FMO DATABASE

FMODB ID: KG963

Calculation Name: 3JTE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JTE

Chain ID: A

ChEMBL ID:

UniProt ID: A3DCZ0

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1092240.988258
FMO2-HF: Nuclear repulsion	1042631.50137
FMO2-HF: Total energy	-49609.486888
FMO2-MP2: Total energy	-49751.347346

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:3:LEU)

Summations of interaction energy for fragment #1(A:3:LEU)

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.
-12.337	-5.276	2.213	-3.972	-5.303	-0.032

Interaction energy analysis for fragmet #1(A:3:LEU)

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 : -0.006

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

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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	5	LYS	1	0.870	0.946	3.475	-0.400	2.019	0.031	-1.254	-1.196	0.003
4	A	6	ILE	0	-0.004	-0.005	6.032	0.587	0.587	0.000	0.000	0.000	0.000
5	A	7	LEU	0	-0.029	-0.006	8.776	0.071	0.071	0.000	0.000	0.000	0.000
6	A	8	VAL	0	-0.002	0.001	12.134	0.068	0.068	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.032	-0.024	14.610	0.034	0.034	0.000	0.000	0.000	0.000
8	A	10	ASP	-1	-0.830	-0.952	18.384	-0.305	-0.305	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.880	-0.951	20.752	-0.245	-0.245	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.928	-0.952	23.348	-0.184	-0.184	0.000	0.000	0.000	0.000
11	A	13	SER	0	-0.036	-0.032	21.264	-0.015	-0.015	0.000	0.000	0.000	0.000
12	A	14	THR	0	0.008	0.001	20.088	-0.020	-0.020	0.000	0.000	0.000	0.000
13	A	15	ILE	0	0.022	0.018	19.554	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	16	LEU	0	0.004	0.010	16.700	-0.036	-0.036	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.040	-0.024	15.590	-0.069	-0.069	0.000	0.000	0.000	0.000
16	A	18	ASN	0	-0.030	-0.013	14.798	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	19	ILE	0	-0.005	-0.004	13.444	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.816	0.898	10.094	0.467	0.467	0.000	0.000	0.000	0.000
19	A	21	PHE	0	0.026	0.011	10.032	-0.089	-0.089	0.000	0.000	0.000	0.000
20	A	22	LEU	0	-0.026	-0.008	10.280	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	23	LEU	0	0.019	-0.002	8.521	0.004	0.004	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.789	-0.876	5.708	-0.926	-0.926	0.000	0.000	0.000	0.000
23	A	25	ILE	0	-0.083	-0.038	5.719	0.023	0.023	0.000	0.000	0.000	0.000
24	A	26	ASP	-1	-0.886	-0.909	7.826	-0.727	-0.727	0.000	0.000	0.000	0.000
25	A	27	GLY	0	-0.009	0.016	3.735	0.072	0.335	0.004	-0.073	-0.194	0.000
26	A	28	ASN	0	-0.111	-0.080	2.625	-7.229	-3.718	2.117	-2.513	-3.116	-0.034
27	A	29	GLU	-1	-0.900	-0.958	3.364	-2.147	-1.308	0.062	-0.126	-0.775	-0.001
28	A	30	VAL	0	-0.028	-0.022	4.670	-0.034	-0.005	-0.001	-0.006	-0.022	0.000
29	A	31	LEU	0	0.012	0.014	8.447	0.267	0.267	0.000	0.000	0.000	0.000
30	A	32	THR	0	-0.004	-0.015	11.223	0.006	0.006	0.000	0.000	0.000	0.000
31	A	33	ALA	0	-0.036	-0.017	14.724	0.035	0.035	0.000	0.000	0.000	0.000
32	A	34	SER	0	-0.008	-0.013	18.217	0.016	0.016	0.000	0.000	0.000	0.000
33	A	35	SER	0	0.039	0.001	21.602	0.031	0.031	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.075	0.010	22.095	-0.032	-0.032	0.000	0.000	0.000	0.000
35	A	37	THR	0	-0.034	-0.014	22.978	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.823	-0.875	19.501	-0.347	-0.347	0.000	0.000	0.000	0.000
37	A	39	GLY	0	0.055	0.018	18.411	-0.036	-0.036	0.000	0.000	0.000	0.000
38	A	40	LEU	0	0.009	0.002	18.521	-0.045	-0.045	0.000	0.000	0.000	0.000
39	A	41	ARG	1	0.808	0.927	19.547	0.343	0.343	0.000	0.000	0.000	0.000
40	A	42	ILE	0	0.054	0.022	14.607	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	43	PHE	0	0.040	0.007	14.951	-0.072	-0.072	0.000	0.000	0.000	0.000
42	A	44	THR	0	-0.022	-0.032	16.647	-0.026	-0.026	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.924	-0.974	17.266	-0.411	-0.411	0.000	0.000	0.000	0.000
44	A	46	ASN	0	-0.029	-0.011	12.176	-0.128	-0.128	0.000	0.000	0.000	0.000
45	A	47	CYS	0	-0.013	0.024	13.057	-0.139	-0.139	0.000	0.000	0.000	0.000
46	A	48	ASN	0	-0.019	-0.026	14.069	-0.046	-0.046	0.000	0.000	0.000	0.000
47	A	49	SER	0	-0.098	-0.056	9.233	-0.044	-0.044	0.000	0.000	0.000	0.000
48	A	50	ILE	0	0.036	0.035	8.621	-0.414	-0.414	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.836	-0.904	6.534	-2.736	-2.736	0.000	0.000	0.000	0.000
50	A	52	VAL	0	-0.022	-0.015	9.582	0.267	0.267	0.000	0.000	0.000	0.000
51	A	53	VAL	0	0.006	0.009	11.426	-0.093	-0.093	0.000	0.000	0.000	0.000
52	A	54	ILE	0	-0.005	0.000	11.849	0.067	0.067	0.000	0.000	0.000	0.000
53	A	55	THR	0	0.002	-0.005	15.647	0.004	0.004	0.000	0.000	0.000	0.000
54	A	56	ASP	-1	-0.750	-0.854	19.175	-0.260	-0.260	0.000	0.000	0.000	0.000
55	A	57	MET	0	-0.003	0.008	22.222	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	58	LYS	1	0.728	0.856	25.361	0.206	0.206	0.000	0.000	0.000	0.000
57	A	59	MET	0	0.048	0.046	22.742	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	60	PRO	0	0.011	0.005	26.618	0.015	0.015	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.887	0.943	28.379	0.164	0.164	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.015	-0.002	27.241	0.007	0.007	0.000	0.000	0.000	0.000
61	A	63	SER	0	0.027	0.009	26.945	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	64	GLY	0	0.045	0.014	23.651	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	65	MET	0	-0.002	0.000	24.081	-0.023	-0.023	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.829	-0.884	26.621	-0.224	-0.224	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.002	0.000	20.780	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	68	LEU	0	0.001	0.007	21.871	-0.027	-0.027	0.000	0.000	0.000	0.000
67	A	69	ARG	1	0.796	0.854	23.150	0.207	0.207	0.000	0.000	0.000	0.000
68	A	70	GLU	-1	-0.828	-0.886	24.360	-0.247	-0.247	0.000	0.000	0.000	0.000
69	A	71	ILE	0	0.023	0.012	18.272	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.754	0.877	20.031	0.395	0.395	0.000	0.000	0.000	0.000
71	A	73	LYS	1	0.782	0.856	23.389	0.265	0.265	0.000	0.000	0.000	0.000
72	A	74	ILE	0	-0.036	0.002	20.297	0.012	0.012	0.000	0.000	0.000	0.000
73	A	75	THR	0	-0.027	-0.022	17.374	-0.026	-0.026	0.000	0.000	0.000	0.000
74	A	76	PRO	0	0.039	0.025	20.122	-0.026	-0.026	0.000	0.000	0.000	0.000
75	A	77	HIS	0	0.000	-0.005	18.474	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	78	MET	0	-0.013	0.021	13.548	-0.045	-0.045	0.000	0.000	0.000	0.000
77	A	79	ALA	0	0.021	0.019	13.988	0.083	0.083	0.000	0.000	0.000	0.000
78	A	80	VAL	0	0.012	-0.002	15.309	-0.068	-0.068	0.000	0.000	0.000	0.000
79	A	81	ILE	0	0.015	0.016	13.844	0.065	0.065	0.000	0.000	0.000	0.000
80	A	82	ILE	0	-0.007	-0.015	17.701	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.027	0.014	17.542	0.026	0.026	0.000	0.000	0.000	0.000
82	A	84	THR	0	-0.020	-0.018	21.344	0.017	0.017	0.000	0.000	0.000	0.000
83	A	85	GLY	0	0.027	-0.002	25.142	0.003	0.003	0.000	0.000	0.000	0.000
84	A	86	HIS	0	0.011	0.000	28.251	0.000	0.000	0.000	0.000	0.000	0.000
85	A	87	GLY	0	0.019	0.007	31.907	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.754	-0.860	28.031	-0.206	-0.206	0.000	0.000	0.000	0.000
87	A	89	LEU	0	-0.014	0.002	29.580	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	90	ASP	-1	-0.854	-0.937	30.652	-0.144	-0.144	0.000	0.000	0.000	0.000
89	A	91	ASN	0	-0.002	-0.003	29.558	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.037	0.016	26.330	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.014	-0.010	27.388	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	94	LEU	0	-0.032	-0.007	29.995	0.005	0.005	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.073	0.026	24.947	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	96	MET	0	-0.050	-0.019	22.784	-0.018	-0.018	0.000	0.000	0.000	0.000
95	A	97	LYS	1	0.828	0.917	26.294	0.171	0.171	0.000	0.000	0.000	0.000
96	A	98	GLU	-1	-0.808	-0.870	27.522	-0.210	-0.210	0.000	0.000	0.000	0.000
97	A	99	GLY	0	0.011	0.013	24.623	-0.012	-0.012	0.000	0.000	0.000	0.000
98	A	100	ALA	0	-0.006	-0.012	21.403	-0.037	-0.037	0.000	0.000	0.000	0.000
99	A	101	PHE	0	-0.077	-0.029	16.618	0.004	0.004	0.000	0.000	0.000	0.000
100	A	102	GLU	-1	-0.856	-0.947	18.108	-0.325	-0.325	0.000	0.000	0.000	0.000
101	A	103	TYR	0	-0.007	-0.018	20.330	-0.015	-0.015	0.000	0.000	0.000	0.000
102	A	104	LEU	0	-0.014	0.007	17.223	0.021	0.021	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.933	0.971	21.650	0.154	0.154	0.000	0.000	0.000	0.000
104	A	106	LYS	1	0.906	0.951	22.712	0.262	0.262	0.000	0.000	0.000	0.000
105	A	107	PRO	0	-0.063	-0.035	24.024	0.014	0.014	0.000	0.000	0.000	0.000
106	A	108	VAL	0	0.038	0.017	18.661	0.009	0.009	0.000	0.000	0.000	0.000
107	A	109	THR	0	-0.038	-0.051	19.297	0.003	0.003	0.000	0.000	0.000	0.000
108	A	110	ALA	0	0.041	0.000	14.072	-0.030	-0.030	0.000	0.000	0.000	0.000
109	A	111	GLN	0	-0.020	-0.001	14.408	-0.024	-0.024	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.807	-0.882	15.631	-0.245	-0.245	0.000	0.000	0.000	0.000
111	A	113	LEU	0	0.006	0.000	13.130	-0.019	-0.019	0.000	0.000	0.000	0.000
112	A	114	SER	0	-0.012	-0.016	10.341	-0.051	-0.051	0.000	0.000	0.000	0.000
113	A	115	ILE	0	-0.018	-0.014	11.983	-0.038	-0.038	0.000	0.000	0.000	0.000
114	A	116	ALA	0	0.028	0.021	14.475	-0.018	-0.018	0.000	0.000	0.000	0.000
115	A	117	ILE	0	0.019	0.005	8.268	-0.023	-0.023	0.000	0.000	0.000	0.000
116	A	118	ASN	0	-0.014	-0.003	10.221	-0.054	-0.054	0.000	0.000	0.000	0.000
117	A	119	ASN	0	-0.034	-0.023	11.254	0.040	0.040	0.000	0.000	0.000	0.000
118	A	120	ALA	0	-0.017	-0.002	12.448	0.030	0.030	0.000	0.000	0.000	0.000
119	A	121	ILE	0	0.017	0.003	6.525	0.007	0.007	0.000	0.000	0.000	0.000
120	A	122	ASN	0	-0.018	-0.008	10.283	0.085	0.085	0.000	0.000	0.000	0.000
121	A	123	ARG	1	0.902	0.951	12.790	0.432	0.432	0.000	0.000	0.000	0.000
122	A	124	LYS	1	0.814	0.884	9.364	1.495	1.495	0.000	0.000	0.000	0.000
123	A	125	LYS	1	0.957	0.956	7.333	0.546	0.546	0.000	0.000	0.000	0.000
124	A	126	LEU	0	-0.044	-0.018	12.850	0.068	0.068	0.000	0.000	0.000	0.000
125	A	127	LEU	0	-0.049	-0.012	15.781	0.042	0.042	0.000	0.000	0.000	0.000
126	A	128	MET	0	-0.071	-0.007	9.303	0.046	0.046	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)