FMO DATABASE

FMODB ID: YVJJ2

Calculation Name: 3LEQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LEQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q82L23

Base Structure: X-ray

Registration Date: 2023-09-23

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-710624.783378
FMO2-HF: Nuclear repulsion	672525.646773
FMO2-HF: Total energy	-38099.136605
FMO2-MP2: Total energy	-38209.325082

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:9:HIS)

Summations of interaction energy for fragment #1(A:9:HIS)

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.
-4.511	1.819	3.217	-3.432	-6.114	0.003

Interaction energy analysis for fragmet #1(A:9:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.008

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	11	GLN	0	0.044	-0.008	3.710	-1.741	-0.164	-0.010	-0.754	-0.813	0.004
4	A	12	LEU	0	0.030	0.010	6.354	-0.040	-0.040	0.000	0.000	0.000	0.000
5	A	13	ASP	-1	-0.697	-0.827	2.762	4.856	7.704	0.534	-1.431	-1.950	-0.012
6	A	14	GLN	0	-0.045	-0.005	3.043	-1.968	-1.135	0.066	-0.210	-0.689	-0.001
7	A	15	LEU	0	-0.026	-0.007	4.995	-0.259	-0.218	-0.001	-0.003	-0.038	0.000
8	A	16	LEU	0	-0.015	0.007	7.790	-0.250	-0.250	0.000	0.000	0.000	0.000
9	A	17	THR	0	0.006	-0.036	5.558	0.077	0.077	0.000	0.000	0.000	0.000
10	A	18	GLY	0	0.025	0.029	8.080	-0.323	-0.323	0.000	0.000	0.000	0.000
11	A	19	LEU	0	-0.083	-0.051	10.217	-0.125	-0.125	0.000	0.000	0.000	0.000
12	A	20	VAL	0	-0.029	-0.020	11.375	-0.060	-0.060	0.000	0.000	0.000	0.000
13	A	21	ASP	-1	-0.910	-0.944	11.245	-0.341	-0.341	0.000	0.000	0.000	0.000
14	A	22	ARG	1	0.818	0.918	13.369	-0.183	-0.183	0.000	0.000	0.000	0.000
15	A	23	VAL	0	-0.041	-0.016	15.884	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	24	ALA	0	0.089	0.053	17.919	0.014	0.014	0.000	0.000	0.000	0.000
17	A	25	GLU	-1	-0.949	-0.989	20.152	0.036	0.036	0.000	0.000	0.000	0.000
18	A	26	VAL	0	-0.051	-0.031	15.270	0.027	0.027	0.000	0.000	0.000	0.000
19	A	27	ASP	-1	-0.822	-0.901	15.846	0.021	0.021	0.000	0.000	0.000	0.000
20	A	28	HIS	1	0.801	0.885	11.832	-0.180	-0.180	0.000	0.000	0.000	0.000
21	A	29	ALA	0	0.044	0.023	11.653	-0.067	-0.067	0.000	0.000	0.000	0.000
22	A	30	VAL	0	-0.003	-0.006	10.887	0.257	0.257	0.000	0.000	0.000	0.000
23	A	31	VAL	0	0.012	0.004	11.597	-0.177	-0.177	0.000	0.000	0.000	0.000
24	A	32	LEU	0	-0.030	-0.008	12.736	0.172	0.172	0.000	0.000	0.000	0.000
25	A	33	SER	0	0.002	-0.038	15.470	-0.038	-0.038	0.000	0.000	0.000	0.000
26	A	34	GLU	-1	-0.913	-0.957	16.959	0.402	0.402	0.000	0.000	0.000	0.000
27	A	35	ASP	-1	-0.889	-0.913	19.047	0.618	0.618	0.000	0.000	0.000	0.000
28	A	36	GLY	0	-0.029	-0.009	19.195	-0.033	-0.033	0.000	0.000	0.000	0.000
29	A	37	LEU	0	-0.032	-0.014	14.395	0.034	0.034	0.000	0.000	0.000	0.000
30	A	38	VAL	0	-0.004	-0.008	10.339	0.008	0.008	0.000	0.000	0.000	0.000
31	A	39	VAL	0	-0.033	-0.008	10.181	0.175	0.175	0.000	0.000	0.000	0.000
32	A	40	SER	0	-0.048	-0.046	6.553	0.223	0.223	0.000	0.000	0.000	0.000
33	A	41	LYS	1	0.903	0.947	4.961	-1.917	-1.917	0.000	0.000	0.000	0.000
34	A	42	SER	0	0.029	0.027	6.270	1.045	1.045	0.000	0.000	0.000	0.000
35	A	43	THR	0	0.007	-0.029	2.593	-2.738	-1.797	2.629	-1.024	-2.544	0.012
36	A	44	GLY	0	0.001	0.020	4.559	-1.709	-1.619	-0.001	-0.010	-0.080	0.000
37	A	45	PHE	0	-0.070	-0.018	7.133	-0.061	-0.061	0.000	0.000	0.000	0.000
38	A	46	LEU	0	0.055	0.012	7.896	0.171	0.171	0.000	0.000	0.000	0.000
39	A	47	ARG	1	0.846	0.894	9.326	-0.530	-0.530	0.000	0.000	0.000	0.000
40	A	48	ASP	-1	-0.880	-0.928	10.329	0.233	0.233	0.000	0.000	0.000	0.000
41	A	49	ASP	-1	-0.876	-0.945	12.541	0.057	0.057	0.000	0.000	0.000	0.000
42	A	50	ALA	0	-0.044	-0.031	10.426	0.046	0.046	0.000	0.000	0.000	0.000
43	A	51	GLU	-1	-0.786	-0.883	12.539	0.694	0.694	0.000	0.000	0.000	0.000
44	A	52	ARG	1	0.971	1.006	14.965	-0.204	-0.204	0.000	0.000	0.000	0.000
45	A	53	LEU	0	-0.031	-0.019	14.742	-0.031	-0.031	0.000	0.000	0.000	0.000
46	A	54	ALA	0	0.014	-0.002	15.390	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	55	ALA	0	0.012	0.005	17.354	-0.024	-0.024	0.000	0.000	0.000	0.000
48	A	56	THR	0	-0.065	-0.031	20.297	-0.043	-0.043	0.000	0.000	0.000	0.000
49	A	57	ALA	0	-0.009	-0.008	19.627	-0.022	-0.022	0.000	0.000	0.000	0.000
50	A	58	SER	0	0.005	0.001	21.293	-0.031	-0.031	0.000	0.000	0.000	0.000
51	A	59	GLY	0	0.038	0.017	22.892	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	60	LEU	0	-0.025	-0.032	23.778	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	61	MET	0	-0.079	-0.034	21.221	-0.020	-0.020	0.000	0.000	0.000	0.000
54	A	62	SER	0	-0.026	0.009	26.741	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	63	LEU	0	-0.075	-0.016	29.031	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	77	ARG	1	0.955	0.964	25.724	-0.287	-0.287	0.000	0.000	0.000	0.000
57	A	78	GLN	0	-0.011	-0.012	24.647	0.008	0.008	0.000	0.000	0.000	0.000
58	A	79	ALA	0	-0.020	0.001	25.061	-0.016	-0.016	0.000	0.000	0.000	0.000
59	A	80	LEU	0	0.032	0.026	25.047	0.018	0.018	0.000	0.000	0.000	0.000
60	A	81	ILE	0	-0.020	-0.008	25.786	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	82	GLU	-1	-0.893	-0.943	26.062	0.094	0.094	0.000	0.000	0.000	0.000
62	A	83	MET	0	-0.063	-0.029	22.743	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	84	GLY	0	0.058	0.021	27.995	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	85	LYS	1	0.930	0.963	19.594	-0.113	-0.113	0.000	0.000	0.000	0.000
65	A	86	GLY	0	0.050	0.028	23.685	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	87	TYR	0	-0.001	0.000	23.372	0.004	0.004	0.000	0.000	0.000	0.000
67	A	88	LEU	0	-0.030	-0.006	20.491	0.017	0.017	0.000	0.000	0.000	0.000
68	A	89	ILE	0	-0.006	-0.011	20.925	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	90	LEU	0	-0.016	-0.002	20.373	0.050	0.050	0.000	0.000	0.000	0.000
70	A	91	THR	0	0.024	-0.001	19.698	-0.059	-0.059	0.000	0.000	0.000	0.000
71	A	92	ALA	0	0.033	0.031	20.065	0.054	0.054	0.000	0.000	0.000	0.000
72	A	93	ALA	0	-0.033	-0.025	16.439	-0.017	-0.017	0.000	0.000	0.000	0.000
73	A	94	GLY	0	-0.001	-0.005	18.119	0.042	0.042	0.000	0.000	0.000	0.000
74	A	95	PRO	0	-0.013	-0.038	20.615	0.008	0.008	0.000	0.000	0.000	0.000
75	A	96	GLY	0	0.037	0.034	19.683	-0.017	-0.017	0.000	0.000	0.000	0.000
76	A	97	ALA	0	0.022	0.012	15.917	0.069	0.069	0.000	0.000	0.000	0.000
77	A	98	HIS	0	0.016	0.014	17.432	-0.112	-0.112	0.000	0.000	0.000	0.000
78	A	99	LEU	0	-0.020	0.005	13.860	0.103	0.103	0.000	0.000	0.000	0.000
79	A	100	VAL	0	-0.023	-0.026	15.785	-0.103	-0.103	0.000	0.000	0.000	0.000
80	A	101	VAL	0	0.018	-0.003	15.655	0.083	0.083	0.000	0.000	0.000	0.000
81	A	102	LEU	0	-0.058	-0.026	16.274	-0.046	-0.046	0.000	0.000	0.000	0.000
82	A	103	THR	0	0.035	0.008	17.717	0.004	0.004	0.000	0.000	0.000	0.000
83	A	104	ARG	1	0.945	1.005	20.414	-0.014	-0.014	0.000	0.000	0.000	0.000
84	A	105	GLN	0	-0.026	-0.036	21.908	0.007	0.007	0.000	0.000	0.000	0.000
85	A	106	GLY	0	-0.006	-0.007	25.641	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	107	ALA	0	-0.056	-0.015	23.750	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	108	ASP	-1	-0.811	-0.907	25.839	0.072	0.072	0.000	0.000	0.000	0.000
88	A	109	VAL	0	0.038	0.004	25.549	0.013	0.013	0.000	0.000	0.000	0.000
89	A	110	GLY	0	0.023	0.024	25.458	0.020	0.020	0.000	0.000	0.000	0.000
90	A	111	VAL	0	-0.001	0.003	22.763	0.012	0.012	0.000	0.000	0.000	0.000
91	A	112	VAL	0	0.014	0.006	20.024	0.017	0.017	0.000	0.000	0.000	0.000
92	A	113	ALA	0	0.029	0.003	20.953	0.033	0.033	0.000	0.000	0.000	0.000
93	A	114	TYR	0	-0.019	-0.003	22.359	0.019	0.019	0.000	0.000	0.000	0.000
94	A	115	GLN	0	0.051	0.007	18.121	0.030	0.030	0.000	0.000	0.000	0.000
95	A	116	MET	0	-0.037	-0.006	17.466	0.022	0.022	0.000	0.000	0.000	0.000
96	A	117	ASN	0	0.002	-0.002	18.230	0.054	0.054	0.000	0.000	0.000	0.000
97	A	118	MET	0	-0.049	-0.022	19.092	0.003	0.003	0.000	0.000	0.000	0.000
98	A	119	LEU	0	-0.023	-0.003	11.831	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	120	VAL	0	0.001	-0.012	15.280	0.037	0.037	0.000	0.000	0.000	0.000
100	A	121	LYS	1	0.928	0.966	17.291	-0.205	-0.205	0.000	0.000	0.000	0.000
101	A	122	LYS	1	0.883	0.971	12.531	-0.265	-0.265	0.000	0.000	0.000	0.000
102	A	123	ILE	0	-0.040	-0.015	12.338	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:HIS)