Detailed ligand analysis report on NAD A 500

ligand picture

Electron density around NAD A 500 :
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 NAD A 500 Statistics

Mogul Analysis:
Database ID	NAD (PDB)
3-letter code	NAD
CC(2mF_o-DF_c)	0.9812
min(B-factor)‡	17.7
avg(B-factor)‡	22.0
max(B-factor)‡	25.5
min(occupancy)‡	1.00
max(occupancy)‡	1.00
‡ hydrogen atoms excluded
'bad' bonds	0/45
'bad' bond angles	0/60
'unusual' dihedrals	0/6
'bad' rings	0/4
bonds rms Z	0.553
angles rms Z	0.907

help? see BUSTER wiki Ligand Statistics Table

Restraints used

restraints for NAD (NICOTINAMIDE-ADENINE-DINUCLEOTIDE) from cif dictionary NAD.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 'ok' → lime (1.5 < Z < 2.5) 'good' → green (Z < 1.5) 'unknown' → gray (Mogul does not find sufficient CSD equivalents).
PN-O2N	1.481	1.527	-0.046	0.030	30	1.54
C3B-C4B	1.543	1.526	0.018	0.014	577	1.28
PA-O2A	1.489	1.527	-0.038	0.030	30	1.28
O4D-C4D	1.455	1.444	0.011	0.011	1633	1.01
C2B-C1B	1.518	1.530	-0.013	0.014	341	0.90
C4N-C3N	1.401	1.391	0.011	0.013	4266	0.84
O3D-C3D	1.434	1.423	0.010	0.013	3264	0.79
C7N-N7N	1.344	1.327	0.016	0.021	568	0.79
C6N-N1N	1.352	1.347	0.006	0.008	44	0.76
C3D-C4D	1.535	1.526	0.010	0.014	577	0.72
C6A-N1A	1.355	1.350	0.005	0.010	239	0.51
C6A-N6A	1.343	1.336	0.007	0.014	531	0.50
O4B-C1B	1.410	1.415	-0.006	0.011	592	0.49
O2B-C2B	1.418	1.423	-0.006	0.013	3264	0.43
O4B-C4B	1.448	1.444	0.005	0.011	1633	0.42
C2A-N1A	1.339	1.335	0.005	0.011	829	0.41
C4A-N3A	1.344	1.339	0.005	0.012	542	0.40
C8A-N7A	1.314	1.311	0.003	0.008	447	0.38
PN-O3	1.598	1.594	0.004	0.011	21	0.38
C2D-C3D	1.526	1.530	-0.005	0.013	510	0.36
C3N-C7N	1.507	1.501	0.006	0.016	409	0.36
C2B-C3B	1.526	1.530	-0.005	0.013	510	0.36
C8A-N9A	1.372	1.370	0.003	0.008	190	0.35
C5N-C4N	1.388	1.384	0.004	0.010	2659	0.34
C2N-N1N	1.346	1.344	0.002	0.006	10	0.33
PA-O3	1.591	1.594	-0.003	0.011	21	0.31
C2A-N3A	1.338	1.335	0.003	0.011	829	0.30
O4D-C1D	1.407	1.404	0.004	0.012	17	0.29
C2N-C3N	1.384	1.381	0.002	0.007	79	0.28
C5B-C4B	1.504	1.508	-0.003	0.012	1182	0.28
C5A-C6A	1.411	1.408	0.003	0.010	166	0.27
O7N-C7N	1.233	1.239	-0.006	0.025	568	0.24
O5D-C5D	1.446	1.443	0.003	0.015	124	0.22
PA-O1A	1.478	1.482	-0.004	0.018	31	0.20
C5D-C4D	1.510	1.508	0.002	0.012	1182	0.20
C5A-N7A	1.388	1.387	0.001	0.007	359	0.16
PN-O1N	1.479	1.482	-0.002	0.018	31	0.12
O2D-C2D	1.425	1.423	0.001	0.013	3264	0.10
C1B-N9A	1.460	1.459	0.001	0.012	78	0.09
O5B-C5B	1.444	1.443	0.001	0.015	124	0.07
C2D-C1D	1.529	1.530	-0.001	0.014	354	0.06
C4A-N9A	1.374	1.374	-0.000	0.008	181	0.05
C5A-C4A	1.387	1.388	-0.001	0.011	332	0.05
C6N-C5N	1.376	1.376	-0.000	0.018	211	0.03
O3B-C3B	1.423	1.423	0.000	0.013	3264	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 '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).
C4B-O4B-C1B	105.7	109.5	-3.8	1.4	434	2.61
C2D-C1D-N1N	117.8	113.6	4.2	1.8	20	2.30
O4B-C1B-N9A	111.3	108.4	2.9	1.3	66	2.25
O5B-C5B-C4B	104.6	109.1	-4.5	2.3	84	1.93
C3D-C2D-C1D	99.4	101.5	-2.1	1.2	285	1.82
O4B-C1B-C2B	104.4	106.5	-2.1	1.2	307	1.82
C4N-C3N-C7N	117.2	120.7	-3.5	2.4	598	1.45
C3B-C2B-C1B	99.8	101.5	-1.7	1.2	273	1.45
O3D-C3D-C2D	108.6	111.9	-3.3	2.6	938	1.26
C4A-N9A-C1B	125.0	127.0	-1.9	1.8	67	1.10
O4D-C1D-C2D	105.9	107.0	-1.1	1.1	17	1.07
O3-PA-O1A	111.2	108.7	2.5	2.4	19	1.02
O4B-C4B-C3B	106.6	105.3	1.3	1.3	448	1.02
O7N-C7N-C3N	118.7	119.5	-0.8	0.8	373	1.00
C1B-N9A-C8A	128.6	126.8	1.8	1.9	65	0.96
O2D-C2D-C1D	113.2	110.6	2.6	2.8	336	0.93
C2B-C1B-N9A	115.5	114.1	1.4	1.5	59	0.92
C6N-C5N-C4N	119.2	119.9	-0.7	0.7	149	0.92
C6N-N1N-C2N	121.8	122.2	-0.3	0.4	10	0.88
C3N-C7N-N7N	118.7	117.9	0.8	1.0	373	0.84
C4D-O4D-C1D	108.4	109.5	-1.1	1.4	447	0.80
O4D-C4D-C3D	106.1	105.3	0.9	1.3	448	0.67
O3D-C3D-C4D	109.3	111.0	-1.7	2.6	541	0.66
C5N-C4N-C3N	119.9	120.4	-0.4	0.7	3664	0.66
C2B-C3B-C4B	103.1	102.5	0.6	1.0	376	0.64
O3B-C3B-C2B	110.3	111.9	-1.6	2.6	938	0.63
C2N-C3N-C4N	118.4	118.8	-0.4	0.7	35	0.55
O3B-C3B-C4B	112.3	111.0	1.3	2.6	541	0.51
C6N-N1N-C1D	118.3	119.3	-1.0	2.1	10	0.48
O7N-C7N-N7N	122.2	122.8	-0.6	1.3	516	0.45
C3N-C2N-N1N	120.4	120.1	0.2	0.5	24	0.44
C5B-C4B-C3B	114.5	115.3	-0.8	1.8	70	0.44
O5D-C5D-C4D	108.1	109.1	-0.9	2.3	84	0.39
C2A-N1A-C6A	118.9	118.5	0.4	1.0	154	0.38
O4D-C4D-C5D	110.1	109.6	0.6	1.5	204	0.37
O4B-C4B-C5B	110.1	109.6	0.5	1.5	204	0.36
O4D-C1D-N1N	108.6	108.4	0.2	0.7	16	0.34
O2B-C2B-C3B	112.7	111.9	0.8	2.6	938	0.29
O3-PN-O1N	109.4	108.7	0.7	2.4	19	0.29
N3A-C4A-N9A	127.4	127.1	0.3	1.2	126	0.28
C6A-C5A-N7A	132.4	132.1	0.3	1.2	118	0.27
O2B-C2B-C1B	111.3	110.6	0.7	2.8	323	0.24
N6A-C6A-N1A	118.5	118.2	0.3	1.2	214	0.24
C5A-C4A-N9A	105.9	105.7	0.1	0.5	148	0.23
C5D-C4D-C3D	114.9	115.3	-0.4	1.8	70	0.23
C2A-N3A-C4A	111.0	111.5	-0.4	2.0	224	0.22
C2N-N1N-C1D	119.8	119.3	0.5	2.1	10	0.22
O2D-C2D-C3D	111.4	111.9	-0.6	2.6	938	0.22
C6A-C5A-C4A	116.9	117.0	-0.1	0.7	127	0.20
C5A-C6A-N6A	123.8	123.7	0.2	1.0	144	0.15
C5A-C4A-N3A	126.8	126.8	-0.1	0.7	212	0.13
C2D-C3D-C4D	102.4	102.5	-0.1	1.0	376	0.11
C5N-C6N-N1N	120.1	120.2	-0.1	0.9	38	0.10
N3A-C2A-N1A	128.7	128.8	-0.1	0.9	329	0.09
C4A-C5A-N7A	110.7	110.7	0.0	0.5	241	0.06
C4A-N9A-C8A	105.7	105.7	-0.0	0.5	150	0.05
C5A-C6A-N1A	117.6	117.6	0.0	0.9	133	0.04
C5A-N7A-C8A	103.7	103.7	-0.0	0.5	265	0.03
N9A-C8A-N7A	114.1	114.1	-0.0	0.7	173	0.02
PN-O3-PA	132.5	132.5	0.0	3.0	21	0.01

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).
…-C1B-N9A-…			common
O4B-C1B-N9A-C8A	71.1	64	12%
O4B-C1B-N9A-C4A	-119.9	68	16%
C2B-C1B-N9A-C4A	121.4	66	18%
C2B-C1B-N9A-C8A	-47.7	63	11%
…-C3N-C7N-…			common
C4N-C3N-C7N-O7N	-19.1	707	39%
C2N-C3N-C7N-N7N	-12.0	111	42%
C2N-C3N-C7N-O7N	160.6	111	43%
C4N-C3N-C7N-N7N	168.4	707	40%
…-C4B-C5B-…			rare
C3B-C4B-C5B-O5B	-67.1	63	40%
O4B-C4B-C5B-O5B	172.8	63	6%
…-C4D-C5D-…			common
C3D-C4D-C5D-O5D	54.8	63	84%
O4D-C4D-C5D-O5D	-65.0	63	90%
…-C5B-O5B-…			common
C4B-C5B-O5B-PA	128.4	74	14%
…-C5D-O5D-…			common
C4D-C5D-O5D-PN	147.5	74	42%

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).
C4B-O4B-C1B-C2B-C3B	191	1.4
C4D-O4D-C1D-C2D-C3D	191	0.5
C5A-C6A-N1A-C2A-N3A-C4A	184	0.2
N9A-C8A-N7A-C5A-C4A	186	0.1

‡ '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

Mogul homepage
Mogul reference