FMO DATABASE

FMODB ID: ZVV8N

Calculation Name: 1EIF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1EIF

Chain ID: A

ChEMBL ID:

UniProt ID: Q58625

Base Structure: X-ray

Registration Date: 2023-09-21

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-970670.653927
FMO2-HF: Nuclear repulsion	921236.066079
FMO2-HF: Total energy	-49434.587848
FMO2-MP2: Total energy	-49576.937974

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:4:MET)

Summations of interaction energy for fragment #1(A:4: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.
-1.632	-0.651	0.02	-0.262	-0.739	0.002

Interaction energy analysis for fragmet #1(A:4:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.004

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	6	GLY	0	0.068	0.036	3.829	-1.349	-0.368	0.020	-0.262	-0.739	0.002
4	A	7	THR	0	-0.059	-0.074	5.972	-0.118	-0.118	0.000	0.000	0.000	0.000
5	A	8	LYS	1	0.935	0.977	8.970	-0.236	-0.236	0.000	0.000	0.000	0.000
6	A	9	GLN	0	0.003	-0.006	11.236	-0.121	-0.121	0.000	0.000	0.000	0.000
7	A	10	VAL	0	0.002	0.007	14.302	-0.005	-0.005	0.000	0.000	0.000	0.000
8	A	11	ASN	0	0.042	0.030	17.706	0.003	0.003	0.000	0.000	0.000	0.000
9	A	12	VAL	0	0.065	0.052	21.365	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	13	GLY	0	-0.010	-0.025	23.491	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	14	SER	0	-0.120	-0.050	21.797	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	15	LEU	0	0.000	0.002	19.686	0.000	0.000	0.000	0.000	0.000	0.000
13	A	16	LYS	1	0.906	0.954	22.932	-0.143	-0.143	0.000	0.000	0.000	0.000
14	A	17	VAL	0	0.034	0.015	23.647	0.008	0.008	0.000	0.000	0.000	0.000
15	A	18	GLY	0	0.028	0.001	23.770	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	19	GLN	0	-0.047	-0.016	19.614	0.008	0.008	0.000	0.000	0.000	0.000
17	A	20	TYR	0	0.043	0.014	15.747	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	21	VAL	0	-0.049	-0.030	16.630	0.013	0.013	0.000	0.000	0.000	0.000
19	A	22	MET	0	0.001	0.020	13.120	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	23	ILE	0	-0.035	-0.028	16.282	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	24	ASP	-1	-0.908	-0.956	19.546	0.154	0.154	0.000	0.000	0.000	0.000
22	A	25	GLY	0	0.006	-0.003	15.569	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	26	VAL	0	0.012	0.005	15.206	0.031	0.031	0.000	0.000	0.000	0.000
24	A	27	PRO	0	0.028	0.020	13.115	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	28	CYS	0	-0.076	-0.041	15.694	-0.026	-0.026	0.000	0.000	0.000	0.000
26	A	29	GLU	-1	-0.884	-0.942	18.529	0.126	0.126	0.000	0.000	0.000	0.000
27	A	30	ILE	0	-0.087	-0.047	20.789	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	31	VAL	0	0.023	0.016	23.431	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	32	ASP	-1	-0.872	-0.930	26.947	0.077	0.077	0.000	0.000	0.000	0.000
30	A	33	ILE	0	-0.032	-0.025	25.090	0.007	0.007	0.000	0.000	0.000	0.000
31	A	34	SER	0	-0.040	-0.005	29.072	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	35	VAL	0	-0.002	-0.006	30.061	0.004	0.004	0.000	0.000	0.000	0.000
33	A	36	SER	0	-0.016	0.002	32.625	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.984	0.966	34.863	-0.058	-0.058	0.000	0.000	0.000	0.000
35	A	38	PRO	0	0.013	0.023	35.817	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	39	GLY	0	0.054	0.021	38.993	0.000	0.000	0.000	0.000	0.000	0.000
37	A	40	LYS	1	0.958	0.985	39.995	-0.044	-0.044	0.000	0.000	0.000	0.000
38	A	41	HIS	0	-0.011	-0.024	39.511	0.002	0.002	0.000	0.000	0.000	0.000
39	A	42	GLY	0	0.044	0.027	36.621	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	43	GLY	0	-0.030	-0.004	32.305	0.001	0.001	0.000	0.000	0.000	0.000
41	A	44	ALA	0	0.001	-0.007	31.678	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	45	LYS	1	0.945	0.970	30.435	-0.073	-0.073	0.000	0.000	0.000	0.000
43	A	46	ALA	0	0.020	0.010	27.577	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	47	ARG	1	0.862	0.925	28.849	-0.085	-0.085	0.000	0.000	0.000	0.000
45	A	48	VAL	0	-0.024	-0.015	23.336	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	49	VAL	0	0.040	0.023	26.317	0.002	0.002	0.000	0.000	0.000	0.000
47	A	50	GLY	0	0.025	0.008	22.834	0.000	0.000	0.000	0.000	0.000	0.000
48	A	51	ILE	0	-0.022	-0.008	23.167	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	52	GLY	0	0.018	0.007	20.055	0.008	0.008	0.000	0.000	0.000	0.000
50	A	53	ILE	0	-0.023	-0.004	15.633	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	54	PHE	0	0.013	-0.009	13.087	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	55	GLU	-1	-0.882	-0.921	18.474	0.183	0.183	0.000	0.000	0.000	0.000
53	A	56	LYS	1	0.957	0.968	21.411	-0.084	-0.084	0.000	0.000	0.000	0.000
54	A	57	VAL	0	0.013	0.019	21.719	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	58	LYS	1	0.967	0.989	24.325	-0.090	-0.090	0.000	0.000	0.000	0.000
56	A	59	LYS	1	0.924	0.966	21.563	-0.156	-0.156	0.000	0.000	0.000	0.000
57	A	60	GLU	-1	-0.802	-0.902	24.892	0.088	0.088	0.000	0.000	0.000	0.000
58	A	61	PHE	0	0.008	0.016	21.841	0.001	0.001	0.000	0.000	0.000	0.000
59	A	62	VAL	0	0.042	0.012	26.209	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	63	ALA	0	-0.019	-0.009	25.152	0.002	0.002	0.000	0.000	0.000	0.000
61	A	64	PRO	0	0.000	0.004	26.180	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	65	THR	0	0.011	0.002	26.088	0.009	0.009	0.000	0.000	0.000	0.000
63	A	66	SER	0	-0.013	-0.014	25.249	0.008	0.008	0.000	0.000	0.000	0.000
64	A	67	SER	0	0.002	-0.010	22.599	0.004	0.004	0.000	0.000	0.000	0.000
65	A	68	LYS	1	0.868	0.925	17.276	-0.201	-0.201	0.000	0.000	0.000	0.000
66	A	69	VAL	0	0.013	0.010	18.370	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	70	GLU	-1	-0.824	-0.888	12.477	0.441	0.441	0.000	0.000	0.000	0.000
68	A	71	VAL	0	-0.019	-0.006	13.302	-0.035	-0.035	0.000	0.000	0.000	0.000
69	A	72	PRO	0	0.040	0.016	10.412	0.060	0.060	0.000	0.000	0.000	0.000
70	A	73	ILE	0	-0.097	-0.046	7.131	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	74	ILE	0	-0.018	-0.004	8.302	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	75	ASP	-1	-0.819	-0.871	7.705	-0.231	-0.231	0.000	0.000	0.000	0.000
73	A	76	ARG	1	0.895	0.946	9.762	-0.042	-0.042	0.000	0.000	0.000	0.000
74	A	77	ARG	1	0.801	0.869	9.470	0.176	0.176	0.000	0.000	0.000	0.000
75	A	78	LYS	1	0.878	0.907	14.556	0.017	0.017	0.000	0.000	0.000	0.000
76	A	79	GLY	0	0.043	0.027	17.411	-0.017	-0.017	0.000	0.000	0.000	0.000
77	A	80	GLN	0	-0.012	-0.002	19.370	0.006	0.006	0.000	0.000	0.000	0.000
78	A	81	VAL	0	0.013	0.019	22.588	0.000	0.000	0.000	0.000	0.000	0.000
79	A	82	LEU	0	-0.035	-0.017	23.258	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	83	ALA	0	-0.004	-0.011	25.693	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	84	ILE	0	0.018	0.028	26.246	0.004	0.004	0.000	0.000	0.000	0.000
82	A	85	MET	0	-0.042	-0.014	27.647	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	86	GLY	0	-0.017	-0.011	29.067	0.004	0.004	0.000	0.000	0.000	0.000
84	A	87	ASP	-1	-0.891	-0.944	27.637	0.050	0.050	0.000	0.000	0.000	0.000
85	A	88	MET	0	-0.019	-0.007	22.393	0.010	0.010	0.000	0.000	0.000	0.000
86	A	89	VAL	0	0.012	-0.003	22.301	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	90	GLN	0	-0.008	0.008	21.670	0.006	0.006	0.000	0.000	0.000	0.000
88	A	91	ILE	0	0.007	-0.007	17.064	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	92	MET	0	-0.002	-0.006	19.016	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	93	ASP	-1	-0.730	-0.824	14.241	-0.105	-0.105	0.000	0.000	0.000	0.000
91	A	94	LEU	0	-0.036	-0.029	16.743	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	95	GLN	0	-0.077	-0.030	12.958	-0.012	-0.012	0.000	0.000	0.000	0.000
93	A	96	THR	0	0.020	0.010	11.356	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	97	TYR	0	-0.043	-0.017	14.707	0.006	0.006	0.000	0.000	0.000	0.000
95	A	98	GLU	-1	-0.930	-0.954	12.149	-0.214	-0.214	0.000	0.000	0.000	0.000
96	A	99	THR	0	-0.083	-0.045	16.192	0.017	0.017	0.000	0.000	0.000	0.000
97	A	100	LEU	0	-0.004	-0.003	13.714	0.006	0.006	0.000	0.000	0.000	0.000
98	A	101	GLU	-1	-0.929	-0.962	17.344	0.039	0.039	0.000	0.000	0.000	0.000
99	A	102	LEU	0	-0.044	-0.028	15.806	0.023	0.023	0.000	0.000	0.000	0.000
100	A	103	PRO	0	0.032	0.023	19.182	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	104	ILE	0	0.046	0.018	22.175	0.001	0.001	0.000	0.000	0.000	0.000
102	A	105	PRO	0	-0.122	-0.065	22.363	0.003	0.003	0.000	0.000	0.000	0.000
103	A	106	GLU	-1	-0.914	-0.972	24.648	0.055	0.055	0.000	0.000	0.000	0.000
104	A	107	GLY	0	-0.012	0.012	27.230	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	108	ILE	0	-0.082	-0.028	24.507	0.002	0.002	0.000	0.000	0.000	0.000
106	A	109	GLU	-1	-0.928	-0.957	28.234	0.024	0.024	0.000	0.000	0.000	0.000
107	A	110	GLY	0	-0.001	-0.012	30.564	0.001	0.001	0.000	0.000	0.000	0.000
108	A	111	LEU	0	-0.065	-0.030	25.226	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	112	GLU	-1	-0.820	-0.955	29.189	0.014	0.014	0.000	0.000	0.000	0.000
110	A	113	PRO	0	-0.062	-0.033	28.563	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	114	GLY	0	-0.030	-0.001	27.918	0.000	0.000	0.000	0.000	0.000	0.000
112	A	115	GLY	0	0.004	0.016	27.705	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	116	GLU	-1	-0.916	-0.961	23.120	-0.014	-0.014	0.000	0.000	0.000	0.000
114	A	117	VAL	0	-0.017	-0.003	20.137	0.007	0.007	0.000	0.000	0.000	0.000
115	A	118	GLU	-1	-0.868	-0.935	17.838	0.031	0.031	0.000	0.000	0.000	0.000
116	A	119	TYR	0	-0.052	-0.069	12.825	0.019	0.019	0.000	0.000	0.000	0.000
117	A	120	ILE	0	-0.077	-0.039	13.128	-0.017	-0.017	0.000	0.000	0.000	0.000
118	A	121	GLU	-1	-0.788	-0.902	6.488	0.852	0.852	0.000	0.000	0.000	0.000
119	A	122	ALA	0	-0.043	-0.043	8.617	-0.061	-0.061	0.000	0.000	0.000	0.000
120	A	123	VAL	0	-0.047	-0.025	7.283	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	124	GLY	0	0.015	0.012	7.544	-0.019	-0.019	0.000	0.000	0.000	0.000
122	A	125	GLN	0	-0.044	-0.001	8.966	-0.196	-0.196	0.000	0.000	0.000	0.000
123	A	126	TYR	0	0.077	0.029	9.256	-0.055	-0.055	0.000	0.000	0.000	0.000
124	A	127	LYS	1	0.866	0.929	13.782	-0.141	-0.141	0.000	0.000	0.000	0.000
125	A	128	ILE	0	0.052	0.041	16.873	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	129	THR	0	-0.091	-0.043	17.854	0.003	0.003	0.000	0.000	0.000	0.000
127	A	130	ARG	1	0.932	0.968	20.610	-0.040	-0.040	0.000	0.000	0.000	0.000
128	A	131	VAL	0	0.083	0.043	22.645	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	132	ILE	0	-0.112	-0.053	21.790	0.002	0.002	0.000	0.000	0.000	0.000
130	A	133	GLY	0	0.039	0.026	25.098	-0.003	-0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:4:MET)