FMO DATABASE

FMODB ID: ZVZ4N

Calculation Name: 3EPU-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EPU

Chain ID: B

ChEMBL ID:

UniProt ID: Q8ZNP3

Base Structure: X-ray

Registration Date: 2023-09-23

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1123852.015036
FMO2-HF: Nuclear repulsion	1069281.186196
FMO2-HF: Total energy	-54570.82884
FMO2-MP2: Total energy	-54728.016541

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:3:SER)

Summations of interaction energy for fragment #1(B:3:SER)

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.
-37.042	-44.607	32.59	-16.321	-8.704	-0.088

Interaction energy analysis for fragmet #1(B:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.044

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	B	5	ALA	0	0.035	0.020	2.770	-1.857	0.648	0.125	-1.288	-1.341	0.004
4	B	6	ASP	-1	-0.768	-0.848	1.531	-36.182	-46.758	32.463	-14.889	-6.999	-0.092
5	B	7	ARG	1	0.942	0.975	3.865	-1.460	-0.954	0.002	-0.144	-0.364	0.000
6	B	8	LEU	0	-0.019	-0.008	6.031	0.348	0.348	0.000	0.000	0.000	0.000
7	B	9	LEU	0	0.070	0.031	6.850	0.318	0.318	0.000	0.000	0.000	0.000
8	B	10	ARG	1	0.946	1.002	7.439	1.688	1.688	0.000	0.000	0.000	0.000
9	B	11	GLN	0	-0.003	-0.013	9.588	0.181	0.181	0.000	0.000	0.000	0.000
10	B	12	PHE	0	-0.007	0.000	11.646	0.114	0.114	0.000	0.000	0.000	0.000
11	B	13	SER	0	0.028	-0.010	11.682	0.056	0.056	0.000	0.000	0.000	0.000
12	B	14	LEU	0	-0.048	-0.020	12.926	0.089	0.089	0.000	0.000	0.000	0.000
13	B	15	LYS	1	0.908	0.950	15.841	0.267	0.267	0.000	0.000	0.000	0.000
14	B	16	LEU	0	0.010	0.007	16.050	0.034	0.034	0.000	0.000	0.000	0.000
15	B	17	ASN	0	0.042	0.026	17.560	0.025	0.025	0.000	0.000	0.000	0.000
16	B	18	THR	0	-0.077	-0.029	20.034	0.050	0.050	0.000	0.000	0.000	0.000
17	B	19	ASP	-1	-0.939	-0.953	21.763	-0.189	-0.189	0.000	0.000	0.000	0.000
18	B	20	SER	0	-0.079	-0.044	23.621	0.010	0.010	0.000	0.000	0.000	0.000
19	B	21	ILE	0	-0.055	-0.025	20.950	0.000	0.000	0.000	0.000	0.000	0.000
20	B	22	VAL	0	0.017	0.010	20.724	-0.019	-0.019	0.000	0.000	0.000	0.000
21	B	23	PHE	0	-0.037	-0.027	13.958	-0.008	-0.008	0.000	0.000	0.000	0.000
22	B	24	ASP	-1	-0.875	-0.924	17.425	-0.505	-0.505	0.000	0.000	0.000	0.000
23	B	25	GLU	-1	-0.971	-0.991	11.581	-1.187	-1.187	0.000	0.000	0.000	0.000
24	B	26	ASN	0	0.037	-0.016	12.467	0.081	0.081	0.000	0.000	0.000	0.000
25	B	27	ARG	1	0.912	0.974	6.669	2.043	2.043	0.000	0.000	0.000	0.000
26	B	28	LEU	0	0.009	0.001	10.686	0.236	0.236	0.000	0.000	0.000	0.000
27	B	29	CYS	0	-0.043	-0.017	10.808	-0.245	-0.245	0.000	0.000	0.000	0.000
28	B	30	SER	0	-0.016	-0.001	12.773	0.154	0.154	0.000	0.000	0.000	0.000
29	B	31	PHE	0	-0.001	-0.004	15.581	-0.031	-0.031	0.000	0.000	0.000	0.000
30	B	32	ILE	0	-0.020	-0.006	18.128	0.009	0.009	0.000	0.000	0.000	0.000
31	B	33	ILE	0	0.046	0.030	20.893	0.006	0.006	0.000	0.000	0.000	0.000
32	B	34	ASP	-1	-0.845	-0.921	23.702	-0.154	-0.154	0.000	0.000	0.000	0.000
33	B	35	ASN	0	-0.133	-0.079	25.178	-0.004	-0.004	0.000	0.000	0.000	0.000
34	B	36	ARG	1	0.935	0.980	26.415	0.159	0.159	0.000	0.000	0.000	0.000
35	B	37	TYR	0	0.039	0.021	25.337	-0.007	-0.007	0.000	0.000	0.000	0.000
36	B	38	ARG	1	0.930	0.973	18.389	0.465	0.465	0.000	0.000	0.000	0.000
37	B	39	ILE	0	0.051	0.022	19.037	0.011	0.011	0.000	0.000	0.000	0.000
38	B	40	LEU	0	-0.061	-0.039	15.953	-0.063	-0.063	0.000	0.000	0.000	0.000
39	B	41	LEU	0	0.033	0.022	14.800	0.039	0.039	0.000	0.000	0.000	0.000
40	B	42	THR	0	-0.018	-0.015	14.631	-0.118	-0.118	0.000	0.000	0.000	0.000
41	B	43	SER	0	0.056	0.022	12.383	0.104	0.104	0.000	0.000	0.000	0.000
42	B	44	THR	0	0.016	-0.004	13.464	-0.142	-0.142	0.000	0.000	0.000	0.000
43	B	45	ASN	0	0.027	0.026	15.933	0.005	0.005	0.000	0.000	0.000	0.000
44	B	46	SER	0	-0.007	-0.020	16.097	-0.015	-0.015	0.000	0.000	0.000	0.000
45	B	47	GLU	-1	-0.953	-0.963	17.018	-0.232	-0.232	0.000	0.000	0.000	0.000
46	B	48	TYR	0	-0.030	-0.017	19.113	0.043	0.043	0.000	0.000	0.000	0.000
47	B	49	ILE	0	-0.027	-0.004	14.598	-0.076	-0.076	0.000	0.000	0.000	0.000
48	B	50	MET	0	-0.056	0.002	18.021	0.080	0.080	0.000	0.000	0.000	0.000
49	B	51	ILE	0	0.016	0.002	18.696	-0.065	-0.065	0.000	0.000	0.000	0.000
50	B	52	TYR	0	0.004	-0.006	19.799	0.030	0.030	0.000	0.000	0.000	0.000
51	B	53	GLY	0	0.074	0.021	22.082	-0.024	-0.024	0.000	0.000	0.000	0.000
52	B	54	PHE	0	-0.086	-0.054	21.152	0.012	0.012	0.000	0.000	0.000	0.000
53	B	55	CYS	0	-0.027	0.006	25.683	0.013	0.013	0.000	0.000	0.000	0.000
54	B	56	GLY	0	0.083	0.027	29.328	0.012	0.012	0.000	0.000	0.000	0.000
55	B	57	LYS	1	0.915	0.955	27.911	0.280	0.280	0.000	0.000	0.000	0.000
56	B	58	PRO	0	0.003	0.010	32.499	0.011	0.011	0.000	0.000	0.000	0.000
57	B	59	PRO	0	0.016	-0.002	35.789	0.000	0.000	0.000	0.000	0.000	0.000
58	B	60	ASP	-1	-0.908	-0.936	37.332	-0.183	-0.183	0.000	0.000	0.000	0.000
59	B	61	ASN	0	-0.022	-0.027	39.918	0.012	0.012	0.000	0.000	0.000	0.000
60	B	62	ASN	0	0.015	-0.007	41.868	-0.008	-0.008	0.000	0.000	0.000	0.000
61	B	63	ASN	0	-0.004	-0.009	43.094	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	64	LEU	0	0.025	0.019	39.585	0.002	0.002	0.000	0.000	0.000	0.000
63	B	65	ALA	0	0.030	0.018	39.043	-0.003	-0.003	0.000	0.000	0.000	0.000
64	B	66	PHE	0	-0.003	-0.006	39.864	-0.004	-0.004	0.000	0.000	0.000	0.000
65	B	67	GLU	-1	-0.924	-0.958	41.934	-0.112	-0.112	0.000	0.000	0.000	0.000
66	B	68	PHE	0	-0.003	-0.010	36.547	-0.002	-0.002	0.000	0.000	0.000	0.000
67	B	69	LEU	0	-0.017	-0.018	37.348	-0.003	-0.003	0.000	0.000	0.000	0.000
68	B	70	ASN	0	0.000	0.003	39.213	0.003	0.003	0.000	0.000	0.000	0.000
69	B	71	ALA	0	0.017	0.013	38.145	0.004	0.004	0.000	0.000	0.000	0.000
70	B	72	ASN	0	-0.024	-0.029	34.711	-0.005	-0.005	0.000	0.000	0.000	0.000
71	B	73	LEU	0	-0.019	0.008	37.504	0.000	0.000	0.000	0.000	0.000	0.000
72	B	74	TRP	0	0.012	0.021	35.927	0.001	0.001	0.000	0.000	0.000	0.000
73	B	75	PHE	0	0.040	0.001	34.059	0.002	0.002	0.000	0.000	0.000	0.000
74	B	76	ALA	0	-0.025	0.003	35.372	-0.002	-0.002	0.000	0.000	0.000	0.000
75	B	77	GLU	-1	-0.978	-0.979	36.871	-0.096	-0.096	0.000	0.000	0.000	0.000
76	B	78	ASN	0	-0.115	-0.066	36.721	0.009	0.009	0.000	0.000	0.000	0.000
77	B	79	ASN	0	-0.069	-0.028	33.263	-0.009	-0.009	0.000	0.000	0.000	0.000
78	B	80	GLY	0	0.024	0.020	31.670	-0.005	-0.005	0.000	0.000	0.000	0.000
79	B	81	PRO	0	-0.048	-0.030	27.941	-0.006	-0.006	0.000	0.000	0.000	0.000
80	B	82	HIS	0	0.019	0.014	29.170	0.012	0.012	0.000	0.000	0.000	0.000
81	B	83	LEU	0	-0.011	0.014	29.768	-0.017	-0.017	0.000	0.000	0.000	0.000
82	B	84	CYS	0	-0.041	-0.037	29.286	0.007	0.007	0.000	0.000	0.000	0.000
83	B	85	TYR	0	0.012	0.003	30.735	-0.004	-0.004	0.000	0.000	0.000	0.000
84	B	86	ASP	-1	-0.788	-0.877	25.296	-0.384	-0.384	0.000	0.000	0.000	0.000
85	B	87	ASN	0	-0.007	-0.035	28.477	0.015	0.015	0.000	0.000	0.000	0.000
86	B	88	ASN	0	-0.069	-0.009	25.545	0.014	0.014	0.000	0.000	0.000	0.000
87	B	89	SER	0	-0.068	-0.041	24.837	0.011	0.011	0.000	0.000	0.000	0.000
88	B	90	GLN	0	-0.011	-0.009	26.895	0.008	0.008	0.000	0.000	0.000	0.000
89	B	91	SER	0	0.005	-0.001	27.502	0.012	0.012	0.000	0.000	0.000	0.000
90	B	92	LEU	0	-0.006	0.009	29.569	-0.005	-0.005	0.000	0.000	0.000	0.000
91	B	93	LEU	0	-0.038	-0.036	24.903	-0.010	-0.010	0.000	0.000	0.000	0.000
92	B	94	LEU	0	0.015	0.024	27.253	0.018	0.018	0.000	0.000	0.000	0.000
93	B	95	ALA	0	-0.017	-0.015	25.127	-0.026	-0.026	0.000	0.000	0.000	0.000
94	B	96	LEU	0	0.032	0.009	24.340	0.022	0.022	0.000	0.000	0.000	0.000
95	B	97	ASN	0	-0.028	-0.017	23.073	-0.031	-0.031	0.000	0.000	0.000	0.000
96	B	98	PHE	0	0.039	0.013	19.070	0.030	0.030	0.000	0.000	0.000	0.000
97	B	99	SER	0	0.044	0.011	20.814	-0.026	-0.026	0.000	0.000	0.000	0.000
98	B	100	LEU	0	0.009	0.010	16.304	0.005	0.005	0.000	0.000	0.000	0.000
99	B	101	ASN	0	-0.043	-0.006	20.168	0.025	0.025	0.000	0.000	0.000	0.000
100	B	102	GLU	-1	-0.960	-0.978	23.334	-0.084	-0.084	0.000	0.000	0.000	0.000
101	B	103	SER	0	-0.056	-0.022	19.421	-0.007	-0.007	0.000	0.000	0.000	0.000
102	B	104	SER	0	0.002	-0.015	19.203	0.016	0.016	0.000	0.000	0.000	0.000
103	B	105	VAL	0	0.012	0.001	16.682	-0.039	-0.039	0.000	0.000	0.000	0.000
104	B	106	GLU	-1	-0.845	-0.925	18.495	-0.070	-0.070	0.000	0.000	0.000	0.000
105	B	107	LYS	1	0.924	0.968	22.229	0.138	0.138	0.000	0.000	0.000	0.000
106	B	108	LEU	0	-0.005	-0.010	16.262	-0.016	-0.016	0.000	0.000	0.000	0.000
107	B	109	GLU	-1	-0.903	-0.961	20.307	-0.170	-0.170	0.000	0.000	0.000	0.000
108	B	110	CYS	0	-0.070	-0.023	21.930	0.007	0.007	0.000	0.000	0.000	0.000
109	B	111	GLU	-1	-0.868	-0.944	23.017	-0.193	-0.193	0.000	0.000	0.000	0.000
110	B	112	ILE	0	-0.010	-0.009	18.511	-0.016	-0.016	0.000	0.000	0.000	0.000
111	B	113	GLU	-1	-0.927	-0.960	23.109	-0.153	-0.153	0.000	0.000	0.000	0.000
112	B	114	VAL	0	-0.012	0.002	26.283	0.010	0.010	0.000	0.000	0.000	0.000
113	B	115	VAL	0	-0.010	-0.010	24.622	0.008	0.008	0.000	0.000	0.000	0.000
114	B	116	ILE	0	0.056	0.017	23.630	0.003	0.003	0.000	0.000	0.000	0.000
115	B	117	ARG	1	0.954	0.967	27.502	0.141	0.141	0.000	0.000	0.000	0.000
116	B	118	SER	0	-0.026	0.004	30.121	0.013	0.013	0.000	0.000	0.000	0.000
117	B	119	MET	0	-0.057	-0.020	26.080	0.000	0.000	0.000	0.000	0.000	0.000
118	B	120	GLU	-1	-0.894	-0.947	30.940	-0.136	-0.136	0.000	0.000	0.000	0.000
119	B	121	ASN	0	-0.012	-0.016	33.031	0.013	0.013	0.000	0.000	0.000	0.000
120	B	122	LEU	0	0.005	0.005	33.389	0.007	0.007	0.000	0.000	0.000	0.000
121	B	123	TYR	0	-0.048	-0.042	29.890	0.004	0.004	0.000	0.000	0.000	0.000
122	B	124	HIS	0	-0.035	-0.013	35.700	0.011	0.011	0.000	0.000	0.000	0.000
123	B	125	ILE	0	0.018	0.021	38.495	0.007	0.007	0.000	0.000	0.000	0.000
124	B	126	LEU	0	-0.065	-0.042	36.241	0.004	0.004	0.000	0.000	0.000	0.000
125	B	127	GLN	0	-0.015	0.000	39.559	0.000	0.000	0.000	0.000	0.000	0.000
126	B	128	ASP	-1	-0.920	-0.938	41.085	-0.095	-0.095	0.000	0.000	0.000	0.000
127	B	129	LYS	1	0.849	0.922	43.152	0.116	0.116	0.000	0.000	0.000	0.000
128	B	130	GLY	0	-0.036	-0.013	43.626	0.000	0.000	0.000	0.000	0.000	0.000
129	B	131	ILE	0	-0.056	-0.030	39.568	-0.001	-0.001	0.000	0.000	0.000	0.000
130	B	132	THR	0	0.021	-0.001	37.153	-0.001	-0.001	0.000	0.000	0.000	0.000
131	B	133	LEU	0	-0.051	-0.023	32.856	0.002	0.002	0.000	0.000	0.000	0.000
132	B	134	ASP	-1	-0.923	-0.946	32.540	-0.207	-0.207	0.000	0.000	0.000	0.000
133	B	135	THR	0	-0.015	0.001	27.880	-0.014	-0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:3:SER)