18-N19 1.486 1.467 0.019 0.018 139 1.10
C58-C57 1.499 1.516 -0.017 0.018 1743 0.97
C2-N1 1.367 1.375 -0.008 0.013 11 0.66
C50-N51 1.349 1.341 0.008 0.013 434 0.60
C50-N49 1.344 1.340 0.004 0.011 146 0.35
C35-C4 1.481 1.478 0.003 0.010 913 0.27
C10-C7 1.517 1.509 0.009 0.040 1023 0.22

help? see BUSTER wiki Ligand Mogul Analysis: Bonds

Mogul angle results

Mogul angles schematic
'bad' → purple (Z > 4)
'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 123.6 115.8 7.8 1.0 10 7.61
C60-C55-N54 97.7 110.6 -12.8 1.7 34 7.49
C56-C55-N54 122.7 110.6 12.1 1.7 34 7.08
C60-C55-C56 114.9 110.7 4.3 0.8 315 5.15
C58-C57-C56 116.0 111.3 4.8 1.0 1421 4.92
C47-C36-C5 116.2 121.1 -5.0 1.1 10 4.38
C5-C4-N3 105.2 110.3 -5.1 1.2 77 4.25
C47-C36-N51 119.7 123.0 -3.2 0.8 691 3.93
C59-C58-C57 114.7 110.9 3.9 1.0 1269 3.74
C57-C56-C55 114.0 111.2 2.8 0.8 586 3.47
C4-N3-C2 110.4 105.2 5.1 1.6 12 3.26
C20-N19-C18 114.6 110.5 4.1 1.3 60 3.10
C41-C40-C39 118.1 120.2 -2.1 0.7 492 2.80
C7-C6-N1 117.5 112.5 5.0 1.9 33 2.67
C6-N1-C5 130.4 126.6 3.7 1.4 14 2.65
C36-N51-C50 119.0 116.7 2.3 0.9 14 2.65
C6-N1-C2 123.1 127.1 -4.0 1.6 26 2.55
C35-C4-N3 122.9 119.3 3.6 1.4 227 2.48
C37-C38-CL45 115.9 118.4 -2.5 1.2 1948 1.99
C18-C17-C16 112.7 109.8 2.9 1.5 90 1.91
N54-C50-N49 119.1 116.5 2.6 1.4 22 1.89
C39-C38-CL45 122.3 120.9 1.5 0.8 728 1.74
C20-C21-C16 112.2 109.8 2.4 1.5 90 1.59
C37-C38-C39 121.7 120.2 1.5 1.0 476 1.57
N49-C50-N51 125.1 126.6 -1.5 1.0 20 1.56
C47-C48-N49 122.8 124.1 -1.3 0.9 427 1.53
C48-C47-C36 116.1 117.1 -1.0 0.7 16 1.44
C48-N49-C50 116.6 115.6 1.0 0.7 106 1.43
C35-C4-C5 131.9 130.0 1.8 1.3 92 1.38
C37-C35-C4 117.9 119.9 -1.9 1.4 31 1.35
C35-C37-C38 120.9 120.1 0.9 0.7 61 1.26
C40-C39-CL46 120.0 118.4 1.6 1.3 2376 1.24
C40-C41-C35 119.9 120.8 -0.9 0.7 3513 1.18
C41-C35-C4 122.5 120.7 1.8 1.7 1605 1.02
C10-C7-C6 114.0 111.8 2.2 2.5 217 0.87
C59-C60-C55 110.5 111.2 -0.6 0.8 586 0.79
C38-C39-CL46 120.2 120.9 -0.6 0.8 728 0.74
C58-C59-C60 111.9 111.3 0.6 1.0 1421 0.65
N54-C50-N51 115.8 116.5 -0.7 1.4 22 0.53
C41-C35-C37 119.6 119.4 0.2 0.9 2010 0.20
C4-C5-N1 105.3 105.4 -0.1 0.9 25 0.12
C40-C39-C38 119.8 119.7 0.0 0.8 229 0.05
C21-C16-C17 109.5 109.5 -0.0 1.2 259 0.03

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-… common
C41-C35-C4-C5 -133.4 452 12%
C37-C35-C4-N3 -131.7 528 19%
C41-C35-C4-N3 48.8 528 16%
C37-C35-C4-C5 46.1 452 15%
…-C50-N54-… unusual
N51-C50-N54-C55 -61.8 22 0%
N49-C50-N54-C55 119.9 22 0%
…-C6-C7-… unusual
N1-C6-C7-C10 0.3 196 0%
…-C6-N1-… common
C7-C6-N1-C5 -90.3 97 64%
C7-C6-N1-C2 91.3 49 76%

help? see BUSTER wiki Ligand Mogul Analysis: Dihedrals

Mogul ring results

Mogul rings schematic
'ok' → lime (ring strangeness score < 6 °)
'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 5.8
N1-C2-N3-C4-C5 58 0.2
C36-C47-C48-N49-C50-N51 41 4.2
C35-C37-C38-C39-C40-C41 246 0.2

‡ '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