FMO DATABASE

FMODB ID: G6531

Calculation Name: 2EK5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EK5

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NLJ5

Base Structure: X-ray

Registration Date: 2023-06-22

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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-770173.965366
FMO2-HF: Nuclear repulsion	726991.476433
FMO2-HF: Total energy	-43182.488933
FMO2-MP2: Total energy	-43311.517083

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:VAL)

Summations of interaction energy for fragment #1(A:3:VAL)

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.
-3.719	-1.486	8.501	-3.416	-7.319	-0.011

Interaction energy analysis for fragmet #1(A:3:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.012

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	5	LEU	0	0.100	0.034	2.403	-3.473	-1.768	1.902	-1.492	-2.116	-0.011
4	A	6	TYR	0	0.045	0.016	4.980	-0.124	0.060	-0.001	-0.008	-0.174	0.000
5	A	7	LYS	1	0.965	0.998	2.232	0.224	-1.461	5.181	-0.870	-2.626	0.003
6	A	8	GLN	0	-0.036	-0.040	2.228	-0.756	1.052	1.412	-1.013	-2.208	-0.003
7	A	9	ILE	0	-0.001	0.003	3.914	0.136	0.288	0.008	-0.031	-0.129	0.000
8	A	10	ALA	0	0.001	-0.004	6.791	0.073	0.073	0.000	0.000	0.000	0.000
9	A	11	SER	0	-0.013	-0.022	4.557	-0.008	0.061	-0.001	-0.002	-0.066	0.000
10	A	12	LEU	0	0.050	0.042	6.975	0.053	0.053	0.000	0.000	0.000	0.000
11	A	13	ILE	0	-0.027	-0.007	9.393	0.091	0.091	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.778	-0.880	8.916	-0.170	-0.170	0.000	0.000	0.000	0.000
13	A	15	ASP	-1	-0.834	-0.916	9.723	-0.673	-0.673	0.000	0.000	0.000	0.000
14	A	16	SER	0	-0.010	-0.001	12.222	0.046	0.046	0.000	0.000	0.000	0.000
15	A	17	ILE	0	-0.059	-0.027	14.629	0.040	0.040	0.000	0.000	0.000	0.000
16	A	18	VAL	0	-0.087	-0.041	13.748	0.031	0.031	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.937	-0.975	15.812	-0.351	-0.351	0.000	0.000	0.000	0.000
18	A	20	GLY	0	-0.030	-0.007	18.043	0.018	0.018	0.000	0.000	0.000	0.000
19	A	21	THR	0	-0.044	-0.020	17.998	0.010	0.010	0.000	0.000	0.000	0.000
20	A	22	LEU	0	-0.059	-0.030	16.319	0.007	0.007	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.015	-0.019	19.767	0.009	0.009	0.000	0.000	0.000	0.000
22	A	24	ILE	0	0.030	-0.008	22.109	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	25	ASP	-1	-0.954	-0.961	23.931	-0.067	-0.067	0.000	0.000	0.000	0.000
24	A	26	GLN	0	0.025	0.023	22.008	0.006	0.006	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.785	0.872	21.305	0.121	0.121	0.000	0.000	0.000	0.000
26	A	28	VAL	0	0.053	0.026	16.277	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	29	PRO	0	-0.001	-0.005	16.456	0.017	0.017	0.000	0.000	0.000	0.000
28	A	30	SER	0	0.014	-0.003	17.077	0.003	0.003	0.000	0.000	0.000	0.000
29	A	31	THR	0	-0.011	-0.016	15.731	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	32	ASN	0	0.005	-0.007	16.514	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	33	GLU	-1	-0.783	-0.855	18.879	-0.156	-0.156	0.000	0.000	0.000	0.000
32	A	34	LEU	0	0.011	0.004	12.648	-0.024	-0.024	0.000	0.000	0.000	0.000
33	A	35	ALA	0	-0.044	-0.021	14.526	-0.043	-0.043	0.000	0.000	0.000	0.000
34	A	36	ALA	0	0.008	0.005	15.520	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	37	PHE	0	-0.017	-0.001	14.946	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	38	HIS	0	0.010	0.004	11.530	-0.049	-0.049	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.966	0.998	13.343	0.202	0.202	0.000	0.000	0.000	0.000
38	A	40	ILE	0	-0.027	-0.012	10.038	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	41	ASN	0	0.008	-0.003	12.654	0.051	0.051	0.000	0.000	0.000	0.000
40	A	42	PRO	0	0.086	0.020	13.194	-0.024	-0.024	0.000	0.000	0.000	0.000
41	A	43	ALA	0	-0.014	-0.015	14.300	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	44	THR	0	0.011	0.018	8.433	0.083	0.083	0.000	0.000	0.000	0.000
43	A	45	ALA	0	0.069	0.033	9.989	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	46	ARG	1	0.925	0.966	11.809	0.012	0.012	0.000	0.000	0.000	0.000
45	A	47	ASN	0	0.024	0.001	10.085	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	48	GLY	0	0.016	0.020	8.749	0.044	0.044	0.000	0.000	0.000	0.000
47	A	49	LEU	0	-0.016	-0.018	9.553	0.027	0.027	0.000	0.000	0.000	0.000
48	A	50	THR	0	-0.047	-0.026	13.077	0.007	0.007	0.000	0.000	0.000	0.000
49	A	51	LEU	0	0.032	0.033	8.207	0.018	0.018	0.000	0.000	0.000	0.000
50	A	52	LEU	0	0.009	-0.004	10.295	0.007	0.007	0.000	0.000	0.000	0.000
51	A	53	VAL	0	-0.076	-0.027	13.273	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.940	-0.978	13.937	0.175	0.175	0.000	0.000	0.000	0.000
53	A	55	ALA	0	-0.020	0.007	13.373	0.013	0.013	0.000	0.000	0.000	0.000
54	A	56	GLY	0	0.004	0.001	15.494	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	57	ILE	0	-0.033	-0.017	13.086	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	58	LEU	0	-0.027	-0.019	15.020	-0.020	-0.020	0.000	0.000	0.000	0.000
57	A	59	TYR	0	0.003	0.003	18.295	0.023	0.023	0.000	0.000	0.000	0.000
58	A	60	LYS	1	0.934	0.954	20.397	0.006	0.006	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.985	1.018	23.390	0.066	0.066	0.000	0.000	0.000	0.000
60	A	62	ARG	1	0.963	0.940	26.677	0.002	0.002	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.016	0.009	28.157	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	64	ILE	0	0.004	0.029	26.668	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	65	GLY	0	0.012	-0.007	23.612	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	66	MET	0	-0.049	-0.006	17.972	0.019	0.019	0.000	0.000	0.000	0.000
65	A	67	PHE	0	0.015	0.007	20.993	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	68	VAL	0	0.093	0.053	18.417	0.007	0.007	0.000	0.000	0.000	0.000
67	A	69	SER	0	0.006	0.004	19.855	0.006	0.006	0.000	0.000	0.000	0.000
68	A	70	ALA	0	0.069	0.016	21.164	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	71	GLN	0	-0.010	0.002	21.187	0.001	0.001	0.000	0.000	0.000	0.000
70	A	72	ALA	0	0.030	0.019	17.297	0.003	0.003	0.000	0.000	0.000	0.000
71	A	73	PRO	0	0.013	-0.002	17.197	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.008	0.009	17.893	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	75	LEU	0	0.039	0.030	16.691	0.003	0.003	0.000	0.000	0.000	0.000
74	A	76	ILE	0	-0.043	-0.013	12.032	0.010	0.010	0.000	0.000	0.000	0.000
75	A	77	ARG	1	0.914	0.963	13.847	0.137	0.137	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.872	-0.942	16.236	-0.027	-0.027	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.792	0.877	9.055	0.093	0.093	0.000	0.000	0.000	0.000
78	A	80	ARG	1	0.795	0.881	9.048	0.418	0.418	0.000	0.000	0.000	0.000
79	A	81	ASP	-1	-0.842	-0.915	12.741	-0.111	-0.111	0.000	0.000	0.000	0.000
80	A	82	ALA	0	-0.022	-0.013	15.560	0.013	0.013	0.000	0.000	0.000	0.000
81	A	83	ALA	0	-0.049	-0.025	10.524	0.029	0.029	0.000	0.000	0.000	0.000
82	A	84	PHE	0	0.005	0.007	12.668	0.015	0.015	0.000	0.000	0.000	0.000
83	A	85	ALA	0	0.039	0.013	14.109	0.013	0.013	0.000	0.000	0.000	0.000
84	A	86	ALA	0	-0.002	-0.002	14.405	0.008	0.008	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.040	-0.026	10.945	0.041	0.041	0.000	0.000	0.000	0.000
86	A	88	TYR	0	-0.043	-0.029	11.123	0.001	0.001	0.000	0.000	0.000	0.000
87	A	89	VAL	0	-0.015	-0.006	16.350	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	90	ALA	0	-0.010	0.002	18.077	0.002	0.002	0.000	0.000	0.000	0.000
89	A	91	PRO	0	0.050	0.029	16.635	0.001	0.001	0.000	0.000	0.000	0.000
90	A	92	LEU	0	-0.010	0.013	19.845	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.020	-0.031	22.088	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.903	-0.949	22.356	0.110	0.110	0.000	0.000	0.000	0.000
93	A	95	GLU	-1	-0.874	-0.953	23.573	0.084	0.084	0.000	0.000	0.000	0.000
94	A	96	SER	0	-0.028	-0.019	25.359	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	97	ILE	0	-0.058	-0.020	27.442	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	98	HIS	0	-0.078	-0.021	27.741	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	99	LEU	0	-0.050	-0.025	28.196	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	100	GLY	0	-0.004	0.022	31.170	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	101	PHE	0	-0.062	-0.032	29.038	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	102	THR	0	0.026	0.008	32.906	0.000	0.000	0.000	0.000	0.000	0.000
101	A	103	ARG	1	1.034	0.992	32.059	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	104	ALA	0	-0.004	-0.012	32.490	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.970	0.993	32.534	-0.010	-0.010	0.000	0.000	0.000	0.000
104	A	106	ILE	0	0.060	0.041	26.276	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	107	HIS	0	-0.037	-0.033	29.138	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	108	ALA	0	0.019	0.017	30.766	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.001	-0.002	28.434	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	110	LEU	0	-0.034	-0.005	24.279	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	111	ASP	-1	-0.878	-0.945	27.645	-0.041	-0.041	0.000	0.000	0.000	0.000
110	A	112	GLN	0	-0.033	-0.014	30.278	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	113	VAL	0	-0.019	-0.014	24.768	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	114	ALA	0	-0.049	-0.019	26.369	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.970	-1.003	27.330	-0.047	-0.047	0.000	0.000	0.000	0.000
114	A	116	SER	0	-0.065	-0.016	29.648	0.000	0.000	0.000	0.000	0.000	0.000
115	A	117	ARG	1	0.895	0.966	23.911	0.093	0.093	0.000	0.000	0.000	0.000

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