FMO DATABASE

FMODB ID: R5LL8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1487076.805401
FMO2-HF: Nuclear repulsion	1424760.140428
FMO2-HF: Total energy	-62316.664973
FMO2-MP2: Total energy	-62491.665302

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.
-17.561	-5.62	4.752	-6.824	-9.87	-0.06

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 : -0.047 / q_NPA : -0.022

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	-0.039	-0.024	2.855	-0.679	1.608	0.081	-0.771	-1.597	0.000
4	A	4	TYR	0	0.007	-0.013	4.926	0.022	0.068	-0.001	-0.006	-0.040	0.000
5	A	5	ARG	1	0.978	0.991	8.665	0.464	0.464	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.751	-0.862	11.347	-0.060	-0.060	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.043	-0.020	15.125	-0.006	-0.006	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.098	-0.047	16.937	0.004	0.004	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.034	-0.024	17.679	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	10	HIS	1	0.845	0.926	14.887	0.124	0.124	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.772	-0.869	13.552	-0.050	-0.050	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.027	-0.030	8.080	-0.049	-0.049	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.029	-0.008	10.757	0.051	0.051	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.006	-0.007	9.079	0.036	0.036	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.034	0.024	3.906	-1.090	-0.714	0.043	-0.113	-0.305	0.000
16	A	16	ASP	-1	-0.800	-0.900	2.427	-9.672	-4.331	2.189	-3.661	-3.870	-0.045
17	A	17	ILE	0	-0.043	-0.004	3.886	-0.508	0.023	0.094	-0.100	-0.526	0.000
18	A	18	TYR	0	-0.047	-0.022	6.208	-0.207	-0.207	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.897	0.948	9.371	-0.162	-0.162	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.025	0.018	8.403	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.901	0.956	12.459	-0.029	-0.029	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.896	-0.936	15.994	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.011	-0.010	17.540	0.009	0.009	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.026	-0.024	21.087	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.941	-0.970	24.039	0.015	0.015	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.043	0.025	19.926	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.100	-0.021	20.299	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	28	CYS	0	-0.024	-0.016	19.353	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.019	-0.009	12.570	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.794	-0.900	16.306	0.034	0.034	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.014	0.008	11.771	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.926	-0.973	14.237	0.075	0.075	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.007	-0.005	13.953	0.032	0.032	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.897	0.929	13.415	-0.166	-0.166	0.000	0.000	0.000	0.000
35	A	35	MET	0	0.016	0.020	17.186	0.013	0.013	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.030	-0.010	15.584	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.008	-0.003	18.909	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	67	ILE	0	-0.020	-0.027	21.487	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	68	THR	0	-0.037	-0.015	21.091	0.008	0.008	0.000	0.000	0.000	0.000
40	A	69	GLY	0	0.075	0.039	20.437	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	70	VAL	0	0.010	0.007	16.374	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	71	ASP	-1	-0.787	-0.895	12.787	0.189	0.189	0.000	0.000	0.000	0.000
43	A	72	ILE	0	0.002	0.007	11.963	0.034	0.034	0.000	0.000	0.000	0.000
44	A	73	VAL	0	0.007	-0.007	12.947	0.020	0.020	0.000	0.000	0.000	0.000
45	A	74	MET	0	-0.043	-0.024	15.340	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	75	ASN	0	-0.036	-0.025	9.848	0.059	0.059	0.000	0.000	0.000	0.000
47	A	76	HIS	0	-0.017	0.001	6.771	0.100	0.100	0.000	0.000	0.000	0.000
48	A	77	HIS	0	0.006	0.020	11.692	-0.064	-0.064	0.000	0.000	0.000	0.000
49	A	78	LEU	0	-0.017	0.002	14.292	-0.031	-0.031	0.000	0.000	0.000	0.000
50	A	79	GLN	0	-0.016	-0.016	16.948	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	80	GLU	-1	-0.914	-0.954	20.716	0.022	0.022	0.000	0.000	0.000	0.000
52	A	81	THR	0	-0.027	-0.009	23.310	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	82	SER	0	-0.016	-0.010	26.172	0.001	0.001	0.000	0.000	0.000	0.000
54	A	83	PHE	0	0.042	0.012	26.151	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	84	THR	0	0.028	0.022	31.380	0.001	0.001	0.000	0.000	0.000	0.000
56	A	85	LYS	1	0.995	0.982	33.565	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	86	GLU	-1	-0.910	-0.974	34.850	0.001	0.001	0.000	0.000	0.000	0.000
58	A	87	ALA	0	-0.016	-0.004	33.225	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	88	TYR	0	0.096	0.055	26.363	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	89	LYS	1	0.874	0.947	30.717	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	90	LYS	1	0.922	0.958	32.980	0.006	0.006	0.000	0.000	0.000	0.000
62	A	91	TYR	0	0.016	-0.013	23.416	0.001	0.001	0.000	0.000	0.000	0.000
63	A	92	ILE	0	0.024	0.022	25.721	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	93	LYS	1	0.915	0.954	28.854	0.002	0.002	0.000	0.000	0.000	0.000
65	A	94	ASP	-1	-0.896	-0.950	29.682	-0.013	-0.013	0.000	0.000	0.000	0.000
66	A	95	TYR	0	0.046	0.022	19.864	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	96	MET	0	-0.031	-0.022	25.640	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	97	LYS	1	0.932	0.963	27.308	0.014	0.014	0.000	0.000	0.000	0.000
69	A	98	SER	0	-0.010	0.000	25.262	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	99	ILE	0	0.020	0.024	20.774	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	100	LYS	1	0.921	0.956	24.073	0.010	0.010	0.000	0.000	0.000	0.000
72	A	101	GLY	0	0.005	-0.001	26.983	0.001	0.001	0.000	0.000	0.000	0.000
73	A	102	LYS	1	0.967	0.989	21.326	0.059	0.059	0.000	0.000	0.000	0.000
74	A	103	LEU	0	-0.032	-0.018	21.156	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	104	GLU	-1	-0.961	-0.989	23.890	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	105	GLU	-1	-0.983	-0.969	24.508	-0.023	-0.023	0.000	0.000	0.000	0.000
77	A	106	GLN	0	0.005	0.007	17.947	0.003	0.003	0.000	0.000	0.000	0.000
78	A	107	ARG	1	0.878	0.941	17.890	0.060	0.060	0.000	0.000	0.000	0.000
79	A	108	PRO	0	0.088	0.043	22.785	0.000	0.000	0.000	0.000	0.000	0.000
80	A	109	GLU	-1	-0.903	-0.960	22.322	0.003	0.003	0.000	0.000	0.000	0.000
81	A	110	ARG	1	0.833	0.890	21.175	0.012	0.012	0.000	0.000	0.000	0.000
82	A	111	VAL	0	0.004	0.018	24.640	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	112	LYS	1	0.939	0.963	27.634	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	113	PRO	0	0.036	0.016	25.368	0.000	0.000	0.000	0.000	0.000	0.000
85	A	114	PHE	0	0.056	0.035	23.319	0.001	0.001	0.000	0.000	0.000	0.000
86	A	115	MET	0	-0.047	-0.027	26.063	0.001	0.001	0.000	0.000	0.000	0.000
87	A	116	THR	0	-0.062	-0.023	29.441	0.001	0.001	0.000	0.000	0.000	0.000
88	A	117	GLY	0	0.063	0.031	27.248	0.001	0.001	0.000	0.000	0.000	0.000
89	A	118	ALA	0	0.036	0.010	26.160	0.001	0.001	0.000	0.000	0.000	0.000
90	A	119	ALA	0	-0.040	-0.013	27.649	0.001	0.001	0.000	0.000	0.000	0.000
91	A	120	GLU	-1	-0.934	-0.968	30.364	0.007	0.007	0.000	0.000	0.000	0.000
92	A	121	GLN	0	0.031	0.012	24.950	0.002	0.002	0.000	0.000	0.000	0.000
93	A	122	ILE	0	-0.044	-0.030	27.908	0.001	0.001	0.000	0.000	0.000	0.000
94	A	123	LYS	1	0.932	0.961	30.281	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	124	HIS	0	0.059	0.042	27.868	0.000	0.000	0.000	0.000	0.000	0.000
96	A	125	ILE	0	-0.004	0.001	25.765	0.001	0.001	0.000	0.000	0.000	0.000
97	A	126	LEU	0	-0.075	-0.058	29.728	0.001	0.001	0.000	0.000	0.000	0.000
98	A	127	ALA	0	-0.051	-0.013	33.184	0.000	0.000	0.000	0.000	0.000	0.000
99	A	128	ASN	0	-0.008	-0.002	30.050	0.000	0.000	0.000	0.000	0.000	0.000
100	A	129	PHE	0	-0.034	-0.019	30.465	0.001	0.001	0.000	0.000	0.000	0.000
101	A	130	LYS	1	0.900	0.929	31.101	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	131	ASN	0	0.016	0.019	29.350	0.000	0.000	0.000	0.000	0.000	0.000
103	A	132	TYR	0	0.001	0.024	25.225	0.000	0.000	0.000	0.000	0.000	0.000
104	A	133	GLN	0	-0.008	0.015	24.420	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	134	PHE	0	-0.025	-0.028	23.769	0.000	0.000	0.000	0.000	0.000	0.000
106	A	135	PHE	0	0.060	0.022	19.154	0.003	0.003	0.000	0.000	0.000	0.000
107	A	136	ILE	0	-0.024	0.001	19.581	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	137	GLY	0	0.037	0.011	16.496	0.012	0.012	0.000	0.000	0.000	0.000
109	A	138	GLU	-1	-0.897	-0.948	15.390	0.046	0.046	0.000	0.000	0.000	0.000
110	A	139	ASN	0	-0.038	-0.021	17.914	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	140	MET	0	-0.072	-0.034	20.211	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	141	ASN	0	0.011	0.009	21.422	0.001	0.001	0.000	0.000	0.000	0.000
113	A	142	PRO	0	0.002	0.003	22.911	0.001	0.001	0.000	0.000	0.000	0.000
114	A	143	ASP	-1	-0.933	-0.970	24.874	-0.021	-0.021	0.000	0.000	0.000	0.000
115	A	144	GLY	0	-0.047	-0.023	20.711	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	145	MET	0	-0.076	-0.015	16.656	0.010	0.010	0.000	0.000	0.000	0.000
117	A	146	VAL	0	-0.005	0.004	20.252	0.005	0.005	0.000	0.000	0.000	0.000
118	A	147	ALA	0	-0.018	0.000	17.776	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	148	LEU	0	-0.039	-0.027	19.829	0.002	0.002	0.000	0.000	0.000	0.000
120	A	149	LEU	0	-0.041	-0.008	19.714	0.005	0.005	0.000	0.000	0.000	0.000
121	A	150	ASP	-1	-0.792	-0.898	22.014	0.020	0.020	0.000	0.000	0.000	0.000
122	A	151	TYR	0	-0.003	-0.015	22.700	0.009	0.009	0.000	0.000	0.000	0.000
123	A	152	ARG	1	0.774	0.884	18.411	-0.047	-0.047	0.000	0.000	0.000	0.000
124	A	153	GLU	-1	-0.898	-0.949	25.005	0.022	0.022	0.000	0.000	0.000	0.000
125	A	154	ASP	-1	-0.842	-0.911	25.281	0.036	0.036	0.000	0.000	0.000	0.000
126	A	155	GLY	0	-0.019	-0.002	27.733	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	156	VAL	0	-0.081	-0.044	24.977	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	157	THR	0	-0.052	-0.046	20.177	0.005	0.005	0.000	0.000	0.000	0.000
129	A	158	PRO	0	-0.006	0.027	18.509	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	159	TYR	0	-0.083	-0.077	17.945	0.011	0.011	0.000	0.000	0.000	0.000
131	A	160	MET	0	0.015	0.007	16.360	0.001	0.001	0.000	0.000	0.000	0.000
132	A	161	ILE	0	-0.044	-0.008	17.265	-0.006	-0.006	0.000	0.000	0.000	0.000
133	A	162	PHE	0	0.072	0.016	14.752	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	163	PHE	0	0.020	-0.014	17.919	0.001	0.001	0.000	0.000	0.000	0.000
135	A	164	LYS	1	0.978	0.977	15.365	0.012	0.012	0.000	0.000	0.000	0.000
136	A	165	ASP	-1	-0.834	-0.919	16.576	-0.047	-0.047	0.000	0.000	0.000	0.000
137	A	166	GLY	0	-0.015	-0.009	18.329	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	167	LEU	0	-0.051	-0.013	12.457	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	168	GLU	-1	-0.921	-0.960	12.385	-0.170	-0.170	0.000	0.000	0.000	0.000
140	A	169	MET	0	-0.065	-0.038	8.644	-0.043	-0.043	0.000	0.000	0.000	0.000
141	A	170	GLU	-1	-0.871	-0.930	6.665	-0.412	-0.412	0.000	0.000	0.000	0.000
142	A	171	LYS	1	0.919	0.959	3.826	-3.745	-3.217	0.006	-0.220	-0.314	0.001
143	A	172	CYS	0	-0.030	0.001	2.474	0.422	2.021	0.271	-0.542	-1.328	0.001
144	A	173	LEU	0	-0.013	-0.030	2.370	-1.810	-0.631	2.070	-1.409	-1.840	-0.017
145	A	174	GLU	-1	-0.909	-0.954	5.151	-0.583	-0.529	-0.001	-0.002	-0.050	0.000
146	A	175	HIS	0	-0.008	-0.002	8.393	0.174	0.174	0.000	0.000	0.000	0.000
147	A	176	HIS	0	-0.036	-0.001	11.256	-0.017	-0.017	0.000	0.000	0.000	0.000

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