FMO DATABASE

FMODB ID: 525GZ

Calculation Name: 5EKQ-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5EKQ

Chain ID: E

ChEMBL ID:

UniProt ID: P0A940

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-562083.413095
FMO2-HF: Nuclear repulsion	527058.485403
FMO2-HF: Total energy	-35024.927692
FMO2-MP2: Total energy	-35127.574903

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(E:22:THR)

Summations of interaction energy for fragment #1(E:22:THR)

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.
-8.022	-2.113	1.111	-3.4	-3.619	-0.023

Interaction energy analysis for fragmet #1(E:22:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.022

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

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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	E	24	GLU	-1	-0.865	-0.934	2.749	-9.796	-3.887	1.111	-3.400	-3.619	-0.023
4	E	25	ARG	1	0.887	0.939	5.427	2.244	2.244	0.000	0.000	0.000	0.000
5	E	26	VAL	0	-0.004	0.005	6.895	-0.564	-0.564	0.000	0.000	0.000	0.000
6	E	27	VAL	0	-0.017	0.003	9.126	0.266	0.266	0.000	0.000	0.000	0.000
7	E	28	TYR	0	0.029	0.003	11.859	-0.051	-0.051	0.000	0.000	0.000	0.000
8	E	29	ARG	1	0.816	0.897	15.091	0.359	0.359	0.000	0.000	0.000	0.000
9	E	30	PRO	0	0.005	0.020	17.294	-0.010	-0.010	0.000	0.000	0.000	0.000
10	E	31	ASP	-1	-0.828	-0.912	20.750	-0.247	-0.247	0.000	0.000	0.000	0.000
11	E	32	ILE	0	-0.042	-0.009	20.066	0.023	0.023	0.000	0.000	0.000	0.000
12	E	33	ASN	0	0.007	0.002	23.683	-0.008	-0.008	0.000	0.000	0.000	0.000
13	E	34	GLN	0	-0.041	-0.032	25.573	0.018	0.018	0.000	0.000	0.000	0.000
14	E	35	GLY	0	0.051	0.028	28.264	-0.002	-0.002	0.000	0.000	0.000	0.000
15	E	36	ASN	0	-0.018	-0.003	31.428	0.001	0.001	0.000	0.000	0.000	0.000
16	E	37	TYR	0	0.039	0.009	32.718	-0.006	-0.006	0.000	0.000	0.000	0.000
17	E	38	LEU	0	-0.021	-0.011	33.858	0.006	0.006	0.000	0.000	0.000	0.000
18	E	39	THR	0	0.000	-0.030	34.856	-0.006	-0.006	0.000	0.000	0.000	0.000
19	E	40	ALA	0	0.027	0.028	35.722	-0.001	-0.001	0.000	0.000	0.000	0.000
20	E	41	ASN	0	0.005	-0.020	37.459	0.006	0.006	0.000	0.000	0.000	0.000
21	E	42	ASP	-1	-0.812	-0.889	40.626	-0.056	-0.056	0.000	0.000	0.000	0.000
22	E	43	VAL	0	0.030	0.017	37.384	0.004	0.004	0.000	0.000	0.000	0.000
23	E	44	SER	0	-0.015	-0.002	40.816	0.003	0.003	0.000	0.000	0.000	0.000
24	E	45	LYS	1	0.790	0.905	43.599	0.052	0.052	0.000	0.000	0.000	0.000
25	E	46	ILE	0	-0.024	0.010	42.673	0.003	0.003	0.000	0.000	0.000	0.000
26	E	47	ARG	1	0.910	0.935	45.838	0.038	0.038	0.000	0.000	0.000	0.000
27	E	48	VAL	0	0.054	0.014	47.366	0.001	0.001	0.000	0.000	0.000	0.000
28	E	49	GLY	0	0.021	0.015	49.262	0.000	0.000	0.000	0.000	0.000	0.000
29	E	50	MET	0	-0.034	-0.008	48.028	0.001	0.001	0.000	0.000	0.000	0.000
30	E	51	THR	0	0.045	0.019	50.145	0.001	0.001	0.000	0.000	0.000	0.000
31	E	52	GLN	0	0.060	0.049	46.687	0.001	0.001	0.000	0.000	0.000	0.000
32	E	53	GLN	0	0.010	-0.011	47.676	-0.002	-0.002	0.000	0.000	0.000	0.000
33	E	54	GLN	0	0.018	-0.009	48.994	-0.001	-0.001	0.000	0.000	0.000	0.000
34	E	55	VAL	0	-0.007	0.009	43.529	-0.002	-0.002	0.000	0.000	0.000	0.000
35	E	56	ALA	0	0.025	0.011	44.375	-0.003	-0.003	0.000	0.000	0.000	0.000
36	E	57	TYR	0	-0.077	-0.028	45.309	-0.002	-0.002	0.000	0.000	0.000	0.000
37	E	58	ALA	0	-0.031	-0.016	45.714	-0.002	-0.002	0.000	0.000	0.000	0.000
38	E	59	LEU	0	0.014	0.012	39.875	-0.003	-0.003	0.000	0.000	0.000	0.000
39	E	60	GLY	0	0.043	0.040	40.353	-0.003	-0.003	0.000	0.000	0.000	0.000
40	E	61	THR	0	0.017	0.004	40.955	0.001	0.001	0.000	0.000	0.000	0.000
41	E	62	PRO	0	-0.029	0.008	38.248	-0.003	-0.003	0.000	0.000	0.000	0.000
42	E	63	LEU	0	-0.008	-0.022	33.632	0.003	0.003	0.000	0.000	0.000	0.000
43	E	64	MET	0	-0.040	-0.013	30.950	0.000	0.000	0.000	0.000	0.000	0.000
44	E	65	SER	0	-0.008	-0.013	35.900	-0.003	-0.003	0.000	0.000	0.000	0.000
45	E	66	ASP	-1	-0.709	-0.823	37.676	-0.009	-0.009	0.000	0.000	0.000	0.000
46	E	67	PRO	0	-0.061	-0.002	37.838	0.000	0.000	0.000	0.000	0.000	0.000
47	E	68	PHE	0	0.000	-0.010	35.281	-0.001	-0.001	0.000	0.000	0.000	0.000
48	E	69	GLY	0	-0.022	-0.017	40.646	0.002	0.002	0.000	0.000	0.000	0.000
49	E	70	THR	0	-0.105	-0.056	41.814	0.001	0.001	0.000	0.000	0.000	0.000
50	E	71	ASN	0	-0.046	-0.033	44.243	-0.001	-0.001	0.000	0.000	0.000	0.000
51	E	72	THR	0	0.008	-0.020	39.685	-0.002	-0.002	0.000	0.000	0.000	0.000
52	E	73	TRP	0	-0.032	-0.020	39.676	-0.001	-0.001	0.000	0.000	0.000	0.000
53	E	74	PHE	0	0.027	0.001	34.198	-0.003	-0.003	0.000	0.000	0.000	0.000
54	E	75	TYR	0	0.008	-0.010	35.120	-0.001	-0.001	0.000	0.000	0.000	0.000
55	E	76	VAL	0	-0.018	-0.012	28.932	-0.004	-0.004	0.000	0.000	0.000	0.000
56	E	77	PHE	0	-0.007	0.015	29.201	0.001	0.001	0.000	0.000	0.000	0.000
57	E	78	ARG	1	0.937	0.942	20.695	0.098	0.098	0.000	0.000	0.000	0.000
58	E	79	GLN	0	-0.014	-0.014	24.902	0.007	0.007	0.000	0.000	0.000	0.000
59	E	80	GLN	0	-0.020	-0.021	17.830	-0.017	-0.017	0.000	0.000	0.000	0.000
60	E	81	PRO	0	0.101	0.066	20.979	-0.002	-0.002	0.000	0.000	0.000	0.000
61	E	82	GLY	0	0.029	0.008	18.998	-0.028	-0.028	0.000	0.000	0.000	0.000
62	E	83	HIS	0	-0.041	-0.032	12.652	-0.005	-0.005	0.000	0.000	0.000	0.000
63	E	84	GLU	-1	-0.943	-0.957	15.101	-0.340	-0.340	0.000	0.000	0.000	0.000
64	E	85	GLY	0	0.039	0.016	16.814	-0.016	-0.016	0.000	0.000	0.000	0.000
65	E	86	VAL	0	-0.077	-0.036	17.779	0.022	0.022	0.000	0.000	0.000	0.000
66	E	87	THR	0	0.020	0.015	20.343	0.001	0.001	0.000	0.000	0.000	0.000
67	E	88	GLN	0	0.019	0.008	23.953	0.005	0.005	0.000	0.000	0.000	0.000
68	E	89	GLN	0	0.040	0.031	26.601	0.003	0.003	0.000	0.000	0.000	0.000
69	E	90	THR	0	-0.053	-0.040	29.455	0.003	0.003	0.000	0.000	0.000	0.000
70	E	91	LEU	0	0.013	0.031	32.062	0.002	0.002	0.000	0.000	0.000	0.000
71	E	92	THR	0	-0.080	-0.058	34.726	0.002	0.002	0.000	0.000	0.000	0.000
72	E	93	LEU	0	0.000	0.002	37.396	0.000	0.000	0.000	0.000	0.000	0.000
73	E	94	THR	0	0.049	0.020	41.169	0.002	0.002	0.000	0.000	0.000	0.000
74	E	95	PHE	0	0.001	-0.002	43.190	-0.001	-0.001	0.000	0.000	0.000	0.000
75	E	96	ASN	0	0.037	0.023	46.910	0.002	0.002	0.000	0.000	0.000	0.000
76	E	97	SER	0	0.023	-0.010	50.057	-0.001	-0.001	0.000	0.000	0.000	0.000
77	E	98	SER	0	-0.038	-0.015	52.040	0.001	0.001	0.000	0.000	0.000	0.000
78	E	99	GLY	0	0.015	0.027	50.211	-0.001	-0.001	0.000	0.000	0.000	0.000
79	E	100	VAL	0	-0.034	-0.018	51.093	-0.002	-0.002	0.000	0.000	0.000	0.000
80	E	101	LEU	0	-0.039	-0.003	45.113	0.001	0.001	0.000	0.000	0.000	0.000
81	E	102	THR	0	-0.012	-0.031	47.152	0.000	0.000	0.000	0.000	0.000	0.000
82	E	103	ASN	0	0.000	-0.006	41.509	0.000	0.000	0.000	0.000	0.000	0.000
83	E	104	ILE	0	-0.004	0.006	40.434	-0.001	-0.001	0.000	0.000	0.000	0.000
84	E	105	ASP	-1	-0.769	-0.838	35.543	-0.039	-0.039	0.000	0.000	0.000	0.000
85	E	106	ASN	0	-0.028	-0.030	35.199	-0.004	-0.004	0.000	0.000	0.000	0.000
86	E	107	LYS	1	0.847	0.918	30.316	0.045	0.045	0.000	0.000	0.000	0.000
87	E	108	PRO	0	0.018	0.004	30.241	-0.003	-0.003	0.000	0.000	0.000	0.000
88	E	109	ALA	0	0.006	0.006	25.346	-0.001	-0.001	0.000	0.000	0.000	0.000
89	E	110	LEU	0	-0.033	-0.025	21.973	0.010	0.010	0.000	0.000	0.000	0.000
90	E	111	SER	0	0.005	0.018	22.701	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:22:THR)