FMO DATABASE

FMODB ID: YV162

Calculation Name: 3EJF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EJF

Chain ID: A

ChEMBL ID:

UniProt ID: P0C6Y1

Base Structure: X-ray

Registration Date: 2023-09-22

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	166
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1685153.697152
FMO2-HF: Nuclear repulsion	1619375.75387
FMO2-HF: Total energy	-65777.943281
FMO2-MP2: Total energy	-65965.796551

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:6:LYS)

Summations of interaction energy for fragment #1(A:6:LYS)

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.
-121.281	-117.6	10.737	-6.298	-8.118	-0.037

Interaction energy analysis for fragmet #1(A:6:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.942 / q_NPA : 0.957

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	8	LYS	1	0.945	0.954	3.284	18.494	20.182	0.050	-0.796	-0.942	-0.001
4	A	9	PHE	0	0.014	0.002	5.994	0.215	0.215	0.000	0.000	0.000	0.000
5	A	10	LEU	0	0.017	0.023	6.733	-1.074	-1.074	0.000	0.000	0.000	0.000
6	A	11	GLU	-1	-0.952	-0.968	7.579	-24.105	-24.105	0.000	0.000	0.000	0.000
7	A	12	TYR	0	0.061	0.013	9.499	-0.761	-0.761	0.000	0.000	0.000	0.000
8	A	13	LYS	1	0.808	0.901	10.672	18.898	18.898	0.000	0.000	0.000	0.000
9	A	14	THR	0	0.045	0.020	14.225	-0.229	-0.229	0.000	0.000	0.000	0.000
10	A	15	CYS	0	-0.049	-0.028	17.619	0.418	0.418	0.000	0.000	0.000	0.000
11	A	16	VAL	0	0.053	0.038	20.090	-0.147	-0.147	0.000	0.000	0.000	0.000
12	A	17	GLY	0	-0.004	-0.008	23.719	0.345	0.345	0.000	0.000	0.000	0.000
13	A	18	ASP	-1	-0.819	-0.904	24.416	-10.834	-10.834	0.000	0.000	0.000	0.000
14	A	19	LEU	0	0.027	0.017	20.771	-0.348	-0.348	0.000	0.000	0.000	0.000
15	A	20	THR	0	-0.046	-0.043	21.921	-0.476	-0.476	0.000	0.000	0.000	0.000
16	A	21	VAL	0	-0.005	0.000	22.131	-0.221	-0.221	0.000	0.000	0.000	0.000
17	A	22	VAL	0	-0.003	-0.010	17.884	-0.445	-0.445	0.000	0.000	0.000	0.000
18	A	23	ILE	0	0.023	0.016	17.732	-0.791	-0.791	0.000	0.000	0.000	0.000
19	A	24	ALA	0	-0.005	0.007	17.801	-0.425	-0.425	0.000	0.000	0.000	0.000
20	A	25	LYS	1	0.845	0.925	15.807	14.228	14.228	0.000	0.000	0.000	0.000
21	A	26	ALA	0	0.006	0.005	13.578	-0.541	-0.541	0.000	0.000	0.000	0.000
22	A	27	LEU	0	-0.011	-0.011	13.252	-0.867	-0.867	0.000	0.000	0.000	0.000
23	A	28	ASP	-1	-0.948	-0.961	14.706	-14.429	-14.429	0.000	0.000	0.000	0.000
24	A	29	GLU	-1	-0.785	-0.882	12.704	-15.955	-15.955	0.000	0.000	0.000	0.000
25	A	30	PHE	0	-0.049	-0.036	8.959	-1.195	-1.195	0.000	0.000	0.000	0.000
26	A	31	LYS	1	0.784	0.911	9.353	14.880	14.880	0.000	0.000	0.000	0.000
27	A	32	GLU	-1	-0.964	-0.989	8.275	-24.223	-24.223	0.000	0.000	0.000	0.000
28	A	33	PHE	0	-0.006	-0.018	9.272	-1.447	-1.447	0.000	0.000	0.000	0.000
29	A	34	CYS	0	-0.007	0.026	10.809	1.691	1.691	0.000	0.000	0.000	0.000
30	A	35	ILE	0	-0.010	-0.001	12.596	-0.132	-0.132	0.000	0.000	0.000	0.000
31	A	36	VAL	0	0.029	0.009	14.527	-0.029	-0.029	0.000	0.000	0.000	0.000
32	A	37	ASN	0	-0.005	-0.016	17.085	0.935	0.935	0.000	0.000	0.000	0.000
33	A	38	ALA	0	-0.007	0.005	20.779	-0.352	-0.352	0.000	0.000	0.000	0.000
34	A	39	ALA	0	-0.010	0.003	22.948	0.625	0.625	0.000	0.000	0.000	0.000
35	A	40	ASN	0	0.001	-0.012	24.626	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	41	GLU	-1	-0.815	-0.923	26.533	-10.781	-10.781	0.000	0.000	0.000	0.000
37	A	42	HIS	0	-0.039	-0.019	27.760	-0.099	-0.099	0.000	0.000	0.000	0.000
38	A	43	MET	0	-0.040	-0.007	22.811	-0.099	-0.099	0.000	0.000	0.000	0.000
39	A	44	THR	0	0.028	0.000	27.197	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	45	HIS	0	0.003	-0.024	24.650	0.279	0.279	0.000	0.000	0.000	0.000
41	A	46	GLY	0	0.054	0.030	29.044	0.139	0.139	0.000	0.000	0.000	0.000
42	A	47	SER	0	-0.070	-0.039	30.943	0.277	0.277	0.000	0.000	0.000	0.000
43	A	48	GLY	0	0.029	0.014	29.304	-0.310	-0.310	0.000	0.000	0.000	0.000
44	A	49	VAL	0	0.048	0.008	22.795	0.110	0.110	0.000	0.000	0.000	0.000
45	A	50	ALA	0	0.055	0.045	25.262	-0.173	-0.173	0.000	0.000	0.000	0.000
46	A	51	LYS	1	0.939	0.983	26.267	9.191	9.191	0.000	0.000	0.000	0.000
47	A	52	ALA	0	0.005	0.010	25.779	0.075	0.075	0.000	0.000	0.000	0.000
48	A	53	ILE	0	-0.012	-0.015	20.906	-0.102	-0.102	0.000	0.000	0.000	0.000
49	A	54	ALA	0	-0.002	-0.005	24.287	-0.127	-0.127	0.000	0.000	0.000	0.000
50	A	55	ASP	-1	-0.928	-0.959	26.871	-9.707	-9.707	0.000	0.000	0.000	0.000
51	A	56	PHE	0	-0.096	-0.049	21.587	0.066	0.066	0.000	0.000	0.000	0.000
52	A	57	CYS	0	-0.071	-0.041	22.198	-0.293	-0.293	0.000	0.000	0.000	0.000
53	A	58	GLY	0	0.032	0.028	24.646	0.040	0.040	0.000	0.000	0.000	0.000
54	A	59	LEU	0	-0.008	-0.013	27.815	-0.241	-0.241	0.000	0.000	0.000	0.000
55	A	60	ASP	-1	-0.826	-0.906	26.714	-10.704	-10.704	0.000	0.000	0.000	0.000
56	A	61	PHE	0	-0.064	-0.036	21.535	-0.340	-0.340	0.000	0.000	0.000	0.000
57	A	62	VAL	0	-0.005	-0.002	25.301	-0.207	-0.207	0.000	0.000	0.000	0.000
58	A	63	GLU	-1	-0.847	-0.934	28.136	-9.630	-9.630	0.000	0.000	0.000	0.000
59	A	64	TYR	0	-0.011	0.002	21.403	-0.161	-0.161	0.000	0.000	0.000	0.000
60	A	65	CYS	0	-0.070	-0.014	24.424	-0.335	-0.335	0.000	0.000	0.000	0.000
61	A	66	GLU	-1	-0.925	-0.964	26.112	-9.514	-9.514	0.000	0.000	0.000	0.000
62	A	67	ASP	-1	-0.928	-0.981	28.575	-9.947	-9.947	0.000	0.000	0.000	0.000
63	A	68	TYR	0	-0.042	-0.023	22.767	-0.043	-0.043	0.000	0.000	0.000	0.000
64	A	69	VAL	0	0.003	-0.004	27.079	0.050	0.050	0.000	0.000	0.000	0.000
65	A	70	LYS	1	0.883	0.955	28.958	9.528	9.528	0.000	0.000	0.000	0.000
66	A	71	LYS	1	0.894	0.949	29.170	10.625	10.625	0.000	0.000	0.000	0.000
67	A	72	HIS	0	-0.056	-0.020	25.694	0.089	0.089	0.000	0.000	0.000	0.000
68	A	73	GLY	0	0.015	0.025	28.725	-0.048	-0.048	0.000	0.000	0.000	0.000
69	A	74	PRO	0	-0.005	-0.017	28.263	-0.393	-0.393	0.000	0.000	0.000	0.000
70	A	75	GLN	0	-0.066	-0.033	23.375	-0.726	-0.726	0.000	0.000	0.000	0.000
71	A	76	GLN	0	0.002	-0.020	22.652	0.115	0.115	0.000	0.000	0.000	0.000
72	A	77	ARG	1	0.877	0.924	12.827	21.127	21.127	0.000	0.000	0.000	0.000
73	A	78	LEU	0	0.003	0.010	19.465	0.152	0.152	0.000	0.000	0.000	0.000
74	A	79	VAL	0	-0.002	0.006	13.857	-0.088	-0.088	0.000	0.000	0.000	0.000
75	A	80	THR	0	-0.003	-0.007	17.106	0.314	0.314	0.000	0.000	0.000	0.000
76	A	81	PRO	0	0.001	0.008	17.685	-0.887	-0.887	0.000	0.000	0.000	0.000
77	A	82	SER	0	0.022	-0.030	17.938	0.696	0.696	0.000	0.000	0.000	0.000
78	A	83	PHE	0	0.026	0.013	20.050	0.426	0.426	0.000	0.000	0.000	0.000
79	A	84	VAL	0	0.032	0.029	19.834	0.582	0.582	0.000	0.000	0.000	0.000
80	A	85	LYS	1	0.953	0.971	18.664	13.067	13.067	0.000	0.000	0.000	0.000
81	A	86	GLY	0	0.027	0.005	14.996	0.287	0.287	0.000	0.000	0.000	0.000
82	A	87	ILE	0	-0.012	0.010	13.960	-1.093	-1.093	0.000	0.000	0.000	0.000
83	A	88	GLN	0	-0.006	0.012	8.433	0.283	0.283	0.000	0.000	0.000	0.000
84	A	89	CYS	0	-0.016	-0.011	12.938	-0.475	-0.475	0.000	0.000	0.000	0.000
85	A	90	VAL	0	0.022	0.017	15.324	-0.314	-0.314	0.000	0.000	0.000	0.000
86	A	91	ASN	0	-0.072	-0.039	13.591	1.006	1.006	0.000	0.000	0.000	0.000
87	A	92	ASN	0	-0.010	-0.015	16.471	0.792	0.792	0.000	0.000	0.000	0.000
88	A	93	VAL	0	0.017	0.003	16.959	-0.047	-0.047	0.000	0.000	0.000	0.000
89	A	94	VAL	0	-0.025	0.013	20.110	0.528	0.528	0.000	0.000	0.000	0.000
90	A	95	GLY	0	-0.014	-0.008	22.736	-0.442	-0.442	0.000	0.000	0.000	0.000
91	A	96	PRO	0	-0.032	-0.025	23.916	0.269	0.269	0.000	0.000	0.000	0.000
92	A	97	ARG	1	0.946	0.974	26.750	10.710	10.710	0.000	0.000	0.000	0.000
93	A	98	HIS	0	0.036	0.008	30.204	-0.085	-0.085	0.000	0.000	0.000	0.000
94	A	99	GLY	0	-0.024	-0.016	33.544	0.103	0.103	0.000	0.000	0.000	0.000
95	A	100	ASP	-1	-0.863	-0.915	28.895	-10.734	-10.734	0.000	0.000	0.000	0.000
96	A	101	ASN	0	0.017	0.002	31.857	0.156	0.156	0.000	0.000	0.000	0.000
97	A	102	ASN	0	-0.008	-0.019	27.680	-0.409	-0.409	0.000	0.000	0.000	0.000
98	A	103	LEU	0	0.062	0.030	27.064	-0.498	-0.498	0.000	0.000	0.000	0.000
99	A	104	HIS	0	0.005	0.003	22.389	0.016	0.016	0.000	0.000	0.000	0.000
100	A	105	GLU	-1	-0.894	-0.949	23.097	-12.840	-12.840	0.000	0.000	0.000	0.000
101	A	106	LYS	1	0.867	0.930	22.040	10.723	10.723	0.000	0.000	0.000	0.000
102	A	107	LEU	0	0.000	-0.002	22.049	-0.530	-0.530	0.000	0.000	0.000	0.000
103	A	108	VAL	0	0.015	0.021	17.663	-0.891	-0.891	0.000	0.000	0.000	0.000
104	A	109	ALA	0	-0.010	-0.008	17.505	-1.225	-1.225	0.000	0.000	0.000	0.000
105	A	110	ALA	0	-0.009	-0.003	17.555	-0.859	-0.859	0.000	0.000	0.000	0.000
106	A	111	TYR	0	0.019	-0.009	15.920	-0.820	-0.820	0.000	0.000	0.000	0.000
107	A	112	LYS	1	0.911	0.964	13.229	20.121	20.121	0.000	0.000	0.000	0.000
108	A	113	ASN	0	-0.019	-0.004	12.881	-2.244	-2.244	0.000	0.000	0.000	0.000
109	A	114	VAL	0	-0.003	0.014	12.171	0.077	0.077	0.000	0.000	0.000	0.000
110	A	115	LEU	0	-0.023	0.003	7.246	-0.853	-0.853	0.000	0.000	0.000	0.000
111	A	116	VAL	0	0.016	-0.004	8.833	2.783	2.783	0.000	0.000	0.000	0.000
112	A	117	ASP	-1	-0.894	-0.936	7.095	-35.512	-35.512	0.000	0.000	0.000	0.000
113	A	118	GLY	0	-0.040	-0.030	4.898	2.642	2.642	0.000	0.000	0.000	0.000
114	A	119	VAL	0	-0.015	0.002	5.179	-1.007	-0.887	-0.001	-0.003	-0.115	0.000
115	A	120	VAL	0	-0.030	-0.015	1.947	-5.426	-8.214	9.907	-3.214	-3.904	-0.019
116	A	121	ASN	0	0.017	0.015	4.509	-0.644	-0.530	-0.001	-0.026	-0.087	0.000
117	A	122	TYR	0	0.045	0.027	6.820	2.457	2.457	0.000	0.000	0.000	0.000
118	A	123	VAL	0	0.010	0.012	10.770	0.546	0.546	0.000	0.000	0.000	0.000
119	A	124	VAL	0	-0.010	-0.012	13.541	0.079	0.079	0.000	0.000	0.000	0.000
120	A	125	PRO	0	0.033	0.034	16.289	0.455	0.455	0.000	0.000	0.000	0.000
121	A	126	VAL	0	0.041	0.004	19.805	-0.479	-0.479	0.000	0.000	0.000	0.000
122	A	127	LEU	0	-0.017	-0.007	19.243	0.718	0.718	0.000	0.000	0.000	0.000
123	A	128	SER	0	0.029	-0.003	23.301	0.294	0.294	0.000	0.000	0.000	0.000
124	A	129	LEU	0	0.030	0.021	26.644	0.346	0.346	0.000	0.000	0.000	0.000
125	A	130	GLY	0	-0.015	0.008	29.098	0.338	0.338	0.000	0.000	0.000	0.000
126	A	131	ILE	0	-0.043	-0.006	28.628	0.359	0.359	0.000	0.000	0.000	0.000
127	A	132	PHE	0	-0.003	-0.014	31.638	0.013	0.013	0.000	0.000	0.000	0.000
128	A	133	GLY	0	0.016	0.003	33.142	-0.113	-0.113	0.000	0.000	0.000	0.000
129	A	134	VAL	0	-0.024	-0.009	27.318	-0.202	-0.202	0.000	0.000	0.000	0.000
130	A	135	ASP	-1	-0.815	-0.901	29.546	-10.311	-10.311	0.000	0.000	0.000	0.000
131	A	136	PHE	0	0.014	-0.036	26.171	-0.459	-0.459	0.000	0.000	0.000	0.000
132	A	137	LYS	1	0.925	0.982	25.368	9.664	9.664	0.000	0.000	0.000	0.000
133	A	138	MET	0	0.025	0.030	25.340	-0.416	-0.416	0.000	0.000	0.000	0.000
134	A	139	SER	0	-0.030	-0.019	23.532	-0.836	-0.836	0.000	0.000	0.000	0.000
135	A	140	ILE	0	0.006	-0.001	20.371	-0.751	-0.751	0.000	0.000	0.000	0.000
136	A	141	ASP	-1	-0.824	-0.868	20.331	-13.431	-13.431	0.000	0.000	0.000	0.000
137	A	142	ALA	0	-0.008	-0.014	20.444	-0.677	-0.677	0.000	0.000	0.000	0.000
138	A	143	MET	0	-0.044	-0.012	16.021	-0.961	-0.961	0.000	0.000	0.000	0.000
139	A	144	ARG	1	0.844	0.905	15.897	14.279	14.279	0.000	0.000	0.000	0.000
140	A	145	GLU	-1	-0.859	-0.914	15.803	-16.363	-16.363	0.000	0.000	0.000	0.000
141	A	146	ALA	0	-0.074	-0.036	14.750	-0.989	-0.989	0.000	0.000	0.000	0.000
142	A	147	PHE	0	0.015	-0.025	11.330	-1.698	-1.698	0.000	0.000	0.000	0.000
143	A	148	GLU	-1	-0.939	-0.957	10.761	-24.677	-24.677	0.000	0.000	0.000	0.000
144	A	149	GLY	0	0.042	0.029	10.388	-0.417	-0.417	0.000	0.000	0.000	0.000
145	A	150	CYS	0	-0.090	-0.032	6.859	-4.595	-4.595	0.000	0.000	0.000	0.000
146	A	151	THR	0	-0.043	-0.038	2.365	-2.885	-1.004	0.666	-0.965	-1.582	-0.009
147	A	152	ILE	0	-0.012	0.003	3.297	-14.209	-12.260	0.086	-1.008	-1.028	-0.008
148	A	153	ARG	1	0.874	0.930	3.305	30.421	31.138	0.030	-0.286	-0.460	0.000
149	A	154	VAL	0	0.026	0.017	7.134	-0.061	-0.061	0.000	0.000	0.000	0.000
150	A	155	LEU	0	-0.038	-0.013	10.740	0.961	0.961	0.000	0.000	0.000	0.000
151	A	156	LEU	0	0.018	0.018	13.589	0.095	0.095	0.000	0.000	0.000	0.000
152	A	157	PHE	0	-0.003	-0.018	16.728	0.678	0.678	0.000	0.000	0.000	0.000
153	A	158	SER	0	0.000	-0.026	19.768	0.159	0.159	0.000	0.000	0.000	0.000
154	A	159	LEU	0	-0.001	0.004	23.476	0.081	0.081	0.000	0.000	0.000	0.000
155	A	160	SER	0	-0.031	-0.013	26.465	0.375	0.375	0.000	0.000	0.000	0.000
156	A	161	GLN	0	0.025	-0.016	25.051	-0.321	-0.321	0.000	0.000	0.000	0.000
157	A	162	GLU	-1	-0.915	-0.947	26.666	-9.766	-9.766	0.000	0.000	0.000	0.000
158	A	163	HIS	0	-0.001	0.009	24.186	-0.496	-0.496	0.000	0.000	0.000	0.000
159	A	164	ILE	0	0.020	0.006	20.573	-0.450	-0.450	0.000	0.000	0.000	0.000
160	A	165	ASP	-1	-0.795	-0.881	22.992	-10.800	-10.800	0.000	0.000	0.000	0.000
161	A	166	TYR	0	-0.110	-0.100	24.295	0.263	0.263	0.000	0.000	0.000	0.000
162	A	167	PHE	0	0.012	0.001	15.971	-0.412	-0.412	0.000	0.000	0.000	0.000
163	A	168	ASP	-1	-0.868	-0.954	20.972	-13.376	-13.376	0.000	0.000	0.000	0.000
164	A	169	VAL	0	-0.085	-0.041	22.259	-0.049	-0.049	0.000	0.000	0.000	0.000
165	A	170	THR	0	-0.051	-0.028	22.337	-0.145	-0.145	0.000	0.000	0.000	0.000
166	A	171	CYS	0	-0.099	-0.004	19.069	-0.745	-0.745	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:LYS)