FMO DATABASE

FMODB ID: P5JLZ

Calculation Name: 2A54-A-Xray26

Preferred Name:

Target Type:

Ligand Name: {(4z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio)propanimidoyl]-5-oxo-4,5-dihydro-1h-imidazol-1-yl}acetic acid

ligand 3-letter code: NRQ

PDB ID: 2A54

Chain ID: A

ChEMBL ID:

UniProt ID: Q9GZ28

Base Structure: X-ray

Registration Date: 2018-07-26

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	Apo structure with with a 3 angstrom solvent shell.
Procedure	Auto-FMO protocol ver. 1.20180227

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	121
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-383369.802561
FMO2-HF: Nuclear repulsion	354089.368606
FMO2-HF: Total energy	-29280.433955
FMO2-MP2: Total energy	-29362.095636

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:-2:ACE)

Summations of interaction energy for fragment #1(A:-2:ACE)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
25.885	-5.892	36.691	0.068	-4.98	-0.01

Interaction energy analysis for fragmet #1(A:-2:ACE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.095 / q_NPA : -0.058

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	0	GLY	0	0.048	0.042	3.804	0.131	1.538	-0.020	-0.564	-0.822	-0.004
4	A	1	SER	0	-0.013	-0.020	6.806	0.353	0.353	0.000	0.000	0.000	0.000
5	A	2	ALA	0	0.103	0.032	8.778	-0.194	-0.194	0.000	0.000	0.000	0.000
6	A	3	SER	0	-0.007	-0.016	10.866	0.045	0.045	0.000	0.000	0.000	0.000
7	A	4	PHE	0	-0.063	-0.016	8.027	0.111	0.111	0.000	0.000	0.000	0.000
8	A	5	LEU	0	-0.038	0.013	6.641	-0.098	-0.098	0.000	0.000	0.000	0.000
9	A	6	LYS	1	0.934	0.961	9.872	0.411	0.411	0.000	0.000	0.000	0.000
10	A	7	LYS	1	0.996	1.000	12.842	0.261	0.261	0.000	0.000	0.000	0.000
11	A	8	THR	0	0.043	0.026	15.586	0.011	0.011	0.000	0.000	0.000	0.000
12	A	9	MET	0	-0.036	-0.005	13.624	-0.014	-0.014	0.000	0.000	0.000	0.000
13	A	10	PRO	0	-0.002	0.012	18.196	0.011	0.011	0.000	0.000	0.000	0.000
14	A	11	PHE	0	0.028	-0.002	20.875	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	12	LYS	1	0.928	0.953	23.292	0.068	0.068	0.000	0.000	0.000	0.000
16	A	13	THR	0	0.036	0.033	26.116	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	14	THR	0	-0.057	-0.029	28.638	0.001	0.001	0.000	0.000	0.000	0.000
18	A	15	ILE	0	0.030	0.021	31.448	0.001	0.001	0.000	0.000	0.000	0.000
19	A	16	GLU	-1	-0.769	-0.846	33.728	-0.018	-0.018	0.000	0.000	0.000	0.000
20	A	17	GLY	0	-0.011	0.003	36.587	0.001	0.001	0.000	0.000	0.000	0.000
21	A	18	THR	0	0.008	-0.002	39.031	0.000	0.000	0.000	0.000	0.000	0.000
22	A	19	VAL	0	-0.005	0.008	40.392	0.001	0.001	0.000	0.000	0.000	0.000
23	A	20	ASN	0	-0.019	-0.012	43.069	0.000	0.000	0.000	0.000	0.000	0.000
24	A	21	GLY	0	0.032	0.018	46.181	0.000	0.000	0.000	0.000	0.000	0.000
25	A	22	HIS	0	-0.032	-0.007	44.341	0.001	0.001	0.000	0.000	0.000	0.000
26	A	23	TYR	0	-0.050	-0.045	40.822	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	24	PHE	0	-0.007	-0.010	37.157	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	25	LYS	1	0.958	0.989	36.847	0.024	0.024	0.000	0.000	0.000	0.000
29	A	26	CYS	0	-0.018	-0.015	34.967	0.000	0.000	0.000	0.000	0.000	0.000
30	A	27	THR	0	0.014	0.075	33.217	0.000	0.000	0.000	0.000	0.000	0.000
31	A	28	GLY	0	0.052	0.028	30.952	0.001	0.001	0.000	0.000	0.000	0.000
32	A	29	LYS	1	0.913	0.963	28.035	0.066	0.066	0.000	0.000	0.000	0.000
33	A	30	GLY	0	0.055	0.035	26.182	0.004	0.004	0.000	0.000	0.000	0.000
34	A	31	GLU	-1	-0.809	-0.857	21.806	-0.142	-0.142	0.000	0.000	0.000	0.000
35	A	32	GLY	0	0.090	0.048	20.601	0.011	0.011	0.000	0.000	0.000	0.000
36	A	33	ASN	0	-0.011	0.003	16.218	-0.047	-0.047	0.000	0.000	0.000	0.000
37	A	34	PRO	0	-0.022	-0.020	12.942	0.014	0.014	0.000	0.000	0.000	0.000
38	A	35	PHE	0	0.016	0.006	8.394	-0.022	-0.022	0.000	0.000	0.000	0.000
39	A	36	GLU	-1	-0.814	-0.837	13.607	-0.199	-0.199	0.000	0.000	0.000	0.000
40	A	37	GLY	0	0.047	0.039	17.020	0.028	0.028	0.000	0.000	0.000	0.000
41	A	38	THR	0	-0.025	-0.018	18.539	0.019	0.019	0.000	0.000	0.000	0.000
42	A	39	GLN	0	-0.002	-0.025	20.856	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	40	GLU	-1	-0.889	-0.912	23.301	-0.067	-0.067	0.000	0.000	0.000	0.000
44	A	41	MET	0	-0.014	-0.003	26.423	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	42	LYS	1	0.969	1.004	28.623	0.054	0.054	0.000	0.000	0.000	0.000
46	A	43	ILE	0	0.020	-0.006	31.296	0.000	0.000	0.000	0.000	0.000	0.000
47	A	44	GLU	-1	-0.952	-0.980	33.874	-0.041	-0.041	0.000	0.000	0.000	0.000
48	A	45	VAL	0	0.013	-0.007	37.099	0.001	0.001	0.000	0.000	0.000	0.000
49	A	46	ILE	0	-0.069	-0.042	37.973	0.000	0.000	0.000	0.000	0.000	0.000
50	A	47	GLU	-1	-0.875	-0.918	40.905	-0.019	-0.019	0.000	0.000	0.000	0.000
51	A	48	GLY	0	0.034	0.016	42.479	0.000	0.000	0.000	0.000	0.000	0.000
52	A	49	GLY	0	-0.003	0.021	44.432	0.000	0.000	0.000	0.000	0.000	0.000
53	A	50	PRO	0	0.005	-0.011	45.031	0.001	0.001	0.000	0.000	0.000	0.000
54	A	51	LEU	0	0.027	0.015	39.602	0.001	0.001	0.000	0.000	0.000	0.000
55	A	52	PRO	0	0.000	0.024	44.348	0.000	0.000	0.000	0.000	0.000	0.000
56	A	53	PHE	0	0.026	0.015	39.856	0.001	0.001	0.000	0.000	0.000	0.000
57	A	54	ALA	0	0.021	0.011	41.615	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	55	PHE	0	0.078	0.019	33.848	0.001	0.001	0.000	0.000	0.000	0.000
59	A	56	HIS	0	0.075	0.035	36.456	0.000	0.000	0.000	0.000	0.000	0.000
60	A	57	ILE	0	-0.015	-0.003	35.739	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	58	LEU	0	0.005	0.014	34.679	0.002	0.002	0.000	0.000	0.000	0.000
62	A	59	SER	0	-0.014	0.001	31.881	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	60	THR	0	-0.043	-0.034	29.107	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	61	SER	0	-0.026	-0.022	28.529	0.002	0.002	0.000	0.000	0.000	0.000
65	A	62	CYS	-1	-0.902	-0.933	27.078	-0.052	-0.052	0.000	0.000	0.000	0.000
66	A	63	HOH	0	0.003	0.002	33.704	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	64	HOH	0	0.007	0.007	33.291	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	65	HOH	0	-0.014	-0.006	32.677	0.000	0.000	0.000	0.000	0.000	0.000
69	A	66	HOH	0	-0.049	-0.033	31.075	0.001	0.001	0.000	0.000	0.000	0.000
70	A	70	HOH	0	-0.037	-0.029	13.812	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	71	HOH	0	-0.024	-0.017	21.948	0.003	0.003	0.000	0.000	0.000	0.000
72	A	72	HOH	0	-0.039	-0.019	19.963	0.005	0.005	0.000	0.000	0.000	0.000
73	A	73	HOH	0	-0.028	-0.019	19.605	0.002	0.002	0.000	0.000	0.000	0.000
74	A	74	HOH	0	-0.033	-0.021	49.502	0.000	0.000	0.000	0.000	0.000	0.000
75	A	75	HOH	0	-0.044	-0.031	46.048	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	HOH	0	-0.039	-0.030	12.681	-0.025	-0.025	0.000	0.000	0.000	0.000
77	A	77	HOH	0	0.001	0.001	15.525	0.006	0.006	0.000	0.000	0.000	0.000
78	A	78	HOH	0	-0.028	-0.021	29.407	0.001	0.001	0.000	0.000	0.000	0.000
79	A	79	HOH	0	0.045	0.026	48.096	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	HOH	0	0.023	0.015	46.858	0.000	0.000	0.000	0.000	0.000	0.000
81	A	81	HOH	0	-0.025	-0.041	20.480	0.003	0.003	0.000	0.000	0.000	0.000
82	A	82	HOH	0	-0.017	-0.017	41.687	0.000	0.000	0.000	0.000	0.000	0.000
83	A	84	HOH	0	0.023	0.013	44.010	0.000	0.000	0.000	0.000	0.000	0.000
84	A	88	HOH	0	-0.020	-0.028	36.074	0.001	0.001	0.000	0.000	0.000	0.000
85	A	92	HOH	0	-0.021	-0.016	47.967	0.001	0.001	0.000	0.000	0.000	0.000
86	A	93	HOH	0	-0.023	-0.014	30.883	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	94	HOH	0	-0.027	-0.024	34.354	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	95	HOH	0	-0.006	-0.015	17.202	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	98	HOH	0	-0.035	-0.027	32.989	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	99	HOH	0	0.055	0.048	13.081	-0.028	-0.028	0.000	0.000	0.000	0.000
91	A	100	HOH	0	-0.024	-0.020	48.881	0.000	0.000	0.000	0.000	0.000	0.000
92	A	102	HOH	0	-0.050	-0.044	12.748	0.024	0.024	0.000	0.000	0.000	0.000
93	A	105	HOH	0	-0.011	-0.016	25.756	0.004	0.004	0.000	0.000	0.000	0.000
94	A	108	HOH	0	-0.027	-0.025	15.297	0.000	0.000	0.000	0.000	0.000	0.000
95	A	111	HOH	0	-0.036	-0.023	35.957	0.000	0.000	0.000	0.000	0.000	0.000
96	A	113	HOH	0	-0.043	-0.005	1.931	3.327	-4.392	9.607	-0.515	-1.372	0.004
97	A	114	HOH	0	-0.049	-0.038	25.814	0.002	0.002	0.000	0.000	0.000	0.000
98	A	115	HOH	0	-0.049	-0.051	20.194	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	116	HOH	0	0.000	0.010	24.313	0.004	0.004	0.000	0.000	0.000	0.000
100	A	117	HOH	0	-0.043	-0.037	23.534	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	120	HOH	0	-0.011	-0.014	47.622	0.000	0.000	0.000	0.000	0.000	0.000
102	A	123	HOH	0	-0.006	-0.016	2.326	6.493	-0.128	5.613	2.183	-1.175	-0.008
103	A	125	HOH	0	-0.060	-0.047	28.694	0.001	0.001	0.000	0.000	0.000	0.000
104	A	126	HOH	0	-0.041	-0.039	48.916	0.000	0.000	0.000	0.000	0.000	0.000
105	A	129	HOH	0	-0.042	-0.027	49.456	0.000	0.000	0.000	0.000	0.000	0.000
106	A	132	HOH	0	-0.081	-0.072	42.189	0.000	0.000	0.000	0.000	0.000	0.000
107	A	136	HOH	0	-0.054	-0.030	38.570	0.000	0.000	0.000	0.000	0.000	0.000
108	A	137	HOH	0	0.044	0.093	1.861	15.403	-3.441	21.491	-1.036	-1.611	-0.002
109	A	139	HOH	0	-0.051	-0.031	23.765	0.000	0.000	0.000	0.000	0.000	0.000
110	A	145	HOH	0	-0.026	-0.019	45.825	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	146	HOH	0	-0.014	0.006	13.372	0.021	0.021	0.000	0.000	0.000	0.000
112	A	153	HOH	0	0.037	0.024	39.751	0.000	0.000	0.000	0.000	0.000	0.000
113	A	154	HOH	0	-0.011	-0.038	35.118	0.000	0.000	0.000	0.000	0.000	0.000
114	A	156	HOH	0	-0.035	-0.022	16.394	-0.014	-0.014	0.000	0.000	0.000	0.000
115	B	606	HOH	0	-0.010	-0.008	35.784	0.000	0.000	0.000	0.000	0.000	0.000
116	B	646	HOH	0	-0.006	0.002	21.494	0.000	0.000	0.000	0.000	0.000	0.000
117	B	659	HOH	0	0.024	0.016	16.405	-0.008	-0.008	0.000	0.000	0.000	0.000
118	B	696	HOH	0	-0.049	-0.026	26.435	0.001	0.001	0.000	0.000	0.000	0.000
119	B	706	HOH	0	0.026	0.026	42.492	-0.001	-0.001	0.000	0.000	0.000	0.000
120	D	245	HOH	0	0.033	0.021	45.218	0.000	0.000	0.000	0.000	0.000	0.000
121	D	356	HOH	0	0.029	0.016	40.033	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:ACE)