Detailed ligand analysis report on 468 A 501

ligand picture

Electron density around 468 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 468 A 501 Statistics

Database ID 468 (PDB)
3-letter code 468
CC(2mFo-DFc) 0.9643
min(B-factor)‡ 26.3
avg(B-factor)‡ 32.7
max(B-factor)‡ 54.8
min(occupancy)‡ 1.00
max(occupancy)‡ 1.00
‡ hydrogen atoms excluded

Mogul Analysis:
'bad' bonds 0/25
'bad' bond angles 0/31
'unusual' dihedrals 0/3
'bad' rings 0/3
bonds rms Z 0.282
angles rms Z 0.486

help? see BUSTER wiki Ligand Statistics Table

Restraints used

restraints for 468 (_3S_-N-_3-CHLORO-2-METHYLPHENYL_-1-CYCLOHEXYL-5-OXOPYRROLIDINE-3-CARBOXAMIDE) from cif dictionary 468.grade_PDB_ligand.cif; generated by GRADE_PDB_LIGAND 1.2.9pre (June 16 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
C20-C15 1.400 1.392 0.008 0.012 3256 0.73
C3-N11 1.477 1.470 0.007 0.013 21 0.51
C6-C5 1.525 1.516 0.009 0.018 1743 0.51
C10-C9 1.539 1.530 0.009 0.019 36 0.45
C15-C16 1.405 1.399 0.006 0.013 49 0.44
C2-C3 1.527 1.522 0.006 0.014 1191 0.39
C18-C17 1.379 1.384 -0.005 0.013 2673 0.34
C6-C1 1.521 1.516 0.005 0.018 1743 0.30
C17-C16 1.393 1.391 0.002 0.008 28 0.26
C8-C9 1.527 1.531 -0.004 0.021 57 0.20
C19-C18 1.383 1.384 -0.002 0.010 2659 0.16
C17-CL1 1.732 1.734 -0.002 0.012 3693 0.15
C5-C4 1.526 1.525 0.001 0.013 1827 0.08
C9-C12 1.511 1.509 0.002 0.019 46 0.08
C23-C16 1.508 1.509 -0.001 0.011 1974 0.07
C1-C2 1.526 1.525 0.001 0.013 1827 0.06
C12-N13 1.351 1.350 0.001 0.014 362 0.05
O15-C7 1.220 1.220 -0.000 0.014 2954 0.04
C19-C20 1.384 1.384 -0.000 0.010 2659 0.04
C7-N11 1.345 1.346 -0.001 0.013 191 0.04
C4-C3 1.522 1.522 0.000 0.014 1191 0.03
O14-C12 1.228 1.228 0.000 0.012 3021 0.03
C15-N13 1.414 1.415 -0.000 0.014 1552 0.02
C8-C7 1.505 1.505 0.000 0.010 228 0.01
C10-N11 1.465 1.465 0.000 0.013 181 0.01

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
C8-C9-C12 109.4 112.1 -2.7 1.8 16 1.47
C18-C17-CL1 117.0 118.4 -1.4 1.3 2376 1.02
C10-N11-C3 122.0 124.2 -2.2 2.4 11 0.90
C3-N11-C7 124.5 122.7 1.8 2.1 16 0.85
C20-C15-N13 120.3 121.9 -1.6 2.2 1192 0.76
C16-C15-N13 118.4 119.3 -0.9 1.6 18 0.58
C4-C3-C2 110.1 111.0 -0.9 1.7 435 0.51
O14-C12-C9 121.6 122.1 -0.5 1.0 39 0.49
C1-C2-C3 110.2 110.9 -0.7 1.4 901 0.46
O14-C12-N13 123.7 124.2 -0.5 1.2 305 0.44
C19-C20-C15 119.6 119.0 0.6 1.7 2995 0.36
C9-C12-N13 114.7 114.8 -0.2 0.6 11 0.30
C10-N11-C7 113.5 113.8 -0.3 1.0 14 0.29
C5-C4-C3 110.5 110.9 -0.4 1.4 901 0.28
C18-C19-C20 120.2 120.4 -0.3 1.0 1853 0.27
C4-C3-N11 111.5 111.7 -0.2 0.9 18 0.22
C23-C16-C17 122.4 122.2 0.2 0.9 26 0.22
C5-C6-C1 111.1 110.9 0.2 1.0 1269 0.20
C18-C17-C16 122.9 123.0 -0.1 0.5 22 0.20
C6-C1-C2 111.4 111.3 0.2 1.0 1421 0.19
C19-C18-C17 119.3 119.4 -0.1 0.7 1865 0.18
O15-C7-C8 127.0 127.3 -0.2 1.1 174 0.18
C2-C3-N11 111.8 111.7 0.1 0.9 18 0.15
O15-C7-N11 124.7 124.8 -0.1 1.1 162 0.10
C6-C5-C4 111.2 111.3 -0.1 1.0 1421 0.07
C15-N13-C12 126.3 126.5 -0.1 2.4 92 0.06
C9-C10-N11 102.0 102.1 -0.1 1.8 10 0.05
C20-C15-C16 121.3 121.3 0.0 0.8 35 0.05
C23-C16-C15 121.2 121.2 0.0 1.0 42 0.04
C8-C7-N11 108.2 108.2 0.0 1.0 22 0.02
C16-C17-CL1 119.5 119.6 -0.0 0.6 26 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°
…-C12-N13-… common
O14-C12-N13-C15 3.7 340 99%
C9-C12-N13-C15 -175.2 87 100%
…-C15-N13-… common
C16-C15-N13-C12 146.5 354 27%
C20-C15-N13-C12 -32.1 934 30%
…-C3-N11-… common
C2-C3-N11-C10 36.5 16 31%
C4-C3-N11-C10 -87.3 16 25%

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 °
C7-C8-C9-C10-N11 10 1.1
C15-C20-C19-C18-C17-C16 167 1.1
C1-C2-C3-C4-C5-C6 67 0.5

‡ '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