FMO DATABASE

FMODB ID: 17VMZ

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	OptH
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	-1064670.234596
FMO2-HF: Nuclear repulsion	1015138.596355
FMO2-HF: Total energy	-49531.638241
FMO2-MP2: Total energy	-49672.137372

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.
-19.079	-5.544	6.152	-6.457	-13.227	-0.047

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 : -0.021 / 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	0.029	0.008	2.819	-1.757	0.843	0.673	-0.975	-2.298	0.003
4	B	5	GLN	0	-0.034	-0.026	4.461	-0.011	0.051	-0.001	-0.014	-0.047	0.000
5	B	6	GLU	-1	-0.751	-0.877	8.126	-0.338	-0.338	0.000	0.000	0.000	0.000
6	B	7	SER	0	-0.054	-0.025	10.996	0.058	0.058	0.000	0.000	0.000	0.000
7	B	8	GLY	0	0.027	0.003	14.328	-0.026	-0.026	0.000	0.000	0.000	0.000
8	B	9	GLY	0	0.015	0.019	17.515	-0.010	-0.010	0.000	0.000	0.000	0.000
9	B	10	GLY	0	-0.012	-0.009	18.988	0.017	0.017	0.000	0.000	0.000	0.000
10	B	11	SER	0	-0.021	-0.023	22.160	-0.010	-0.010	0.000	0.000	0.000	0.000
11	B	12	VAL	0	0.013	0.010	25.061	0.005	0.005	0.000	0.000	0.000	0.000
12	B	13	GLN	0	0.011	0.014	27.375	-0.004	-0.004	0.000	0.000	0.000	0.000
13	B	14	ALA	0	0.029	0.002	29.769	-0.005	-0.005	0.000	0.000	0.000	0.000
14	B	15	GLY	0	-0.020	-0.003	30.628	0.005	0.005	0.000	0.000	0.000	0.000
15	B	16	GLY	0	-0.037	-0.013	29.083	0.002	0.002	0.000	0.000	0.000	0.000
16	B	17	SER	0	-0.050	-0.036	25.328	-0.006	-0.006	0.000	0.000	0.000	0.000
17	B	18	LEU	0	0.021	0.011	20.915	0.007	0.007	0.000	0.000	0.000	0.000
18	B	19	ARG	1	0.930	0.981	17.632	0.072	0.072	0.000	0.000	0.000	0.000
19	B	20	LEU	0	-0.006	0.014	14.832	0.015	0.015	0.000	0.000	0.000	0.000
20	B	21	SER	0	0.004	-0.012	12.821	-0.011	-0.011	0.000	0.000	0.000	0.000
21	B	22	CYS	0	-0.056	-0.010	7.352	-0.020	-0.020	0.000	0.000	0.000	0.000
22	B	23	ALA	0	0.013	0.017	7.668	-0.041	-0.041	0.000	0.000	0.000	0.000
23	B	24	ALA	0	0.038	0.016	2.533	-0.494	-0.126	0.530	-0.227	-0.671	0.002
24	B	25	SER	0	-0.042	-0.008	2.758	-2.016	-0.320	0.815	-0.975	-1.536	-0.007
25	B	26	GLY	0	0.007	-0.007	2.735	-2.837	-0.532	0.593	-1.289	-1.609	-0.015
26	B	27	ASP	-1	-0.908	-0.964	4.734	-0.033	0.019	-0.001	-0.004	-0.046	0.000
27	B	28	THR	0	0.006	0.000	3.088	-1.179	-0.526	0.077	-0.235	-0.495	-0.001
28	B	29	PHE	0	0.027	0.018	4.595	-0.485	-0.348	-0.001	-0.008	-0.128	0.000
29	B	30	SER	0	0.019	0.008	6.045	-0.137	-0.137	0.000	0.000	0.000	0.000
30	B	31	SER	0	-0.076	-0.027	7.027	0.023	0.023	0.000	0.000	0.000	0.000
31	B	32	TYR	0	0.000	0.014	3.195	-1.408	-0.370	0.135	-0.348	-0.824	-0.003
32	B	33	SER	0	0.004	0.008	7.584	0.265	0.265	0.000	0.000	0.000	0.000
33	B	34	MET	0	-0.038	-0.011	5.504	-0.245	-0.245	0.000	0.000	0.000	0.000
34	B	35	ALA	0	0.017	0.011	9.424	0.116	0.116	0.000	0.000	0.000	0.000
35	B	36	TRP	0	-0.028	-0.013	10.998	-0.039	-0.039	0.000	0.000	0.000	0.000
36	B	37	PHE	0	0.050	0.014	12.139	0.036	0.036	0.000	0.000	0.000	0.000
37	B	38	ARG	1	0.758	0.872	15.449	0.191	0.191	0.000	0.000	0.000	0.000
38	B	39	GLN	0	0.004	-0.005	18.120	-0.011	-0.011	0.000	0.000	0.000	0.000
39	B	40	ALA	0	0.003	0.009	20.473	0.012	0.012	0.000	0.000	0.000	0.000
40	B	41	PRO	0	0.016	-0.012	23.768	-0.005	-0.005	0.000	0.000	0.000	0.000
41	B	42	GLY	0	-0.007	-0.005	25.883	0.005	0.005	0.000	0.000	0.000	0.000
42	B	43	LYS	1	0.910	0.967	25.428	0.118	0.118	0.000	0.000	0.000	0.000
43	B	44	GLU	-1	-0.855	-0.933	23.926	-0.189	-0.189	0.000	0.000	0.000	0.000
44	B	100	CYS	0	-0.084	-0.025	15.069	-0.003	-0.003	0.000	0.000	0.000	0.000
45	B	46	GLU	-1	-0.838	-0.921	19.852	-0.189	-0.189	0.000	0.000	0.000	0.000
46	B	47	LEU	0	-0.004	0.015	15.186	-0.009	-0.009	0.000	0.000	0.000	0.000
47	B	48	VAL	0	-0.024	-0.027	17.479	0.026	0.026	0.000	0.000	0.000	0.000
48	B	49	SER	0	-0.039	-0.031	16.712	0.028	0.028	0.000	0.000	0.000	0.000
49	B	50	ASN	0	0.029	0.009	14.232	-0.089	-0.089	0.000	0.000	0.000	0.000
50	B	51	ILE	0	-0.032	-0.025	12.021	0.058	0.058	0.000	0.000	0.000	0.000
51	B	52	LEU	0	0.036	0.014	12.366	-0.085	-0.085	0.000	0.000	0.000	0.000
52	B	53	ARG	1	0.960	0.986	11.698	0.533	0.533	0.000	0.000	0.000	0.000
53	B	54	ASP	-1	-0.888	-0.927	13.186	-0.284	-0.284	0.000	0.000	0.000	0.000
54	B	55	GLY	0	0.010	0.009	15.624	0.039	0.039	0.000	0.000	0.000	0.000
55	B	56	THR	0	-0.046	-0.036	16.960	0.033	0.033	0.000	0.000	0.000	0.000
56	B	57	THR	0	-0.044	-0.022	17.159	-0.026	-0.026	0.000	0.000	0.000	0.000
57	B	58	THR	0	-0.025	-0.009	18.482	0.015	0.015	0.000	0.000	0.000	0.000
58	B	59	TYR	0	-0.004	-0.002	19.214	-0.014	-0.014	0.000	0.000	0.000	0.000
59	B	60	ALA	0	0.090	0.053	21.570	0.011	0.011	0.000	0.000	0.000	0.000
60	B	61	GLY	0	0.009	-0.012	23.426	0.010	0.010	0.000	0.000	0.000	0.000
61	B	62	SER	0	-0.006	0.003	26.083	0.006	0.006	0.000	0.000	0.000	0.000
62	B	63	VAL	0	0.030	0.015	21.817	0.010	0.010	0.000	0.000	0.000	0.000
63	B	64	LYS	1	0.985	1.007	25.070	0.151	0.151	0.000	0.000	0.000	0.000
64	B	65	GLY	0	-0.032	-0.017	25.794	0.010	0.010	0.000	0.000	0.000	0.000
65	B	66	ARG	1	0.738	0.851	26.202	0.125	0.125	0.000	0.000	0.000	0.000
66	B	67	PHE	0	0.018	-0.001	20.269	0.004	0.004	0.000	0.000	0.000	0.000
67	B	68	THR	0	-0.038	-0.018	20.089	0.002	0.002	0.000	0.000	0.000	0.000
68	B	69	ILE	0	-0.010	0.004	13.212	0.010	0.010	0.000	0.000	0.000	0.000
69	B	70	SER	0	-0.044	-0.024	15.241	0.021	0.021	0.000	0.000	0.000	0.000
70	B	71	ARG	1	0.856	0.919	8.797	0.576	0.576	0.000	0.000	0.000	0.000
71	B	72	ASP	-1	-0.856	-0.924	11.777	-0.050	-0.050	0.000	0.000	0.000	0.000
72	B	73	ASP	-1	-0.825	-0.932	10.730	-0.384	-0.384	0.000	0.000	0.000	0.000
73	B	74	ALA	0	-0.036	-0.006	11.657	0.017	0.017	0.000	0.000	0.000	0.000
74	B	75	LYS	1	0.881	0.926	11.494	0.040	0.040	0.000	0.000	0.000	0.000
75	B	76	ASN	0	0.016	0.021	6.224	-0.042	-0.042	0.000	0.000	0.000	0.000
76	B	77	THR	0	-0.005	0.003	7.132	0.032	0.032	0.000	0.000	0.000	0.000
77	B	78	VAL	0	0.048	0.019	8.806	-0.025	-0.025	0.000	0.000	0.000	0.000
78	B	79	TYR	0	-0.092	-0.059	10.806	0.048	0.048	0.000	0.000	0.000	0.000
79	B	80	LEU	0	0.019	0.006	14.201	-0.023	-0.023	0.000	0.000	0.000	0.000
80	B	81	GLN	0	-0.027	-0.017	16.793	0.025	0.025	0.000	0.000	0.000	0.000
81	B	82	MET	0	-0.019	0.011	19.914	-0.012	-0.012	0.000	0.000	0.000	0.000
82	B	82	VAL	0	0.046	0.009	22.686	0.014	0.014	0.000	0.000	0.000	0.000
83	B	82	ASN	0	-0.014	-0.010	26.423	-0.002	-0.002	0.000	0.000	0.000	0.000
84	B	82	LEU	0	0.020	0.017	23.388	-0.006	-0.006	0.000	0.000	0.000	0.000
85	B	83	LYS	1	1.003	0.991	27.550	0.103	0.103	0.000	0.000	0.000	0.000
86	B	84	SER	0	0.064	0.022	27.950	-0.004	-0.004	0.000	0.000	0.000	0.000
87	B	85	GLU	-1	-0.994	-1.001	27.612	-0.109	-0.109	0.000	0.000	0.000	0.000
88	B	86	ASP	-1	-0.728	-0.841	23.912	-0.132	-0.132	0.000	0.000	0.000	0.000
89	B	87	THR	0	-0.021	0.017	23.219	-0.006	-0.006	0.000	0.000	0.000	0.000
90	B	88	ALA	0	-0.019	-0.013	20.756	-0.004	-0.004	0.000	0.000	0.000	0.000
91	B	89	ARG	1	0.851	0.949	15.019	0.154	0.154	0.000	0.000	0.000	0.000
92	B	90	TYR	0	-0.022	-0.040	15.435	-0.025	-0.025	0.000	0.000	0.000	0.000
93	B	91	TYR	0	0.023	0.003	11.506	0.038	0.038	0.000	0.000	0.000	0.000
94	B	93	ALA	0	0.032	0.012	7.351	-0.058	-0.058	0.000	0.000	0.000	0.000
95	B	94	ALA	0	0.004	-0.012	4.102	0.042	0.162	0.000	-0.012	-0.107	0.000
96	B	95	ASP	-1	-0.770	-0.892	6.154	-1.342	-1.342	0.000	0.000	0.000	0.000
97	B	96	SER	0	-0.078	-0.066	6.999	0.221	0.221	0.000	0.000	0.000	0.000
98	B	97	GLY	0	0.045	0.037	8.812	0.162	0.162	0.000	0.000	0.000	0.000
99	B	98	THR	0	-0.072	-0.049	12.267	0.049	0.049	0.000	0.000	0.000	0.000
100	B	99	GLN	0	0.029	0.024	12.120	0.073	0.073	0.000	0.000	0.000	0.000
101	B	100	LEU	0	0.005	-0.011	15.489	0.029	0.029	0.000	0.000	0.000	0.000
102	B	100	GLY	0	0.017	0.020	17.347	0.031	0.031	0.000	0.000	0.000	0.000
103	B	100	TYR	0	-0.033	-0.022	18.575	0.033	0.033	0.000	0.000	0.000	0.000
104	B	100	VAL	0	-0.015	-0.001	18.582	-0.025	-0.025	0.000	0.000	0.000	0.000
105	B	100	GLY	0	0.007	0.004	20.795	0.022	0.022	0.000	0.000	0.000	0.000
106	B	100	ALA	0	-0.020	-0.008	21.389	-0.022	-0.022	0.000	0.000	0.000	0.000
107	B	100	VAL	0	-0.010	-0.006	18.046	-0.008	-0.008	0.000	0.000	0.000	0.000
108	B	100	GLY	0	0.101	0.076	21.176	-0.010	-0.010	0.000	0.000	0.000	0.000
109	B	100	LEU	0	-0.022	-0.032	22.290	0.000	0.000	0.000	0.000	0.000	0.000
110	B	100	SER	0	0.009	0.021	18.248	0.004	0.004	0.000	0.000	0.000	0.000
111	B	100	LEU	0	-0.025	-0.018	12.582	-0.038	-0.038	0.000	0.000	0.000	0.000
112	B	100	ASP	-1	-0.884	-0.934	15.220	-0.301	-0.301	0.000	0.000	0.000	0.000
113	B	100	TYR	0	-0.099	-0.066	14.168	0.040	0.040	0.000	0.000	0.000	0.000
114	B	100	VAL	0	-0.006	-0.021	12.261	-0.058	-0.058	0.000	0.000	0.000	0.000
115	B	100	MET	0	-0.062	-0.016	9.049	0.031	0.031	0.000	0.000	0.000	0.000
116	B	101	ASP	-1	-0.807	-0.868	5.593	-1.679	-1.679	0.000	0.000	0.000	0.000
117	B	102	TYR	0	-0.056	-0.032	2.708	-6.971	-2.575	3.333	-2.367	-5.362	-0.026
118	B	103	TRP	0	0.041	0.012	5.200	0.357	0.465	-0.001	-0.003	-0.104	0.000
119	B	104	GLY	0	0.009	0.016	6.844	-0.040	-0.040	0.000	0.000	0.000	0.000
120	B	105	LYS	1	0.926	0.946	7.920	0.043	0.043	0.000	0.000	0.000	0.000
121	B	106	GLY	0	0.041	0.020	11.024	0.043	0.043	0.000	0.000	0.000	0.000
122	B	107	THR	0	-0.079	-0.041	13.000	0.060	0.060	0.000	0.000	0.000	0.000
123	B	108	GLN	0	-0.010	-0.003	15.809	-0.027	-0.027	0.000	0.000	0.000	0.000
124	B	109	VAL	0	0.030	0.026	18.967	0.013	0.013	0.000	0.000	0.000	0.000
125	B	110	THR	0	-0.021	-0.025	21.524	-0.009	-0.009	0.000	0.000	0.000	0.000
126	B	111	VAL	0	-0.002	0.010	25.258	0.008	0.008	0.000	0.000	0.000	0.000
127	B	112	SER	0	-0.018	-0.008	27.805	0.002	0.002	0.000	0.000	0.000	0.000

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