Detailed ligand analysis report on ANP A 502

ligand picture

Electron density around ANP A 502 :
2mF_o-DF_c (at 0.7 rmsd) in grey.
mF_o-DF_c (at 3 rmsd) in red (negative) and green (positive),
(picture produced with PyMOL)

help? see BUSTER wiki Ligand Electron Density Picture

Residue ANP A 502 Statistics

Mogul Analysis:
Database ID	ANP (PDB)
3-letter code	ANP
CC(2mF_o-DF_c)	0.7687
min(B-factor)‡	43.6
avg(B-factor)‡	48.9
max(B-factor)‡	54.1
min(occupancy)‡	0.50
max(occupancy)‡	0.50
‡ hydrogen atoms excluded
'bad' bonds	6/28
'bad' bond angles	9/33
'unusual' dihedrals	0/3
'bad' rings	0/3
bonds rms Z	4.275
angles rms Z	4.310

help? see BUSTER wiki Ligand Statistics Table

Restraints used

restraints for ANP (PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER) from cif dictionary ANP.cif; bUSTER common-compounds v 3.0, 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

atoms	actual in Å	Mogul mean in Å	difference in Å	Mogul σ in Å	Mogul # samples	Zscore
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).
O5'-C5'	1.626	1.443	0.183	0.015	124	11.89
PG-O2G	1.546	1.454	0.092	0.009	68	9.72
PB-O1B	1.532	1.454	0.078	0.009	68	8.25
C5-C4	1.476	1.388	0.088	0.011	332	7.92
C4-N3	1.424	1.339	0.085	0.012	542	7.10
C8-N7	1.350	1.311	0.039	0.008	447	5.17
C6-N6	1.384	1.336	0.048	0.014	531	3.35
PB-N3B	1.562	1.631	-0.068	0.022	23	3.06
O2'-C2'	1.458	1.423	0.035	0.013	3264	2.67
PG-N3B	1.572	1.631	-0.059	0.022	23	2.65
C5'-C4'	1.539	1.508	0.031	0.012	1182	2.55
C4-N9	1.395	1.374	0.020	0.008	181	2.52
C6-N1	1.370	1.350	0.020	0.010	239	2.03
C3'-C4'	1.551	1.526	0.026	0.014	577	1.87
C8-N9	1.381	1.370	0.011	0.008	190	1.47
O3'-C3'	1.442	1.423	0.019	0.013	3264	1.45
C2'-C1'	1.549	1.530	0.019	0.014	341	1.39
O4'-C4'	1.458	1.444	0.015	0.011	1633	1.31
PA-O1A	1.492	1.527	-0.035	0.030	30	1.17
O4'-C1'	1.427	1.415	0.012	0.011	592	1.06
C2'-C3'	1.541	1.530	0.011	0.013	510	0.82
C2-N3	1.343	1.335	0.009	0.011	829	0.81
C2-N1	1.342	1.335	0.008	0.011	829	0.70
C1'-N9	1.452	1.459	-0.007	0.012	78	0.62
C5-N7	1.385	1.387	-0.002	0.007	359	0.31
PA-O2A	1.485	1.482	0.004	0.018	31	0.19
PA-O3A	1.593	1.594	-0.001	0.011	21	0.07
C5-C6	1.408	1.408	0.000	0.010	166	0.01

help? see BUSTER wiki Ligand Mogul Analysis: Bonds

Mogul angle results

atoms	actual in °	Mogul mean in °	difference in °	Mogul σ in °	Mogul # samples	Zscore
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).
C4-N9-C8	111.3	105.7	5.5	0.5	150	11.81
C5-N7-C8	108.5	103.7	4.9	0.5	265	10.64
N9-C8-N7	109.0	114.1	-5.1	0.7	173	7.20
C5-C4-N9	102.5	105.7	-3.3	0.5	148	7.10
N3-C2-N1	123.3	128.8	-5.5	0.9	329	6.26
C6-C5-C4	113.3	117.0	-3.7	0.7	127	5.67
N3-C4-N9	133.5	127.1	6.4	1.2	126	5.53
C2-N1-C6	123.4	118.5	4.8	1.0	154	5.05
C6-C5-N7	138.0	132.1	5.9	1.2	118	5.02
C5-C4-N3	124.1	126.8	-2.8	0.7	212	3.88
C4-C5-N7	108.7	110.7	-2.0	0.5	241	3.77
C5-C6-N1	120.6	117.6	3.0	0.9	133	3.48
O4'-C1'-C2'	110.4	106.5	3.9	1.2	307	3.37
C5-C6-N6	120.6	123.7	-3.0	1.0	144	2.95
O5'-C5'-C4'	102.3	109.1	-6.8	2.3	84	2.93
C5'-C4'-C3'	110.3	115.3	-5.0	1.8	70	2.81
O4'-C1'-N9	111.8	108.4	3.4	1.3	66	2.63
C2-N3-C4	115.4	111.5	3.9	2.0	224	1.98
C1'-N9-C8	123.3	126.8	-3.5	1.9	65	1.83
O4'-C4'-C5'	112.2	109.6	2.7	1.5	204	1.79
O3A-PA-O2A	112.7	108.7	3.9	2.4	19	1.62
O4'-C4'-C3'	107.2	105.3	2.0	1.3	448	1.55
O1B-PB-N3B	110.3	112.1	-1.8	1.7	15	1.11
C2'-C3'-C4'	103.4	102.5	1.0	1.0	376	0.98
C4-N9-C1'	125.5	127.0	-1.5	1.8	67	0.86
C4'-O4'-C1'	108.3	109.5	-1.2	1.4	434	0.85
O2'-C2'-C1'	112.9	110.6	2.3	2.8	323	0.82
N6-C6-N1	118.7	118.2	0.5	1.2	214	0.45
C3'-C2'-C1'	101.9	101.5	0.4	1.2	273	0.33
O3'-C3'-C4'	111.6	111.0	0.6	2.6	541	0.24
C2'-C1'-N9	114.3	114.1	0.1	1.5	59	0.10
O3'-C3'-C2'	111.7	111.9	-0.3	2.6	938	0.10
O2'-C2'-C3'	112.2	111.9	0.2	2.6	938	0.09

help? see BUSTER wiki Ligand Mogul Analysis: Angles

Mogul dihedral results

atoms	actual torsion angle in °	Mogul # samples	classification or % Mogul population within ± 10°
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).
…-C1'-N9-…			common
C2'-C1'-N9-C4	102.5	66	18%
O4'-C1'-N9-C8	47.0	64	17%
O4'-C1'-N9-C4	-131.2	68	15%
C2'-C1'-N9-C8	-79.3	63	22%
…-C4'-C5'-…			rare
O4'-C4'-C5'-O5'	59.6	63	71%
C3'-C4'-C5'-O5'	179.1	63	10%
…-C5'-O5'-…			common
C4'-C5'-O5'-PA	-171.5	74	43%

help? see BUSTER wiki Ligand Mogul Analysis: Dihedrals

Mogul ring results

atoms	Mogul # samples	Ring strangeness score‡ in °
Mogul rings schematic 'good' → green (ring strangeness score < 3 °) 'unknown' → gray (Mogul does not find sufficient CSD equivalents).
N9-C8-N7-C5-C4	186	0.0
C5-C6-N1-C2-N3-C4	184	0.2
C4'-O4'-C1'-C2'-C3'	191	1.1

‡ '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

Mogul executable is/scratch/software/CSDS/latest/bin/mogul

Mogul minimum # samples to report for BOND, ANGLE, RING 10

Mogul minimum # samples to report for TORSIONS 15

Mogul instructions used:

MOGUL EDIT HYDROGENS GENERATE MISSING
CONFIG SEARCH ALL GENERALISATION ON
CONFIG SEARCH BOND MIN_OBSERVATIONS EXACT 10
CONFIG SEARCH ANGLE MIN_OBSERVATIONS EXACT 10
# no generalisation for torsion or ring
CONFIG SEARCH TORSION MIN_OBSERVATIONS EXACT 0
CONFIG SEARCH RING MIN_OBSERVATIONS EXACT 0
CONFIG SEARCH BOND MIN_RELEVANCE 0.9
CONFIG SEARCH ANGLE MIN_RELEVANCE 0.9
CONFIG SEARCH ALL FILTER RFACTOR 0.05
CONFIG SEARCH ALL FILTER EXCLUDE_SOLVENTS
CONFIG SEARCH ALL FILTER EXCLUDE_ORGANOMETALLICS

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