FMO DATABASE

FMODB ID: R89J8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1088365.267255
FMO2-HF: Nuclear repulsion	1038756.565723
FMO2-HF: Total energy	-49608.701532
FMO2-MP2: Total energy	-49750.641616

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.
-13.214	-6.292	1.197	-3.598	-4.522	-0.022

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 : -0.011 / 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

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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	0.919	0.962	3.619	0.055	2.419	0.011	-1.182	-1.193	0.005
4	A	6	ILE	0	-0.012	-0.015	5.955	0.719	0.719	0.000	0.000	0.000	0.000
5	A	7	LEU	0	-0.016	0.006	8.853	0.082	0.082	0.000	0.000	0.000	0.000
6	A	8	VAL	0	-0.014	-0.019	11.960	0.081	0.081	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.030	-0.033	14.499	0.038	0.038	0.000	0.000	0.000	0.000
8	A	10	ASP	-1	-0.797	-0.924	18.265	-0.352	-0.352	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.889	-0.951	20.859	-0.297	-0.297	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.963	-0.971	23.173	-0.230	-0.230	0.000	0.000	0.000	0.000
11	A	13	SER	0	-0.010	-0.022	21.325	-0.030	-0.030	0.000	0.000	0.000	0.000
12	A	14	THR	0	0.027	0.004	20.231	-0.022	-0.022	0.000	0.000	0.000	0.000
13	A	15	ILE	0	0.011	0.026	19.745	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	16	LEU	0	-0.001	-0.005	16.570	-0.042	-0.042	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.050	-0.028	15.796	-0.074	-0.074	0.000	0.000	0.000	0.000
16	A	18	ASN	0	-0.016	-0.009	15.209	-0.020	-0.020	0.000	0.000	0.000	0.000
17	A	19	ILE	0	0.005	0.001	13.443	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.892	0.949	10.577	0.671	0.671	0.000	0.000	0.000	0.000
19	A	21	PHE	0	0.015	0.008	10.262	-0.101	-0.101	0.000	0.000	0.000	0.000
20	A	22	LEU	0	-0.011	-0.007	10.584	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	23	LEU	0	-0.001	-0.015	8.493	0.000	0.000	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.858	-0.920	5.965	-1.139	-1.139	0.000	0.000	0.000	0.000
23	A	25	ILE	0	-0.081	-0.028	5.793	0.012	0.012	0.000	0.000	0.000	0.000
24	A	26	ASP	-1	-0.930	-0.961	7.739	-0.693	-0.693	0.000	0.000	0.000	0.000
25	A	27	GLY	0	-0.009	0.016	3.556	0.038	0.271	0.008	-0.056	-0.185	0.000
26	A	28	ASN	0	-0.103	-0.057	2.733	-6.814	-3.301	1.141	-2.211	-2.443	-0.027
27	A	29	GLU	-1	-0.902	-0.953	3.165	-3.160	-2.368	0.038	-0.141	-0.690	0.000
28	A	30	VAL	0	-0.026	-0.026	4.643	0.043	0.063	-0.001	-0.008	-0.011	0.000
29	A	31	LEU	0	-0.012	-0.004	8.371	0.228	0.228	0.000	0.000	0.000	0.000
30	A	32	THR	0	-0.002	-0.009	11.276	0.014	0.014	0.000	0.000	0.000	0.000
31	A	33	ALA	0	-0.022	-0.005	14.739	0.033	0.033	0.000	0.000	0.000	0.000
32	A	34	SER	0	0.006	0.009	18.223	0.016	0.016	0.000	0.000	0.000	0.000
33	A	35	SER	0	0.022	0.000	21.512	0.043	0.043	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.083	0.010	22.011	-0.038	-0.038	0.000	0.000	0.000	0.000
35	A	37	THR	0	-0.021	-0.004	22.879	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.934	-0.966	19.425	-0.445	-0.445	0.000	0.000	0.000	0.000
37	A	39	GLY	0	0.056	0.017	18.396	-0.039	-0.039	0.000	0.000	0.000	0.000
38	A	40	LEU	0	0.029	0.007	18.399	-0.052	-0.052	0.000	0.000	0.000	0.000
39	A	41	ARG	1	0.925	0.995	20.460	0.370	0.370	0.000	0.000	0.000	0.000
40	A	42	ILE	0	0.060	0.025	14.542	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	43	PHE	0	0.027	-0.006	15.074	-0.069	-0.069	0.000	0.000	0.000	0.000
42	A	44	THR	0	-0.026	-0.035	16.596	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.988	-0.996	17.170	-0.456	-0.456	0.000	0.000	0.000	0.000
44	A	46	ASN	0	-0.077	-0.034	12.091	-0.051	-0.051	0.000	0.000	0.000	0.000
45	A	47	CYS	0	-0.011	0.010	12.766	-0.155	-0.155	0.000	0.000	0.000	0.000
46	A	48	ASN	0	0.030	0.000	13.051	-0.030	-0.030	0.000	0.000	0.000	0.000
47	A	49	SER	0	-0.089	-0.033	8.355	-0.048	-0.048	0.000	0.000	0.000	0.000
48	A	50	ILE	0	-0.004	0.019	7.955	-0.539	-0.539	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.847	-0.913	6.192	-3.025	-3.025	0.000	0.000	0.000	0.000
50	A	52	VAL	0	-0.021	-0.010	9.586	0.316	0.316	0.000	0.000	0.000	0.000
51	A	53	VAL	0	0.006	0.014	11.535	-0.108	-0.108	0.000	0.000	0.000	0.000
52	A	54	ILE	0	0.001	0.006	12.052	0.091	0.091	0.000	0.000	0.000	0.000
53	A	55	THR	0	0.009	-0.005	15.544	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	56	ASP	-1	-0.705	-0.808	19.000	-0.296	-0.296	0.000	0.000	0.000	0.000
55	A	57	MET	0	-0.021	-0.011	21.976	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	58	LYS	1	0.837	0.931	24.951	0.232	0.232	0.000	0.000	0.000	0.000
57	A	59	MET	0	0.046	0.042	22.772	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	60	PRO	0	0.013	0.007	26.701	0.019	0.019	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.876	0.945	28.481	0.198	0.198	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.005	0.001	26.625	0.007	0.007	0.000	0.000	0.000	0.000
61	A	63	SER	0	0.037	0.032	26.829	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	64	GLY	0	0.070	0.019	23.754	-0.016	-0.016	0.000	0.000	0.000	0.000
63	A	65	MET	0	-0.012	-0.002	24.242	-0.020	-0.020	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.872	-0.936	26.702	-0.245	-0.245	0.000	0.000	0.000	0.000
65	A	67	ILE	0	-0.004	-0.004	20.905	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.009	0.000	21.781	-0.024	-0.024	0.000	0.000	0.000	0.000
67	A	69	ARG	1	0.884	0.936	23.181	0.226	0.226	0.000	0.000	0.000	0.000
68	A	70	GLU	-1	-0.921	-0.966	24.326	-0.276	-0.276	0.000	0.000	0.000	0.000
69	A	71	ILE	0	0.008	0.011	18.159	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.830	0.936	20.573	0.386	0.386	0.000	0.000	0.000	0.000
71	A	73	LYS	1	0.920	0.959	22.771	0.261	0.261	0.000	0.000	0.000	0.000
72	A	74	ILE	0	-0.010	0.019	19.760	0.017	0.017	0.000	0.000	0.000	0.000
73	A	75	THR	0	-0.008	-0.007	16.356	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	76	PRO	0	0.024	0.009	19.372	-0.026	-0.026	0.000	0.000	0.000	0.000
75	A	77	HIS	0	-0.058	-0.045	17.703	0.009	0.009	0.000	0.000	0.000	0.000
76	A	78	MET	0	-0.029	0.018	13.328	-0.048	-0.048	0.000	0.000	0.000	0.000
77	A	79	ALA	0	-0.014	0.001	13.858	0.083	0.083	0.000	0.000	0.000	0.000
78	A	80	VAL	0	0.019	0.006	15.193	-0.083	-0.083	0.000	0.000	0.000	0.000
79	A	81	ILE	0	0.011	0.004	13.872	0.067	0.067	0.000	0.000	0.000	0.000
80	A	82	ILE	0	0.002	-0.006	17.633	-0.018	-0.018	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.015	0.017	17.559	0.031	0.031	0.000	0.000	0.000	0.000
82	A	84	THR	0	-0.030	-0.028	21.309	0.015	0.015	0.000	0.000	0.000	0.000
83	A	85	GLY	0	0.012	-0.005	25.089	0.003	0.003	0.000	0.000	0.000	0.000
84	A	86	HIS	0	-0.005	-0.018	27.927	0.003	0.003	0.000	0.000	0.000	0.000
85	A	87	GLY	0	-0.014	-0.008	31.723	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.785	-0.890	28.282	-0.229	-0.229	0.000	0.000	0.000	0.000
87	A	89	LEU	0	-0.022	-0.008	29.634	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	90	ASP	-1	-0.868	-0.938	30.738	-0.152	-0.152	0.000	0.000	0.000	0.000
89	A	91	ASN	0	0.024	-0.003	29.429	0.004	0.004	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.006	0.001	26.385	-0.014	-0.014	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.009	-0.008	27.107	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	94	LEU	0	-0.026	-0.015	29.380	0.000	0.000	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.077	0.019	24.990	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	96	MET	0	-0.039	-0.005	23.023	-0.019	-0.019	0.000	0.000	0.000	0.000
95	A	97	LYS	1	0.860	0.940	26.148	0.168	0.168	0.000	0.000	0.000	0.000
96	A	98	GLU	-1	-0.911	-0.949	26.922	-0.208	-0.208	0.000	0.000	0.000	0.000
97	A	99	GLY	0	-0.046	-0.015	24.358	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	100	ALA	0	-0.034	-0.022	21.463	-0.037	-0.037	0.000	0.000	0.000	0.000
99	A	101	PHE	0	-0.071	-0.033	16.188	0.017	0.017	0.000	0.000	0.000	0.000
100	A	102	GLU	-1	-0.891	-0.966	18.535	-0.321	-0.321	0.000	0.000	0.000	0.000
101	A	103	TYR	0	-0.006	-0.006	20.197	-0.024	-0.024	0.000	0.000	0.000	0.000
102	A	104	LEU	0	0.007	0.008	16.984	0.019	0.019	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.925	0.965	21.547	0.175	0.175	0.000	0.000	0.000	0.000
104	A	106	LYS	1	0.829	0.910	23.004	0.294	0.294	0.000	0.000	0.000	0.000
105	A	107	PRO	0	-0.046	-0.040	23.985	0.018	0.018	0.000	0.000	0.000	0.000
106	A	108	VAL	0	0.052	0.026	17.900	0.011	0.011	0.000	0.000	0.000	0.000
107	A	109	THR	0	-0.048	-0.029	19.388	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	110	ALA	0	0.060	0.009	14.359	-0.032	-0.032	0.000	0.000	0.000	0.000
109	A	111	GLN	0	-0.003	0.004	14.631	-0.022	-0.022	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.820	-0.907	16.001	-0.273	-0.273	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.004	-0.013	12.924	-0.016	-0.016	0.000	0.000	0.000	0.000
112	A	114	SER	0	-0.007	-0.004	10.400	-0.045	-0.045	0.000	0.000	0.000	0.000
113	A	115	ILE	0	-0.027	-0.011	11.934	-0.010	-0.010	0.000	0.000	0.000	0.000
114	A	116	ALA	0	0.027	0.014	14.331	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	117	ILE	0	0.024	0.004	8.138	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	118	ASN	0	0.017	0.015	9.956	-0.076	-0.076	0.000	0.000	0.000	0.000
117	A	119	ASN	0	-0.025	-0.018	11.014	0.086	0.086	0.000	0.000	0.000	0.000
118	A	120	ALA	0	-0.023	-0.006	12.078	0.042	0.042	0.000	0.000	0.000	0.000
119	A	121	ILE	0	0.022	0.006	6.105	0.032	0.032	0.000	0.000	0.000	0.000
120	A	122	ASN	0	-0.017	-0.008	10.006	0.153	0.153	0.000	0.000	0.000	0.000
121	A	123	ARG	1	0.965	0.980	12.455	0.402	0.402	0.000	0.000	0.000	0.000
122	A	124	LYS	1	0.875	0.925	8.950	1.460	1.460	0.000	0.000	0.000	0.000
123	A	125	LYS	1	0.929	0.948	7.020	0.090	0.090	0.000	0.000	0.000	0.000
124	A	126	LEU	0	-0.046	-0.011	12.659	0.066	0.066	0.000	0.000	0.000	0.000
125	A	127	LEU	0	-0.048	-0.022	15.683	0.029	0.029	0.000	0.000	0.000	0.000
126	A	128	MET	0	-0.069	0.000	8.959	0.062	0.062	0.000	0.000	0.000	0.000

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