FMO DATABASE

FMODB ID: MVQJZ

Calculation Name: 3EMX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EMX

Chain ID: A

ChEMBL ID:

UniProt ID: Q9YED4

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	124
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1098458.055464
FMO2-HF: Nuclear repulsion	1049660.978086
FMO2-HF: Total energy	-48797.077378
FMO2-MP2: Total energy	-48940.190446

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:224:SER)

Summations of interaction energy for fragment #1(A:224:SER)

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.
-11.814	-4.034	3.695	-4.313	-7.164	0.01

Interaction energy analysis for fragmet #1(A:224:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.000

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	226	SER	0	-0.013	-0.030	2.453	-9.092	-5.652	1.613	-2.142	-2.912	0.019
4	A	227	TYR	0	-0.088	-0.044	2.807	-3.914	-1.388	1.781	-1.491	-2.816	-0.012
5	A	228	VAL	0	0.011	0.030	4.355	0.086	0.344	-0.001	-0.041	-0.216	0.000
6	A	229	LYS	1	0.916	0.967	6.319	0.304	0.304	0.000	0.000	0.000	0.000
7	A	230	GLU	-1	-0.789	-0.880	9.956	-0.049	-0.049	0.000	0.000	0.000	0.000
8	A	231	GLY	0	0.022	0.006	12.353	-0.080	-0.080	0.000	0.000	0.000	0.000
9	A	232	LEU	0	-0.057	-0.013	15.466	0.071	0.071	0.000	0.000	0.000	0.000
10	A	233	ALA	0	0.003	-0.008	13.953	-0.040	-0.040	0.000	0.000	0.000	0.000
11	A	234	VAL	0	0.023	0.026	16.003	0.027	0.027	0.000	0.000	0.000	0.000
12	A	235	LEU	0	-0.057	-0.028	11.435	0.030	0.030	0.000	0.000	0.000	0.000
13	A	236	GLU	-1	-0.837	-0.927	14.779	0.255	0.255	0.000	0.000	0.000	0.000
14	A	237	ASP	-1	-0.768	-0.877	16.058	0.337	0.337	0.000	0.000	0.000	0.000
15	A	238	GLY	0	-0.050	-0.029	12.310	0.008	0.008	0.000	0.000	0.000	0.000
16	A	239	ARG	1	0.726	0.843	11.018	-0.195	-0.195	0.000	0.000	0.000	0.000
17	A	240	LEU	0	-0.045	-0.021	8.861	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	241	ILE	0	0.029	0.035	12.457	-0.086	-0.086	0.000	0.000	0.000	0.000
19	A	242	TYR	0	-0.064	-0.056	10.417	0.011	0.011	0.000	0.000	0.000	0.000
20	A	243	ILE	0	-0.001	0.011	16.402	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	244	THR	0	0.020	0.007	19.708	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	245	PRO	0	0.005	-0.017	22.598	0.018	0.018	0.000	0.000	0.000	0.000
23	A	246	GLU	-1	-0.870	-0.933	24.248	0.083	0.083	0.000	0.000	0.000	0.000
24	A	247	GLU	-1	-0.846	-0.919	23.422	0.144	0.144	0.000	0.000	0.000	0.000
25	A	248	PHE	0	-0.001	-0.001	19.698	0.013	0.013	0.000	0.000	0.000	0.000
26	A	249	ARG	1	0.849	0.899	23.387	-0.092	-0.092	0.000	0.000	0.000	0.000
27	A	250	GLN	0	0.021	0.015	26.920	0.004	0.004	0.000	0.000	0.000	0.000
28	A	251	LEU	0	0.009	0.003	22.022	0.006	0.006	0.000	0.000	0.000	0.000
29	A	252	LEU	0	-0.043	-0.017	22.678	0.009	0.009	0.000	0.000	0.000	0.000
30	A	253	GLN	0	-0.070	-0.035	26.465	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	254	GLY	0	0.007	0.012	28.538	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	255	ASP	-1	-0.834	-0.920	27.378	0.198	0.198	0.000	0.000	0.000	0.000
33	A	256	ALA	0	0.002	-0.014	22.876	0.006	0.006	0.000	0.000	0.000	0.000
34	A	257	ILE	0	-0.016	0.003	19.189	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	258	LEU	0	0.020	0.024	18.858	0.023	0.023	0.000	0.000	0.000	0.000
36	A	259	ALA	0	-0.011	-0.013	14.330	0.021	0.021	0.000	0.000	0.000	0.000
37	A	260	VAL	0	-0.018	-0.009	15.932	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	261	TYR	0	0.025	-0.060	8.542	0.165	0.165	0.000	0.000	0.000	0.000
39	A	262	SER	0	0.023	0.005	11.522	-0.143	-0.143	0.000	0.000	0.000	0.000
40	A	263	LYS	1	0.854	0.917	7.501	0.577	0.577	0.000	0.000	0.000	0.000
41	A	264	THR	0	-0.026	-0.011	7.336	0.267	0.267	0.000	0.000	0.000	0.000
42	A	265	CYS	0	-0.025	0.022	9.534	-0.093	-0.093	0.000	0.000	0.000	0.000
43	A	266	PRO	0	0.049	0.021	8.628	0.384	0.384	0.000	0.000	0.000	0.000
44	A	267	HIS	0	0.078	0.018	9.513	0.283	0.283	0.000	0.000	0.000	0.000
45	A	268	CYS	0	0.005	0.015	9.437	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	269	HIS	0	0.008	0.016	3.218	1.340	2.615	0.291	-0.575	-0.992	0.003
47	A	270	ARG	1	0.871	0.934	6.183	-0.566	-0.566	0.000	0.000	0.000	0.000
48	A	271	ASP	-1	-0.748	-0.837	8.828	1.010	1.010	0.000	0.000	0.000	0.000
49	A	272	TRP	0	0.052	0.031	3.493	-0.786	-0.505	0.011	-0.064	-0.228	0.000
50	A	273	PRO	0	0.000	-0.004	5.654	-0.187	-0.187	0.000	0.000	0.000	0.000
51	A	274	GLN	0	0.025	0.013	7.919	-0.414	-0.414	0.000	0.000	0.000	0.000
52	A	275	LEU	0	0.001	-0.005	10.552	-0.179	-0.179	0.000	0.000	0.000	0.000
53	A	276	ILE	0	-0.006	-0.004	7.813	-0.175	-0.175	0.000	0.000	0.000	0.000
54	A	277	GLN	0	0.028	0.026	11.030	-0.144	-0.144	0.000	0.000	0.000	0.000
55	A	278	ALA	0	0.062	0.032	13.615	-0.111	-0.111	0.000	0.000	0.000	0.000
56	A	279	SER	0	-0.047	-0.028	13.997	-0.087	-0.087	0.000	0.000	0.000	0.000
57	A	280	LYS	1	0.853	0.926	13.183	-0.764	-0.764	0.000	0.000	0.000	0.000
58	A	281	GLU	-1	-0.973	-0.974	17.603	0.383	0.383	0.000	0.000	0.000	0.000
59	A	282	VAL	0	-0.084	-0.042	19.383	-0.036	-0.036	0.000	0.000	0.000	0.000
60	A	283	ASP	-1	-0.877	-0.931	21.438	0.266	0.266	0.000	0.000	0.000	0.000
61	A	284	VAL	0	-0.080	-0.021	22.088	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	285	PRO	0	0.040	0.012	20.946	0.039	0.039	0.000	0.000	0.000	0.000
63	A	286	ILE	0	0.015	0.015	15.352	0.013	0.013	0.000	0.000	0.000	0.000
64	A	287	VAL	0	0.029	0.015	17.399	0.011	0.011	0.000	0.000	0.000	0.000
65	A	288	MET	0	-0.065	-0.025	10.703	0.072	0.072	0.000	0.000	0.000	0.000
66	A	289	PHE	0	0.047	0.021	15.788	-0.080	-0.080	0.000	0.000	0.000	0.000
67	A	290	ILE	0	-0.006	-0.002	9.673	0.103	0.103	0.000	0.000	0.000	0.000
68	A	291	TRP	0	0.013	-0.010	13.046	-0.110	-0.110	0.000	0.000	0.000	0.000
69	A	292	GLY	0	0.037	-0.011	11.922	0.089	0.089	0.000	0.000	0.000	0.000
70	A	293	SER	0	-0.009	-0.006	13.138	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	294	LEU	0	-0.027	-0.010	13.969	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	295	ILE	0	-0.080	-0.015	16.288	0.000	0.000	0.000	0.000	0.000	0.000
73	A	296	GLY	0	0.055	0.031	17.846	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	297	GLU	-1	-0.920	-0.967	21.365	0.038	0.038	0.000	0.000	0.000	0.000
75	A	298	ARG	1	0.957	0.963	24.431	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	299	GLU	-1	-0.816	-0.911	18.272	0.076	0.076	0.000	0.000	0.000	0.000
77	A	300	LEU	0	0.017	0.011	19.639	0.028	0.028	0.000	0.000	0.000	0.000
78	A	301	SER	0	-0.085	-0.038	21.910	0.014	0.014	0.000	0.000	0.000	0.000
79	A	302	ALA	0	0.009	-0.005	23.683	0.008	0.008	0.000	0.000	0.000	0.000
80	A	303	ALA	0	0.083	0.041	20.266	0.009	0.009	0.000	0.000	0.000	0.000
81	A	304	ARG	1	0.971	0.979	22.279	-0.092	-0.092	0.000	0.000	0.000	0.000
82	A	305	LEU	0	-0.050	-0.014	24.012	0.000	0.000	0.000	0.000	0.000	0.000
83	A	306	GLU	-1	-0.772	-0.868	23.749	0.174	0.174	0.000	0.000	0.000	0.000
84	A	307	MET	0	-0.004	-0.002	19.855	0.011	0.011	0.000	0.000	0.000	0.000
85	A	308	ASN	0	-0.035	-0.016	23.925	0.006	0.006	0.000	0.000	0.000	0.000
86	A	309	LYS	1	0.827	0.918	27.432	-0.162	-0.162	0.000	0.000	0.000	0.000
87	A	310	ALA	0	0.027	0.031	24.855	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	311	GLY	0	0.029	0.020	26.760	0.009	0.009	0.000	0.000	0.000	0.000
89	A	312	VAL	0	-0.085	-0.048	20.362	0.013	0.013	0.000	0.000	0.000	0.000
90	A	313	GLU	-1	-0.904	-0.952	22.726	0.209	0.209	0.000	0.000	0.000	0.000
91	A	314	GLY	0	-0.025	-0.014	19.099	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	315	THR	0	-0.060	0.014	14.341	0.044	0.044	0.000	0.000	0.000	0.000
93	A	316	PRO	0	0.029	-0.025	12.829	0.009	0.009	0.000	0.000	0.000	0.000
94	A	317	THR	0	-0.014	-0.017	14.800	-0.062	-0.062	0.000	0.000	0.000	0.000
95	A	318	LEU	0	-0.038	0.000	15.409	0.021	0.021	0.000	0.000	0.000	0.000
96	A	319	VAL	0	0.008	-0.004	18.985	-0.033	-0.033	0.000	0.000	0.000	0.000
97	A	320	PHE	0	0.021	-0.007	21.051	0.014	0.014	0.000	0.000	0.000	0.000
98	A	321	TYR	0	-0.004	-0.025	23.891	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	322	LYS	1	0.924	0.963	26.963	-0.175	-0.175	0.000	0.000	0.000	0.000
100	A	323	GLU	-1	-0.865	-0.909	29.953	0.136	0.136	0.000	0.000	0.000	0.000
101	A	324	GLY	0	0.061	0.047	29.790	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	325	ARG	1	0.699	0.823	30.799	-0.150	-0.150	0.000	0.000	0.000	0.000
103	A	326	ILE	0	-0.020	-0.009	26.929	0.011	0.011	0.000	0.000	0.000	0.000
104	A	327	VAL	0	-0.046	-0.033	28.227	-0.013	-0.013	0.000	0.000	0.000	0.000
105	A	328	ASP	-1	-0.758	-0.864	26.096	0.261	0.261	0.000	0.000	0.000	0.000
106	A	329	LYS	1	0.791	0.893	23.172	-0.246	-0.246	0.000	0.000	0.000	0.000
107	A	330	LEU	0	0.014	0.021	18.962	-0.008	-0.008	0.000	0.000	0.000	0.000
108	A	331	VAL	0	-0.001	-0.005	19.417	0.042	0.042	0.000	0.000	0.000	0.000
109	A	332	GLY	0	0.018	0.017	16.676	-0.016	-0.016	0.000	0.000	0.000	0.000
110	A	333	ALA	0	-0.065	-0.046	12.853	0.037	0.037	0.000	0.000	0.000	0.000
111	A	334	THR	0	-0.005	0.003	14.378	-0.089	-0.089	0.000	0.000	0.000	0.000
112	A	335	PRO	0	0.005	0.003	14.557	0.107	0.107	0.000	0.000	0.000	0.000
113	A	336	TRP	0	0.053	0.004	14.369	-0.033	-0.033	0.000	0.000	0.000	0.000
114	A	337	SER	0	0.013	0.010	16.185	-0.024	-0.024	0.000	0.000	0.000	0.000
115	A	338	LEU	0	0.050	0.031	19.426	-0.025	-0.025	0.000	0.000	0.000	0.000
116	A	339	LYS	1	0.800	0.881	13.439	-0.853	-0.853	0.000	0.000	0.000	0.000
117	A	340	VAL	0	-0.005	0.004	18.976	-0.031	-0.031	0.000	0.000	0.000	0.000
118	A	341	GLU	-1	-0.951	-0.983	21.305	0.306	0.306	0.000	0.000	0.000	0.000
119	A	342	LYS	1	0.807	0.897	22.474	-0.299	-0.299	0.000	0.000	0.000	0.000
120	A	343	ALA	0	0.034	0.012	22.155	-0.022	-0.022	0.000	0.000	0.000	0.000
121	A	344	ARG	1	0.923	0.962	23.948	-0.331	-0.331	0.000	0.000	0.000	0.000
122	A	345	GLU	-1	-0.877	-0.907	27.104	0.232	0.232	0.000	0.000	0.000	0.000
123	A	346	ILE	0	-0.037	-0.009	25.929	-0.018	-0.018	0.000	0.000	0.000	0.000
124	A	347	TYR	0	-0.102	-0.061	24.228	-0.015	-0.015	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:224:SER)