FMO DATABASE

FMODB ID: G67J1

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	OptHSide
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	-1065388.48893
FMO2-HF: Nuclear repulsion	1015856.668741
FMO2-HF: Total energy	-49531.820188
FMO2-MP2: Total energy	-49672.339035

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.
-19.909	-6.561	8.952	-7.491	-14.807	-0.054

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 : -0.030 / q_NPA : -0.008

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	0.011	2.733	-1.829	0.791	0.674	-1.023	-2.271	0.003
4	B	5	GLN	0	-0.030	-0.023	4.531	-0.068	-0.013	-0.001	-0.012	-0.042	0.000
5	B	6	GLU	-1	-0.752	-0.873	8.189	-0.247	-0.247	0.000	0.000	0.000	0.000
6	B	7	SER	0	-0.046	-0.025	11.045	0.053	0.053	0.000	0.000	0.000	0.000
7	B	8	GLY	0	0.021	0.001	14.370	-0.028	-0.028	0.000	0.000	0.000	0.000
8	B	9	GLY	0	0.018	0.019	17.546	-0.013	-0.013	0.000	0.000	0.000	0.000
9	B	10	GLY	0	-0.012	-0.007	19.032	0.015	0.015	0.000	0.000	0.000	0.000
10	B	11	SER	0	-0.022	-0.022	22.215	-0.009	-0.009	0.000	0.000	0.000	0.000
11	B	12	VAL	0	0.011	0.008	25.087	0.004	0.004	0.000	0.000	0.000	0.000
12	B	13	GLN	0	0.013	0.016	27.414	-0.004	-0.004	0.000	0.000	0.000	0.000
13	B	14	ALA	0	0.029	-0.001	29.797	-0.005	-0.005	0.000	0.000	0.000	0.000
14	B	15	GLY	0	-0.016	0.000	30.644	0.004	0.004	0.000	0.000	0.000	0.000
15	B	16	GLY	0	-0.033	-0.009	29.103	0.001	0.001	0.000	0.000	0.000	0.000
16	B	17	SER	0	-0.023	-0.022	25.304	-0.006	-0.006	0.000	0.000	0.000	0.000
17	B	18	LEU	0	-0.020	-0.008	20.956	0.008	0.008	0.000	0.000	0.000	0.000
18	B	19	ARG	1	0.895	0.971	16.669	0.060	0.060	0.000	0.000	0.000	0.000
19	B	20	LEU	0	-0.007	0.015	14.848	0.017	0.017	0.000	0.000	0.000	0.000
20	B	21	SER	0	-0.004	-0.014	13.045	-0.018	-0.018	0.000	0.000	0.000	0.000
21	B	22	CYS	0	-0.049	-0.012	7.343	-0.021	-0.021	0.000	0.000	0.000	0.000
22	B	23	ALA	0	0.008	0.013	7.673	-0.057	-0.057	0.000	0.000	0.000	0.000
23	B	24	ALA	0	0.035	0.016	2.541	-0.445	-0.071	0.504	-0.221	-0.656	0.002
24	B	25	SER	0	-0.014	0.001	2.574	-1.889	-0.215	0.804	-1.006	-1.472	-0.006
25	B	26	GLY	0	-0.024	-0.019	2.694	-2.961	-0.544	0.704	-1.377	-1.744	-0.016
26	B	27	ASP	-1	-0.898	-0.957	4.611	-0.195	-0.135	-0.001	-0.004	-0.055	0.000
27	B	28	THR	0	0.009	-0.004	3.463	-1.130	-0.481	0.055	-0.249	-0.454	-0.001
28	B	29	PHE	0	0.018	0.011	4.615	-0.504	-0.361	-0.001	-0.008	-0.134	0.000
29	B	30	SER	0	0.026	0.006	5.971	-0.120	-0.120	0.000	0.000	0.000	0.000
30	B	31	SER	0	-0.093	-0.033	6.798	0.048	0.048	0.000	0.000	0.000	0.000
31	B	32	TYR	0	0.005	0.010	2.719	-1.903	-0.419	0.617	-0.623	-1.478	-0.005
32	B	33	SER	0	0.004	0.012	7.583	0.272	0.272	0.000	0.000	0.000	0.000
33	B	34	MET	0	-0.042	-0.012	5.489	-0.245	-0.245	0.000	0.000	0.000	0.000
34	B	35	ALA	0	0.016	0.010	9.402	0.111	0.111	0.000	0.000	0.000	0.000
35	B	36	TRP	0	-0.021	-0.014	11.028	-0.023	-0.023	0.000	0.000	0.000	0.000
36	B	37	PHE	0	0.055	0.016	12.234	0.032	0.032	0.000	0.000	0.000	0.000
37	B	38	ARG	1	0.742	0.857	15.476	0.173	0.173	0.000	0.000	0.000	0.000
38	B	39	GLN	0	0.000	-0.020	18.162	-0.015	-0.015	0.000	0.000	0.000	0.000
39	B	40	ALA	0	0.005	0.012	20.529	0.014	0.014	0.000	0.000	0.000	0.000
40	B	41	PRO	0	0.020	-0.010	23.828	-0.005	-0.005	0.000	0.000	0.000	0.000
41	B	42	GLY	0	-0.009	-0.008	25.954	0.003	0.003	0.000	0.000	0.000	0.000
42	B	43	LYS	1	0.911	0.970	25.402	0.096	0.096	0.000	0.000	0.000	0.000
43	B	44	GLU	-1	-0.856	-0.927	23.969	-0.168	-0.168	0.000	0.000	0.000	0.000
44	B	100	CYS	0	-0.086	-0.027	15.209	-0.005	-0.005	0.000	0.000	0.000	0.000
45	B	46	GLU	-1	-0.812	-0.903	19.873	-0.171	-0.171	0.000	0.000	0.000	0.000
46	B	47	LEU	0	-0.006	0.016	15.158	-0.005	-0.005	0.000	0.000	0.000	0.000
47	B	48	VAL	0	-0.018	-0.023	17.435	0.022	0.022	0.000	0.000	0.000	0.000
48	B	49	SER	0	-0.048	-0.041	16.744	0.025	0.025	0.000	0.000	0.000	0.000
49	B	50	ASN	0	0.019	0.003	14.220	-0.084	-0.084	0.000	0.000	0.000	0.000
50	B	51	ILE	0	-0.026	-0.024	12.010	0.057	0.057	0.000	0.000	0.000	0.000
51	B	52	LEU	0	0.034	0.016	12.320	-0.086	-0.086	0.000	0.000	0.000	0.000
52	B	53	ARG	1	0.969	0.992	11.298	0.652	0.652	0.000	0.000	0.000	0.000
53	B	54	ASP	-1	-0.882	-0.925	13.137	-0.323	-0.323	0.000	0.000	0.000	0.000
54	B	55	GLY	0	0.010	0.007	15.548	0.041	0.041	0.000	0.000	0.000	0.000
55	B	56	THR	0	-0.048	-0.036	16.894	0.037	0.037	0.000	0.000	0.000	0.000
56	B	57	THR	0	-0.043	-0.022	17.059	-0.025	-0.025	0.000	0.000	0.000	0.000
57	B	58	THR	0	-0.048	-0.031	18.463	0.015	0.015	0.000	0.000	0.000	0.000
58	B	59	TYR	0	0.005	0.003	19.205	-0.011	-0.011	0.000	0.000	0.000	0.000
59	B	60	ALA	0	0.087	0.055	21.575	0.010	0.010	0.000	0.000	0.000	0.000
60	B	61	GLY	0	0.009	-0.012	23.436	0.010	0.010	0.000	0.000	0.000	0.000
61	B	62	SER	0	-0.015	0.000	25.866	0.006	0.006	0.000	0.000	0.000	0.000
62	B	63	VAL	0	0.024	0.004	21.830	0.010	0.010	0.000	0.000	0.000	0.000
63	B	64	LYS	1	0.984	1.010	25.084	0.146	0.146	0.000	0.000	0.000	0.000
64	B	65	GLY	0	-0.026	-0.013	25.814	0.009	0.009	0.000	0.000	0.000	0.000
65	B	66	ARG	1	0.742	0.845	26.152	0.111	0.111	0.000	0.000	0.000	0.000
66	B	67	PHE	0	0.023	-0.005	20.351	0.005	0.005	0.000	0.000	0.000	0.000
67	B	68	THR	0	-0.049	-0.023	20.145	0.000	0.000	0.000	0.000	0.000	0.000
68	B	69	ILE	0	-0.003	0.010	13.185	0.012	0.012	0.000	0.000	0.000	0.000
69	B	70	SER	0	-0.031	-0.018	15.250	0.018	0.018	0.000	0.000	0.000	0.000
70	B	71	ARG	1	0.824	0.898	8.811	0.600	0.600	0.000	0.000	0.000	0.000
71	B	72	ASP	-1	-0.805	-0.884	11.754	-0.049	-0.049	0.000	0.000	0.000	0.000
72	B	73	ASP	-1	-0.796	-0.913	10.609	-0.442	-0.442	0.000	0.000	0.000	0.000
73	B	74	ALA	0	-0.016	0.007	11.550	0.007	0.007	0.000	0.000	0.000	0.000
74	B	75	LYS	1	0.826	0.885	11.426	0.062	0.062	0.000	0.000	0.000	0.000
75	B	76	ASN	0	-0.006	0.012	6.152	-0.041	-0.041	0.000	0.000	0.000	0.000
76	B	77	THR	0	0.018	0.020	7.076	0.059	0.059	0.000	0.000	0.000	0.000
77	B	78	VAL	0	0.034	0.017	8.732	-0.037	-0.037	0.000	0.000	0.000	0.000
78	B	79	TYR	0	-0.051	-0.061	10.816	0.055	0.055	0.000	0.000	0.000	0.000
79	B	80	LEU	0	0.023	0.010	14.226	-0.027	-0.027	0.000	0.000	0.000	0.000
80	B	81	GLN	0	-0.017	-0.009	16.801	0.025	0.025	0.000	0.000	0.000	0.000
81	B	82	MET	0	-0.021	0.008	19.956	-0.014	-0.014	0.000	0.000	0.000	0.000
82	B	82	VAL	0	0.039	0.001	22.685	0.014	0.014	0.000	0.000	0.000	0.000
83	B	82	ASN	0	-0.021	-0.012	26.420	-0.002	-0.002	0.000	0.000	0.000	0.000
84	B	82	LEU	0	0.023	0.020	23.398	-0.005	-0.005	0.000	0.000	0.000	0.000
85	B	83	LYS	1	0.888	0.929	27.568	0.098	0.098	0.000	0.000	0.000	0.000
86	B	84	SER	0	0.043	0.012	27.982	-0.005	-0.005	0.000	0.000	0.000	0.000
87	B	85	GLU	-1	-0.848	-0.925	27.469	-0.097	-0.097	0.000	0.000	0.000	0.000
88	B	86	ASP	-1	-0.731	-0.826	23.912	-0.115	-0.115	0.000	0.000	0.000	0.000
89	B	87	THR	0	-0.012	0.020	23.257	-0.003	-0.003	0.000	0.000	0.000	0.000
90	B	88	ALA	0	-0.022	-0.012	20.788	-0.005	-0.005	0.000	0.000	0.000	0.000
91	B	89	ARG	1	0.846	0.936	14.887	0.091	0.091	0.000	0.000	0.000	0.000
92	B	90	TYR	0	-0.015	-0.040	15.490	-0.026	-0.026	0.000	0.000	0.000	0.000
93	B	91	TYR	0	0.019	-0.003	11.618	0.043	0.043	0.000	0.000	0.000	0.000
94	B	93	ALA	0	0.031	0.012	7.382	-0.035	-0.035	0.000	0.000	0.000	0.000
95	B	94	ALA	0	0.004	-0.012	4.109	0.016	0.137	0.000	-0.013	-0.108	0.000
96	B	95	ASP	-1	-0.779	-0.890	6.144	-1.306	-1.306	0.000	0.000	0.000	0.000
97	B	96	SER	0	-0.080	-0.065	6.995	0.192	0.192	0.000	0.000	0.000	0.000
98	B	97	GLY	0	0.037	0.036	8.843	0.154	0.154	0.000	0.000	0.000	0.000
99	B	98	THR	0	-0.064	-0.049	12.314	0.017	0.017	0.000	0.000	0.000	0.000
100	B	99	GLN	0	0.026	0.014	12.057	0.085	0.085	0.000	0.000	0.000	0.000
101	B	100	LEU	0	0.007	-0.011	15.436	0.027	0.027	0.000	0.000	0.000	0.000
102	B	100	GLY	0	0.029	0.026	17.315	0.031	0.031	0.000	0.000	0.000	0.000
103	B	100	TYR	0	-0.042	-0.019	18.541	0.034	0.034	0.000	0.000	0.000	0.000
104	B	100	VAL	0	-0.013	0.002	18.573	-0.023	-0.023	0.000	0.000	0.000	0.000
105	B	100	GLY	0	0.008	0.006	20.795	0.020	0.020	0.000	0.000	0.000	0.000
106	B	100	ALA	0	-0.021	-0.008	21.411	-0.019	-0.019	0.000	0.000	0.000	0.000
107	B	100	VAL	0	-0.010	-0.003	18.014	-0.009	-0.009	0.000	0.000	0.000	0.000
108	B	100	GLY	0	0.094	0.074	21.245	-0.010	-0.010	0.000	0.000	0.000	0.000
109	B	100	LEU	0	-0.035	-0.038	22.338	0.002	0.002	0.000	0.000	0.000	0.000
110	B	100	SER	0	-0.038	-0.030	18.654	0.007	0.007	0.000	0.000	0.000	0.000
111	B	100	LEU	0	-0.005	-0.003	12.668	-0.041	-0.041	0.000	0.000	0.000	0.000
112	B	100	ASP	-1	-0.857	-0.895	15.308	-0.270	-0.270	0.000	0.000	0.000	0.000
113	B	100	TYR	0	-0.072	-0.042	14.253	0.036	0.036	0.000	0.000	0.000	0.000
114	B	100	VAL	0	-0.012	-0.021	12.372	-0.052	-0.052	0.000	0.000	0.000	0.000
115	B	100	MET	0	-0.050	-0.011	9.084	0.023	0.023	0.000	0.000	0.000	0.000
116	B	101	ASP	-1	-0.818	-0.877	5.587	-1.730	-1.730	0.000	0.000	0.000	0.000
117	B	102	TYR	0	-0.049	-0.027	2.213	-6.990	-3.348	5.598	-2.952	-6.288	-0.031
118	B	103	TRP	0	0.035	0.010	5.285	0.310	0.419	-0.001	-0.003	-0.105	0.000
119	B	104	GLY	0	0.008	0.015	6.938	0.012	0.012	0.000	0.000	0.000	0.000
120	B	105	LYS	1	0.930	0.951	8.004	-0.122	-0.122	0.000	0.000	0.000	0.000
121	B	106	GLY	0	0.042	0.030	11.100	0.027	0.027	0.000	0.000	0.000	0.000
122	B	107	THR	0	-0.077	-0.043	13.076	0.056	0.056	0.000	0.000	0.000	0.000
123	B	108	GLN	0	-0.017	-0.011	15.877	-0.028	-0.028	0.000	0.000	0.000	0.000
124	B	109	VAL	0	0.035	0.028	18.986	0.012	0.012	0.000	0.000	0.000	0.000
125	B	110	THR	0	-0.025	-0.021	21.576	-0.008	-0.008	0.000	0.000	0.000	0.000
126	B	111	VAL	0	-0.003	0.010	25.313	0.007	0.007	0.000	0.000	0.000	0.000
127	B	112	SER	0	-0.020	-0.007	27.849	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)