FMO DATABASE

FMODB ID: N9NYQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-771641.185993
FMO2-HF: Nuclear repulsion	728457.782279
FMO2-HF: Total energy	-43183.403714
FMO2-MP2: Total energy	-43312.290799

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.
-4.632	0.738	2.469	-2.356	-5.482	-0.007

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 : 0.049 / q_NPA : 0.018

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	0.063	0.023	2.788	-2.860	-0.613	0.414	-1.164	-1.497	-0.006
4	A	6	TYR	0	0.034	0.011	5.105	-0.101	0.074	-0.001	-0.010	-0.164	0.000
5	A	7	LYS	1	0.892	0.945	2.582	-0.518	0.261	0.773	-0.274	-1.278	0.002
6	A	8	GLN	0	-0.038	-0.007	2.447	-1.222	0.691	1.275	-0.876	-2.312	-0.003
7	A	9	ILE	0	0.012	0.002	3.908	0.039	0.175	0.009	-0.016	-0.128	0.000
8	A	10	ALA	0	0.012	0.002	6.701	0.058	0.058	0.000	0.000	0.000	0.000
9	A	11	SER	0	-0.012	-0.023	4.012	-0.091	0.029	-0.001	-0.016	-0.103	0.000
10	A	12	LEU	0	0.058	0.040	6.593	0.084	0.084	0.000	0.000	0.000	0.000
11	A	13	ILE	0	-0.024	0.009	9.193	0.093	0.093	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.754	-0.846	8.289	-0.312	-0.312	0.000	0.000	0.000	0.000
13	A	15	ASP	-1	-0.788	-0.888	8.765	-0.694	-0.694	0.000	0.000	0.000	0.000
14	A	16	SER	0	-0.023	-0.019	11.868	0.051	0.051	0.000	0.000	0.000	0.000
15	A	17	ILE	0	-0.041	-0.019	14.285	0.042	0.042	0.000	0.000	0.000	0.000
16	A	18	VAL	0	-0.057	-0.023	13.523	0.030	0.030	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.907	-0.947	15.877	-0.336	-0.336	0.000	0.000	0.000	0.000
18	A	20	GLY	0	-0.047	-0.022	17.790	0.019	0.019	0.000	0.000	0.000	0.000
19	A	21	THR	0	-0.080	-0.039	17.372	0.010	0.010	0.000	0.000	0.000	0.000
20	A	22	LEU	0	-0.013	-0.010	16.174	0.010	0.010	0.000	0.000	0.000	0.000
21	A	23	SER	0	0.012	-0.005	19.386	0.007	0.007	0.000	0.000	0.000	0.000
22	A	24	ILE	0	0.015	-0.001	22.015	0.000	0.000	0.000	0.000	0.000	0.000
23	A	25	ASP	-1	-0.863	-0.943	23.762	-0.069	-0.069	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.013	0.006	21.488	0.010	0.010	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.717	0.815	20.634	0.113	0.113	0.000	0.000	0.000	0.000
26	A	28	VAL	0	0.047	0.028	16.451	-0.012	-0.012	0.000	0.000	0.000	0.000
27	A	29	PRO	0	0.014	0.017	16.188	0.019	0.019	0.000	0.000	0.000	0.000
28	A	30	SER	0	-0.010	-0.030	17.060	0.003	0.003	0.000	0.000	0.000	0.000
29	A	31	THR	0	-0.020	-0.025	15.732	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	32	ASN	0	0.017	0.004	16.560	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	33	GLU	-1	-0.723	-0.804	18.905	-0.140	-0.140	0.000	0.000	0.000	0.000
32	A	34	LEU	0	0.008	0.004	12.643	-0.021	-0.021	0.000	0.000	0.000	0.000
33	A	35	ALA	0	-0.014	-0.009	14.628	-0.034	-0.034	0.000	0.000	0.000	0.000
34	A	36	ALA	0	0.005	0.003	15.900	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	37	PHE	0	-0.024	-0.011	15.078	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	38	HIS	0	0.025	0.006	11.821	-0.051	-0.051	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.930	0.981	13.601	0.153	0.153	0.000	0.000	0.000	0.000
38	A	40	ILE	0	-0.036	-0.008	10.438	0.008	0.008	0.000	0.000	0.000	0.000
39	A	41	ASN	0	0.046	0.014	13.212	0.026	0.026	0.000	0.000	0.000	0.000
40	A	42	PRO	0	0.090	0.021	13.453	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	43	ALA	0	-0.037	-0.021	14.394	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	44	THR	0	0.018	0.015	8.312	0.060	0.060	0.000	0.000	0.000	0.000
43	A	45	ALA	0	0.052	0.032	9.925	-0.033	-0.033	0.000	0.000	0.000	0.000
44	A	46	ARG	1	0.929	0.971	12.056	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	47	ASN	0	0.025	0.019	10.219	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	48	GLY	0	0.028	0.025	8.651	0.025	0.025	0.000	0.000	0.000	0.000
47	A	49	LEU	0	-0.018	-0.016	9.475	0.005	0.005	0.000	0.000	0.000	0.000
48	A	50	THR	0	-0.075	-0.056	13.021	0.007	0.007	0.000	0.000	0.000	0.000
49	A	51	LEU	0	0.050	0.037	8.154	0.004	0.004	0.000	0.000	0.000	0.000
50	A	52	LEU	0	-0.008	-0.007	10.030	0.002	0.002	0.000	0.000	0.000	0.000
51	A	53	VAL	0	-0.066	-0.026	13.226	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.922	-0.970	13.637	0.141	0.141	0.000	0.000	0.000	0.000
53	A	55	ALA	0	-0.037	-0.010	12.794	0.007	0.007	0.000	0.000	0.000	0.000
54	A	56	GLY	0	0.038	0.021	14.946	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	57	ILE	0	-0.018	-0.006	12.854	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	58	LEU	0	-0.035	-0.018	14.674	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	59	TYR	0	0.025	0.010	18.074	0.024	0.024	0.000	0.000	0.000	0.000
58	A	60	LYS	1	0.883	0.916	19.919	0.027	0.027	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.868	0.957	23.148	0.078	0.078	0.000	0.000	0.000	0.000
60	A	62	ARG	1	0.980	0.962	26.327	0.007	0.007	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.012	0.010	28.066	0.000	0.000	0.000	0.000	0.000	0.000
62	A	64	ILE	0	-0.005	0.017	27.079	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	65	GLY	0	0.023	-0.003	23.567	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	66	MET	0	0.002	0.032	17.552	0.019	0.019	0.000	0.000	0.000	0.000
65	A	67	PHE	0	0.026	0.015	20.816	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	68	VAL	0	0.073	0.044	18.084	0.005	0.005	0.000	0.000	0.000	0.000
67	A	69	SER	0	-0.019	-0.010	19.406	0.010	0.010	0.000	0.000	0.000	0.000
68	A	70	ALA	0	0.041	0.007	20.992	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	71	GLN	0	0.024	0.019	20.975	0.001	0.001	0.000	0.000	0.000	0.000
70	A	72	ALA	0	0.004	0.009	16.956	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	73	PRO	0	0.022	-0.003	16.864	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	74	ALA	0	-0.016	0.016	17.640	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	75	LEU	0	0.048	0.022	16.636	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	76	ILE	0	-0.059	-0.033	11.870	0.003	0.003	0.000	0.000	0.000	0.000
75	A	77	ARG	1	0.904	0.964	13.370	0.154	0.154	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.888	-0.950	15.613	-0.059	-0.059	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.825	0.885	8.656	0.190	0.190	0.000	0.000	0.000	0.000
78	A	80	ARG	1	0.748	0.845	8.845	0.497	0.497	0.000	0.000	0.000	0.000
79	A	81	ASP	-1	-0.823	-0.920	12.661	-0.156	-0.156	0.000	0.000	0.000	0.000
80	A	82	ALA	0	-0.005	0.000	15.520	0.016	0.016	0.000	0.000	0.000	0.000
81	A	83	ALA	0	-0.009	-0.001	10.372	0.027	0.027	0.000	0.000	0.000	0.000
82	A	84	PHE	0	0.000	0.009	12.526	0.019	0.019	0.000	0.000	0.000	0.000
83	A	85	ALA	0	0.029	0.006	13.765	0.019	0.019	0.000	0.000	0.000	0.000
84	A	86	ALA	0	-0.015	-0.014	13.872	0.013	0.013	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.058	-0.038	10.607	0.039	0.039	0.000	0.000	0.000	0.000
86	A	88	TYR	0	-0.036	-0.028	10.592	0.010	0.010	0.000	0.000	0.000	0.000
87	A	89	VAL	0	-0.028	-0.007	16.242	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	90	ALA	0	0.000	0.006	18.098	0.004	0.004	0.000	0.000	0.000	0.000
89	A	91	PRO	0	0.068	0.038	16.520	0.000	0.000	0.000	0.000	0.000	0.000
90	A	92	LEU	0	-0.002	0.014	19.821	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.028	-0.011	21.876	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.895	-0.949	21.604	0.091	0.091	0.000	0.000	0.000	0.000
93	A	95	GLU	-1	-0.834	-0.917	23.360	0.072	0.072	0.000	0.000	0.000	0.000
94	A	96	SER	0	-0.049	-0.047	25.148	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	97	ILE	0	-0.058	-0.026	27.246	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	98	HIS	0	-0.121	-0.057	26.943	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	99	LEU	0	-0.024	-0.011	28.026	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	100	GLY	0	-0.014	0.009	31.010	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	101	PHE	0	-0.060	-0.035	28.367	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	102	THR	0	0.030	0.009	32.488	0.000	0.000	0.000	0.000	0.000	0.000
101	A	103	ARG	1	0.934	0.945	31.371	0.009	0.009	0.000	0.000	0.000	0.000
102	A	104	ALA	0	0.002	-0.004	32.090	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.960	0.997	32.300	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	106	ILE	0	0.069	0.033	25.773	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	107	HIS	0	0.014	0.008	28.677	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	108	ALA	0	0.063	0.031	30.351	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.032	-0.013	28.543	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	110	LEU	0	-0.015	0.003	24.089	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	111	ASP	-1	-0.883	-0.944	27.362	-0.047	-0.047	0.000	0.000	0.000	0.000
110	A	112	GLN	0	0.001	-0.001	29.984	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	113	VAL	0	-0.033	-0.020	24.627	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	114	ALA	0	-0.023	-0.005	26.107	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.968	-0.978	27.095	-0.052	-0.052	0.000	0.000	0.000	0.000
114	A	116	SER	0	-0.073	-0.032	30.143	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	117	ARG	1	0.861	0.934	24.093	0.095	0.095	0.000	0.000	0.000	0.000

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