Detailed ligand analysis report on 880 A 501

ligand picture

Density around 880 A 501 :
2mFo-DFc (at 1.3 rmsd) in grey.
mFo-DFc (at 3 rmsd) in red (negative) and green (positive),
(picture produced with PyMOL)

Residue 880 A 501 Statistics

CC(2Fo-Fc) 0.9558
min(B-factor)‡ 28.7
avg(B-factor)‡ 36.2
max(B-factor)‡ 44.2
min(occ)‡ 1.00
max(occ)‡ 1.00
‡ hydrogen atoms excluded
Mogul Analysis:
"bad" bonds 0/38
"bad" angles 0/43
"unusual" dihedrals 0/4
"bad" rings 0/4
bonds rms Z 0.539
angles rms Z 1.043

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 using refmacdict2tnt revision 1.20.2.13; generated by GRADE_PDB_LIGAND 1.2.8 (April 29 2014) using MOGUL 1.6(RC5), CSD as535be, with quantum mechanics RM1

Mogul bond results

Mogul bonds schematic
blue "good" bonds Z < 1.5
gray "unknown" where 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 3673 1.31
C5-C4 1.391 1.377 0.014 0.014 109 1.00
C2-N3 1.302 1.316 -0.014 0.015 17 0.95
C50-N51 1.353 1.341 0.012 0.013 403 0.93
C39-C38 1.376 1.388 -0.012 0.013 374 0.93
C7-C6 1.533 1.514 0.019 0.024 204 0.80
C36-C5 1.483 1.478 0.005 0.007 10 0.72
C50-N54 1.351 1.342 0.009 0.013 12 0.71
C36-N51 1.345 1.341 0.005 0.007 809 0.67
C58-C57 1.528 1.516 0.012 0.018 1790 0.65
C21-C20 1.521 1.512 0.008 0.014 29 0.60
C5-N1 1.398 1.389 0.009 0.015 68 0.58
C59-C58 1.526 1.516 0.010 0.018 1790 0.54
C56-C55 1.510 1.518 -0.008 0.015 678 0.53
C55-N54 1.465 1.459 0.006 0.013 40 0.49
C17-C18 1.519 1.512 0.006 0.014 29 0.45
C4-N3 1.378 1.384 -0.006 0.013 236 0.44
C10-C7 1.494 1.511 -0.016 0.038 1047 0.43
C20-N19 1.473 1.466 0.007 0.018 124 0.41
C50-N49 1.345 1.341 0.004 0.012 117 0.39
C41-C35 1.396 1.391 0.005 0.012 4132 0.38
C18-N19 1.473 1.466 0.007 0.018 124 0.37
C6-N1 1.471 1.467 0.004 0.013 485 0.35
C40-C39 1.388 1.384 0.004 0.013 2440 0.32
C41-C40 1.385 1.383 0.002 0.009 5145 0.24
C60-C55 1.514 1.518 -0.003 0.015 678 0.22
C39-CL46 1.736 1.734 0.002 0.012 3673 0.17
C48-N49 1.341 1.340 0.002 0.011 2639 0.16
C57-C56 1.526 1.524 0.002 0.012 1741 0.16
C35-C4 1.480 1.478 0.002 0.010 779 0.15
C21-C16 1.533 1.531 0.002 0.015 973 0.14
C37-C38 1.382 1.381 0.000 0.010 1971 0.05
C47-C48 1.380 1.381 -0.001 0.012 2594 0.05
C17-C16 1.531 1.531 -0.001 0.015 973 0.04
C37-C35 1.392 1.391 0.000 0.009 1932 0.04
C47-C36 1.388 1.388 -0.000 0.010 1480 0.03
C2-N1 1.375 1.375 -0.000 0.013 11 0.01
C59-C60 1.524 1.524 -0.000 0.012 1741 0.01

Mogul angle results

Mogul angles schematic
orange "poor" 2.5 < Z < 4
green "ok" 1.5 < Z < 2.5
blue "good" angles Z < 1.5
gray "unknown" where Mogul does not find sufficient CSD equivalents

atoms actual
in °		 Mogul
mean
in °		 difference
in °		 Mogul σ
in °		 Mogul
#samples		 Zscore
C56-C55-N54 114.8 110.4 4.4 1.6 34 2.80
C5-C36-N51 118.5 115.8 2.6 1.0 10 2.60
C60-C55-N54 114.4 110.4 4.0 1.6 34 2.55
N54-C50-N51 119.2 116.5 2.7 1.4 22 1.94
C35-C4-C5 132.2 130.0 2.1 1.3 84 1.63
C40-C39-CL46 120.3 118.4 1.9 1.3 2378 1.44
N54-C50-N49 114.6 116.5 -1.9 1.4 22 1.38
C47-C36-N51 121.8 123.0 -1.1 0.8 669 1.37
C35-C4-N3 117.2 119.3 -2.1 1.5 206 1.36
C47-C36-C5 119.7 121.1 -1.5 1.1 10 1.29
C39-C38-CL45 119.8 120.8 -1.1 0.8 742 1.25
C4-C5-N1 104.5 105.5 -1.0 1.0 21 1.00
C38-C39-CL46 120.0 120.8 -0.8 0.8 742 0.96
C47-C48-N49 123.3 124.1 -0.8 0.9 387 0.87
C37-C38-C39 121.0 120.2 0.7 1.0 484 0.77
C59-C58-C57 111.7 110.9 0.8 1.1 1272 0.74
C6-N1-C5 127.8 126.8 1.0 1.3 19 0.73
C20-N19-C18 111.4 110.5 0.9 1.4 56 0.63
C6-N1-C2 125.6 126.6 -1.0 1.7 24 0.60
C10-C7-C6 113.3 111.8 1.5 2.6 197 0.58
C59-C60-C55 110.7 111.2 -0.4 0.8 548 0.54
C37-C38-CL45 119.1 118.5 0.7 1.2 1937 0.54
C41-C40-C39 119.8 120.2 -0.4 0.7 472 0.53
N49-C50-N51 126.0 126.5 -0.5 0.9 22 0.52
C18-C17-C16 108.9 109.7 -0.7 1.5 89 0.50
C58-C57-C56 111.8 111.3 0.5 1.1 1467 0.49
C37-C35-C4 120.6 119.8 0.7 1.5 27 0.48
C4-N3-C2 105.9 105.2 0.7 1.6 12 0.42
C48-C47-C36 116.8 117.0 -0.2 0.6 14 0.38
C36-N51-C50 116.3 116.6 -0.3 0.9 16 0.37
C41-C35-C37 119.0 119.4 -0.4 1.0 1907 0.36
C40-C41-C35 120.6 120.8 -0.2 0.8 3393 0.30
C48-N49-C50 115.4 115.6 -0.2 0.7 94 0.26
C5-C4-N3 110.6 110.3 0.3 1.2 71 0.25
C35-C37-C38 119.9 120.0 -0.1 0.7 60 0.19
C41-C35-C4 120.4 120.7 -0.3 1.7 1509 0.18
C7-C6-N1 112.7 112.3 0.3 2.0 25 0.17
C20-C21-C16 109.4 109.7 -0.2 1.5 89 0.15
C60-C55-C56 110.8 110.7 0.1 0.8 294 0.14
C57-C56-C55 111.1 111.2 -0.1 0.8 548 0.14
C21-C16-C17 109.3 109.4 -0.1 1.2 283 0.10
C40-C39-C38 119.7 119.7 -0.0 0.9 229 0.05
C58-C59-C60 111.3 111.3 0.0 1.1 1467 0.02

Mogul dihedral results

Mogul dihedrals schematic
green "rare" dihedrals with all torsions having > 0.5% of Mogul population within ±10°
blue "common" dihedrals with all torsions having > 10% of Mogul population within ±10°
gray "unknown" where Mogul does not find sufficient CSD equivalents

atoms actual torsion
angle in °		 classification or
% Mogul population
within ±10°		 Mogul
histogram		 Mogul
# samples
…-C35-C4-…   rare
C41-C35-C4-C5 -129.7 7% 362
C37-C35-C4-N3 -130.9 19% 450
C41-C35-C4-N3 46.7 17% 450
C37-C35-C4-C5 52.6 9% 362
…-C50-N54-…   common
N51-C50-N54-C55 -8.0 45% 22
N49-C50-N54-C55 167.3 55% 22
…-C6-C7-…   rare
N1-C6-C7-C10 31.4 1% 163
…-C6-N1-…   common
C7-C6-N1-C5 -107.8 31% 75
C7-C6-N1-C2 71.7 44% 41

Mogul ring results

Mogul rings schematic
blue "good" ring strangeness score < 3 °
gray "unknown" where Mogul does not find sufficient CSD equivalents

atoms Mogul
# samples		 Ring strangeness
score‡ in °
C55-C56-C57-C58-C59-C60 143 0.3
N1-C2-N3-C4-C5 51 0.1
C36-C47-C48-N49-C50-N51 37 0.7
C35-C37-C38-C39-C40-C41 238 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.

Mogul Run Conditions