FMO DATABASE

FMODB ID: 859YY

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	OptHSide
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	-770519.19748
FMO2-HF: Nuclear repulsion	727336.030543
FMO2-HF: Total energy	-43183.166936
FMO2-MP2: Total energy	-43312.131528

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.
-4.843	0.129	3.115	-2.484	-5.605	-0.009

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 : 0.030 / 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	5	LEU	0	0.080	0.027	2.617	-3.418	-1.141	0.798	-1.316	-1.760	-0.008
4	A	6	TYR	0	0.039	0.014	5.238	-0.093	0.079	-0.001	-0.009	-0.162	0.000
5	A	7	LYS	1	0.911	0.964	2.372	-0.543	-0.059	1.549	-0.406	-1.627	0.002
6	A	8	GLN	0	-0.023	-0.016	2.449	-0.892	0.935	0.766	-0.723	-1.870	-0.003
7	A	9	ILE	0	0.000	-0.001	4.042	0.053	0.189	0.004	-0.027	-0.114	0.000
8	A	10	ALA	0	0.008	0.001	6.845	0.053	0.053	0.000	0.000	0.000	0.000
9	A	11	SER	0	0.008	-0.021	4.435	-0.010	0.066	-0.001	-0.003	-0.072	0.000
10	A	12	LEU	0	0.051	0.049	6.985	0.049	0.049	0.000	0.000	0.000	0.000
11	A	13	ILE	0	-0.018	0.000	9.392	0.083	0.083	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.775	-0.857	8.949	-0.270	-0.270	0.000	0.000	0.000	0.000
13	A	15	ASP	-1	-0.791	-0.882	9.294	-0.672	-0.672	0.000	0.000	0.000	0.000
14	A	16	SER	0	-0.022	-0.011	12.147	0.044	0.044	0.000	0.000	0.000	0.000
15	A	17	ILE	0	-0.048	-0.028	14.611	0.038	0.038	0.000	0.000	0.000	0.000
16	A	18	VAL	0	-0.069	-0.030	13.955	0.029	0.029	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.932	-0.971	16.064	-0.339	-0.339	0.000	0.000	0.000	0.000
18	A	20	GLY	0	-0.034	-0.007	17.943	0.019	0.019	0.000	0.000	0.000	0.000
19	A	21	THR	0	-0.049	-0.019	17.785	0.013	0.013	0.000	0.000	0.000	0.000
20	A	22	LEU	0	-0.049	-0.029	16.527	0.010	0.010	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.015	-0.022	19.775	0.006	0.006	0.000	0.000	0.000	0.000
22	A	24	ILE	0	0.044	0.005	22.153	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	25	ASP	-1	-0.916	-0.962	23.974	-0.066	-0.066	0.000	0.000	0.000	0.000
24	A	26	GLN	0	0.004	0.021	21.951	0.008	0.008	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.728	0.835	21.021	0.106	0.106	0.000	0.000	0.000	0.000
26	A	28	VAL	0	0.047	0.027	16.387	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	29	PRO	0	0.019	0.018	16.635	0.018	0.018	0.000	0.000	0.000	0.000
28	A	30	SER	0	-0.002	-0.019	17.180	0.001	0.001	0.000	0.000	0.000	0.000
29	A	31	THR	0	-0.001	-0.012	15.710	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	32	ASN	0	0.009	-0.004	16.695	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	33	GLU	-1	-0.735	-0.826	19.211	-0.129	-0.129	0.000	0.000	0.000	0.000
32	A	34	LEU	0	-0.001	0.001	12.732	-0.020	-0.020	0.000	0.000	0.000	0.000
33	A	35	ALA	0	-0.041	-0.024	14.753	-0.035	-0.035	0.000	0.000	0.000	0.000
34	A	36	ALA	0	0.007	0.006	15.745	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	37	PHE	0	-0.012	-0.001	15.064	0.000	0.000	0.000	0.000	0.000	0.000
36	A	38	HIS	0	0.006	0.002	11.769	-0.044	-0.044	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.957	0.994	13.613	0.145	0.145	0.000	0.000	0.000	0.000
38	A	40	ILE	0	-0.026	-0.008	10.078	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	41	ASN	0	0.032	0.005	12.912	0.030	0.030	0.000	0.000	0.000	0.000
40	A	42	PRO	0	0.092	0.023	13.414	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	43	ALA	0	-0.029	-0.017	14.655	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	44	THR	0	0.017	0.015	8.594	0.063	0.063	0.000	0.000	0.000	0.000
43	A	45	ALA	0	0.070	0.037	10.134	-0.027	-0.027	0.000	0.000	0.000	0.000
44	A	46	ARG	1	0.915	0.958	11.971	-0.020	-0.020	0.000	0.000	0.000	0.000
45	A	47	ASN	0	0.020	0.012	10.260	-0.023	-0.023	0.000	0.000	0.000	0.000
46	A	48	GLY	0	0.026	0.028	8.776	0.028	0.028	0.000	0.000	0.000	0.000
47	A	49	LEU	0	-0.018	-0.020	9.600	0.013	0.013	0.000	0.000	0.000	0.000
48	A	50	THR	0	-0.060	-0.047	13.103	0.004	0.004	0.000	0.000	0.000	0.000
49	A	51	LEU	0	0.035	0.040	8.347	0.009	0.009	0.000	0.000	0.000	0.000
50	A	52	LEU	0	-0.004	-0.008	10.325	0.001	0.001	0.000	0.000	0.000	0.000
51	A	53	VAL	0	-0.068	-0.026	13.351	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.928	-0.969	13.953	0.131	0.131	0.000	0.000	0.000	0.000
53	A	55	ALA	0	-0.025	0.003	13.311	0.009	0.009	0.000	0.000	0.000	0.000
54	A	56	GLY	0	0.009	0.003	15.461	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	57	ILE	0	-0.042	-0.023	13.286	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	58	LEU	0	-0.022	-0.014	14.971	-0.015	-0.015	0.000	0.000	0.000	0.000
57	A	59	TYR	0	0.010	0.003	18.419	0.022	0.022	0.000	0.000	0.000	0.000
58	A	60	LYS	1	0.896	0.929	20.321	0.019	0.019	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.910	0.990	23.384	0.071	0.071	0.000	0.000	0.000	0.000
60	A	62	ARG	1	0.971	0.945	26.682	0.005	0.005	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.016	0.008	28.206	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	64	ILE	0	0.004	0.028	27.003	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	65	GLY	0	0.030	0.002	23.678	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	66	MET	0	-0.025	0.013	18.015	0.018	0.018	0.000	0.000	0.000	0.000
65	A	67	PHE	0	0.040	0.016	21.029	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	68	VAL	0	0.082	0.046	18.203	0.005	0.005	0.000	0.000	0.000	0.000
67	A	69	SER	0	0.008	0.007	19.935	0.008	0.008	0.000	0.000	0.000	0.000
68	A	70	ALA	0	0.063	0.016	21.205	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	71	GLN	0	0.003	0.006	21.354	0.000	0.000	0.000	0.000	0.000	0.000
70	A	72	ALA	0	0.024	0.014	17.226	0.000	0.000	0.000	0.000	0.000	0.000
71	A	73	PRO	0	0.020	0.001	17.190	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.002	0.008	17.837	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	75	LEU	0	0.044	0.031	16.691	0.000	0.000	0.000	0.000	0.000	0.000
74	A	76	ILE	0	-0.048	-0.022	11.976	0.002	0.002	0.000	0.000	0.000	0.000
75	A	77	ARG	1	0.902	0.965	13.772	0.159	0.159	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.871	-0.939	16.133	-0.065	-0.065	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.799	0.875	9.041	0.184	0.184	0.000	0.000	0.000	0.000
78	A	80	ARG	1	0.747	0.830	9.432	0.475	0.475	0.000	0.000	0.000	0.000
79	A	81	ASP	-1	-0.838	-0.922	12.751	-0.162	-0.162	0.000	0.000	0.000	0.000
80	A	82	ALA	0	-0.018	-0.009	15.527	0.013	0.013	0.000	0.000	0.000	0.000
81	A	83	ALA	0	-0.030	-0.015	10.587	0.025	0.025	0.000	0.000	0.000	0.000
82	A	84	PHE	0	0.005	0.019	12.737	0.013	0.013	0.000	0.000	0.000	0.000
83	A	85	ALA	0	0.040	0.013	14.139	0.015	0.015	0.000	0.000	0.000	0.000
84	A	86	ALA	0	-0.004	-0.001	14.465	0.012	0.012	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.054	-0.044	10.651	0.035	0.035	0.000	0.000	0.000	0.000
86	A	88	TYR	0	-0.044	-0.029	10.766	0.006	0.006	0.000	0.000	0.000	0.000
87	A	89	VAL	0	-0.016	-0.007	16.268	0.005	0.005	0.000	0.000	0.000	0.000
88	A	90	ALA	0	-0.009	0.002	18.150	0.006	0.006	0.000	0.000	0.000	0.000
89	A	91	PRO	0	0.057	0.035	16.562	0.005	0.005	0.000	0.000	0.000	0.000
90	A	92	LEU	0	-0.003	0.013	19.783	0.000	0.000	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.017	-0.016	21.999	0.000	0.000	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.901	-0.947	21.967	0.071	0.071	0.000	0.000	0.000	0.000
93	A	95	GLU	-1	-0.839	-0.922	23.470	0.057	0.057	0.000	0.000	0.000	0.000
94	A	96	SER	0	-0.051	-0.041	25.270	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	97	ILE	0	-0.057	-0.020	27.401	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	98	HIS	0	-0.125	-0.057	27.021	0.001	0.001	0.000	0.000	0.000	0.000
97	A	99	LEU	0	-0.034	-0.018	28.091	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	100	GLY	0	-0.008	0.020	31.065	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	101	PHE	0	-0.064	-0.036	28.480	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	102	THR	0	0.026	0.006	32.811	0.000	0.000	0.000	0.000	0.000	0.000
101	A	103	ARG	1	0.985	0.974	31.818	0.016	0.016	0.000	0.000	0.000	0.000
102	A	104	ALA	0	0.007	-0.001	32.413	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.979	0.998	32.390	0.005	0.005	0.000	0.000	0.000	0.000
104	A	106	ILE	0	0.065	0.033	25.976	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	107	HIS	0	-0.011	-0.021	29.025	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	108	ALA	0	0.032	0.021	30.720	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.024	-0.010	28.437	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	110	LEU	0	-0.026	-0.002	24.358	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	111	ASP	-1	-0.882	-0.947	27.568	-0.056	-0.056	0.000	0.000	0.000	0.000
110	A	112	GLN	0	-0.030	-0.015	30.192	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	113	VAL	0	-0.011	-0.011	24.607	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	114	ALA	0	-0.033	-0.009	26.254	-0.008	-0.008	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.962	-0.983	27.216	-0.057	-0.057	0.000	0.000	0.000	0.000
114	A	116	SER	0	-0.071	-0.020	29.510	0.001	0.001	0.000	0.000	0.000	0.000
115	A	117	ARG	1	0.877	0.943	23.921	0.107	0.107	0.000	0.000	0.000	0.000

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