FMO DATABASE

FMODB ID: 5JY9Z

Calculation Name: 3EJG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EJG

Chain ID: A

ChEMBL ID:

UniProt ID: P0C6X1

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	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	165
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1629907.781528
FMO2-HF: Nuclear repulsion	1566988.196996
FMO2-HF: Total energy	-62919.584532
FMO2-MP2: Total energy	-63103.71642

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:GLU)

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

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.
-18.392	-29.854	57.516	-24.315	-21.739	0.193

Interaction energy analysis for fragmet #1(A:1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.770 / q_NPA : -0.840

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	LEU	0	-0.039	0.001	3.279	-8.334	-5.518	0.000	-1.330	-1.485	0.000
4	A	4	ASN	0	-0.006	-0.013	3.156	11.844	12.833	0.096	-0.479	-0.606	-0.004
5	A	5	ALA	0	0.038	0.027	4.460	-4.492	-4.200	-0.001	-0.025	-0.267	0.000
6	A	6	PHE	0	-0.054	-0.036	5.886	-4.863	-4.863	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.009	-0.019	8.812	-3.472	-3.472	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.006	-0.011	6.762	4.375	4.375	0.000	0.000	0.000	0.000
9	A	9	HIS	0	-0.038	-0.018	9.515	-2.295	-2.295	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.867	-0.927	12.347	19.861	19.861	0.000	0.000	0.000	0.000
11	A	11	ASN	0	-0.070	-0.048	11.358	0.575	0.575	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.001	-0.003	9.783	2.124	2.124	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.011	0.015	5.364	-0.479	-0.479	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.009	-0.006	7.356	-0.342	-0.342	0.000	0.000	0.000	0.000
15	A	15	TYR	0	-0.017	-0.047	1.575	-32.827	-41.735	23.448	-9.512	-5.029	0.086
16	A	16	GLN	0	-0.047	-0.049	8.062	-2.704	-2.704	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.020	0.008	10.336	1.269	1.269	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.865	-0.912	12.203	20.698	20.698	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.020	-0.008	11.764	1.749	1.749	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.892	-0.945	11.176	20.844	20.844	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.019	-0.024	9.214	1.397	1.397	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.013	-0.009	7.091	3.003	3.003	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.027	-0.023	6.373	4.779	4.779	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.093	-0.053	7.684	-0.036	-0.036	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.010	0.001	4.688	-1.457	-1.329	-0.001	-0.045	-0.082	0.000
26	A	26	VAL	0	-0.043	-0.012	2.216	-1.995	0.996	5.142	-3.787	-4.346	0.005
27	A	27	ASP	-1	-0.919	-0.957	1.821	30.234	24.762	13.637	-3.415	-4.749	0.035
28	A	28	PHE	0	0.004	-0.011	3.533	3.090	3.489	0.016	0.098	-0.513	0.001
29	A	29	ASP	-1	-0.782	-0.857	6.626	25.537	25.537	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.053	-0.051	10.223	-3.210	-3.210	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.007	0.020	10.260	1.855	1.855	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.021	-0.020	11.858	-2.542	-2.542	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.040	-0.033	14.627	0.584	0.584	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.017	0.004	17.440	-0.626	-0.626	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.003	0.015	19.783	-0.599	-0.599	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.020	-0.036	22.817	-0.628	-0.628	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.766	-0.872	26.618	9.842	9.842	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.062	-0.034	29.184	-0.335	-0.335	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.007	0.003	24.148	-0.055	-0.055	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.043	0.040	26.883	0.049	0.049	0.000	0.000	0.000	0.000
41	A	41	HIS	0	0.013	-0.005	23.015	0.164	0.164	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.009	-0.020	25.205	0.131	0.131	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.007	-0.010	25.456	-0.269	-0.269	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.004	-0.002	22.301	0.294	0.294	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.053	0.028	14.901	-0.242	-0.242	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.055	0.039	18.635	0.327	0.327	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.844	0.921	20.731	-12.367	-12.367	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.019	0.012	17.654	-0.165	-0.165	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.048	0.026	14.241	0.147	0.147	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.792	-0.883	17.821	12.800	12.800	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.026	-0.014	20.439	-0.462	-0.462	0.000	0.000	0.000	0.000
52	A	52	TYR	0	0.037	0.045	12.607	-0.415	-0.415	0.000	0.000	0.000	0.000
53	A	53	THR	0	-0.025	-0.029	17.556	-0.389	-0.389	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.859	0.922	18.555	-16.144	-16.144	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.009	0.013	22.887	-0.602	-0.602	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.759	0.854	21.626	-14.094	-14.094	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.085	0.046	19.373	-0.328	-0.328	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.028	-0.009	22.613	-0.324	-0.324	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.819	0.905	25.921	-11.737	-11.737	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.035	0.015	23.222	-0.403	-0.403	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.006	-0.005	24.292	-0.064	-0.064	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.934	0.966	26.630	-9.750	-9.750	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.845	-0.919	29.569	10.279	10.279	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.052	0.030	27.621	-0.126	-0.126	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.038	-0.019	29.291	-0.330	-0.330	0.000	0.000	0.000	0.000
66	A	66	GLY	0	-0.052	-0.029	31.673	-0.310	-0.310	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.046	-0.017	32.512	-0.329	-0.329	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.017	-0.008	31.339	-0.195	-0.195	0.000	0.000	0.000	0.000
69	A	69	GLY	0	-0.012	0.011	33.484	-0.079	-0.079	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.807	0.872	31.530	-9.035	-9.035	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.014	0.018	25.384	-0.098	-0.098	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.960	0.980	28.855	-10.200	-10.200	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.030	0.016	27.463	0.420	0.420	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.024	-0.010	25.352	-0.370	-0.370	0.000	0.000	0.000	0.000
75	A	75	THR	0	-0.065	-0.043	24.406	0.098	0.098	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.056	0.003	21.977	0.302	0.302	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.026	0.003	22.279	-0.343	-0.343	0.000	0.000	0.000	0.000
78	A	78	MET	0	-0.017	0.023	16.003	0.560	0.560	0.000	0.000	0.000	0.000
79	A	79	VAL	0	-0.029	-0.021	19.504	-0.908	-0.908	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.893	-0.946	18.010	17.448	17.448	0.000	0.000	0.000	0.000
81	A	81	CYS	0	-0.064	-0.030	17.909	-1.224	-1.224	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.791	-0.873	17.462	15.275	15.275	0.000	0.000	0.000	0.000
83	A	83	SER	0	0.015	-0.002	13.110	-0.610	-0.610	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.018	0.007	11.762	1.523	1.523	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.881	0.950	13.950	-21.171	-21.171	0.000	0.000	0.000	0.000
86	A	86	ILE	0	0.023	0.004	13.979	1.456	1.456	0.000	0.000	0.000	0.000
87	A	87	PHE	0	0.032	-0.001	15.774	-1.418	-1.418	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.009	-0.011	17.472	0.368	0.368	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.039	0.027	18.625	-0.927	-0.927	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.055	-0.008	20.986	0.090	0.090	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.062	0.035	23.110	-0.238	-0.238	0.000	0.000	0.000	0.000
92	A	92	PRO	0	-0.025	-0.016	23.899	-0.519	-0.519	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.901	0.960	26.689	-10.379	-10.379	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.875	0.940	29.360	-10.856	-10.856	0.000	0.000	0.000	0.000
95	A	95	GLY	0	-0.009	-0.018	30.924	-0.334	-0.334	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.945	0.962	32.983	-7.861	-7.861	0.000	0.000	0.000	0.000
97	A	97	HIS	0	0.060	0.039	33.021	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.829	-0.911	28.715	11.322	11.322	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.828	0.875	25.346	-12.088	-12.088	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.810	-0.902	27.080	10.935	10.935	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.019	-0.013	27.946	0.159	0.159	0.000	0.000	0.000	0.000
102	A	102	LEU	0	0.016	0.007	22.472	0.345	0.345	0.000	0.000	0.000	0.000
103	A	103	ILE	0	0.040	0.030	22.932	0.625	0.625	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.800	0.908	23.577	-10.692	-10.692	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.025	0.016	21.893	0.302	0.302	0.000	0.000	0.000	0.000
106	A	106	TYR	0	0.055	0.005	16.875	0.923	0.923	0.000	0.000	0.000	0.000
107	A	107	ASN	0	-0.004	-0.005	18.864	0.695	0.695	0.000	0.000	0.000	0.000
108	A	108	THR	0	-0.056	-0.024	20.440	0.112	0.112	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.026	-0.009	14.574	0.170	0.170	0.000	0.000	0.000	0.000
110	A	110	ASN	0	0.012	-0.006	15.785	2.211	2.211	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.026	-0.027	17.170	0.735	0.735	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.827	-0.894	16.351	16.828	16.828	0.000	0.000	0.000	0.000
113	A	113	GLN	0	-0.070	-0.039	16.439	1.407	1.407	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.035	0.011	13.009	0.055	0.055	0.000	0.000	0.000	0.000
115	A	115	THR	0	-0.008	-0.016	6.724	-1.532	-1.532	0.000	0.000	0.000	0.000
116	A	116	PRO	0	-0.041	-0.014	9.225	1.080	1.080	0.000	0.000	0.000	0.000
117	A	117	LEU	0	0.052	0.041	6.364	3.063	3.063	0.000	0.000	0.000	0.000
118	A	118	THR	0	-0.025	-0.040	8.885	-4.168	-4.168	0.000	0.000	0.000	0.000
119	A	119	PRO	0	-0.003	0.023	12.003	0.990	0.990	0.000	0.000	0.000	0.000
120	A	120	ILE	0	0.063	0.028	14.481	-0.438	-0.438	0.000	0.000	0.000	0.000
121	A	121	LEU	0	0.013	0.016	16.926	-1.084	-1.084	0.000	0.000	0.000	0.000
122	A	122	SER	0	-0.017	-0.037	19.694	-0.210	-0.210	0.000	0.000	0.000	0.000
123	A	123	CYS	0	0.009	0.025	20.191	-0.741	-0.741	0.000	0.000	0.000	0.000
124	A	124	GLY	0	0.026	0.013	22.912	-0.134	-0.134	0.000	0.000	0.000	0.000
125	A	125	ILE	0	0.030	0.003	25.245	-0.452	-0.452	0.000	0.000	0.000	0.000
126	A	126	PHE	0	-0.047	-0.017	25.342	-0.664	-0.664	0.000	0.000	0.000	0.000
127	A	127	GLY	0	0.027	0.019	27.515	-0.379	-0.379	0.000	0.000	0.000	0.000
128	A	128	ILE	0	-0.011	-0.001	24.921	-0.366	-0.366	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.845	0.934	25.164	-12.086	-12.086	0.000	0.000	0.000	0.000
130	A	130	LEU	0	0.072	0.030	18.356	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.731	-0.867	20.837	13.844	13.844	0.000	0.000	0.000	0.000
132	A	132	THR	0	0.020	0.014	21.902	0.130	0.130	0.000	0.000	0.000	0.000
133	A	133	SER	0	-0.029	-0.040	21.021	0.099	0.099	0.000	0.000	0.000	0.000
134	A	134	LEU	0	0.009	0.002	15.340	0.403	0.403	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.814	-0.881	18.593	13.179	13.179	0.000	0.000	0.000	0.000
136	A	136	VAL	0	-0.035	-0.021	20.952	0.025	0.025	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.036	-0.009	13.886	0.045	0.045	0.000	0.000	0.000	0.000
138	A	138	LEU	0	0.048	0.008	14.356	0.613	0.613	0.000	0.000	0.000	0.000
139	A	139	ASP	-1	-0.862	-0.907	17.690	13.689	13.689	0.000	0.000	0.000	0.000
140	A	140	VAL	0	-0.101	-0.043	19.636	-0.476	-0.476	0.000	0.000	0.000	0.000
141	A	141	CYS	0	-0.064	-0.024	14.558	0.020	0.020	0.000	0.000	0.000	0.000
142	A	142	ASN	0	-0.018	-0.001	15.179	1.506	1.506	0.000	0.000	0.000	0.000
143	A	143	THR	0	0.010	0.001	16.131	-0.499	-0.499	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.781	0.927	12.992	-21.523	-21.523	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.859	-0.927	5.741	51.889	51.889	0.000	0.000	0.000	0.000
146	A	146	VAL	0	-0.045	-0.031	9.615	-0.665	-0.665	0.000	0.000	0.000	0.000
147	A	147	LYS	1	0.810	0.914	1.734	-115.103	-119.800	15.179	-5.820	-4.662	0.070
148	A	148	VAL	0	-0.001	-0.005	7.553	-4.480	-4.480	0.000	0.000	0.000	0.000
149	A	149	PHE	0	-0.022	-0.020	9.069	2.026	2.026	0.000	0.000	0.000	0.000
150	A	150	VAL	0	-0.031	-0.016	10.875	-2.586	-2.586	0.000	0.000	0.000	0.000
151	A	151	TYR	0	-0.040	-0.019	13.481	0.749	0.749	0.000	0.000	0.000	0.000
152	A	152	THR	0	-0.012	-0.052	16.113	-0.141	-0.141	0.000	0.000	0.000	0.000
153	A	153	ASP	-1	-0.795	-0.908	17.413	17.868	17.868	0.000	0.000	0.000	0.000
154	A	154	THR	0	-0.015	-0.003	18.467	-0.355	-0.355	0.000	0.000	0.000	0.000
155	A	155	GLU	-1	-0.817	-0.875	17.118	17.813	17.813	0.000	0.000	0.000	0.000
156	A	156	VAL	0	0.001	0.009	13.725	0.286	0.286	0.000	0.000	0.000	0.000
157	A	157	CYS	0	-0.073	-0.028	15.850	0.166	0.166	0.000	0.000	0.000	0.000
158	A	158	LYS	1	0.892	0.929	18.933	-13.682	-13.682	0.000	0.000	0.000	0.000
159	A	159	VAL	0	-0.017	-0.002	13.147	-0.390	-0.390	0.000	0.000	0.000	0.000
160	A	160	LYS	1	0.924	0.974	13.657	-21.314	-21.314	0.000	0.000	0.000	0.000
161	A	161	ASP	-1	-0.907	-0.961	16.929	14.218	14.218	0.000	0.000	0.000	0.000
162	A	162	PHE	0	-0.077	-0.053	18.617	-0.725	-0.725	0.000	0.000	0.000	0.000
163	A	163	VAL	0	-0.009	0.001	14.711	-0.306	-0.306	0.000	0.000	0.000	0.000
164	A	164	SER	0	-0.050	-0.026	16.807	0.514	0.514	0.000	0.000	0.000	0.000
165	A	165	GLY	0	-0.044	0.005	19.126	-0.634	-0.634	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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