FMO DATABASE

FMODB ID: 7215K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1102082.985247
FMO2-HF: Nuclear repulsion	1053285.632105
FMO2-HF: Total energy	-48797.353142
FMO2-MP2: Total energy	-48940.48696

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.
-11.716	-4.149	4.654	-4.53	-7.692	0.008

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 : 0.024 / 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	-0.006	-0.027	2.457	-8.164	-4.828	1.494	-2.086	-2.744	0.017
4	A	227	TYR	0	-0.071	-0.045	2.682	-4.667	-2.392	2.724	-1.678	-3.321	-0.013
5	A	228	VAL	0	0.013	0.037	4.441	0.147	0.379	-0.001	-0.036	-0.195	0.000
6	A	229	LYS	1	0.852	0.938	6.692	0.245	0.245	0.000	0.000	0.000	0.000
7	A	230	GLU	-1	-0.752	-0.862	10.448	-0.048	-0.048	0.000	0.000	0.000	0.000
8	A	231	GLY	0	0.012	-0.004	12.339	-0.092	-0.092	0.000	0.000	0.000	0.000
9	A	232	LEU	0	-0.065	-0.013	15.154	0.081	0.081	0.000	0.000	0.000	0.000
10	A	233	ALA	0	-0.006	-0.013	14.320	-0.045	-0.045	0.000	0.000	0.000	0.000
11	A	234	VAL	0	0.019	0.021	16.337	0.020	0.020	0.000	0.000	0.000	0.000
12	A	235	LEU	0	-0.048	-0.030	11.293	0.018	0.018	0.000	0.000	0.000	0.000
13	A	236	GLU	-1	-0.816	-0.896	15.070	0.226	0.226	0.000	0.000	0.000	0.000
14	A	237	ASP	-1	-0.768	-0.872	15.893	0.309	0.309	0.000	0.000	0.000	0.000
15	A	238	GLY	0	-0.037	-0.020	12.293	0.026	0.026	0.000	0.000	0.000	0.000
16	A	239	ARG	1	0.696	0.812	10.945	-0.172	-0.172	0.000	0.000	0.000	0.000
17	A	240	LEU	0	-0.026	-0.013	8.649	0.030	0.030	0.000	0.000	0.000	0.000
18	A	241	ILE	0	0.008	0.017	12.425	-0.098	-0.098	0.000	0.000	0.000	0.000
19	A	242	TYR	0	-0.047	-0.050	10.682	0.007	0.007	0.000	0.000	0.000	0.000
20	A	243	ILE	0	-0.013	0.012	16.532	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	244	THR	0	0.021	0.013	20.111	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	245	PRO	0	0.016	-0.016	22.746	0.019	0.019	0.000	0.000	0.000	0.000
23	A	246	GLU	-1	-0.846	-0.920	24.154	0.085	0.085	0.000	0.000	0.000	0.000
24	A	247	GLU	-1	-0.841	-0.923	23.697	0.136	0.136	0.000	0.000	0.000	0.000
25	A	248	PHE	0	-0.015	-0.011	19.371	0.013	0.013	0.000	0.000	0.000	0.000
26	A	249	ARG	1	0.807	0.877	23.333	-0.092	-0.092	0.000	0.000	0.000	0.000
27	A	250	GLN	0	0.011	0.021	26.768	0.004	0.004	0.000	0.000	0.000	0.000
28	A	251	LEU	0	0.019	0.003	22.090	0.005	0.005	0.000	0.000	0.000	0.000
29	A	252	LEU	0	-0.042	-0.012	22.525	0.012	0.012	0.000	0.000	0.000	0.000
30	A	253	GLN	0	-0.067	-0.034	26.414	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	254	GLY	0	0.008	-0.003	28.553	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	255	ASP	-1	-0.831	-0.924	27.674	0.202	0.202	0.000	0.000	0.000	0.000
33	A	256	ALA	0	0.000	-0.004	23.122	0.003	0.003	0.000	0.000	0.000	0.000
34	A	257	ILE	0	-0.019	-0.008	18.980	0.002	0.002	0.000	0.000	0.000	0.000
35	A	258	LEU	0	0.022	0.015	18.667	0.026	0.026	0.000	0.000	0.000	0.000
36	A	259	ALA	0	-0.006	-0.004	14.165	0.020	0.020	0.000	0.000	0.000	0.000
37	A	260	VAL	0	-0.009	-0.002	15.808	-0.017	-0.017	0.000	0.000	0.000	0.000
38	A	261	TYR	0	0.023	-0.063	8.463	0.186	0.186	0.000	0.000	0.000	0.000
39	A	262	SER	0	0.011	-0.004	11.241	-0.157	-0.157	0.000	0.000	0.000	0.000
40	A	263	LYS	1	0.819	0.905	7.181	0.656	0.656	0.000	0.000	0.000	0.000
41	A	264	THR	0	-0.022	-0.012	7.276	0.294	0.294	0.000	0.000	0.000	0.000
42	A	265	CYS	0	-0.014	0.044	9.318	-0.097	-0.097	0.000	0.000	0.000	0.000
43	A	266	PRO	0	0.052	0.019	8.241	0.467	0.467	0.000	0.000	0.000	0.000
44	A	267	HIS	0	0.069	0.020	9.317	0.281	0.281	0.000	0.000	0.000	0.000
45	A	268	CYS	0	0.007	0.019	9.103	-0.016	-0.016	0.000	0.000	0.000	0.000
46	A	269	HIS	0	-0.003	0.015	3.058	1.349	2.818	0.431	-0.678	-1.223	0.004
47	A	270	ARG	1	0.868	0.928	5.746	-0.688	-0.688	0.000	0.000	0.000	0.000
48	A	271	ASP	-1	-0.752	-0.832	8.445	1.022	1.022	0.000	0.000	0.000	0.000
49	A	272	TRP	0	0.063	0.039	3.648	-0.810	-0.555	0.006	-0.052	-0.209	0.000
50	A	273	PRO	0	-0.003	-0.012	5.727	-0.245	-0.245	0.000	0.000	0.000	0.000
51	A	274	GLN	0	0.021	0.013	8.256	-0.474	-0.474	0.000	0.000	0.000	0.000
52	A	275	LEU	0	0.031	0.009	10.710	-0.196	-0.196	0.000	0.000	0.000	0.000
53	A	276	ILE	0	-0.018	0.003	7.906	-0.181	-0.181	0.000	0.000	0.000	0.000
54	A	277	GLN	0	0.018	0.017	11.328	-0.176	-0.176	0.000	0.000	0.000	0.000
55	A	278	ALA	0	0.048	0.017	14.055	-0.111	-0.111	0.000	0.000	0.000	0.000
56	A	279	SER	0	-0.042	-0.035	14.003	-0.085	-0.085	0.000	0.000	0.000	0.000
57	A	280	LYS	1	0.856	0.932	13.461	-0.728	-0.728	0.000	0.000	0.000	0.000
58	A	281	GLU	-1	-0.894	-0.932	17.676	0.356	0.356	0.000	0.000	0.000	0.000
59	A	282	VAL	0	-0.052	-0.029	19.936	-0.034	-0.034	0.000	0.000	0.000	0.000
60	A	283	ASP	-1	-0.870	-0.922	21.495	0.268	0.268	0.000	0.000	0.000	0.000
61	A	284	VAL	0	-0.063	-0.009	22.066	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	285	PRO	0	0.023	0.001	21.152	0.039	0.039	0.000	0.000	0.000	0.000
63	A	286	ILE	0	0.022	0.025	15.488	0.011	0.011	0.000	0.000	0.000	0.000
64	A	287	VAL	0	0.033	0.023	17.215	0.021	0.021	0.000	0.000	0.000	0.000
65	A	288	MET	0	-0.046	-0.015	10.866	0.083	0.083	0.000	0.000	0.000	0.000
66	A	289	PHE	0	0.024	0.006	15.782	-0.088	-0.088	0.000	0.000	0.000	0.000
67	A	290	ILE	0	-0.002	0.002	9.478	0.113	0.113	0.000	0.000	0.000	0.000
68	A	291	TRP	0	0.024	0.005	12.765	-0.117	-0.117	0.000	0.000	0.000	0.000
69	A	292	GLY	0	0.033	-0.011	11.584	0.117	0.117	0.000	0.000	0.000	0.000
70	A	293	SER	0	-0.007	-0.002	12.801	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	294	LEU	0	-0.022	0.001	13.422	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	295	ILE	0	-0.024	0.004	15.906	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	296	GLY	0	0.036	0.015	17.642	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	297	GLU	-1	-0.921	-0.971	21.357	0.041	0.041	0.000	0.000	0.000	0.000
75	A	298	ARG	1	0.965	0.976	24.351	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	299	GLU	-1	-0.788	-0.887	18.398	0.079	0.079	0.000	0.000	0.000	0.000
77	A	300	LEU	0	0.034	0.018	19.413	0.028	0.028	0.000	0.000	0.000	0.000
78	A	301	SER	0	-0.118	-0.068	21.652	0.013	0.013	0.000	0.000	0.000	0.000
79	A	302	ALA	0	0.021	0.009	23.634	0.005	0.005	0.000	0.000	0.000	0.000
80	A	303	ALA	0	0.074	0.030	20.138	0.009	0.009	0.000	0.000	0.000	0.000
81	A	304	ARG	1	0.973	0.986	22.125	-0.102	-0.102	0.000	0.000	0.000	0.000
82	A	305	LEU	0	-0.031	-0.005	24.056	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	306	GLU	-1	-0.779	-0.853	23.438	0.185	0.185	0.000	0.000	0.000	0.000
84	A	307	MET	0	-0.006	-0.009	19.761	0.009	0.009	0.000	0.000	0.000	0.000
85	A	308	ASN	0	-0.031	-0.012	23.800	0.007	0.007	0.000	0.000	0.000	0.000
86	A	309	LYS	1	0.818	0.899	27.413	-0.173	-0.173	0.000	0.000	0.000	0.000
87	A	310	ALA	0	0.013	0.020	24.684	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	311	GLY	0	0.014	0.006	26.256	0.011	0.011	0.000	0.000	0.000	0.000
89	A	312	VAL	0	-0.059	-0.036	20.028	0.013	0.013	0.000	0.000	0.000	0.000
90	A	313	GLU	-1	-0.810	-0.900	23.084	0.279	0.279	0.000	0.000	0.000	0.000
91	A	314	GLY	0	-0.027	-0.014	19.101	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	315	THR	0	-0.040	0.011	14.084	0.001	0.001	0.000	0.000	0.000	0.000
93	A	316	PRO	0	-0.021	-0.048	12.218	0.030	0.030	0.000	0.000	0.000	0.000
94	A	317	THR	0	0.000	-0.018	14.214	-0.055	-0.055	0.000	0.000	0.000	0.000
95	A	318	LEU	0	-0.045	-0.003	15.195	0.022	0.022	0.000	0.000	0.000	0.000
96	A	319	VAL	0	0.021	0.005	18.610	-0.033	-0.033	0.000	0.000	0.000	0.000
97	A	320	PHE	0	0.007	-0.002	20.866	0.016	0.016	0.000	0.000	0.000	0.000
98	A	321	TYR	0	-0.012	-0.040	23.678	-0.014	-0.014	0.000	0.000	0.000	0.000
99	A	322	LYS	1	0.907	0.954	26.673	-0.180	-0.180	0.000	0.000	0.000	0.000
100	A	323	GLU	-1	-0.850	-0.908	29.714	0.143	0.143	0.000	0.000	0.000	0.000
101	A	324	GLY	0	-0.001	0.024	30.234	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	325	ARG	1	0.750	0.856	31.158	-0.156	-0.156	0.000	0.000	0.000	0.000
103	A	326	ILE	0	-0.003	-0.002	26.732	0.011	0.011	0.000	0.000	0.000	0.000
104	A	327	VAL	0	-0.058	-0.035	27.895	-0.015	-0.015	0.000	0.000	0.000	0.000
105	A	328	ASP	-1	-0.785	-0.873	25.928	0.275	0.275	0.000	0.000	0.000	0.000
106	A	329	LYS	1	0.745	0.866	22.993	-0.267	-0.267	0.000	0.000	0.000	0.000
107	A	330	LEU	0	0.005	0.013	18.846	-0.008	-0.008	0.000	0.000	0.000	0.000
108	A	331	VAL	0	0.008	0.006	18.903	0.056	0.056	0.000	0.000	0.000	0.000
109	A	332	GLY	0	0.010	0.007	16.659	-0.024	-0.024	0.000	0.000	0.000	0.000
110	A	333	ALA	0	-0.071	-0.043	12.578	0.049	0.049	0.000	0.000	0.000	0.000
111	A	334	THR	0	0.010	0.005	14.192	-0.087	-0.087	0.000	0.000	0.000	0.000
112	A	335	PRO	0	0.000	-0.002	14.422	0.114	0.114	0.000	0.000	0.000	0.000
113	A	336	TRP	0	0.038	0.001	14.382	-0.024	-0.024	0.000	0.000	0.000	0.000
114	A	337	SER	0	-0.050	-0.019	16.061	-0.025	-0.025	0.000	0.000	0.000	0.000
115	A	338	LEU	0	0.066	0.035	19.505	-0.020	-0.020	0.000	0.000	0.000	0.000
116	A	339	LYS	1	0.784	0.875	13.264	-0.913	-0.913	0.000	0.000	0.000	0.000
117	A	340	VAL	0	0.013	0.013	18.763	-0.032	-0.032	0.000	0.000	0.000	0.000
118	A	341	GLU	-1	-0.904	-0.945	21.205	0.338	0.338	0.000	0.000	0.000	0.000
119	A	342	LYS	1	0.816	0.895	22.580	-0.311	-0.311	0.000	0.000	0.000	0.000
120	A	343	ALA	0	0.016	0.006	21.983	-0.022	-0.022	0.000	0.000	0.000	0.000
121	A	344	ARG	1	0.831	0.893	23.238	-0.357	-0.357	0.000	0.000	0.000	0.000
122	A	345	GLU	-1	-0.891	-0.918	26.829	0.243	0.243	0.000	0.000	0.000	0.000
123	A	346	ILE	0	-0.022	0.006	25.871	-0.019	-0.019	0.000	0.000	0.000	0.000
124	A	347	TYR	0	-0.100	-0.063	24.098	-0.020	-0.020	0.000	0.000	0.000	0.000

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