FMO DATABASE

FMODB ID: 5J51Z

Calculation Name: 3EPU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EPU

Chain ID: A

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	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	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1252917.655626
FMO2-HF: Nuclear repulsion	1196640.944878
FMO2-HF: Total energy	-56276.710748
FMO2-MP2: Total energy	-56438.067434

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:1:MET)

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

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.
-0.765	0.817	-0.009	-0.663	-0.91	0.002

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.018

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	3	SER	0	-0.003	-0.032	3.877	1.011	2.426	-0.008	-0.646	-0.761	0.002
4	A	4	ARG	1	0.811	0.862	6.146	0.615	0.615	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.074	0.048	8.560	0.141	0.141	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.755	-0.835	7.161	-0.777	-0.777	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.878	0.929	4.523	-1.438	-1.271	-0.001	-0.017	-0.149	0.000
8	A	8	LEU	0	0.010	0.035	8.306	0.066	0.066	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.024	0.013	11.865	0.014	0.014	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.845	0.906	8.529	-0.762	-0.762	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.027	-0.025	11.183	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.041	0.014	13.254	-0.029	-0.029	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.028	-0.034	13.941	-0.035	-0.035	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.036	-0.020	11.787	0.009	0.009	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.765	0.875	15.790	-0.298	-0.298	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.024	-0.003	18.568	-0.031	-0.031	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.080	-0.041	19.372	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	18	THR	0	0.026	0.016	17.955	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.808	-0.872	13.816	0.632	0.632	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.065	-0.036	14.493	0.002	0.002	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.003	0.010	15.969	-0.047	-0.047	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.018	-0.008	10.764	0.044	0.044	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.023	-0.013	12.070	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.759	-0.876	13.319	-0.150	-0.150	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.958	-0.977	15.245	-0.201	-0.201	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.093	-0.051	16.433	-0.045	-0.045	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.753	0.855	10.785	0.454	0.454	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.026	0.003	16.618	0.019	0.019	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.029	-0.015	16.603	0.017	0.017	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.058	-0.028	18.725	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.025	0.006	19.496	0.016	0.016	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.016	-0.009	23.578	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	33	ILE	0	0.012	0.024	23.601	0.012	0.012	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.852	-0.940	27.485	0.085	0.085	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.102	-0.051	29.820	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.821	0.891	31.246	-0.051	-0.051	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.001	-0.024	29.302	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.890	0.935	28.146	-0.024	-0.024	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.015	0.017	23.054	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.013	0.008	22.178	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.010	0.010	18.007	0.001	0.001	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.012	-0.018	18.628	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	43	SER	0	0.022	0.018	13.563	-0.016	-0.016	0.000	0.000	0.000	0.000
44	A	44	THR	0	0.046	0.020	14.900	-0.064	-0.064	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.019	-0.006	15.874	-0.051	-0.051	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.007	-0.007	11.660	-0.039	-0.039	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.818	-0.885	12.805	-0.234	-0.234	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.008	-0.005	15.530	0.033	0.033	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.011	0.010	14.504	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	50	MET	0	-0.065	0.005	17.840	0.009	0.009	0.000	0.000	0.000	0.000
51	A	51	ILE	0	0.025	0.001	21.207	0.005	0.005	0.000	0.000	0.000	0.000
52	A	52	TYR	0	0.000	-0.008	23.488	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.095	0.028	26.559	0.007	0.007	0.000	0.000	0.000	0.000
54	A	54	PHE	0	-0.038	-0.024	26.992	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	55	CYS	0	-0.051	-0.020	30.926	0.006	0.006	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.068	0.045	34.502	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.860	0.917	36.422	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.028	-0.007	38.923	0.003	0.003	0.000	0.000	0.000	0.000
59	A	59	PRO	0	0.002	0.006	41.979	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.887	-0.955	45.522	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.016	0.010	47.528	0.002	0.002	0.000	0.000	0.000	0.000
62	A	62	ASN	0	-0.006	-0.008	48.874	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.091	-0.074	49.517	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.083	0.055	45.615	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.010	0.005	43.512	0.001	0.001	0.000	0.000	0.000	0.000
66	A	66	PHE	0	-0.003	-0.015	43.437	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.796	-0.877	45.240	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	PHE	0	0.023	0.014	40.152	0.002	0.002	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.008	-0.008	39.685	0.000	0.000	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.058	-0.034	41.724	0.000	0.000	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.026	0.013	40.985	0.001	0.001	0.000	0.000	0.000	0.000
72	A	72	ASN	0	0.013	0.002	36.042	0.004	0.004	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.022	0.001	38.394	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	74	TRP	0	0.019	0.026	38.109	0.001	0.001	0.000	0.000	0.000	0.000
75	A	75	PHE	0	0.039	0.010	35.213	0.003	0.003	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.011	0.001	35.569	0.001	0.001	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.961	-0.971	36.434	0.007	0.007	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.131	-0.080	37.066	0.004	0.004	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.100	-0.046	32.034	0.002	0.002	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.040	0.033	31.502	0.003	0.003	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.056	-0.036	29.387	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	82	HIS	0	0.019	0.013	30.726	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.012	0.003	32.379	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	CYS	0	-0.090	-0.050	32.413	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	85	TYR	0	-0.005	-0.016	34.502	0.004	0.004	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.779	-0.845	31.788	-0.044	-0.044	0.000	0.000	0.000	0.000
87	A	87	ASN	0	-0.012	-0.018	33.900	0.007	0.007	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.073	-0.037	30.058	0.003	0.003	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.049	-0.050	31.843	0.005	0.005	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.019	-0.008	33.805	0.008	0.008	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.033	-0.022	33.603	0.005	0.005	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.029	0.011	35.273	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.034	-0.015	29.534	0.004	0.004	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.011	0.017	31.294	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	95	ALA	0	-0.011	-0.007	27.910	0.003	0.003	0.000	0.000	0.000	0.000
96	A	96	LEU	0	0.034	0.012	24.984	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	97	ASN	0	-0.054	-0.042	21.322	0.000	0.000	0.000	0.000	0.000	0.000
98	A	98	PHE	0	0.028	0.018	16.534	0.015	0.015	0.000	0.000	0.000	0.000
99	A	99	SER	0	0.021	0.003	18.513	-0.028	-0.028	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.002	-0.007	12.444	0.031	0.031	0.000	0.000	0.000	0.000
101	A	101	ASN	0	-0.034	-0.001	14.305	0.032	0.032	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.879	-0.943	16.114	0.010	0.010	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.049	-0.013	14.282	0.030	0.030	0.000	0.000	0.000	0.000
104	A	104	SER	0	-0.038	-0.049	15.465	0.025	0.025	0.000	0.000	0.000	0.000
105	A	105	VAL	0	0.024	0.005	15.491	-0.034	-0.034	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.761	-0.854	17.257	0.263	0.263	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.885	0.943	19.531	-0.119	-0.119	0.000	0.000	0.000	0.000
108	A	108	LEU	0	0.013	0.011	16.600	-0.018	-0.018	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.817	-0.914	20.161	0.210	0.210	0.000	0.000	0.000	0.000
110	A	110	CYS	0	-0.049	-0.019	22.421	-0.014	-0.014	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.862	-0.947	22.915	0.043	0.043	0.000	0.000	0.000	0.000
112	A	112	ILE	0	-0.028	-0.018	20.506	-0.013	-0.013	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.823	-0.895	24.856	0.079	0.079	0.000	0.000	0.000	0.000
114	A	114	VAL	0	-0.007	0.002	27.824	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	115	VAL	0	-0.005	0.003	26.679	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	116	ILE	0	0.026	0.012	26.924	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	117	ARG	1	0.844	0.898	30.522	-0.074	-0.074	0.000	0.000	0.000	0.000
118	A	118	SER	0	-0.023	-0.013	32.420	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	119	MET	0	-0.034	-0.013	30.913	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.803	-0.845	34.402	0.042	0.042	0.000	0.000	0.000	0.000
121	A	121	ASN	0	0.012	0.006	36.736	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	122	LEU	0	0.013	0.009	36.830	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	123	TYR	0	-0.020	-0.037	35.013	0.000	0.000	0.000	0.000	0.000	0.000
124	A	124	HIS	0	-0.083	-0.045	40.152	0.000	0.000	0.000	0.000	0.000	0.000
125	A	125	ILE	0	0.013	0.004	41.128	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.031	-0.018	40.766	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	127	GLN	0	-0.034	0.002	43.713	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	ASP	-1	-0.933	-0.966	45.746	0.017	0.017	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.832	0.907	46.028	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	130	GLY	0	-0.017	0.000	48.856	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	131	ILE	0	-0.083	-0.046	46.062	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	132	THR	0	-0.008	-0.012	42.781	0.000	0.000	0.000	0.000	0.000	0.000
133	A	133	LEU	0	-0.002	0.019	38.061	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	134	ASP	-1	-0.777	-0.861	38.453	0.012	0.012	0.000	0.000	0.000	0.000
135	A	135	THR	0	0.017	-0.007	37.038	0.001	0.001	0.000	0.000	0.000	0.000
136	A	136	ASP	-1	-0.973	-0.980	34.316	0.016	0.016	0.000	0.000	0.000	0.000

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