FMO DATABASE

FMODB ID: 85KRY

Calculation Name: 3G9A-B-Xray372

Preferred Name:

Target Type:

Ligand Name: [(4z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic acid

ligand 3-letter code: GYS

PDB ID: 3G9A

Chain ID: B

ChEMBL ID:

UniProt ID: P42212

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1066134.940011
FMO2-HF: Nuclear repulsion	1016603.024834
FMO2-HF: Total energy	-49531.915178
FMO2-MP2: Total energy	-49672.478498

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(B:2:VAL)

Summations of interaction energy for fragment #1(B:2:VAL)

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.
-18.173	-5.987	10.502	-7.608	-15.076	-0.058

Interaction energy analysis for fragmet #1(B:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : 0.005

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	B	4	LEU	0	0.031	0.022	2.662	-1.387	0.861	0.986	-0.893	-2.341	0.000
4	B	5	GLN	0	-0.033	-0.027	4.452	-0.013	0.043	-0.001	-0.013	-0.042	0.000
5	B	6	GLU	-1	-0.733	-0.860	8.141	-0.267	-0.267	0.000	0.000	0.000	0.000
6	B	7	SER	0	-0.044	-0.023	11.139	0.056	0.056	0.000	0.000	0.000	0.000
7	B	8	GLY	0	0.034	0.007	14.417	-0.027	-0.027	0.000	0.000	0.000	0.000
8	B	9	GLY	0	0.021	0.019	17.398	-0.010	-0.010	0.000	0.000	0.000	0.000
9	B	10	GLY	0	-0.002	-0.008	19.036	0.016	0.016	0.000	0.000	0.000	0.000
10	B	11	SER	0	-0.030	-0.020	22.442	-0.010	-0.010	0.000	0.000	0.000	0.000
11	B	12	VAL	0	0.007	0.015	25.401	0.004	0.004	0.000	0.000	0.000	0.000
12	B	13	GLN	0	0.009	0.022	27.643	-0.001	-0.001	0.000	0.000	0.000	0.000
13	B	14	ALA	0	0.040	0.006	29.974	-0.005	-0.005	0.000	0.000	0.000	0.000
14	B	15	GLY	0	-0.014	0.001	31.284	0.004	0.004	0.000	0.000	0.000	0.000
15	B	16	GLY	0	-0.019	-0.006	29.324	0.000	0.000	0.000	0.000	0.000	0.000
16	B	17	SER	0	-0.021	-0.030	25.558	-0.006	-0.006	0.000	0.000	0.000	0.000
17	B	18	LEU	0	-0.029	-0.014	20.985	0.009	0.009	0.000	0.000	0.000	0.000
18	B	19	ARG	1	0.895	0.972	16.279	0.098	0.098	0.000	0.000	0.000	0.000
19	B	20	LEU	0	0.012	0.020	15.232	0.013	0.013	0.000	0.000	0.000	0.000
20	B	21	SER	0	-0.007	-0.019	13.589	-0.019	-0.019	0.000	0.000	0.000	0.000
21	B	22	CYS	0	-0.077	-0.020	7.705	-0.006	-0.006	0.000	0.000	0.000	0.000
22	B	23	ALA	0	0.025	0.022	7.721	-0.045	-0.045	0.000	0.000	0.000	0.000
23	B	24	ALA	0	0.030	0.006	2.846	-0.478	-0.054	0.273	-0.165	-0.532	0.001
24	B	25	SER	0	-0.056	-0.030	2.445	-1.553	-0.139	0.512	-0.754	-1.171	-0.001
25	B	26	GLY	0	0.031	0.010	2.706	-2.486	0.331	1.206	-1.809	-2.214	-0.022
26	B	27	ASP	-1	-0.851	-0.918	4.355	-0.349	-0.276	-0.001	-0.007	-0.064	0.000
27	B	28	THR	0	0.011	-0.005	3.795	-0.789	-0.446	0.008	-0.100	-0.251	0.000
28	B	29	PHE	0	0.004	0.015	4.684	-0.323	-0.217	-0.001	-0.007	-0.098	0.000
29	B	30	SER	0	0.045	0.011	5.995	-0.080	-0.080	0.000	0.000	0.000	0.000
30	B	31	SER	0	-0.104	-0.046	6.659	0.049	0.049	0.000	0.000	0.000	0.000
31	B	32	TYR	0	-0.008	0.003	2.881	-1.749	-0.396	0.293	-0.509	-1.137	-0.004
32	B	33	SER	0	0.022	0.013	7.953	0.219	0.219	0.000	0.000	0.000	0.000
33	B	34	MET	0	-0.033	-0.005	5.709	-0.234	-0.234	0.000	0.000	0.000	0.000
34	B	35	ALA	0	0.005	0.005	9.713	0.108	0.108	0.000	0.000	0.000	0.000
35	B	36	TRP	0	-0.025	-0.017	11.115	-0.023	-0.023	0.000	0.000	0.000	0.000
36	B	37	PHE	0	0.037	0.006	12.442	0.031	0.031	0.000	0.000	0.000	0.000
37	B	38	ARG	1	0.744	0.846	15.627	0.164	0.164	0.000	0.000	0.000	0.000
38	B	39	GLN	0	-0.006	-0.020	18.204	-0.017	-0.017	0.000	0.000	0.000	0.000
39	B	40	ALA	0	0.022	0.013	20.540	0.012	0.012	0.000	0.000	0.000	0.000
40	B	41	PRO	0	0.001	-0.009	23.827	-0.003	-0.003	0.000	0.000	0.000	0.000
41	B	42	GLY	0	0.001	-0.003	26.334	0.002	0.002	0.000	0.000	0.000	0.000
42	B	43	LYS	1	0.895	0.954	25.330	0.086	0.086	0.000	0.000	0.000	0.000
43	B	44	GLU	-1	-0.815	-0.906	23.810	-0.151	-0.151	0.000	0.000	0.000	0.000
44	B	100	CYS	0	-0.100	-0.038	15.074	-0.004	-0.004	0.000	0.000	0.000	0.000
45	B	46	GLU	-1	-0.773	-0.878	20.146	-0.158	-0.158	0.000	0.000	0.000	0.000
46	B	47	LEU	0	0.002	0.013	15.578	-0.003	-0.003	0.000	0.000	0.000	0.000
47	B	48	VAL	0	-0.008	-0.012	17.569	0.018	0.018	0.000	0.000	0.000	0.000
48	B	49	SER	0	-0.036	-0.043	17.068	0.021	0.021	0.000	0.000	0.000	0.000
49	B	50	ASN	0	0.006	0.000	14.461	-0.079	-0.079	0.000	0.000	0.000	0.000
50	B	51	ILE	0	-0.027	-0.025	12.371	0.051	0.051	0.000	0.000	0.000	0.000
51	B	52	LEU	0	0.051	0.025	12.538	-0.081	-0.081	0.000	0.000	0.000	0.000
52	B	53	ARG	1	0.925	0.969	10.942	0.670	0.670	0.000	0.000	0.000	0.000
53	B	54	ASP	-1	-0.858	-0.913	13.237	-0.329	-0.329	0.000	0.000	0.000	0.000
54	B	55	GLY	0	0.003	0.005	15.818	0.038	0.038	0.000	0.000	0.000	0.000
55	B	56	THR	0	-0.047	-0.038	17.077	0.035	0.035	0.000	0.000	0.000	0.000
56	B	57	THR	0	-0.052	-0.029	17.327	-0.024	-0.024	0.000	0.000	0.000	0.000
57	B	58	THR	0	-0.048	-0.038	18.849	0.014	0.014	0.000	0.000	0.000	0.000
58	B	59	TYR	0	0.009	0.009	19.628	-0.010	-0.010	0.000	0.000	0.000	0.000
59	B	60	ALA	0	0.077	0.056	21.954	0.010	0.010	0.000	0.000	0.000	0.000
60	B	61	GLY	0	-0.007	-0.017	23.834	0.009	0.009	0.000	0.000	0.000	0.000
61	B	62	SER	0	-0.030	-0.013	25.177	0.007	0.007	0.000	0.000	0.000	0.000
62	B	63	VAL	0	0.029	0.005	22.114	0.010	0.010	0.000	0.000	0.000	0.000
63	B	64	LYS	1	0.964	0.992	25.113	0.142	0.142	0.000	0.000	0.000	0.000
64	B	65	GLY	0	-0.014	-0.003	25.797	0.009	0.009	0.000	0.000	0.000	0.000
65	B	66	ARG	1	0.717	0.830	26.346	0.112	0.112	0.000	0.000	0.000	0.000
66	B	67	PHE	0	0.021	-0.004	20.470	0.004	0.004	0.000	0.000	0.000	0.000
67	B	68	THR	0	-0.061	-0.040	20.650	0.005	0.005	0.000	0.000	0.000	0.000
68	B	69	ILE	0	-0.004	0.010	13.557	0.009	0.009	0.000	0.000	0.000	0.000
69	B	70	SER	0	-0.027	-0.020	15.440	0.019	0.019	0.000	0.000	0.000	0.000
70	B	71	ARG	1	0.797	0.878	9.262	0.601	0.601	0.000	0.000	0.000	0.000
71	B	72	ASP	-1	-0.789	-0.885	11.724	-0.098	-0.098	0.000	0.000	0.000	0.000
72	B	73	ASP	-1	-0.782	-0.887	10.688	-0.474	-0.474	0.000	0.000	0.000	0.000
73	B	74	ALA	0	-0.016	0.006	11.772	0.010	0.010	0.000	0.000	0.000	0.000
74	B	75	LYS	1	0.776	0.863	11.652	0.137	0.137	0.000	0.000	0.000	0.000
75	B	76	ASN	0	-0.010	0.001	6.253	-0.014	-0.014	0.000	0.000	0.000	0.000
76	B	77	THR	0	0.032	0.024	7.073	0.027	0.027	0.000	0.000	0.000	0.000
77	B	78	VAL	0	0.003	0.003	8.763	-0.034	-0.034	0.000	0.000	0.000	0.000
78	B	79	TYR	0	-0.033	-0.044	10.815	0.056	0.056	0.000	0.000	0.000	0.000
79	B	80	LEU	0	0.019	0.009	14.202	-0.023	-0.023	0.000	0.000	0.000	0.000
80	B	81	GLN	0	0.022	0.013	16.980	0.021	0.021	0.000	0.000	0.000	0.000
81	B	82	MET	0	-0.035	0.001	20.286	-0.014	-0.014	0.000	0.000	0.000	0.000
82	B	82	VAL	0	0.024	-0.003	22.931	0.013	0.013	0.000	0.000	0.000	0.000
83	B	82	ASN	0	-0.007	0.002	26.743	-0.002	-0.002	0.000	0.000	0.000	0.000
84	B	82	LEU	0	0.020	0.026	23.671	-0.005	-0.005	0.000	0.000	0.000	0.000
85	B	83	LYS	1	0.847	0.907	27.830	0.099	0.099	0.000	0.000	0.000	0.000
86	B	84	SER	0	0.045	0.014	28.241	-0.005	-0.005	0.000	0.000	0.000	0.000
87	B	85	GLU	-1	-0.820	-0.910	27.472	-0.097	-0.097	0.000	0.000	0.000	0.000
88	B	86	ASP	-1	-0.733	-0.816	24.148	-0.113	-0.113	0.000	0.000	0.000	0.000
89	B	87	THR	0	-0.022	0.008	23.531	-0.003	-0.003	0.000	0.000	0.000	0.000
90	B	88	ALA	0	-0.021	-0.012	21.047	-0.001	-0.001	0.000	0.000	0.000	0.000
91	B	89	ARG	1	0.859	0.941	14.951	0.078	0.078	0.000	0.000	0.000	0.000
92	B	90	TYR	0	0.007	-0.025	15.749	-0.022	-0.022	0.000	0.000	0.000	0.000
93	B	91	TYR	0	0.016	-0.006	11.759	0.037	0.037	0.000	0.000	0.000	0.000
94	B	93	ALA	0	0.040	0.015	7.474	-0.038	-0.038	0.000	0.000	0.000	0.000
95	B	94	ALA	0	0.006	-0.011	4.319	0.032	0.123	-0.001	-0.006	-0.084	0.000
96	B	95	ASP	-1	-0.775	-0.880	6.426	-1.232	-1.232	0.000	0.000	0.000	0.000
97	B	96	SER	0	-0.067	-0.060	7.490	0.187	0.187	0.000	0.000	0.000	0.000
98	B	97	GLY	0	0.045	0.037	9.278	0.140	0.140	0.000	0.000	0.000	0.000
99	B	98	THR	0	-0.045	-0.032	12.814	0.008	0.008	0.000	0.000	0.000	0.000
100	B	99	GLN	0	-0.016	-0.006	12.175	0.117	0.117	0.000	0.000	0.000	0.000
101	B	100	LEU	0	0.006	-0.011	15.498	0.021	0.021	0.000	0.000	0.000	0.000
102	B	100	GLY	0	0.026	0.023	17.306	0.031	0.031	0.000	0.000	0.000	0.000
103	B	100	TYR	0	-0.018	0.000	18.587	0.032	0.032	0.000	0.000	0.000	0.000
104	B	100	VAL	0	-0.022	-0.008	18.893	-0.021	-0.021	0.000	0.000	0.000	0.000
105	B	100	GLY	0	0.001	0.006	21.189	0.020	0.020	0.000	0.000	0.000	0.000
106	B	100	ALA	0	-0.023	-0.011	21.606	-0.018	-0.018	0.000	0.000	0.000	0.000
107	B	100	VAL	0	-0.018	-0.004	18.146	-0.010	-0.010	0.000	0.000	0.000	0.000
108	B	100	GLY	0	0.074	0.061	21.269	-0.010	-0.010	0.000	0.000	0.000	0.000
109	B	100	LEU	0	-0.028	-0.026	22.435	0.005	0.005	0.000	0.000	0.000	0.000
110	B	100	SER	0	-0.051	-0.043	18.411	0.007	0.007	0.000	0.000	0.000	0.000
111	B	100	LEU	0	0.007	0.008	12.395	-0.038	-0.038	0.000	0.000	0.000	0.000
112	B	100	ASP	-1	-0.839	-0.880	15.113	-0.226	-0.226	0.000	0.000	0.000	0.000
113	B	100	TYR	0	-0.065	-0.039	14.295	0.034	0.034	0.000	0.000	0.000	0.000
114	B	100	VAL	0	0.010	-0.009	12.501	-0.052	-0.052	0.000	0.000	0.000	0.000
115	B	100	MET	0	-0.053	-0.017	9.132	0.036	0.036	0.000	0.000	0.000	0.000
116	B	101	ASP	-1	-0.838	-0.885	5.704	-1.519	-1.519	0.000	0.000	0.000	0.000
117	B	102	TYR	0	-0.049	-0.030	2.177	-7.361	-4.216	7.229	-3.341	-7.032	-0.032
118	B	103	TRP	0	0.049	0.013	5.184	0.309	0.425	-0.001	-0.004	-0.110	0.000
119	B	104	GLY	0	-0.022	0.005	6.193	-0.059	-0.059	0.000	0.000	0.000	0.000
120	B	105	LYS	1	0.893	0.931	7.787	-0.145	-0.145	0.000	0.000	0.000	0.000
121	B	106	GLY	0	0.012	0.018	11.162	0.036	0.036	0.000	0.000	0.000	0.000
122	B	107	THR	0	-0.057	-0.032	13.255	0.048	0.048	0.000	0.000	0.000	0.000
123	B	108	GLN	0	-0.021	-0.013	15.881	-0.023	-0.023	0.000	0.000	0.000	0.000
124	B	109	VAL	0	0.023	0.012	19.356	0.006	0.006	0.000	0.000	0.000	0.000
125	B	110	THR	0	-0.017	-0.015	21.912	-0.006	-0.006	0.000	0.000	0.000	0.000
126	B	111	VAL	0	-0.014	0.011	25.661	0.006	0.006	0.000	0.000	0.000	0.000
127	B	112	SER	0	-0.013	-0.022	28.133	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:VAL)