FMO DATABASE

FMODB ID: V5391

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1102826.046741
FMO2-HF: Nuclear repulsion	1051672.709285
FMO2-HF: Total energy	-51153.337457
FMO2-MP2: Total energy	-51301.704188

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.
-15.714	-14.848	15.945	-7.669	-9.143	-0.062

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 : -0.040 / q_NPA : -0.031

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	0.026	0.008	3.558	-1.271	0.444	0.023	-0.863	-0.875	0.002
4	A	4	ILE	0	0.002	-0.010	6.300	0.318	0.318	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.798	-0.881	1.879	-13.401	-16.530	14.158	-5.721	-5.309	-0.061
6	A	6	GLN	0	-0.051	-0.039	2.837	-1.541	0.591	1.756	-1.084	-2.804	-0.003
7	A	7	LEU	0	-0.029	0.002	4.437	-0.353	-0.205	0.008	-0.001	-0.155	0.000
8	A	8	ASN	0	-0.012	0.000	5.362	-0.156	-0.156	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.001	0.000	6.347	0.207	0.207	0.000	0.000	0.000	0.000
10	A	10	THR	0	0.026	-0.002	8.642	-0.115	-0.115	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.882	-0.938	11.067	-0.290	-0.290	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.019	-0.006	13.504	0.051	0.051	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.046	-0.013	15.196	0.018	0.018	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.003	-0.012	18.779	0.014	0.014	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.006	0.000	21.692	0.005	0.005	0.000	0.000	0.000	0.000
16	A	16	THR	0	0.009	-0.006	25.330	0.003	0.003	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.818	-0.877	29.005	-0.118	-0.118	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.825	-0.917	31.169	-0.116	-0.116	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.022	-0.022	33.936	0.009	0.009	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.014	-0.007	33.362	0.005	0.005	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.915	-0.936	35.813	-0.089	-0.089	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.945	0.957	36.993	0.073	0.073	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.016	0.013	37.714	0.004	0.004	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.023	-0.001	37.877	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.037	-0.018	35.746	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.825	0.904	31.954	0.102	0.102	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.028	0.020	30.751	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	28	TYR	0	0.017	-0.001	26.617	0.000	0.000	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.820	0.888	25.423	0.131	0.131	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.027	0.009	18.600	-0.012	-0.012	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.010	-0.005	19.859	0.029	0.029	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.020	-0.010	14.448	-0.040	-0.040	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.889	0.937	13.789	0.297	0.297	0.000	0.000	0.000	0.000
34	A	34	MET	0	-0.003	0.027	10.466	-0.082	-0.082	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.012	0.003	9.813	0.083	0.083	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.056	-0.022	9.942	0.021	0.021	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.004	-0.012	9.622	0.106	0.106	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.869	-0.950	11.632	0.580	0.580	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.004	0.009	7.386	-0.030	-0.030	0.000	0.000	0.000	0.000
40	A	40	HIS	0	-0.025	-0.016	8.431	0.007	0.007	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.066	0.027	12.763	-0.073	-0.073	0.000	0.000	0.000	0.000
42	A	42	GLN	0	0.006	-0.016	16.109	0.002	0.002	0.000	0.000	0.000	0.000
43	A	43	PRO	0	-0.008	-0.024	19.212	0.006	0.006	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.022	0.006	21.798	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.017	0.027	20.174	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.043	-0.016	20.550	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.014	-0.003	15.353	0.021	0.021	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.049	-0.028	15.986	-0.043	-0.043	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.055	0.024	17.369	-0.023	-0.023	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.018	0.003	16.834	-0.024	-0.024	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.030	0.017	13.207	-0.037	-0.037	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.017	0.000	14.578	-0.057	-0.057	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.002	-0.012	17.149	-0.025	-0.025	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.010	0.016	12.680	-0.023	-0.023	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.034	0.010	13.016	-0.055	-0.055	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.003	0.018	14.493	-0.031	-0.031	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.931	-0.971	16.731	-0.216	-0.216	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.001	0.005	10.670	-0.016	-0.016	0.000	0.000	0.000	0.000
59	A	59	THR	0	-0.023	-0.034	14.250	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.033	0.023	16.195	0.013	0.013	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.004	0.005	17.062	0.019	0.019	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.039	-0.023	12.505	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.009	0.017	16.497	0.021	0.021	0.000	0.000	0.000	0.000
64	A	64	SER	0	0.013	-0.028	20.087	0.020	0.020	0.000	0.000	0.000	0.000
65	A	65	ASN	0	0.005	0.006	16.882	0.046	0.046	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.014	0.002	19.170	0.016	0.016	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.052	-0.024	20.700	0.020	0.020	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.002	-0.002	23.276	0.017	0.017	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.037	-0.022	22.427	0.012	0.012	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.013	0.011	22.775	0.011	0.011	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.040	-0.018	23.741	0.017	0.017	0.000	0.000	0.000	0.000
72	A	72	TYR	0	-0.056	-0.010	23.813	0.014	0.014	0.000	0.000	0.000	0.000
73	A	73	PHE	0	0.021	0.021	17.682	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.080	-0.033	19.450	0.022	0.022	0.000	0.000	0.000	0.000
75	A	75	PHE	0	-0.003	-0.002	17.830	-0.031	-0.031	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.065	0.042	18.891	0.016	0.016	0.000	0.000	0.000	0.000
77	A	77	GLN	0	-0.077	-0.048	20.481	0.019	0.019	0.000	0.000	0.000	0.000
78	A	78	SER	0	-0.027	-0.028	24.102	0.015	0.015	0.000	0.000	0.000	0.000
79	A	79	ILE	0	0.045	0.035	21.172	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.035	-0.013	24.326	0.013	0.013	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.038	0.006	23.212	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	82	ASN	0	-0.024	0.002	25.297	0.016	0.016	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.032	-0.026	21.314	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.044	-0.023	25.721	0.005	0.005	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.017	-0.015	26.009	0.011	0.011	0.000	0.000	0.000	0.000
86	A	86	PRO	0	-0.005	0.006	24.426	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.827	0.919	18.122	0.039	0.039	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.865	0.915	20.847	-0.052	-0.052	0.000	0.000	0.000	0.000
89	A	89	CYS	0	-0.062	-0.005	14.982	-0.023	-0.023	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.816	-0.894	16.204	0.095	0.095	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.015	0.009	16.503	-0.023	-0.023	0.000	0.000	0.000	0.000
92	A	92	PHE	0	-0.027	-0.029	14.624	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.012	0.014	15.189	0.023	0.023	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.014	-0.014	15.888	-0.058	-0.058	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.019	0.004	16.577	0.021	0.021	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.750	0.846	18.538	0.126	0.126	0.000	0.000	0.000	0.000
97	A	97	GLY	0	0.034	0.023	21.301	0.012	0.012	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.021	-0.005	23.621	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.019	-0.002	26.107	0.005	0.005	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.006	0.003	28.051	0.009	0.009	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.926	0.956	30.083	0.091	0.091	0.000	0.000	0.000	0.000
102	A	102	ASN	0	0.086	0.056	29.593	-0.012	-0.012	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.007	0.004	30.481	0.008	0.008	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.890	0.922	30.285	0.100	0.100	0.000	0.000	0.000	0.000
105	A	105	ARG	1	1.000	0.997	29.544	0.074	0.074	0.000	0.000	0.000	0.000
106	A	106	ASN	0	0.035	0.025	27.584	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	107	HIS	0	0.022	0.048	25.029	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.038	-0.016	26.053	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	109	TRP	0	0.024	0.000	22.921	0.004	0.004	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.816	-0.874	25.941	-0.102	-0.102	0.000	0.000	0.000	0.000
111	A	111	ILE	0	0.006	-0.010	20.478	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.811	0.900	23.116	0.117	0.117	0.000	0.000	0.000	0.000
113	A	113	ILE	0	0.025	0.017	18.068	-0.015	-0.015	0.000	0.000	0.000	0.000
114	A	114	THR	0	-0.024	-0.012	20.528	0.023	0.023	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.712	-0.845	20.404	-0.070	-0.070	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.803	-0.893	19.220	-0.064	-0.064	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.077	-0.049	21.545	0.001	0.001	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.818	-0.865	23.735	-0.118	-0.118	0.000	0.000	0.000	0.000
119	A	119	THR	0	-0.024	-0.012	25.409	0.004	0.004	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.007	-0.016	24.652	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.026	0.029	20.758	0.009	0.009	0.000	0.000	0.000	0.000
122	A	122	SER	0	-0.040	-0.036	22.003	0.010	0.010	0.000	0.000	0.000	0.000
123	A	123	GLN	0	0.008	0.017	23.918	-0.013	-0.013	0.000	0.000	0.000	0.000
124	A	124	ILE	0	0.008	-0.012	20.652	0.007	0.007	0.000	0.000	0.000	0.000
125	A	125	THR	0	-0.058	-0.033	24.682	0.001	0.001	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.033	0.025	20.880	0.006	0.006	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.048	-0.026	24.162	0.003	0.003	0.000	0.000	0.000	0.000
128	A	128	ASN	0	0.040	0.008	20.670	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.029	0.013	23.429	0.013	0.013	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.063	-0.028	23.351	-0.015	-0.015	0.000	0.000	0.000	0.000
131	A	131	VAL	0	0.019	0.012	22.658	0.016	0.016	0.000	0.000	0.000	0.000
132	A	132	PRO	0	-0.031	-0.029	24.383	-0.011	-0.011	0.000	0.000	0.000	0.000

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