FMO DATABASE

FMODB ID: 941K2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1098211.191903
FMO2-HF: Nuclear repulsion	1049414.820344
FMO2-HF: Total energy	-48796.371559
FMO2-MP2: Total energy	-48939.515056

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.
-12.342	-8.154	7.229	-4.317	-7.1	0.019

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 : 0.025 / q_NPA : -0.002

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	-0.001	-0.022	2.095	-7.592	-7.486	6.168	-2.661	-3.613	0.026
4	A	227	TYR	0	-0.098	-0.051	2.937	-4.916	-2.104	1.018	-1.262	-2.567	-0.008
5	A	228	VAL	0	0.015	0.030	4.160	-0.442	-0.159	-0.001	-0.049	-0.233	0.000
6	A	229	LYS	1	0.943	1.001	6.223	0.359	0.359	0.000	0.000	0.000	0.000
7	A	230	GLU	-1	-0.825	-0.896	9.875	0.122	0.122	0.000	0.000	0.000	0.000
8	A	231	GLY	0	0.043	0.002	12.258	-0.081	-0.081	0.000	0.000	0.000	0.000
9	A	232	LEU	0	-0.066	-0.020	15.352	0.064	0.064	0.000	0.000	0.000	0.000
10	A	233	ALA	0	0.000	-0.004	13.786	-0.037	-0.037	0.000	0.000	0.000	0.000
11	A	234	VAL	0	0.037	0.033	15.854	0.024	0.024	0.000	0.000	0.000	0.000
12	A	235	LEU	0	-0.069	-0.032	11.202	0.026	0.026	0.000	0.000	0.000	0.000
13	A	236	GLU	-1	-0.887	-0.963	14.616	0.249	0.249	0.000	0.000	0.000	0.000
14	A	237	ASP	-1	-0.866	-0.930	15.912	0.335	0.335	0.000	0.000	0.000	0.000
15	A	238	GLY	0	-0.092	-0.065	12.355	0.015	0.015	0.000	0.000	0.000	0.000
16	A	239	ARG	1	0.896	0.947	10.882	-0.190	-0.190	0.000	0.000	0.000	0.000
17	A	240	LEU	0	-0.026	-0.008	8.543	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	241	ILE	0	0.020	0.032	12.309	-0.078	-0.078	0.000	0.000	0.000	0.000
19	A	242	TYR	0	-0.060	-0.065	10.350	0.008	0.008	0.000	0.000	0.000	0.000
20	A	243	ILE	0	-0.007	0.004	16.270	-0.019	-0.019	0.000	0.000	0.000	0.000
21	A	244	THR	0	0.035	0.018	19.580	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	245	PRO	0	0.016	-0.016	22.470	0.016	0.016	0.000	0.000	0.000	0.000
23	A	246	GLU	-1	-0.953	-0.982	24.116	0.092	0.092	0.000	0.000	0.000	0.000
24	A	247	GLU	-1	-0.841	-0.919	23.211	0.142	0.142	0.000	0.000	0.000	0.000
25	A	248	PHE	0	-0.012	-0.003	19.720	0.012	0.012	0.000	0.000	0.000	0.000
26	A	249	ARG	1	0.934	0.947	23.238	-0.107	-0.107	0.000	0.000	0.000	0.000
27	A	250	GLN	0	0.007	0.003	26.770	0.001	0.001	0.000	0.000	0.000	0.000
28	A	251	LEU	0	0.018	0.006	21.858	0.004	0.004	0.000	0.000	0.000	0.000
29	A	252	LEU	0	-0.048	-0.019	22.777	0.008	0.008	0.000	0.000	0.000	0.000
30	A	253	GLN	0	-0.044	-0.013	26.444	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	254	GLY	0	-0.022	-0.003	28.519	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	255	ASP	-1	-0.847	-0.917	27.482	0.183	0.183	0.000	0.000	0.000	0.000
33	A	256	ALA	0	0.009	-0.013	22.799	0.006	0.006	0.000	0.000	0.000	0.000
34	A	257	ILE	0	-0.010	0.007	19.021	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	258	LEU	0	0.023	0.024	18.710	0.023	0.023	0.000	0.000	0.000	0.000
36	A	259	ALA	0	-0.017	-0.015	14.316	0.017	0.017	0.000	0.000	0.000	0.000
37	A	260	VAL	0	-0.018	-0.006	15.907	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	261	TYR	0	0.014	-0.067	8.503	0.155	0.155	0.000	0.000	0.000	0.000
39	A	262	SER	0	0.027	0.008	11.531	-0.105	-0.105	0.000	0.000	0.000	0.000
40	A	263	LYS	1	0.868	0.925	7.015	0.056	0.056	0.000	0.000	0.000	0.000
41	A	264	THR	0	0.001	0.005	7.240	0.322	0.322	0.000	0.000	0.000	0.000
42	A	265	CYS	0	-0.057	0.033	9.560	-0.136	-0.136	0.000	0.000	0.000	0.000
43	A	266	PRO	0	0.043	0.027	8.926	0.341	0.341	0.000	0.000	0.000	0.000
44	A	267	HIS	0	0.054	-0.012	9.850	0.193	0.193	0.000	0.000	0.000	0.000
45	A	268	CYS	0	0.016	0.016	9.581	-0.039	-0.039	0.000	0.000	0.000	0.000
46	A	269	HIS	0	-0.005	0.012	3.568	1.110	1.786	0.027	-0.263	-0.440	0.001
47	A	270	ARG	1	0.913	0.959	6.168	-0.555	-0.555	0.000	0.000	0.000	0.000
48	A	271	ASP	-1	-0.760	-0.845	8.815	0.916	0.916	0.000	0.000	0.000	0.000
49	A	272	TRP	0	0.050	0.038	3.389	-0.793	-0.482	0.017	-0.082	-0.247	0.000
50	A	273	PRO	0	0.003	-0.004	5.673	-0.114	-0.114	0.000	0.000	0.000	0.000
51	A	274	GLN	0	0.020	0.018	7.917	-0.368	-0.368	0.000	0.000	0.000	0.000
52	A	275	LEU	0	0.016	0.000	10.564	-0.148	-0.148	0.000	0.000	0.000	0.000
53	A	276	ILE	0	-0.013	-0.008	7.894	-0.163	-0.163	0.000	0.000	0.000	0.000
54	A	277	GLN	0	-0.026	-0.012	11.025	-0.110	-0.110	0.000	0.000	0.000	0.000
55	A	278	ALA	0	0.056	0.032	13.615	-0.100	-0.100	0.000	0.000	0.000	0.000
56	A	279	SER	0	-0.060	-0.026	14.116	-0.081	-0.081	0.000	0.000	0.000	0.000
57	A	280	LYS	1	0.922	0.968	12.586	-0.763	-0.763	0.000	0.000	0.000	0.000
58	A	281	GLU	-1	-0.970	-0.976	17.603	0.369	0.369	0.000	0.000	0.000	0.000
59	A	282	VAL	0	-0.104	-0.047	19.385	-0.033	-0.033	0.000	0.000	0.000	0.000
60	A	283	ASP	-1	-0.851	-0.918	21.432	0.243	0.243	0.000	0.000	0.000	0.000
61	A	284	VAL	0	-0.102	-0.031	22.113	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	285	PRO	0	0.052	0.020	20.872	0.035	0.035	0.000	0.000	0.000	0.000
63	A	286	ILE	0	0.014	0.011	15.215	0.013	0.013	0.000	0.000	0.000	0.000
64	A	287	VAL	0	0.032	0.013	17.341	0.012	0.012	0.000	0.000	0.000	0.000
65	A	288	MET	0	-0.063	-0.030	10.924	0.070	0.070	0.000	0.000	0.000	0.000
66	A	289	PHE	0	0.054	0.021	15.765	-0.066	-0.066	0.000	0.000	0.000	0.000
67	A	290	ILE	0	-0.011	0.002	9.728	0.105	0.105	0.000	0.000	0.000	0.000
68	A	291	TRP	0	0.021	-0.002	13.046	-0.083	-0.083	0.000	0.000	0.000	0.000
69	A	292	GLY	0	0.039	-0.016	11.708	0.128	0.128	0.000	0.000	0.000	0.000
70	A	293	SER	0	-0.004	-0.008	12.846	-0.032	-0.032	0.000	0.000	0.000	0.000
71	A	294	LEU	0	-0.055	-0.021	14.330	-0.023	-0.023	0.000	0.000	0.000	0.000
72	A	295	ILE	0	-0.064	0.000	16.280	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	296	GLY	0	0.042	0.025	17.568	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	297	GLU	-1	-0.923	-0.970	21.235	0.066	0.066	0.000	0.000	0.000	0.000
75	A	298	ARG	1	0.962	0.967	24.117	-0.031	-0.031	0.000	0.000	0.000	0.000
76	A	299	GLU	-1	-0.852	-0.928	18.735	0.116	0.116	0.000	0.000	0.000	0.000
77	A	300	LEU	0	0.019	0.010	19.752	0.023	0.023	0.000	0.000	0.000	0.000
78	A	301	SER	0	-0.034	-0.031	21.676	0.009	0.009	0.000	0.000	0.000	0.000
79	A	302	ALA	0	-0.036	-0.017	23.626	0.004	0.004	0.000	0.000	0.000	0.000
80	A	303	ALA	0	0.089	0.048	20.282	0.006	0.006	0.000	0.000	0.000	0.000
81	A	304	ARG	1	0.971	0.978	22.279	-0.118	-0.118	0.000	0.000	0.000	0.000
82	A	305	LEU	0	-0.058	-0.019	23.888	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	306	GLU	-1	-0.795	-0.898	23.752	0.176	0.176	0.000	0.000	0.000	0.000
84	A	307	MET	0	-0.019	-0.008	19.602	0.009	0.009	0.000	0.000	0.000	0.000
85	A	308	ASN	0	-0.028	-0.009	23.897	0.003	0.003	0.000	0.000	0.000	0.000
86	A	309	LYS	1	0.866	0.945	27.408	-0.160	-0.160	0.000	0.000	0.000	0.000
87	A	310	ALA	0	0.029	0.027	24.781	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	311	GLY	0	0.018	0.012	26.734	0.006	0.006	0.000	0.000	0.000	0.000
89	A	312	VAL	0	-0.085	-0.050	20.394	0.011	0.011	0.000	0.000	0.000	0.000
90	A	313	GLU	-1	-0.922	-0.960	22.789	0.195	0.195	0.000	0.000	0.000	0.000
91	A	314	GLY	0	-0.022	-0.012	19.202	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	315	THR	0	-0.057	-0.004	14.369	0.005	0.005	0.000	0.000	0.000	0.000
93	A	316	PRO	0	0.029	-0.032	12.850	0.009	0.009	0.000	0.000	0.000	0.000
94	A	317	THR	0	-0.023	-0.020	14.775	-0.061	-0.061	0.000	0.000	0.000	0.000
95	A	318	LEU	0	-0.042	0.000	15.605	0.023	0.023	0.000	0.000	0.000	0.000
96	A	319	VAL	0	0.016	-0.001	18.963	-0.030	-0.030	0.000	0.000	0.000	0.000
97	A	320	PHE	0	0.012	-0.012	21.302	0.013	0.013	0.000	0.000	0.000	0.000
98	A	321	TYR	0	-0.011	-0.018	23.553	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	322	LYS	1	0.926	0.956	26.942	-0.163	-0.163	0.000	0.000	0.000	0.000
100	A	323	GLU	-1	-0.864	-0.914	29.934	0.127	0.127	0.000	0.000	0.000	0.000
101	A	324	GLY	0	0.059	0.043	29.770	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	325	ARG	1	0.698	0.818	30.778	-0.140	-0.140	0.000	0.000	0.000	0.000
103	A	326	ILE	0	-0.015	-0.003	27.027	0.010	0.010	0.000	0.000	0.000	0.000
104	A	327	VAL	0	-0.044	-0.030	28.213	-0.012	-0.012	0.000	0.000	0.000	0.000
105	A	328	ASP	-1	-0.791	-0.901	26.116	0.239	0.239	0.000	0.000	0.000	0.000
106	A	329	LYS	1	0.814	0.916	23.176	-0.232	-0.232	0.000	0.000	0.000	0.000
107	A	330	LEU	0	0.009	0.019	19.044	-0.011	-0.011	0.000	0.000	0.000	0.000
108	A	331	VAL	0	-0.003	-0.003	19.396	0.038	0.038	0.000	0.000	0.000	0.000
109	A	332	GLY	0	0.022	0.016	16.654	-0.017	-0.017	0.000	0.000	0.000	0.000
110	A	333	ALA	0	-0.067	-0.044	12.884	0.034	0.034	0.000	0.000	0.000	0.000
111	A	334	THR	0	-0.010	-0.003	14.368	-0.077	-0.077	0.000	0.000	0.000	0.000
112	A	335	PRO	0	-0.002	0.002	14.547	0.095	0.095	0.000	0.000	0.000	0.000
113	A	336	TRP	0	0.065	0.003	14.292	-0.028	-0.028	0.000	0.000	0.000	0.000
114	A	337	SER	0	0.027	0.015	16.180	-0.022	-0.022	0.000	0.000	0.000	0.000
115	A	338	LEU	0	0.047	0.020	19.430	-0.023	-0.023	0.000	0.000	0.000	0.000
116	A	339	LYS	1	0.816	0.901	13.439	-0.763	-0.763	0.000	0.000	0.000	0.000
117	A	340	VAL	0	-0.004	0.005	18.968	-0.027	-0.027	0.000	0.000	0.000	0.000
118	A	341	GLU	-1	-0.971	-0.988	21.297	0.252	0.252	0.000	0.000	0.000	0.000
119	A	342	LYS	1	0.874	0.960	22.530	-0.282	-0.282	0.000	0.000	0.000	0.000
120	A	343	ALA	0	0.038	0.015	22.171	-0.019	-0.019	0.000	0.000	0.000	0.000
121	A	344	ARG	1	0.914	0.953	24.198	-0.289	-0.289	0.000	0.000	0.000	0.000
122	A	345	GLU	-1	-0.919	-0.943	27.095	0.208	0.208	0.000	0.000	0.000	0.000
123	A	346	ILE	0	-0.027	-0.005	26.064	-0.015	-0.015	0.000	0.000	0.000	0.000
124	A	347	TYR	0	-0.080	-0.036	24.305	-0.009	-0.009	0.000	0.000	0.000	0.000

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