FMO DATABASE

FMODB ID: KG8R3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1625923.97718
FMO2-HF: Nuclear repulsion	1563005.386987
FMO2-HF: Total energy	-62918.590193
FMO2-MP2: Total energy	-63102.749271

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.
-9.734	-18.568	58.006	-26.911	-22.26	0.191

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 : -0.768 / q_NPA : -0.837

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	-0.037	0.000	2.855	-7.886	-5.028	0.082	-1.222	-1.718	0.002
4	A	4	ASN	0	0.023	0.003	2.530	12.134	13.287	1.015	-0.849	-1.319	-0.012
5	A	5	ALA	0	0.030	0.025	4.501	-3.735	-3.469	-0.001	-0.020	-0.245	0.000
6	A	6	PHE	0	-0.079	-0.057	5.821	-4.872	-4.872	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.014	-0.018	8.775	-3.205	-3.205	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.003	0.001	6.891	3.660	3.660	0.000	0.000	0.000	0.000
9	A	9	HIS	0	-0.025	-0.014	9.625	-1.887	-1.887	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.889	-0.943	12.866	19.292	19.292	0.000	0.000	0.000	0.000
11	A	11	ASN	0	-0.059	-0.039	11.433	1.135	1.135	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.003	0.001	10.225	2.207	2.207	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.016	0.023	5.564	-0.707	-0.707	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.005	-0.009	7.583	0.198	0.198	0.000	0.000	0.000	0.000
15	A	15	TYR	0	-0.019	-0.062	1.494	-31.139	-45.671	32.662	-12.957	-5.172	0.091
16	A	16	GLN	0	-0.054	-0.055	8.065	-2.987	-2.987	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.005	-0.002	9.813	1.286	1.286	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.875	-0.934	11.642	20.026	20.026	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.020	-0.009	11.768	1.576	1.576	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.887	-0.935	11.190	20.438	20.438	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.042	-0.024	8.766	1.342	1.342	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.015	-0.014	7.086	2.927	2.927	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.029	-0.022	6.491	4.156	4.156	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.070	-0.039	7.294	1.068	1.068	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.034	-0.005	4.410	-0.320	-0.075	-0.001	-0.087	-0.157	0.000
26	A	26	VAL	0	-0.042	-0.014	2.304	-2.326	0.763	5.853	-4.164	-4.777	0.005
27	A	27	ASP	-1	-0.935	-0.954	1.877	29.788	27.263	10.149	-3.186	-4.439	0.040
28	A	28	PHE	0	0.000	-0.007	3.730	2.674	3.117	0.008	0.018	-0.469	0.001
29	A	29	ASP	-1	-0.793	-0.875	6.595	26.245	26.245	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.091	-0.056	10.345	-2.732	-2.732	0.000	0.000	0.000	0.000
31	A	31	ILE	0	0.003	0.025	10.608	1.643	1.643	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.011	-0.015	12.005	-2.416	-2.416	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.018	-0.023	14.829	0.519	0.519	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.011	0.009	17.661	-0.520	-0.520	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.016	0.005	19.939	-0.590	-0.590	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.013	-0.031	22.968	-0.442	-0.442	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.886	-0.956	26.731	10.016	10.016	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.023	-0.014	29.125	-0.276	-0.276	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.012	0.008	24.272	-0.021	-0.021	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.026	0.030	26.825	-0.027	-0.027	0.000	0.000	0.000	0.000
41	A	41	HIS	0	0.026	-0.011	23.332	0.095	0.095	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.017	-0.017	25.334	0.087	0.087	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.000	-0.016	25.647	-0.292	-0.292	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.016	-0.005	22.518	0.332	0.332	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.065	0.033	15.336	-0.200	-0.200	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.048	0.041	18.928	0.331	0.331	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.936	0.980	20.946	-12.220	-12.220	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.002	-0.003	17.844	-0.140	-0.140	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.046	0.021	14.529	0.256	0.256	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.855	-0.934	17.909	12.995	12.995	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.051	-0.032	20.123	-0.393	-0.393	0.000	0.000	0.000	0.000
52	A	52	TYR	0	0.027	0.033	12.530	-0.237	-0.237	0.000	0.000	0.000	0.000
53	A	53	THR	0	-0.042	-0.023	17.423	-0.283	-0.283	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.920	0.950	19.207	-14.841	-14.841	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.016	0.019	22.423	-0.608	-0.608	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.823	0.913	21.570	-13.852	-13.852	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.072	0.032	19.564	-0.349	-0.349	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.013	0.001	22.430	-0.272	-0.272	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.861	0.927	25.787	-11.824	-11.824	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.038	0.011	22.920	-0.418	-0.418	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.009	0.001	24.292	-0.073	-0.073	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.932	0.965	26.624	-9.752	-9.752	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.890	-0.941	29.533	10.271	10.271	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.054	0.032	27.695	-0.205	-0.205	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.043	-0.024	29.255	-0.316	-0.316	0.000	0.000	0.000	0.000
66	A	66	GLY	0	-0.049	-0.024	31.567	-0.303	-0.303	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.045	-0.018	32.310	-0.336	-0.336	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.025	-0.009	31.448	-0.233	-0.233	0.000	0.000	0.000	0.000
69	A	69	GLY	0	-0.016	0.004	33.586	-0.139	-0.139	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.907	0.941	31.768	-8.764	-8.764	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.041	0.027	25.781	-0.101	-0.101	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.929	0.973	29.220	-10.232	-10.232	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.045	0.022	27.741	0.416	0.416	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.024	-0.021	25.264	-0.344	-0.344	0.000	0.000	0.000	0.000
75	A	75	THR	0	-0.088	-0.047	24.859	0.226	0.226	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.072	0.019	21.862	0.294	0.294	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.038	-0.007	22.376	-0.451	-0.451	0.000	0.000	0.000	0.000
78	A	78	MET	0	-0.009	0.020	16.383	0.617	0.617	0.000	0.000	0.000	0.000
79	A	79	VAL	0	-0.027	-0.024	19.785	-0.870	-0.870	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.932	-0.956	18.511	16.951	16.951	0.000	0.000	0.000	0.000
81	A	81	CYS	0	-0.079	-0.042	17.911	-1.262	-1.262	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.849	-0.925	17.453	15.328	15.328	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.002	-0.002	13.022	-0.239	-0.239	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.022	0.027	11.517	1.382	1.382	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.977	0.992	13.937	-21.278	-21.278	0.000	0.000	0.000	0.000
86	A	86	ILE	0	0.028	0.007	14.199	1.394	1.394	0.000	0.000	0.000	0.000
87	A	87	PHE	0	0.039	0.004	15.919	-1.443	-1.443	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.028	-0.018	17.713	0.474	0.474	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.046	0.023	18.710	-0.836	-0.836	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.035	0.007	21.157	0.025	0.025	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.058	0.035	23.637	-0.189	-0.189	0.000	0.000	0.000	0.000
92	A	92	PRO	0	-0.032	-0.015	24.348	-0.479	-0.479	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.943	0.980	26.987	-10.204	-10.204	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.964	0.991	29.647	-10.223	-10.223	0.000	0.000	0.000	0.000
95	A	95	GLY	0	-0.037	-0.027	31.080	-0.337	-0.337	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.961	0.973	33.157	-7.835	-7.835	0.000	0.000	0.000	0.000
97	A	97	HIS	0	0.043	0.026	33.547	0.089	0.089	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.845	-0.931	29.058	11.180	11.180	0.000	0.000	0.000	0.000
99	A	99	ARG	1	1.040	1.019	25.939	-11.650	-11.650	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.871	-0.934	27.561	10.642	10.642	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.101	-0.056	28.126	0.236	0.236	0.000	0.000	0.000	0.000
102	A	102	LEU	0	0.023	0.008	22.580	0.358	0.358	0.000	0.000	0.000	0.000
103	A	103	ILE	0	0.057	0.037	23.186	0.644	0.644	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.907	0.957	23.783	-10.318	-10.318	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.014	0.014	22.118	0.264	0.264	0.000	0.000	0.000	0.000
106	A	106	TYR	0	0.050	-0.002	17.050	0.914	0.914	0.000	0.000	0.000	0.000
107	A	107	ASN	0	-0.018	-0.014	19.160	0.864	0.864	0.000	0.000	0.000	0.000
108	A	108	THR	0	-0.062	-0.029	20.682	0.112	0.112	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.018	-0.003	14.926	0.167	0.167	0.000	0.000	0.000	0.000
110	A	110	ASN	0	0.039	0.001	16.343	2.051	2.051	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.040	-0.036	17.411	0.475	0.475	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.962	-0.951	16.988	15.831	15.831	0.000	0.000	0.000	0.000
113	A	113	GLN	0	-0.036	-0.040	16.183	1.930	1.930	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.035	0.018	13.113	-0.072	-0.072	0.000	0.000	0.000	0.000
115	A	115	THR	0	0.009	-0.007	6.836	-1.481	-1.481	0.000	0.000	0.000	0.000
116	A	116	PRO	0	-0.027	-0.003	9.487	1.050	1.050	0.000	0.000	0.000	0.000
117	A	117	LEU	0	0.047	0.036	6.553	3.003	3.003	0.000	0.000	0.000	0.000
118	A	118	THR	0	-0.021	-0.045	9.015	-3.923	-3.923	0.000	0.000	0.000	0.000
119	A	119	PRO	0	-0.010	0.022	12.178	1.058	1.058	0.000	0.000	0.000	0.000
120	A	120	ILE	0	0.069	0.028	14.550	-0.438	-0.438	0.000	0.000	0.000	0.000
121	A	121	LEU	0	-0.010	-0.005	17.145	-0.976	-0.976	0.000	0.000	0.000	0.000
122	A	122	SER	0	-0.016	-0.036	19.997	-0.196	-0.196	0.000	0.000	0.000	0.000
123	A	123	CYS	0	0.042	0.049	20.603	-0.701	-0.701	0.000	0.000	0.000	0.000
124	A	124	GLY	0	0.017	0.004	23.222	-0.152	-0.152	0.000	0.000	0.000	0.000
125	A	125	ILE	0	0.019	-0.007	25.122	-0.472	-0.472	0.000	0.000	0.000	0.000
126	A	126	PHE	0	-0.078	-0.035	25.372	-0.623	-0.623	0.000	0.000	0.000	0.000
127	A	127	GLY	0	0.025	0.013	27.428	-0.357	-0.357	0.000	0.000	0.000	0.000
128	A	128	ILE	0	-0.026	-0.010	25.327	-0.368	-0.368	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.906	0.967	25.275	-11.408	-11.408	0.000	0.000	0.000	0.000
130	A	130	LEU	0	0.062	0.023	18.676	0.007	0.007	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.813	-0.930	21.221	14.033	14.033	0.000	0.000	0.000	0.000
132	A	132	THR	0	-0.034	-0.008	22.529	0.001	0.001	0.000	0.000	0.000	0.000
133	A	133	SER	0	-0.016	-0.027	21.150	0.182	0.182	0.000	0.000	0.000	0.000
134	A	134	LEU	0	0.003	-0.002	15.743	0.382	0.382	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.906	-0.946	18.982	13.331	13.331	0.000	0.000	0.000	0.000
136	A	136	VAL	0	-0.063	-0.026	21.395	-0.100	-0.100	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.044	-0.014	14.254	0.079	0.079	0.000	0.000	0.000	0.000
138	A	138	LEU	0	0.019	-0.007	14.876	0.640	0.640	0.000	0.000	0.000	0.000
139	A	139	ASP	-1	-0.906	-0.936	17.819	14.071	14.071	0.000	0.000	0.000	0.000
140	A	140	VAL	0	-0.136	-0.070	19.712	-0.344	-0.344	0.000	0.000	0.000	0.000
141	A	141	CYS	0	-0.063	-0.025	15.007	-0.012	-0.012	0.000	0.000	0.000	0.000
142	A	142	ASN	0	0.057	0.039	15.908	1.326	1.326	0.000	0.000	0.000	0.000
143	A	143	THR	0	-0.025	-0.014	16.814	-0.329	-0.329	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.803	0.940	13.189	-20.820	-20.820	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.893	-0.944	6.200	48.434	48.434	0.000	0.000	0.000	0.000
146	A	146	VAL	0	-0.037	-0.026	9.998	-0.634	-0.634	0.000	0.000	0.000	0.000
147	A	147	LYS	1	0.830	0.923	1.882	-112.143	-111.974	8.239	-4.444	-3.964	0.064
148	A	148	VAL	0	0.022	0.010	7.860	-4.101	-4.101	0.000	0.000	0.000	0.000
149	A	149	PHE	0	-0.027	-0.017	9.208	2.269	2.269	0.000	0.000	0.000	0.000
150	A	150	VAL	0	-0.032	-0.014	10.916	-2.629	-2.629	0.000	0.000	0.000	0.000
151	A	151	TYR	0	0.016	0.015	13.335	0.676	0.676	0.000	0.000	0.000	0.000
152	A	152	THR	0	-0.013	-0.018	15.788	-0.231	-0.231	0.000	0.000	0.000	0.000
153	A	153	ASP	-1	-0.779	-0.895	17.336	17.514	17.514	0.000	0.000	0.000	0.000
154	A	154	THR	0	-0.047	-0.029	18.452	-0.300	-0.300	0.000	0.000	0.000	0.000
155	A	155	GLU	-1	-0.876	-0.943	17.434	17.351	17.351	0.000	0.000	0.000	0.000
156	A	156	VAL	0	0.024	0.017	13.776	0.214	0.214	0.000	0.000	0.000	0.000
157	A	157	CYS	0	-0.065	-0.030	16.086	0.094	0.094	0.000	0.000	0.000	0.000
158	A	158	LYS	1	0.974	0.987	19.116	-13.725	-13.725	0.000	0.000	0.000	0.000
159	A	159	VAL	0	-0.013	0.011	13.699	-0.338	-0.338	0.000	0.000	0.000	0.000
160	A	160	LYS	1	0.927	0.965	14.150	-20.206	-20.206	0.000	0.000	0.000	0.000
161	A	161	ASP	-1	-0.906	-0.951	17.076	13.877	13.877	0.000	0.000	0.000	0.000
162	A	162	PHE	0	-0.075	-0.040	19.077	-0.525	-0.525	0.000	0.000	0.000	0.000
163	A	163	VAL	0	-0.018	-0.003	15.214	-0.291	-0.291	0.000	0.000	0.000	0.000
164	A	164	SER	0	-0.047	-0.033	16.798	0.106	0.106	0.000	0.000	0.000	0.000
165	A	165	GLY	0	-0.058	-0.002	19.170	-0.669	-0.669	0.000	0.000	0.000	0.000

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