FMO DATABASE

FMODB ID: ZNVGN

Calculation Name: 2H09-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H09

Chain ID: A

ChEMBL ID:

UniProt ID: P0A9F1

Base Structure: X-ray

Registration Date: 2023-09-27

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

DOI:

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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1071507.534588
FMO2-HF: Nuclear repulsion	1020111.357502
FMO2-HF: Total energy	-51396.177086
FMO2-MP2: Total energy	-51545.415681

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:24:GLU)

Summations of interaction energy for fragment #1(A:24:GLU)

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.
-46.505	-42.077	0.653	-2.623	-2.456	0.013

Interaction energy analysis for fragmet #1(A:24:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.915 / q_NPA : -0.960

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

Sort

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	26	PHE	0	0.007	0.009	3.792	-1.892	1.619	-0.044	-2.189	-1.277	0.009
4	A	27	ARG	1	0.927	0.968	6.547	-20.694	-20.694	0.000	0.000	0.000	0.000
5	A	28	GLN	0	0.027	0.008	7.948	0.547	0.547	0.000	0.000	0.000	0.000
6	A	29	VAL	0	0.076	0.042	6.837	-0.675	-0.675	0.000	0.000	0.000	0.000
7	A	30	ARG	1	0.890	0.934	2.337	-48.123	-47.206	0.697	-0.434	-1.179	0.004
8	A	31	GLU	-1	-0.925	-0.981	6.466	22.887	22.887	0.000	0.000	0.000	0.000
9	A	32	ALA	0	-0.006	-0.007	9.908	-1.457	-1.457	0.000	0.000	0.000	0.000
10	A	33	HIS	0	0.054	0.035	8.014	2.477	2.477	0.000	0.000	0.000	0.000
11	A	34	ARG	1	0.827	0.916	7.495	-33.744	-33.744	0.000	0.000	0.000	0.000
12	A	35	ARG	1	0.996	0.981	10.877	-21.259	-21.259	0.000	0.000	0.000	0.000
13	A	36	GLU	-1	-0.813	-0.894	13.431	21.480	21.480	0.000	0.000	0.000	0.000
14	A	37	LEU	0	-0.018	-0.011	9.873	-0.206	-0.206	0.000	0.000	0.000	0.000
15	A	38	ILE	0	-0.087	-0.055	13.936	-0.792	-0.792	0.000	0.000	0.000	0.000
16	A	39	ASP	-1	-0.828	-0.917	16.321	15.821	15.821	0.000	0.000	0.000	0.000
17	A	40	ASP	-1	-0.816	-0.908	16.691	17.432	17.432	0.000	0.000	0.000	0.000
18	A	41	TYR	0	-0.084	-0.066	14.125	-0.723	-0.723	0.000	0.000	0.000	0.000
19	A	42	VAL	0	-0.033	-0.018	18.772	-0.768	-0.768	0.000	0.000	0.000	0.000
20	A	43	GLU	-1	-0.808	-0.920	21.688	12.716	12.716	0.000	0.000	0.000	0.000
21	A	44	LEU	0	0.018	0.038	20.037	-0.652	-0.652	0.000	0.000	0.000	0.000
22	A	45	ILE	0	-0.052	-0.040	21.093	-0.603	-0.603	0.000	0.000	0.000	0.000
23	A	46	SER	0	-0.050	-0.028	24.574	-0.569	-0.569	0.000	0.000	0.000	0.000
24	A	47	ASP	-1	-0.844	-0.932	26.090	11.492	11.492	0.000	0.000	0.000	0.000
25	A	48	LEU	0	-0.048	-0.030	24.439	-0.363	-0.363	0.000	0.000	0.000	0.000
26	A	49	ILE	0	-0.084	-0.034	27.953	-0.419	-0.419	0.000	0.000	0.000	0.000
27	A	50	ARG	1	0.921	0.952	30.633	-10.519	-10.519	0.000	0.000	0.000	0.000
28	A	51	GLU	-1	-0.946	-0.956	30.946	9.442	9.442	0.000	0.000	0.000	0.000
29	A	52	VAL	0	-0.076	-0.041	30.407	-0.297	-0.297	0.000	0.000	0.000	0.000
30	A	53	GLY	0	-0.012	0.009	33.154	-0.167	-0.167	0.000	0.000	0.000	0.000
31	A	54	GLU	-1	-1.014	-1.017	30.414	9.943	9.943	0.000	0.000	0.000	0.000
32	A	55	ALA	0	0.098	0.060	25.226	0.203	0.203	0.000	0.000	0.000	0.000
33	A	56	ARG	1	0.923	0.964	26.009	-10.311	-10.311	0.000	0.000	0.000	0.000
34	A	57	GLN	0	0.043	-0.020	20.849	0.762	0.762	0.000	0.000	0.000	0.000
35	A	58	VAL	0	-0.041	-0.026	21.422	0.620	0.620	0.000	0.000	0.000	0.000
36	A	59	ASP	-1	-0.837	-0.925	23.236	12.277	12.277	0.000	0.000	0.000	0.000
37	A	60	MET	0	-0.003	0.026	20.292	0.363	0.363	0.000	0.000	0.000	0.000
38	A	61	ALA	0	-0.013	-0.014	18.383	0.523	0.523	0.000	0.000	0.000	0.000
39	A	62	ALA	0	-0.007	-0.004	19.180	0.567	0.567	0.000	0.000	0.000	0.000
40	A	63	ARG	1	0.919	0.964	21.859	-12.312	-12.312	0.000	0.000	0.000	0.000
41	A	64	LEU	0	-0.013	0.016	16.093	0.247	0.247	0.000	0.000	0.000	0.000
42	A	65	GLY	0	0.016	0.025	17.205	0.649	0.649	0.000	0.000	0.000	0.000
43	A	66	VAL	0	-0.061	-0.019	13.106	1.310	1.310	0.000	0.000	0.000	0.000
44	A	67	SER	0	0.012	-0.003	14.425	-1.125	-1.125	0.000	0.000	0.000	0.000
45	A	68	GLN	0	0.087	0.018	16.246	0.743	0.743	0.000	0.000	0.000	0.000
46	A	69	PRO	0	0.007	-0.011	14.695	0.241	0.241	0.000	0.000	0.000	0.000
47	A	70	THR	0	-0.063	-0.030	11.268	1.137	1.137	0.000	0.000	0.000	0.000
48	A	71	VAL	0	0.128	0.087	13.125	0.664	0.664	0.000	0.000	0.000	0.000
49	A	72	ALA	0	0.009	0.005	15.989	-0.274	-0.274	0.000	0.000	0.000	0.000
50	A	73	LYS	1	0.839	0.917	9.625	-28.223	-28.223	0.000	0.000	0.000	0.000
51	A	74	MET	0	0.004	0.004	11.969	0.716	0.716	0.000	0.000	0.000	0.000
52	A	75	LEU	0	0.087	0.045	14.150	-0.611	-0.611	0.000	0.000	0.000	0.000
53	A	76	LYS	1	0.931	0.973	16.444	-17.322	-17.322	0.000	0.000	0.000	0.000
54	A	77	ARG	1	0.910	0.956	9.127	-28.593	-28.593	0.000	0.000	0.000	0.000
55	A	78	LEU	0	0.083	0.036	15.761	-0.280	-0.280	0.000	0.000	0.000	0.000
56	A	79	ALA	0	-0.009	0.009	18.414	-0.688	-0.688	0.000	0.000	0.000	0.000
57	A	80	THR	0	-0.069	-0.033	17.918	-0.580	-0.580	0.000	0.000	0.000	0.000
58	A	81	MET	0	-0.072	-0.032	14.620	0.098	0.098	0.000	0.000	0.000	0.000
59	A	82	GLY	0	0.031	0.027	20.349	-0.407	-0.407	0.000	0.000	0.000	0.000
60	A	83	LEU	0	0.004	0.011	19.588	-0.337	-0.337	0.000	0.000	0.000	0.000
61	A	84	ILE	0	-0.032	-0.019	21.012	-0.210	-0.210	0.000	0.000	0.000	0.000
62	A	85	GLU	-1	-0.882	-0.934	23.923	10.894	10.894	0.000	0.000	0.000	0.000
63	A	86	MET	0	-0.095	-0.052	21.656	0.244	0.244	0.000	0.000	0.000	0.000
64	A	87	ILE	0	0.057	0.027	26.485	-0.290	-0.290	0.000	0.000	0.000	0.000
65	A	88	PRO	0	0.012	0.001	30.001	0.073	0.073	0.000	0.000	0.000	0.000
66	A	89	TRP	0	-0.018	-0.024	30.999	-0.191	-0.191	0.000	0.000	0.000	0.000
67	A	90	ARG	1	0.928	0.952	31.196	-9.146	-9.146	0.000	0.000	0.000	0.000
68	A	91	GLY	0	-0.041	0.005	27.449	0.022	0.022	0.000	0.000	0.000	0.000
69	A	92	VAL	0	-0.038	-0.024	22.834	0.017	0.017	0.000	0.000	0.000	0.000
70	A	93	PHE	0	0.047	0.022	26.098	-0.302	-0.302	0.000	0.000	0.000	0.000
71	A	94	LEU	0	-0.010	0.007	23.875	0.441	0.441	0.000	0.000	0.000	0.000
72	A	95	THR	0	0.007	0.000	26.105	-0.401	-0.401	0.000	0.000	0.000	0.000
73	A	96	ALA	0	0.037	0.008	28.206	0.023	0.023	0.000	0.000	0.000	0.000
74	A	97	GLU	-1	-0.914	-0.969	25.778	11.056	11.056	0.000	0.000	0.000	0.000
75	A	98	GLY	0	-0.005	-0.010	24.135	0.354	0.354	0.000	0.000	0.000	0.000
76	A	99	GLU	-1	-0.956	-0.999	25.052	10.808	10.808	0.000	0.000	0.000	0.000
77	A	100	LYS	1	0.936	1.000	26.879	-11.555	-11.555	0.000	0.000	0.000	0.000
78	A	101	LEU	0	-0.050	-0.019	20.483	0.061	0.061	0.000	0.000	0.000	0.000
79	A	102	ALA	0	0.022	0.002	24.165	0.237	0.237	0.000	0.000	0.000	0.000
80	A	103	GLN	0	-0.034	-0.013	25.103	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	104	GLU	-1	-0.877	-0.960	25.280	11.816	11.816	0.000	0.000	0.000	0.000
82	A	105	SER	0	0.006	0.016	22.229	0.243	0.243	0.000	0.000	0.000	0.000
83	A	106	ARG	1	0.910	0.976	24.133	-11.613	-11.613	0.000	0.000	0.000	0.000
84	A	107	GLU	-1	-0.966	-0.993	27.047	10.909	10.909	0.000	0.000	0.000	0.000
85	A	108	ARG	1	0.894	0.951	21.667	-14.205	-14.205	0.000	0.000	0.000	0.000
86	A	109	HIS	0	0.016	0.018	21.597	0.169	0.169	0.000	0.000	0.000	0.000
87	A	110	GLN	0	0.006	0.002	26.328	-0.425	-0.425	0.000	0.000	0.000	0.000
88	A	111	ILE	0	-0.063	-0.014	28.930	-0.391	-0.391	0.000	0.000	0.000	0.000
89	A	112	VAL	0	0.009	0.003	25.311	-0.277	-0.277	0.000	0.000	0.000	0.000
90	A	113	GLU	-1	-0.836	-0.924	28.695	10.234	10.234	0.000	0.000	0.000	0.000
91	A	114	ASN	0	-0.014	-0.030	30.574	-0.383	-0.383	0.000	0.000	0.000	0.000
92	A	115	PHE	0	-0.001	0.012	30.497	-0.308	-0.308	0.000	0.000	0.000	0.000
93	A	116	LEU	0	0.004	-0.006	28.070	-0.242	-0.242	0.000	0.000	0.000	0.000
94	A	117	LEU	0	-0.028	-0.006	32.715	-0.250	-0.250	0.000	0.000	0.000	0.000
95	A	118	VAL	0	-0.058	-0.018	35.744	-0.279	-0.279	0.000	0.000	0.000	0.000
96	A	119	LEU	0	-0.056	-0.031	32.856	-0.221	-0.221	0.000	0.000	0.000	0.000
97	A	120	GLY	0	-0.028	0.002	36.612	-0.170	-0.170	0.000	0.000	0.000	0.000
98	A	121	VAL	0	-0.060	-0.023	31.526	-0.083	-0.083	0.000	0.000	0.000	0.000
99	A	122	SER	0	-0.030	-0.012	33.661	-0.037	-0.037	0.000	0.000	0.000	0.000
100	A	123	PRO	0	0.084	0.000	33.514	0.272	0.272	0.000	0.000	0.000	0.000
101	A	124	GLU	-1	-0.945	-0.968	31.351	9.962	9.962	0.000	0.000	0.000	0.000
102	A	125	ILE	0	-0.047	-0.020	29.011	0.362	0.362	0.000	0.000	0.000	0.000
103	A	126	ALA	0	-0.003	0.018	28.676	0.376	0.376	0.000	0.000	0.000	0.000
104	A	127	ARG	1	0.949	0.966	28.181	-9.924	-9.924	0.000	0.000	0.000	0.000
105	A	128	ARG	1	0.892	0.955	23.332	-12.321	-12.321	0.000	0.000	0.000	0.000
106	A	129	ASP	-1	-0.878	-0.957	24.207	12.700	12.700	0.000	0.000	0.000	0.000
107	A	130	ALA	0	0.022	0.005	23.925	0.518	0.518	0.000	0.000	0.000	0.000
108	A	131	GLU	-1	-0.967	-0.984	21.210	15.395	15.395	0.000	0.000	0.000	0.000
109	A	132	GLY	0	0.010	0.003	19.568	0.799	0.799	0.000	0.000	0.000	0.000
110	A	133	MET	0	-0.068	-0.044	19.350	0.640	0.640	0.000	0.000	0.000	0.000
111	A	134	GLU	-1	-0.799	-0.906	20.822	14.955	14.955	0.000	0.000	0.000	0.000
112	A	135	HIS	1	0.892	0.971	16.588	-17.110	-17.110	0.000	0.000	0.000	0.000
113	A	136	HIS	0	-0.121	-0.062	14.233	1.007	1.007	0.000	0.000	0.000	0.000
114	A	137	VAL	0	-0.055	-0.008	18.502	-0.490	-0.490	0.000	0.000	0.000	0.000
115	A	138	SER	0	-0.027	-0.013	21.643	0.042	0.042	0.000	0.000	0.000	0.000
116	A	139	GLU	-1	-0.883	-0.959	22.482	11.370	11.370	0.000	0.000	0.000	0.000
117	A	140	GLU	-1	-0.936	-0.964	25.261	10.310	10.310	0.000	0.000	0.000	0.000
118	A	141	THR	0	-0.045	-0.019	25.264	-0.420	-0.420	0.000	0.000	0.000	0.000
119	A	142	LEU	0	0.041	0.022	25.704	-0.339	-0.339	0.000	0.000	0.000	0.000
120	A	143	ASP	-1	-0.865	-0.932	27.799	10.024	10.024	0.000	0.000	0.000	0.000
121	A	144	ALA	0	-0.014	-0.022	30.527	-0.405	-0.405	0.000	0.000	0.000	0.000
122	A	145	PHE	0	-0.033	-0.024	26.520	-0.224	-0.224	0.000	0.000	0.000	0.000
123	A	146	ARG	1	0.905	0.955	30.119	-10.267	-10.267	0.000	0.000	0.000	0.000
124	A	147	LEU	0	-0.110	-0.042	33.585	-0.327	-0.327	0.000	0.000	0.000	0.000
125	A	148	PHE	0	-0.053	-0.033	35.303	-0.359	-0.359	0.000	0.000	0.000	0.000
126	A	149	THR	0	-0.013	0.022	37.181	0.071	0.071	0.000	0.000	0.000	0.000
127	A	150	GLN	0	-0.005	-0.003	40.020	-0.114	-0.114	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:24:GLU)