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) 0.9043
min(B-factor)‡ 30.3
avg(B-factor)‡ 32.4
max(B-factor)‡ 36.2
min(occupancy)‡ 1.00
max(occupancy)‡ 1.00
‡ hydrogen atoms excluded

Mogul Analysis:
'bad' bonds 14/25
'bad' bond angles 16/31
'unusual' dihedrals 0/3
'bad' rings 1/3
bonds rms Z 9.335
angles rms Z 5.532

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
'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
C17-C16 1.610 1.391 0.219 0.008 28 26.28
C15-N13 1.098 1.415 -0.317 0.014 1552 22.23
C10-N11 1.654 1.465 0.188 0.013 181 14.69
C19-C20 1.524 1.384 0.139 0.010 2659 13.39
C8-C7 1.402 1.505 -0.103 0.010 228 10.42
C12-N13 1.492 1.350 0.142 0.014 362 9.82
C3-N11 1.577 1.470 0.107 0.013 21 8.20
C15-C16 1.502 1.399 0.103 0.013 49 7.79
C19-C18 1.455 1.384 0.071 0.010 2659 6.81
C6-C5 1.622 1.516 0.106 0.018 1743 5.99
C5-C4 1.600 1.525 0.074 0.013 1827 5.61
C2-C3 1.596 1.522 0.074 0.014 1191 5.24
C8-C9 1.424 1.531 -0.107 0.021 57 5.06
C7-N11 1.410 1.346 0.064 0.013 191 4.82
C20-C15 1.436 1.392 0.044 0.012 3256 3.76
C6-C1 1.582 1.516 0.066 0.018 1743 3.75
C10-C9 1.595 1.530 0.064 0.019 36 3.40
C18-C17 1.429 1.384 0.045 0.013 2673 3.38
O14-C12 1.188 1.228 -0.040 0.012 3021 3.38
C17-CL1 1.771 1.734 0.037 0.012 3693 3.12
C9-C12 1.486 1.509 -0.023 0.019 46 1.16
O15-C7 1.234 1.220 0.013 0.014 2954 0.98
C4-C3 1.533 1.522 0.011 0.014 1191 0.76
C1-C2 1.531 1.525 0.006 0.013 1827 0.43
C23-C16 1.512 1.509 0.003 0.011 1974 0.28

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
C2-C3-N11 99.4 111.7 -12.3 0.9 18 14.33
C4-C3-N11 121.0 111.7 9.3 0.9 18 10.84
C10-N11-C7 105.2 113.8 -8.6 1.0 14 8.84
C9-C12-N13 110.1 114.8 -4.8 0.6 11 8.23
C18-C17-C16 119.2 123.0 -3.9 0.5 22 8.13
O15-C7-C8 118.5 127.3 -8.8 1.1 174 7.84
C16-C17-CL1 123.7 119.6 4.1 0.6 26 7.02
C3-N11-C7 107.9 122.7 -14.8 2.1 16 6.92
C16-C15-N13 110.5 119.3 -8.9 1.6 18 5.62
C1-C2-C3 118.7 110.9 7.8 1.4 901 5.41
C8-C7-N11 113.3 108.2 5.1 1.0 22 5.12
C5-C6-C1 115.9 110.9 5.1 1.0 1269 4.88
C6-C1-C2 115.9 111.3 4.6 1.0 1421 4.74
C6-C5-C4 115.8 111.3 4.6 1.0 1421 4.71
O14-C12-N13 129.2 124.2 5.0 1.2 305 4.30
C20-C15-N13 130.9 121.9 9.0 2.2 1192 4.11
C5-C4-C3 105.7 110.9 -5.1 1.4 901 3.55
C20-C15-C16 118.7 121.3 -2.6 0.8 35 3.36
C23-C16-C17 119.1 122.2 -3.0 0.9 26 3.17
O15-C7-N11 128.2 124.8 3.4 1.1 162 3.04
C8-C9-C12 108.0 112.1 -4.0 1.8 16 2.24
C15-N13-C12 121.6 126.5 -4.9 2.4 92 2.00
C19-C18-C17 120.6 119.4 1.2 0.7 1865 1.68
C19-C20-C15 121.8 119.0 2.8 1.7 2995 1.63
O14-C12-C9 120.6 122.1 -1.5 1.0 39 1.61
C10-N11-C3 121.1 124.2 -3.1 2.4 11 1.27
C23-C16-C15 122.1 121.2 0.9 1.0 42 0.96
C18-C17-CL1 117.1 118.4 -1.2 1.3 2376 0.93
C18-C19-C20 121.0 120.4 0.6 1.0 1853 0.62
C4-C3-C2 111.8 111.0 0.8 1.7 435 0.44
C9-C10-N11 101.9 102.1 -0.2 1.8 10 0.11

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 9.6 340 100%
C9-C12-N13-C15 -165.3 87 100%
…-C15-N13-… common
C16-C15-N13-C12 140.3 354 21%
C20-C15-N13-C12 -39.9 934 28%
…-C3-N11-… common
C2-C3-N11-C10 82.3 16 38%
C4-C3-N11-C10 -40.2 16 44%

help? see BUSTER wiki Ligand Mogul Analysis: Dihedrals

Mogul ring results

Mogul rings schematic
'bad' → purple (ring strangeness score > 9 °)
'poor' → violet (ring strangeness score < 9 °)
'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 °
C7-C8-C9-C10-N11 10 8.1
C15-C20-C19-C18-C17-C16 167 0.1
C1-C2-C3-C4-C5-C6 67 14.7

‡ '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