FMO DATABASE

FMODB ID: Q1LLY

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	OptHSide
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	-1489437.701936
FMO2-HF: Nuclear repulsion	1427119.921177
FMO2-HF: Total energy	-62317.780759
FMO2-MP2: Total energy	-62492.869968

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.
-17.874	-6.024	4.979	-6.82	-10.009	-0.056

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 : -0.045 / 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	ILE	0	-0.019	-0.016	2.920	-0.724	1.605	0.087	-0.803	-1.613	0.000
4	A	4	TYR	0	0.006	-0.009	5.149	0.031	0.081	-0.001	-0.005	-0.044	0.000
5	A	5	ARG	1	0.806	0.867	8.911	0.211	0.211	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.752	-0.847	11.515	-0.014	-0.014	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.042	-0.015	15.302	0.005	0.005	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.087	-0.053	17.058	0.006	0.006	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.046	-0.056	17.895	0.005	0.005	0.000	0.000	0.000	0.000
10	A	10	HIS	1	0.807	0.909	14.928	0.020	0.020	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.733	-0.824	13.595	0.090	0.090	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.015	-0.023	8.123	-0.052	-0.052	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.031	-0.008	10.989	0.029	0.029	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.014	-0.005	9.012	0.009	0.009	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.029	0.022	4.146	-0.979	-0.655	0.032	-0.111	-0.244	0.001
16	A	16	ASP	-1	-0.822	-0.917	2.421	-10.074	-5.113	2.402	-3.513	-3.850	-0.044
17	A	17	ILE	0	-0.050	-0.008	3.877	-0.662	-0.137	0.029	-0.081	-0.473	0.000
18	A	18	TYR	0	-0.051	-0.016	6.272	-0.046	-0.046	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.862	0.916	9.476	0.033	0.033	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.011	0.012	8.475	0.035	0.035	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.868	0.926	12.554	0.057	0.057	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.797	-0.873	16.096	-0.050	-0.050	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.031	-0.011	17.630	0.010	0.010	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.004	-0.021	21.165	0.001	0.001	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.932	-0.965	24.022	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.051	0.025	19.959	0.003	0.003	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.085	-0.018	20.324	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	28	CYS	0	-0.030	-0.015	19.346	0.000	0.000	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.012	-0.004	12.611	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.798	-0.887	16.341	-0.037	-0.037	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.030	0.014	11.695	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.789	-0.876	14.312	-0.055	-0.055	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.011	-0.010	13.994	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.785	0.872	12.557	0.028	0.028	0.000	0.000	0.000	0.000
35	A	35	MET	0	0.019	0.019	16.962	0.016	0.016	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.021	-0.010	15.296	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.010	-0.005	18.699	0.009	0.009	0.000	0.000	0.000	0.000
38	A	67	ILE	0	0.024	0.011	21.405	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	68	THR	0	-0.081	-0.050	20.985	0.002	0.002	0.000	0.000	0.000	0.000
40	A	69	GLY	0	0.075	0.033	20.298	0.006	0.006	0.000	0.000	0.000	0.000
41	A	70	VAL	0	0.015	0.007	16.612	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	71	ASP	-1	-0.723	-0.852	12.644	0.039	0.039	0.000	0.000	0.000	0.000
43	A	72	ILE	0	0.005	0.005	12.185	0.046	0.046	0.000	0.000	0.000	0.000
44	A	73	VAL	0	-0.005	-0.009	13.097	0.043	0.043	0.000	0.000	0.000	0.000
45	A	74	MET	0	-0.046	-0.018	15.156	0.013	0.013	0.000	0.000	0.000	0.000
46	A	75	ASN	0	-0.050	-0.029	9.802	0.103	0.103	0.000	0.000	0.000	0.000
47	A	76	HIS	0	-0.008	-0.001	7.133	0.038	0.038	0.000	0.000	0.000	0.000
48	A	77	HIS	0	0.006	0.025	11.716	-0.051	-0.051	0.000	0.000	0.000	0.000
49	A	78	LEU	0	-0.025	0.001	14.108	-0.029	-0.029	0.000	0.000	0.000	0.000
50	A	79	GLN	0	-0.020	-0.022	16.996	-0.020	-0.020	0.000	0.000	0.000	0.000
51	A	80	GLU	-1	-0.875	-0.918	20.751	0.020	0.020	0.000	0.000	0.000	0.000
52	A	81	THR	0	-0.028	-0.013	23.398	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	82	SER	0	-0.020	-0.012	26.248	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	83	PHE	0	0.040	0.010	26.403	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	84	THR	0	0.026	0.017	31.614	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	85	LYS	1	0.941	0.959	33.881	0.000	0.000	0.000	0.000	0.000	0.000
57	A	86	GLU	-1	-0.817	-0.900	35.170	0.004	0.004	0.000	0.000	0.000	0.000
58	A	87	ALA	0	-0.004	0.002	33.515	0.000	0.000	0.000	0.000	0.000	0.000
59	A	88	TYR	0	0.102	0.053	25.836	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	89	LYS	1	0.791	0.880	31.009	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	90	LYS	1	0.825	0.902	33.254	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	91	TYR	0	0.008	-0.016	23.693	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	92	ILE	0	0.028	0.020	25.957	0.000	0.000	0.000	0.000	0.000	0.000
64	A	93	LYS	1	0.928	0.965	29.111	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	94	ASP	-1	-0.797	-0.878	30.069	0.008	0.008	0.000	0.000	0.000	0.000
66	A	95	TYR	0	0.058	0.040	20.077	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	96	MET	0	-0.030	-0.021	25.848	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	97	LYS	1	0.878	0.924	27.510	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	98	SER	0	-0.010	-0.004	25.509	0.001	0.001	0.000	0.000	0.000	0.000
70	A	99	ILE	0	0.006	0.016	20.961	0.000	0.000	0.000	0.000	0.000	0.000
71	A	100	LYS	1	0.767	0.868	24.244	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	101	GLY	0	0.012	0.002	27.146	0.001	0.001	0.000	0.000	0.000	0.000
73	A	102	LYS	1	0.957	0.984	21.311	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	103	LEU	0	-0.022	-0.012	21.445	0.001	0.001	0.000	0.000	0.000	0.000
75	A	104	GLU	-1	-0.826	-0.908	24.005	0.010	0.010	0.000	0.000	0.000	0.000
76	A	105	GLU	-1	-0.986	-0.970	24.497	0.019	0.019	0.000	0.000	0.000	0.000
77	A	106	GLN	0	0.006	0.003	18.194	0.002	0.002	0.000	0.000	0.000	0.000
78	A	107	ARG	1	0.824	0.914	18.005	0.024	0.024	0.000	0.000	0.000	0.000
79	A	108	PRO	0	0.091	0.039	22.817	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	109	GLU	-1	-0.899	-0.957	22.184	0.012	0.012	0.000	0.000	0.000	0.000
81	A	110	ARG	1	0.827	0.884	21.195	0.012	0.012	0.000	0.000	0.000	0.000
82	A	111	VAL	0	-0.001	0.012	24.672	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	112	LYS	1	0.962	0.974	27.683	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	113	PRO	0	0.042	0.028	25.394	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	114	PHE	0	0.053	0.037	23.387	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	115	MET	0	-0.036	-0.020	26.184	0.000	0.000	0.000	0.000	0.000	0.000
87	A	116	THR	0	-0.079	-0.047	29.689	0.001	0.001	0.000	0.000	0.000	0.000
88	A	117	GLY	0	0.061	0.030	27.271	0.000	0.000	0.000	0.000	0.000	0.000
89	A	118	ALA	0	0.034	0.011	26.391	0.000	0.000	0.000	0.000	0.000	0.000
90	A	119	ALA	0	-0.020	-0.006	27.765	0.001	0.001	0.000	0.000	0.000	0.000
91	A	120	GLU	-1	-0.807	-0.892	30.607	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	121	GLN	0	0.028	0.016	25.071	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	122	ILE	0	-0.036	-0.028	27.849	0.001	0.001	0.000	0.000	0.000	0.000
94	A	123	LYS	1	0.791	0.882	30.370	0.003	0.003	0.000	0.000	0.000	0.000
95	A	124	HIS	0	0.047	0.032	27.946	0.001	0.001	0.000	0.000	0.000	0.000
96	A	125	ILE	0	0.007	0.005	25.625	0.000	0.000	0.000	0.000	0.000	0.000
97	A	126	LEU	0	-0.060	-0.044	29.717	0.001	0.001	0.000	0.000	0.000	0.000
98	A	127	ALA	0	-0.029	-0.011	33.209	0.001	0.001	0.000	0.000	0.000	0.000
99	A	128	ASN	0	-0.028	-0.006	30.759	0.000	0.000	0.000	0.000	0.000	0.000
100	A	129	PHE	0	-0.014	-0.013	30.961	0.000	0.000	0.000	0.000	0.000	0.000
101	A	130	LYS	1	0.909	0.936	31.181	0.002	0.002	0.000	0.000	0.000	0.000
102	A	131	ASN	0	0.011	0.014	29.288	0.002	0.002	0.000	0.000	0.000	0.000
103	A	132	TYR	0	-0.024	0.012	25.330	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	133	GLN	0	-0.041	-0.016	24.622	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	134	PHE	0	-0.018	-0.027	23.927	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	135	PHE	0	0.061	0.024	19.251	0.004	0.004	0.000	0.000	0.000	0.000
107	A	136	ILE	0	-0.027	-0.004	19.866	-0.008	-0.008	0.000	0.000	0.000	0.000
108	A	137	GLY	0	0.039	0.014	16.673	0.011	0.011	0.000	0.000	0.000	0.000
109	A	138	GLU	-1	-0.881	-0.943	15.212	0.177	0.177	0.000	0.000	0.000	0.000
110	A	139	ASN	0	-0.070	-0.063	17.610	-0.016	-0.016	0.000	0.000	0.000	0.000
111	A	140	MET	0	-0.075	-0.029	20.312	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	141	ASN	0	0.018	0.011	21.468	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	142	PRO	0	-0.001	0.004	23.087	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	143	ASP	-1	-0.943	-0.975	24.931	0.014	0.014	0.000	0.000	0.000	0.000
115	A	144	GLY	0	-0.003	-0.004	20.899	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	145	MET	0	-0.068	-0.007	17.172	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	146	VAL	0	-0.017	-0.002	20.512	0.007	0.007	0.000	0.000	0.000	0.000
118	A	147	ALA	0	-0.023	-0.001	18.118	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	148	LEU	0	-0.037	-0.025	20.173	0.004	0.004	0.000	0.000	0.000	0.000
120	A	149	LEU	0	-0.040	-0.009	19.902	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	150	ASP	-1	-0.788	-0.884	22.038	-0.012	-0.012	0.000	0.000	0.000	0.000
122	A	151	TYR	0	0.006	-0.016	22.721	0.000	0.000	0.000	0.000	0.000	0.000
123	A	152	ARG	1	0.747	0.866	18.809	0.046	0.046	0.000	0.000	0.000	0.000
124	A	153	GLU	-1	-0.894	-0.948	25.059	-0.019	-0.019	0.000	0.000	0.000	0.000
125	A	154	ASP	-1	-0.840	-0.896	25.166	-0.030	-0.030	0.000	0.000	0.000	0.000
126	A	155	GLY	0	-0.009	0.004	27.763	0.001	0.001	0.000	0.000	0.000	0.000
127	A	156	VAL	0	-0.091	-0.058	25.249	0.002	0.002	0.000	0.000	0.000	0.000
128	A	157	THR	0	-0.061	-0.056	20.363	0.000	0.000	0.000	0.000	0.000	0.000
129	A	158	PRO	0	-0.003	0.025	18.772	0.001	0.001	0.000	0.000	0.000	0.000
130	A	159	TYR	0	-0.089	-0.081	17.960	-0.008	-0.008	0.000	0.000	0.000	0.000
131	A	160	MET	0	0.014	0.007	16.365	0.012	0.012	0.000	0.000	0.000	0.000
132	A	161	ILE	0	-0.037	-0.008	17.270	-0.014	-0.014	0.000	0.000	0.000	0.000
133	A	162	PHE	0	0.074	0.018	14.955	0.008	0.008	0.000	0.000	0.000	0.000
134	A	163	PHE	0	0.020	-0.016	18.012	-0.006	-0.006	0.000	0.000	0.000	0.000
135	A	164	LYS	1	0.864	0.910	15.355	0.044	0.044	0.000	0.000	0.000	0.000
136	A	165	ASP	-1	-0.790	-0.880	16.822	-0.029	-0.029	0.000	0.000	0.000	0.000
137	A	166	GLY	0	-0.008	-0.006	18.553	0.004	0.004	0.000	0.000	0.000	0.000
138	A	167	LEU	0	-0.038	-0.009	12.918	0.005	0.005	0.000	0.000	0.000	0.000
139	A	168	GLU	-1	-0.884	-0.935	12.415	-0.042	-0.042	0.000	0.000	0.000	0.000
140	A	169	MET	0	-0.038	-0.028	8.709	-0.006	-0.006	0.000	0.000	0.000	0.000
141	A	170	GLU	-1	-0.796	-0.864	6.949	-0.051	-0.051	0.000	0.000	0.000	0.000
142	A	171	LYS	1	0.929	0.965	3.496	-3.828	-3.175	0.018	-0.316	-0.354	0.002
143	A	172	CYS	0	-0.030	0.006	2.539	0.049	1.711	0.395	-0.570	-1.488	0.002
144	A	173	LEU	0	-0.011	-0.029	2.378	-1.972	-0.672	2.018	-1.419	-1.900	-0.017
145	A	174	GLU	-1	-0.876	-0.932	5.153	-0.416	-0.370	-0.001	-0.002	-0.043	0.000
146	A	175	HIS	0	-0.015	-0.004	8.364	0.151	0.151	0.000	0.000	0.000	0.000
147	A	176	HIS	0	-0.068	-0.026	11.243	-0.003	-0.003	0.000	0.000	0.000	0.000

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