FMO DATABASE

FMODB ID: 6644Z

Calculation Name: 3EMF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EMF

Chain ID: A

ChEMBL ID:

UniProt ID: Q48152

Base Structure: X-ray

Registration Date: 2023-03-14

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	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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-729605.74108
FMO2-HF: Nuclear repulsion	687207.428164
FMO2-HF: Total energy	-42398.312916
FMO2-MP2: Total energy	-42524.549691

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:53:THR)

Summations of interaction energy for fragment #1(A:53:THR)

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.
0.655	2.837	0.135	-0.747	-1.571	0

Interaction energy analysis for fragmet #1(A:53:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.009

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].
3	A	55	VAL	0	0.013	0.012	3.110	-0.950	1.171	0.135	-0.733	-1.523
4	A	56	THR	0	-0.040	-0.026	4.317	0.612	0.673	0.000	-0.014	-0.048
5	A	57	ASN	0	0.007	-0.025	7.757	0.107	0.107	0.000	0.000	0.000
6	A	58	LYS	1	0.972	0.975	10.916	0.241	0.241	0.000	0.000	0.000
7	A	59	LEU	0	-0.006	0.019	14.439	0.048	0.048	0.000	0.000	0.000
8	A	60	LYS	1	0.898	0.971	16.452	0.167	0.167	0.000	0.000	0.000
9	A	61	ALA	0	-0.031	-0.015	19.235	-0.022	-0.022	0.000	0.000	0.000
10	A	62	TYR	0	0.030	0.000	21.667	0.018	0.018	0.000	0.000	0.000
11	A	63	GLY	0	0.018	0.001	25.340	-0.003	-0.003	0.000	0.000	0.000
12	A	64	ASP	-1	-0.927	-0.962	21.373	-0.147	-0.147	0.000	0.000	0.000
13	A	65	ALA	0	0.030	0.011	24.781	0.005	0.005	0.000	0.000	0.000
14	A	66	ASN	0	-0.062	-0.025	22.481	-0.003	-0.003	0.000	0.000	0.000
15	A	67	PHE	0	0.033	0.041	25.341	-0.003	-0.003	0.000	0.000	0.000
16	A	68	ASN	0	-0.016	-0.016	26.236	0.012	0.012	0.000	0.000	0.000
17	A	69	PHE	0	0.054	-0.002	28.663	-0.005	-0.005	0.000	0.000	0.000
18	A	70	THR	0	-0.021	0.005	31.746	0.000	0.000	0.000	0.000	0.000
19	A	71	ASN	0	-0.020	-0.010	27.215	0.008	0.008	0.000	0.000	0.000
20	A	72	ASN	0	-0.012	0.006	26.535	-0.020	-0.020	0.000	0.000	0.000
21	A	73	SER	0	0.023	-0.002	30.087	0.010	0.010	0.000	0.000	0.000
22	A	74	ILE	0	0.068	0.010	32.596	-0.002	-0.002	0.000	0.000	0.000
23	A	75	ALA	0	0.052	0.037	32.587	0.000	0.000	0.000	0.000	0.000
24	A	76	ASP	-1	-0.822	-0.886	28.321	-0.166	-0.166	0.000	0.000	0.000
25	A	77	ALA	0	0.012	0.007	30.247	-0.003	-0.003	0.000	0.000	0.000
26	A	78	GLU	-1	-0.900	-0.962	32.250	-0.097	-0.097	0.000	0.000	0.000
27	A	79	LYS	1	0.841	0.935	28.166	0.170	0.170	0.000	0.000	0.000
28	A	80	GLN	0	-0.020	-0.007	27.122	-0.014	-0.014	0.000	0.000	0.000
29	A	81	VAL	0	-0.044	-0.022	29.668	0.002	0.002	0.000	0.000	0.000
30	A	82	GLN	0	-0.029	-0.009	32.280	0.007	0.007	0.000	0.000	0.000
31	A	83	GLU	-1	-0.785	-0.897	31.437	-0.107	-0.107	0.000	0.000	0.000
32	A	84	ALA	0	-0.013	-0.001	31.125	-0.007	-0.007	0.000	0.000	0.000
33	A	85	TYR	0	0.053	0.016	28.311	-0.014	-0.014	0.000	0.000	0.000
34	A	86	LYS	1	0.821	0.922	26.887	0.086	0.086	0.000	0.000	0.000
35	A	87	GLY	0	-0.028	-0.005	23.421	0.000	0.000	0.000	0.000	0.000
36	A	88	LEU	0	-0.033	-0.009	22.432	-0.029	-0.029	0.000	0.000	0.000
37	A	89	LEU	0	-0.067	-0.042	16.889	-0.001	-0.001	0.000	0.000	0.000
38	A	90	ASN	0	0.019	0.005	20.732	0.015	0.015	0.000	0.000	0.000
39	A	91	LEU	0	-0.015	-0.023	18.647	-0.016	-0.016	0.000	0.000	0.000
40	A	92	ASN	0	-0.038	-0.028	21.267	-0.007	-0.007	0.000	0.000	0.000
41	A	93	GLU	-1	-0.859	-0.923	21.677	-0.172	-0.172	0.000	0.000	0.000
42	A	94	LYS	1	0.911	0.969	22.733	0.152	0.152	0.000	0.000	0.000
43	A	95	ASN	0	-0.005	-0.030	22.540	0.014	0.014	0.000	0.000	0.000
44	A	96	ALA	0	0.028	0.003	25.575	0.003	0.003	0.000	0.000	0.000
45	A	97	SER	0	-0.076	-0.038	27.010	0.004	0.004	0.000	0.000	0.000
46	A	98	ASP	-1	-0.874	-0.928	28.526	-0.123	-0.123	0.000	0.000	0.000
47	A	99	LYS	1	0.844	0.929	21.268	0.152	0.152	0.000	0.000	0.000
48	A	100	LEU	0	0.006	-0.002	21.035	0.008	0.008	0.000	0.000	0.000
49	A	101	LEU	0	-0.064	-0.031	19.079	0.003	0.003	0.000	0.000	0.000
50	A	102	VAL	0	-0.060	-0.034	14.592	-0.013	-0.013	0.000	0.000	0.000
51	A	103	GLU	-1	-0.815	-0.901	16.747	-0.227	-0.227	0.000	0.000	0.000
52	A	104	ASP	-1	-0.860	-0.918	16.288	-0.344	-0.344	0.000	0.000	0.000
53	A	105	ASN	0	-0.088	-0.028	15.004	-0.070	-0.070	0.000	0.000	0.000
54	A	106	THR	0	-0.038	-0.033	11.240	-0.007	-0.007	0.000	0.000	0.000
55	A	107	ALA	0	-0.008	-0.002	8.038	-0.026	-0.026	0.000	0.000	0.000
56	A	108	ALA	0	0.052	0.036	9.954	0.056	0.056	0.000	0.000	0.000
57	A	109	THR	0	-0.003	-0.021	8.122	-0.212	-0.212	0.000	0.000	0.000
58	A	110	VAL	0	0.060	0.006	9.549	0.204	0.204	0.000	0.000	0.000
59	A	111	GLY	0	-0.009	-0.009	11.744	0.167	0.167	0.000	0.000	0.000
60	A	112	ASN	0	0.023	0.029	12.666	-0.002	-0.002	0.000	0.000	0.000
61	A	113	LEU	0	0.084	0.043	14.011	0.079	0.079	0.000	0.000	0.000
62	A	114	ARG	1	0.924	0.973	13.008	0.552	0.552	0.000	0.000	0.000
63	A	115	LYS	1	0.916	0.963	16.049	0.457	0.457	0.000	0.000	0.000
64	A	116	LEU	0	0.010	0.025	18.434	0.024	0.024	0.000	0.000	0.000
65	A	117	GLY	0	0.044	0.009	21.592	0.009	0.009	0.000	0.000	0.000
66	A	118	TRP	0	-0.027	0.005	25.289	0.005	0.005	0.000	0.000	0.000
67	A	119	VAL	0	0.019	0.007	28.790	0.003	0.003	0.000	0.000	0.000
68	A	120	LEU	0	0.000	0.020	31.739	0.004	0.004	0.000	0.000	0.000
69	A	121	SER	0	0.037	-0.007	34.794	0.002	0.002	0.000	0.000	0.000
70	A	122	SER	0	-0.067	-0.012	38.093	0.003	0.003	0.000	0.000	0.000
71	A	123	LYS	1	0.953	0.959	41.750	0.072	0.072	0.000	0.000	0.000
72	A	124	ASN	0	-0.002	0.004	44.681	0.003	0.003	0.000	0.000	0.000
73	A	125	GLY	0	0.049	0.008	48.234	0.002	0.002	0.000	0.000	0.000
74	A	126	THR	0	0.031	0.000	49.536	-0.002	-0.002	0.000	0.000	0.000
75	A	127	ARG	1	0.910	0.974	47.771	0.054	0.054	0.000	0.000	0.000
76	A	128	ASN	0	0.032	0.015	43.529	-0.002	-0.002	0.000	0.000	0.000
77	A	129	GLU	-1	-0.885	-0.925	39.103	-0.097	-0.097	0.000	0.000	0.000
78	A	130	LYS	1	0.843	0.936	36.913	0.097	0.097	0.000	0.000	0.000
79	A	131	SER	0	0.014	-0.011	35.061	-0.001	-0.001	0.000	0.000	0.000
80	A	132	GLN	0	0.009	-0.001	33.040	0.010	0.010	0.000	0.000	0.000
81	A	133	GLN	0	-0.050	-0.043	26.812	-0.015	-0.015	0.000	0.000	0.000
82	A	134	VAL	0	0.005	0.015	28.767	0.004	0.004	0.000	0.000	0.000
83	A	135	LYS	1	0.890	0.928	21.959	0.240	0.240	0.000	0.000	0.000
84	A	136	HIS	0	0.006	-0.013	20.548	0.009	0.009	0.000	0.000	0.000
85	A	137	ALA	0	-0.079	-0.042	23.445	0.003	0.003	0.000	0.000	0.000
86	A	138	ASP	-1	-0.820	-0.877	25.233	-0.178	-0.178	0.000	0.000	0.000
87	A	139	GLU	-1	-0.968	-0.986	28.137	-0.131	-0.131	0.000	0.000	0.000
88	A	140	VAL	0	-0.064	-0.034	31.671	0.006	0.006	0.000	0.000	0.000
89	A	141	LEU	0	0.019	0.019	34.652	0.001	0.001	0.000	0.000	0.000
90	A	142	PHE	0	-0.030	-0.024	37.292	0.003	0.003	0.000	0.000	0.000
91	A	143	GLU	-1	-0.807	-0.886	41.119	-0.073	-0.073	0.000	0.000	0.000
92	A	144	GLY	0	-0.012	0.000	44.056	0.001	0.001	0.000	0.000	0.000
93	A	145	LYS	1	0.876	0.901	45.594	0.070	0.070	0.000	0.000	0.000
94	A	146	GLY	0	-0.014	-0.009	50.419	0.000	0.000	0.000	0.000	0.000
95	A	147	GLY	0	0.026	0.015	53.717	0.001	0.001	0.000	0.000	0.000
96	A	148	VAL	0	-0.041	0.008	49.571	0.000	0.000	0.000	0.000	0.000
97	A	149	GLN	0	-0.013	-0.007	50.210	-0.002	-0.002	0.000	0.000	0.000
98	A	150	VAL	0	0.022	0.003	43.921	-0.001	-0.001	0.000	0.000	0.000
99	A	151	THR	0	0.006	0.010	45.507	0.000	0.000	0.000	0.000	0.000
100	A	152	SER	0	-0.009	-0.015	40.830	-0.004	-0.004	0.000	0.000	0.000
101	A	153	THR	0	0.009	0.013	42.054	0.002	0.002	0.000	0.000	0.000
102	A	154	SER	0	-0.004	-0.013	37.220	-0.008	-0.008	0.000	0.000	0.000
103	A	155	GLU	-1	-0.873	-0.922	38.516	-0.113	-0.113	0.000	0.000	0.000
104	A	156	ASN	0	-0.023	-0.015	35.532	-0.007	-0.007	0.000	0.000	0.000
105	A	157	GLY	0	0.000	0.010	33.250	-0.003	-0.003	0.000	0.000	0.000
106	A	158	LYS	1	0.919	0.975	33.913	0.113	0.113	0.000	0.000	0.000
107	A	159	HIS	0	-0.016	-0.026	33.816	-0.002	-0.002	0.000	0.000	0.000
108	A	160	THR	0	-0.028	-0.025	37.980	0.000	0.000	0.000	0.000	0.000
109	A	161	ILE	0	0.011	0.014	38.919	0.002	0.002	0.000	0.000	0.000
110	A	162	THR	0	-0.016	-0.006	42.605	0.001	0.001	0.000	0.000	0.000
111	A	163	PHE	0	-0.007	-0.009	43.103	0.001	0.001	0.000	0.000	0.000
112	A	164	ALA	0	0.018	0.015	48.647	0.002	0.002	0.000	0.000	0.000
113	A	165	LEU	0	-0.020	-0.022	52.328	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:53:THR)