FMO DATABASE

FMODB ID: 72GQK

Calculation Name: 3LFH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LFH

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RD55

Base Structure: X-ray

Registration Date: 2023-06-21

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	129
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1108087.813524
FMO2-HF: Nuclear repulsion	1057944.643005
FMO2-HF: Total energy	-50143.170519
FMO2-MP2: Total energy	-50289.083064

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:1:MET)

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

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.
-15.992	-15.032	17.502	-6.219	-12.246	-0.014

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.007

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	3	GLU	-1	-0.853	-0.921	2.777	-5.996	-3.364	0.420	-1.395	-1.657	-0.008
4	A	4	LYS	1	0.836	0.899	2.467	-6.898	-9.380	8.614	-2.853	-3.280	0.023
5	A	5	PHE	0	-0.004	-0.007	6.542	-0.102	-0.102	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.014	0.008	10.316	0.197	0.197	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.012	-0.002	12.616	-0.049	-0.049	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.009	-0.004	15.977	0.057	0.057	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.009	0.000	18.732	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	10	THR	0	0.010	0.002	21.675	0.012	0.012	0.000	0.000	0.000	0.000
11	A	11	HIS	0	-0.053	-0.044	24.778	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.001	-0.010	28.450	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.868	-0.930	28.096	-0.081	-0.081	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.031	-0.004	23.663	-0.014	-0.014	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.067	0.016	22.549	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.865	0.926	22.336	0.063	0.063	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.030	0.011	24.129	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.039	-0.017	19.761	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.026	0.010	17.644	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.030	0.014	20.619	-0.028	-0.028	0.000	0.000	0.000	0.000
21	A	21	GLY	0	-0.026	-0.021	23.448	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.046	-0.003	17.970	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.859	-0.928	18.784	-0.383	-0.383	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.082	-0.025	20.507	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.080	-0.034	19.617	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.041	-0.025	14.553	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.010	0.021	17.350	-0.060	-0.060	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.866	0.932	18.192	0.382	0.382	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.026	-0.016	13.467	-0.118	-0.118	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.907	-0.950	14.049	-0.452	-0.452	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.082	-0.055	10.427	0.116	0.116	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.054	0.030	12.635	0.040	0.040	0.000	0.000	0.000	0.000
33	A	33	HIS	0	-0.017	0.002	15.193	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.034	-0.012	18.245	0.031	0.031	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.010	-0.012	21.064	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	36	GLY	0	-0.018	-0.003	23.472	0.010	0.010	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.024	-0.019	26.590	0.003	0.003	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.029	-0.013	29.122	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.024	-0.003	32.582	0.007	0.007	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.018	-0.008	35.973	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.802	-0.878	31.209	-0.025	-0.025	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.014	-0.016	33.866	0.011	0.011	0.000	0.000	0.000	0.000
43	A	43	ILE	0	0.044	0.001	29.176	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.790	-0.887	29.222	0.070	0.070	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.041	-0.012	29.639	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.030	0.008	25.862	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.830	0.908	25.249	-0.089	-0.089	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.850	0.924	24.545	-0.040	-0.040	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.817	-0.918	24.999	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.004	-0.009	19.925	-0.015	-0.015	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.807	-0.879	20.183	0.085	0.085	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.793	0.903	20.459	0.026	0.026	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.017	0.014	17.090	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.008	-0.004	15.223	-0.031	-0.031	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.933	0.975	15.749	-0.092	-0.092	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.859	-0.925	17.121	-0.065	-0.065	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.896	0.956	12.714	0.383	0.383	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.004	0.006	11.863	-0.056	-0.056	0.000	0.000	0.000	0.000
59	A	59	GLN	0	-0.093	-0.052	13.208	0.035	0.035	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.982	-0.983	13.186	-0.458	-0.458	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.960	-0.987	8.591	-0.084	-0.084	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.883	0.956	8.043	0.773	0.773	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.915	-0.941	4.522	2.108	2.346	-0.001	-0.010	-0.226	0.000
64	A	64	ILE	0	-0.028	-0.019	7.522	-0.142	-0.142	0.000	0.000	0.000	0.000
65	A	65	ILE	0	0.015	0.012	7.981	0.186	0.186	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.009	-0.011	11.451	-0.139	-0.139	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.008	0.002	14.564	0.055	0.055	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.010	-0.016	17.076	-0.035	-0.035	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.756	-0.883	20.807	0.030	0.030	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.038	-0.017	23.814	0.004	0.004	0.000	0.000	0.000	0.000
71	A	71	PHE	0	-0.019	0.000	23.881	0.009	0.009	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.033	0.016	25.949	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.038	0.010	28.227	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.014	-0.021	27.910	0.013	0.013	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.063	0.034	24.578	0.009	0.009	0.000	0.000	0.000	0.000
76	A	76	PHE	0	0.068	0.042	22.444	0.010	0.010	0.000	0.000	0.000	0.000
77	A	77	ASN	0	0.001	-0.010	23.612	0.029	0.029	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.017	-0.007	22.367	0.013	0.013	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.057	0.045	19.377	0.010	0.010	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.015	-0.009	19.970	0.031	0.031	0.000	0.000	0.000	0.000
81	A	81	SER	0	-0.095	-0.053	21.756	0.013	0.013	0.000	0.000	0.000	0.000
82	A	82	MET	0	0.033	0.023	18.373	0.003	0.003	0.000	0.000	0.000	0.000
83	A	83	MET	0	-0.031	-0.002	16.376	0.032	0.032	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.887	0.941	18.291	-0.168	-0.168	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.964	-0.980	20.730	0.212	0.212	0.000	0.000	0.000	0.000
86	A	86	TYR	0	-0.088	-0.093	16.133	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.960	-0.954	13.373	0.735	0.735	0.000	0.000	0.000	0.000
88	A	88	VAL	0	-0.018	0.007	12.414	0.084	0.084	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.971	0.982	9.424	-1.185	-1.185	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.010	-0.010	13.158	-0.092	-0.092	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.006	0.020	15.014	0.034	0.034	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.034	-0.027	17.268	-0.041	-0.041	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.011	0.005	20.439	0.007	0.007	0.000	0.000	0.000	0.000
94	A	94	ILE	0	-0.036	-0.004	16.734	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	95	ASN	0	0.068	0.002	19.750	-0.023	-0.023	0.000	0.000	0.000	0.000
96	A	96	MET	0	0.014	0.012	19.374	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	97	PRO	0	-0.006	0.000	18.618	-0.030	-0.030	0.000	0.000	0.000	0.000
98	A	98	MET	0	-0.006	0.039	15.843	-0.031	-0.031	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.022	0.016	14.417	-0.012	-0.012	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.025	0.003	14.331	-0.059	-0.059	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.894	-0.939	11.337	-0.479	-0.479	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.036	-0.002	9.214	-0.093	-0.093	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.024	-0.027	9.306	-0.130	-0.130	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.078	-0.027	10.404	-0.178	-0.178	0.000	0.000	0.000	0.000
105	A	105	SER	0	0.004	-0.012	7.395	-0.133	-0.133	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.025	0.020	5.374	-0.388	-0.388	0.000	0.000	0.000	0.000
107	A	107	ASN	0	0.001	-0.016	2.762	-0.544	0.171	0.218	-0.280	-0.654	-0.001
108	A	108	VAL	0	-0.060	-0.016	2.532	-4.177	-4.061	3.165	-1.154	-2.127	-0.016
109	A	109	TYR	0	0.034	0.020	3.091	-1.738	-0.733	0.220	-0.300	-0.926	-0.003
110	A	110	ASP	-1	-0.819	-0.915	2.846	5.228	6.257	4.865	-2.841	-3.054	-0.008
111	A	111	THR	0	0.003	-0.031	3.721	-0.469	-2.762	0.001	2.614	-0.322	-0.001
112	A	112	THR	0	-0.030	-0.023	6.624	-0.858	-0.858	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.912	-0.957	7.413	0.416	0.416	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.034	-0.003	5.678	-0.440	-0.440	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.032	-0.033	8.330	-0.352	-0.352	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.939	-0.959	11.701	0.275	0.275	0.000	0.000	0.000	0.000
117	A	117	ASN	0	0.029	0.008	8.987	-0.055	-0.055	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.014	-0.015	11.361	-0.099	-0.099	0.000	0.000	0.000	0.000
119	A	119	SER	0	-0.015	0.006	13.981	-0.071	-0.071	0.000	0.000	0.000	0.000
120	A	120	LYS	1	0.869	0.938	16.178	-0.105	-0.105	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.041	0.017	13.944	-0.022	-0.022	0.000	0.000	0.000	0.000
122	A	122	GLY	0	-0.005	-0.022	17.674	-0.026	-0.026	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.884	0.933	19.553	-0.165	-0.165	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.848	-0.922	20.767	0.023	0.023	0.000	0.000	0.000	0.000
125	A	125	GLY	0	-0.050	-0.011	21.779	-0.016	-0.016	0.000	0.000	0.000	0.000
126	A	126	ILE	0	-0.073	-0.024	23.020	-0.011	-0.011	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.948	0.973	26.133	0.041	0.041	0.000	0.000	0.000	0.000
128	A	128	VAL	0	0.014	0.010	29.107	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	129	ILE	0	-0.014	-0.011	30.686	0.002	0.002	0.000	0.000	0.000	0.000

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