FMO DATABASE

FMODB ID: 521VZ

Calculation Name: 3GEK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GEK

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CHK5

Base Structure: X-ray

Registration Date: 2023-09-20

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1101442.292784
FMO2-HF: Nuclear repulsion	1050289.803957
FMO2-HF: Total energy	-51152.488827
FMO2-MP2: Total energy	-51300.874402

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.
-17.629	-10.475	10.462	-7.877	-9.741	-0.064

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 : -0.004 / 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

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	MET	0	0.040	0.001	3.165	-2.280	-0.161	0.150	-1.071	-1.199	0.001
4	A	4	ILE	0	-0.002	-0.005	5.917	0.264	0.264	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.835	-0.915	2.128	-14.033	-10.322	6.762	-5.609	-4.864	-0.063
6	A	6	GLN	0	-0.075	-0.053	2.583	-1.049	0.274	3.527	-1.361	-3.489	-0.002
7	A	7	LEU	0	-0.035	-0.004	4.328	-0.697	-0.696	0.023	0.164	-0.189	0.000
8	A	8	ASN	0	0.002	0.014	5.410	-0.331	-0.331	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.001	-0.002	6.117	0.210	0.210	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.001	-0.016	8.869	-0.158	-0.158	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.860	-0.934	10.841	-0.369	-0.369	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.022	-0.011	13.566	0.064	0.064	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.021	-0.010	15.206	0.025	0.025	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.005	0.000	18.873	0.019	0.019	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.019	-0.015	21.624	0.001	0.001	0.000	0.000	0.000	0.000
16	A	16	THR	0	0.017	0.004	25.209	0.007	0.007	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.856	-0.927	28.924	-0.120	-0.120	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.833	-0.931	31.351	-0.123	-0.123	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.030	-0.014	33.977	0.009	0.009	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.046	-0.028	33.614	0.007	0.007	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.940	-0.942	35.719	-0.091	-0.091	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.958	0.967	36.624	0.065	0.065	0.000	0.000	0.000	0.000
23	A	23	PHE	0	0.014	0.020	37.979	0.006	0.006	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.000	-0.009	37.981	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.072	-0.039	35.620	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.913	0.965	31.821	0.086	0.086	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.025	0.015	30.508	0.001	0.001	0.000	0.000	0.000	0.000
28	A	28	TYR	0	0.017	0.001	26.173	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.870	0.927	25.163	0.129	0.129	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.019	0.014	18.255	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.014	0.005	19.411	0.029	0.029	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.022	-0.002	14.168	-0.035	-0.035	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.906	0.959	13.590	0.375	0.375	0.000	0.000	0.000	0.000
34	A	34	MET	0	-0.025	0.018	10.201	-0.067	-0.067	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.007	-0.006	8.720	0.099	0.099	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.060	-0.027	9.312	0.025	0.025	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.004	0.000	9.016	0.048	0.048	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.885	-0.962	11.244	0.449	0.449	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.001	0.014	7.414	0.023	0.023	0.000	0.000	0.000	0.000
40	A	40	HIS	0	0.000	-0.014	8.224	0.043	0.043	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.044	0.013	12.753	-0.066	-0.066	0.000	0.000	0.000	0.000
42	A	42	GLN	0	-0.003	-0.016	16.011	0.019	0.019	0.000	0.000	0.000	0.000
43	A	43	PRO	0	-0.009	-0.028	18.976	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.026	0.003	21.628	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.007	0.023	20.031	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.031	-0.016	20.052	-0.014	-0.014	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.022	-0.011	15.068	0.022	0.022	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.001	-0.007	15.855	-0.035	-0.035	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.058	0.026	17.256	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.012	-0.005	16.384	-0.019	-0.019	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.036	0.020	13.086	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.012	0.005	14.096	-0.053	-0.053	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.015	-0.017	16.840	-0.027	-0.027	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.017	0.017	12.143	-0.019	-0.019	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.020	0.009	12.834	-0.046	-0.046	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.018	0.004	14.198	-0.039	-0.039	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.921	-0.968	15.878	-0.073	-0.073	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.008	-0.003	9.997	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	59	THR	0	-0.017	-0.031	13.832	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.016	0.018	15.794	0.003	0.003	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.001	0.007	16.330	0.012	0.012	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.027	-0.014	12.294	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.010	0.003	15.841	0.011	0.011	0.000	0.000	0.000	0.000
64	A	64	SER	0	0.001	-0.038	19.430	0.016	0.016	0.000	0.000	0.000	0.000
65	A	65	ASN	0	0.067	0.030	15.767	0.042	0.042	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.016	0.006	18.884	0.011	0.011	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.065	-0.023	20.362	0.013	0.013	0.000	0.000	0.000	0.000
68	A	68	GLY	0	-0.021	-0.013	23.060	0.012	0.012	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.001	-0.001	21.795	0.007	0.007	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.009	0.007	21.821	0.012	0.012	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.096	-0.051	23.319	0.011	0.011	0.000	0.000	0.000	0.000
72	A	72	TYR	0	-0.034	-0.008	23.022	0.009	0.009	0.000	0.000	0.000	0.000
73	A	73	PHE	0	0.003	0.003	16.360	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.054	-0.024	19.137	0.017	0.017	0.000	0.000	0.000	0.000
75	A	75	PHE	0	-0.025	-0.006	17.786	-0.011	-0.011	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.066	0.050	18.380	0.002	0.002	0.000	0.000	0.000	0.000
77	A	77	GLN	0	-0.057	-0.023	19.942	0.015	0.015	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.001	-0.031	23.490	0.013	0.013	0.000	0.000	0.000	0.000
79	A	79	ILE	0	0.029	0.032	20.376	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.050	-0.017	23.532	0.008	0.008	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.044	0.012	22.756	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	82	ASN	0	-0.014	0.009	24.885	0.014	0.014	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.039	-0.038	21.064	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.051	-0.026	25.768	0.005	0.005	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.021	-0.019	26.051	0.010	0.010	0.000	0.000	0.000	0.000
86	A	86	PRO	0	-0.010	0.011	24.158	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.912	0.966	17.986	0.072	0.072	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.958	0.978	20.388	0.000	0.000	0.000	0.000	0.000	0.000
89	A	89	CYS	0	-0.053	-0.009	14.521	-0.020	-0.020	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.911	-0.958	15.603	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.017	0.012	15.599	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	92	PHE	0	-0.024	-0.018	13.877	-0.026	-0.026	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.015	0.024	14.840	0.029	0.029	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.019	-0.028	15.646	-0.073	-0.073	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.023	0.014	16.586	0.030	0.030	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.797	0.886	18.476	0.140	0.140	0.000	0.000	0.000	0.000
97	A	97	GLY	0	0.017	0.010	21.473	0.018	0.018	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.011	-0.007	23.295	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.035	-0.014	25.568	0.008	0.008	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.019	-0.001	27.658	0.006	0.006	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.924	0.952	29.498	0.055	0.055	0.000	0.000	0.000	0.000
102	A	102	ASN	0	0.062	0.038	29.013	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	103	GLY	0	-0.011	-0.012	29.874	0.006	0.006	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.927	0.949	30.044	0.054	0.054	0.000	0.000	0.000	0.000
105	A	105	ARG	1	1.002	0.999	29.029	0.033	0.033	0.000	0.000	0.000	0.000
106	A	106	ASN	0	0.044	0.027	26.987	0.001	0.001	0.000	0.000	0.000	0.000
107	A	107	HIS	0	0.018	0.058	24.318	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.028	-0.012	25.644	0.004	0.004	0.000	0.000	0.000	0.000
109	A	109	TRP	0	0.023	0.002	22.421	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.885	-0.958	25.387	-0.073	-0.073	0.000	0.000	0.000	0.000
111	A	111	ILE	0	-0.016	-0.018	20.224	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.867	0.951	23.386	0.105	0.105	0.000	0.000	0.000	0.000
113	A	113	ILE	0	0.026	0.005	18.456	-0.016	-0.016	0.000	0.000	0.000	0.000
114	A	114	THR	0	-0.034	0.002	20.451	0.022	0.022	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.762	-0.889	20.002	-0.099	-0.099	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.802	-0.924	18.913	-0.123	-0.123	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.075	-0.034	21.329	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.839	-0.918	23.871	-0.135	-0.135	0.000	0.000	0.000	0.000
119	A	119	THR	0	-0.018	0.010	25.275	0.009	0.009	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.019	-0.009	24.498	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.011	0.018	20.827	0.010	0.010	0.000	0.000	0.000	0.000
122	A	122	SER	0	-0.008	-0.019	21.780	0.017	0.017	0.000	0.000	0.000	0.000
123	A	123	GLN	0	0.049	0.044	23.633	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	124	ILE	0	0.000	-0.015	20.335	0.011	0.011	0.000	0.000	0.000	0.000
125	A	125	THR	0	-0.042	-0.008	24.260	-0.010	-0.010	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.027	0.018	20.204	0.009	0.009	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.073	-0.035	23.442	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	128	ASN	0	0.028	0.000	19.997	0.011	0.011	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.020	0.002	22.794	0.004	0.004	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.065	-0.039	22.823	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	131	VAL	0	-0.015	-0.009	22.551	0.011	0.011	0.000	0.000	0.000	0.000
132	A	132	PRO	0	0.036	0.022	24.083	-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:1:MET)