FMO DATABASE

FMODB ID: K3VV3

Calculation Name: 3EBM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EBM

Chain ID: A

ChEMBL ID:

UniProt ID: P13693

Base Structure: X-ray

Registration Date: 2023-03-14

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	147
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1491579.817733
FMO2-HF: Nuclear repulsion	1429261.744738
FMO2-HF: Total energy	-62318.072996
FMO2-MP2: Total energy	-62493.147607

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.
-20.12	-10.326	9.078	-7.904	-10.967	-0.069

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 : -0.024 / q_NPA : -0.011

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	ILE	0	0.002	-0.011	3.272	-1.070	1.217	0.091	-0.874	-1.505	0.001
4	A	4	TYR	0	0.003	0.001	5.650	-0.097	-0.097	0.000	0.000	0.000	0.000
5	A	5	ARG	1	0.817	0.880	9.295	-0.008	-0.008	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.714	-0.832	12.205	-0.020	-0.020	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.053	-0.013	16.000	0.013	0.013	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.077	-0.046	17.785	0.005	0.005	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.030	-0.061	18.361	0.009	0.009	0.000	0.000	0.000	0.000
10	A	10	HIS	1	0.743	0.874	15.191	-0.025	-0.025	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.763	-0.850	14.060	0.156	0.156	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.015	-0.022	8.547	-0.048	-0.048	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.033	-0.010	11.517	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.005	-0.008	8.981	-0.035	-0.035	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.017	0.006	4.047	-0.566	-0.278	0.014	-0.086	-0.216	0.000
16	A	16	ASP	-1	-0.797	-0.913	2.442	-11.035	-6.942	3.757	-3.785	-4.064	-0.046
17	A	17	ILE	0	-0.044	0.004	3.081	-0.517	0.074	0.084	-0.095	-0.581	0.000
18	A	18	TYR	0	-0.050	-0.040	5.767	0.238	0.238	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.859	0.915	9.562	0.199	0.199	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.013	0.018	8.261	0.063	0.063	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.849	0.914	12.482	0.139	0.139	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.793	-0.880	15.945	-0.088	-0.088	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.028	-0.018	17.786	0.010	0.010	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.004	-0.012	21.407	0.004	0.004	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.910	-0.957	24.123	-0.027	-0.027	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.048	0.024	19.991	0.005	0.005	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.099	-0.036	20.159	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	28	CYS	0	-0.051	-0.018	19.327	0.004	0.004	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.012	0.005	12.602	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.785	-0.859	16.170	-0.106	-0.106	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.031	0.012	11.700	-0.036	-0.036	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.785	-0.873	14.417	-0.146	-0.146	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.029	0.014	14.016	-0.042	-0.042	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.737	0.838	12.113	0.260	0.260	0.000	0.000	0.000	0.000
35	A	35	MET	0	0.031	0.020	16.742	0.012	0.012	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.009	-0.001	15.049	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.002	0.005	18.537	0.016	0.016	0.000	0.000	0.000	0.000
38	A	67	ILE	0	0.032	0.013	21.383	0.001	0.001	0.000	0.000	0.000	0.000
39	A	68	THR	0	-0.098	-0.060	20.822	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	69	GLY	0	0.057	0.017	19.798	0.011	0.011	0.000	0.000	0.000	0.000
41	A	70	VAL	0	0.009	0.004	16.311	-0.015	-0.015	0.000	0.000	0.000	0.000
42	A	71	ASP	-1	-0.701	-0.846	12.277	-0.163	-0.163	0.000	0.000	0.000	0.000
43	A	72	ILE	0	-0.003	0.001	12.018	0.042	0.042	0.000	0.000	0.000	0.000
44	A	73	VAL	0	-0.016	-0.006	13.092	0.053	0.053	0.000	0.000	0.000	0.000
45	A	74	MET	0	-0.059	-0.020	14.699	0.025	0.025	0.000	0.000	0.000	0.000
46	A	75	ASN	0	-0.078	-0.044	8.316	0.100	0.100	0.000	0.000	0.000	0.000
47	A	76	HIS	0	-0.007	0.012	7.402	0.011	0.011	0.000	0.000	0.000	0.000
48	A	77	HIS	0	0.018	0.026	11.859	-0.035	-0.035	0.000	0.000	0.000	0.000
49	A	78	LEU	0	-0.012	0.016	14.433	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	79	GLN	0	-0.030	-0.025	17.150	-0.024	-0.024	0.000	0.000	0.000	0.000
51	A	80	GLU	-1	-0.856	-0.915	20.928	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	81	THR	0	-0.027	-0.018	23.604	0.003	0.003	0.000	0.000	0.000	0.000
53	A	82	SER	0	-0.029	-0.013	26.471	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	83	PHE	0	0.051	0.016	26.791	0.002	0.002	0.000	0.000	0.000	0.000
55	A	84	THR	0	0.037	0.018	31.990	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	85	LYS	1	0.915	0.950	34.365	0.014	0.014	0.000	0.000	0.000	0.000
57	A	86	GLU	-1	-0.825	-0.897	35.519	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	87	ALA	0	0.003	0.007	33.844	0.001	0.001	0.000	0.000	0.000	0.000
59	A	88	TYR	0	0.093	0.048	25.777	0.001	0.001	0.000	0.000	0.000	0.000
60	A	89	LYS	1	0.819	0.890	31.563	0.006	0.006	0.000	0.000	0.000	0.000
61	A	90	LYS	1	0.823	0.905	34.123	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	91	TYR	0	0.035	0.002	24.136	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	92	ILE	0	0.022	0.018	26.308	0.001	0.001	0.000	0.000	0.000	0.000
64	A	93	LYS	1	0.873	0.930	29.296	0.002	0.002	0.000	0.000	0.000	0.000
65	A	94	ASP	-1	-0.783	-0.859	30.582	0.008	0.008	0.000	0.000	0.000	0.000
66	A	95	TYR	0	0.059	0.050	20.282	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	96	MET	0	-0.028	-0.018	26.369	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	97	LYS	1	0.861	0.917	27.979	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	98	SER	0	0.000	-0.007	26.084	0.002	0.002	0.000	0.000	0.000	0.000
70	A	99	ILE	0	0.005	0.014	21.447	0.001	0.001	0.000	0.000	0.000	0.000
71	A	100	LYS	1	0.763	0.862	24.632	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	101	GLY	0	0.010	0.000	27.606	0.001	0.001	0.000	0.000	0.000	0.000
73	A	102	LYS	1	0.940	0.974	20.646	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	103	LEU	0	-0.035	-0.014	21.999	0.001	0.001	0.000	0.000	0.000	0.000
75	A	104	GLU	-1	-0.816	-0.910	24.617	0.009	0.009	0.000	0.000	0.000	0.000
76	A	105	GLU	-1	-0.995	-0.971	24.449	0.024	0.024	0.000	0.000	0.000	0.000
77	A	106	GLN	0	0.031	0.008	18.684	0.002	0.002	0.000	0.000	0.000	0.000
78	A	107	ARG	1	0.802	0.902	18.344	0.024	0.024	0.000	0.000	0.000	0.000
79	A	108	PRO	0	0.071	0.031	23.068	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	109	GLU	-1	-0.892	-0.951	21.995	0.001	0.001	0.000	0.000	0.000	0.000
81	A	110	ARG	1	0.850	0.901	21.374	0.026	0.026	0.000	0.000	0.000	0.000
82	A	111	VAL	0	0.004	0.019	24.842	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	112	LYS	1	0.919	0.952	27.723	0.004	0.004	0.000	0.000	0.000	0.000
84	A	113	PRO	0	0.019	0.025	25.343	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	114	PHE	0	0.059	0.038	23.637	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	115	MET	0	-0.020	-0.005	25.979	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	116	THR	0	-0.068	-0.055	29.410	0.001	0.001	0.000	0.000	0.000	0.000
88	A	117	GLY	0	0.056	0.034	27.346	0.000	0.000	0.000	0.000	0.000	0.000
89	A	118	ALA	0	0.017	0.000	26.504	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	119	ALA	0	-0.017	-0.005	27.794	0.000	0.000	0.000	0.000	0.000	0.000
91	A	120	GLU	-1	-0.781	-0.880	30.738	-0.016	-0.016	0.000	0.000	0.000	0.000
92	A	121	GLN	0	0.033	0.020	24.886	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	122	ILE	0	-0.016	-0.015	27.485	0.000	0.000	0.000	0.000	0.000	0.000
94	A	123	LYS	1	0.790	0.879	30.180	0.015	0.015	0.000	0.000	0.000	0.000
95	A	124	HIS	0	0.028	0.022	27.707	0.003	0.003	0.000	0.000	0.000	0.000
96	A	125	ILE	0	0.024	0.018	25.567	0.000	0.000	0.000	0.000	0.000	0.000
97	A	126	LEU	0	-0.055	-0.033	29.770	0.002	0.002	0.000	0.000	0.000	0.000
98	A	127	ALA	0	-0.041	-0.023	33.389	0.002	0.002	0.000	0.000	0.000	0.000
99	A	128	ASN	0	-0.026	-0.016	30.678	0.001	0.001	0.000	0.000	0.000	0.000
100	A	129	PHE	0	-0.008	-0.005	31.060	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	130	LYS	1	0.907	0.936	31.528	0.020	0.020	0.000	0.000	0.000	0.000
102	A	131	ASN	0	0.009	0.011	29.236	0.004	0.004	0.000	0.000	0.000	0.000
103	A	132	TYR	0	-0.033	0.004	24.930	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	133	GLN	0	-0.011	-0.006	24.408	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	134	PHE	0	-0.032	-0.031	24.180	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	135	PHE	0	0.035	0.010	19.515	0.003	0.003	0.000	0.000	0.000	0.000
107	A	136	ILE	0	-0.027	-0.004	20.107	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	137	GLY	0	0.050	0.013	16.880	0.007	0.007	0.000	0.000	0.000	0.000
109	A	138	GLU	-1	-0.874	-0.934	15.258	0.216	0.216	0.000	0.000	0.000	0.000
110	A	139	ASN	0	-0.077	-0.060	17.836	-0.022	-0.022	0.000	0.000	0.000	0.000
111	A	140	MET	0	-0.065	-0.030	20.497	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	141	ASN	0	0.017	0.009	21.797	-0.015	-0.015	0.000	0.000	0.000	0.000
113	A	142	PRO	0	-0.005	0.005	23.560	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	143	ASP	-1	-0.935	-0.974	25.406	0.019	0.019	0.000	0.000	0.000	0.000
115	A	144	GLY	0	0.020	0.002	21.523	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	145	MET	0	-0.078	-0.019	17.446	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	146	VAL	0	-0.019	-0.005	20.475	0.006	0.006	0.000	0.000	0.000	0.000
118	A	147	ALA	0	-0.013	0.009	18.271	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	148	LEU	0	-0.048	-0.024	20.262	0.006	0.006	0.000	0.000	0.000	0.000
120	A	149	LEU	0	-0.027	-0.008	19.680	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	150	ASP	-1	-0.791	-0.882	22.084	-0.047	-0.047	0.000	0.000	0.000	0.000
122	A	151	TYR	0	-0.013	-0.024	22.605	-0.010	-0.010	0.000	0.000	0.000	0.000
123	A	152	ARG	1	0.748	0.858	19.193	0.126	0.126	0.000	0.000	0.000	0.000
124	A	153	GLU	-1	-0.890	-0.954	25.163	-0.059	-0.059	0.000	0.000	0.000	0.000
125	A	154	ASP	-1	-0.849	-0.879	24.716	-0.087	-0.087	0.000	0.000	0.000	0.000
126	A	155	GLY	0	-0.020	-0.004	27.887	0.003	0.003	0.000	0.000	0.000	0.000
127	A	156	VAL	0	-0.078	-0.049	24.903	0.004	0.004	0.000	0.000	0.000	0.000
128	A	157	THR	0	-0.047	-0.058	19.883	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	158	PRO	0	-0.006	0.014	18.454	0.004	0.004	0.000	0.000	0.000	0.000
130	A	159	TYR	0	-0.094	-0.080	18.039	-0.025	-0.025	0.000	0.000	0.000	0.000
131	A	160	MET	0	0.018	0.016	16.431	0.019	0.019	0.000	0.000	0.000	0.000
132	A	161	ILE	0	-0.029	-0.009	17.413	-0.021	-0.021	0.000	0.000	0.000	0.000
133	A	162	PHE	0	0.071	0.019	15.047	0.016	0.016	0.000	0.000	0.000	0.000
134	A	163	PHE	0	0.018	-0.017	18.073	-0.010	-0.010	0.000	0.000	0.000	0.000
135	A	164	LYS	1	0.853	0.919	15.478	0.078	0.078	0.000	0.000	0.000	0.000
136	A	165	ASP	-1	-0.779	-0.879	17.029	-0.035	-0.035	0.000	0.000	0.000	0.000
137	A	166	GLY	0	0.003	-0.001	19.183	0.008	0.008	0.000	0.000	0.000	0.000
138	A	167	LEU	0	-0.031	-0.007	12.887	0.008	0.008	0.000	0.000	0.000	0.000
139	A	168	GLU	-1	-0.851	-0.917	12.816	0.007	0.007	0.000	0.000	0.000	0.000
140	A	169	MET	0	-0.036	-0.022	9.138	0.020	0.020	0.000	0.000	0.000	0.000
141	A	170	GLU	-1	-0.801	-0.866	6.984	0.178	0.178	0.000	0.000	0.000	0.000
142	A	171	LYS	1	0.926	0.954	3.801	-2.763	-2.391	0.003	-0.123	-0.251	0.000
143	A	172	CYS	0	-0.015	0.013	2.269	0.490	1.966	1.259	-0.776	-1.958	0.002
144	A	173	LEU	0	-0.017	-0.025	2.100	-5.493	-4.870	3.871	-2.159	-2.336	-0.026
145	A	174	GLU	-1	-0.870	-0.924	4.814	-0.078	-0.014	-0.001	-0.006	-0.056	0.000
146	A	175	HIS	0	-0.012	-0.010	8.269	0.081	0.081	0.000	0.000	0.000	0.000
147	A	176	HIS	0	-0.071	-0.030	11.317	0.014	0.014	0.000	0.000	0.000	0.000

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