FMO DATABASE

FMODB ID: 9L892

Calculation Name: 5EKQ-E-Xray540

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: 2025-07-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	168
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-562625.321073
FMO2-HF: Nuclear repulsion	527618.17268
FMO2-HF: Total energy	-35007.148393
FMO2-MP2: Total energy	-35109.435673

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.
-1.598	0.516	0.01	-0.938	-1.187	0.002

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 : 0.055 / q_NPA : 0.017

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].
4	E	23	LEU	0	-0.087	0.097	3.545	-0.359	0.200	0.030	-0.223	-0.367	0.001
5	E	24	GLU	0	0.092	-0.081	3.802	0.061	1.431	-0.019	-0.705	-0.646	0.001
6	E	24	GLU	-1	-1.016	-0.873	4.558	-2.048	-1.863	-0.001	-0.010	-0.174	0.000
7	E	25	ARG	0	0.021	-0.137	6.429	0.705	0.705	0.000	0.000	0.000	0.000
8	E	25	ARG	1	0.909	1.069	9.073	0.867	0.867	0.000	0.000	0.000	0.000
9	E	26	VAL	0	-0.002	-0.065	8.021	-0.538	-0.538	0.000	0.000	0.000	0.000
10	E	26	VAL	0	-0.047	0.088	7.095	0.068	0.068	0.000	0.000	0.000	0.000
11	E	27	VAL	0	0.074	-0.100	9.684	0.031	0.031	0.000	0.000	0.000	0.000
12	E	27	VAL	0	-0.037	0.092	12.471	0.003	0.003	0.000	0.000	0.000	0.000
13	E	28	TYR	0	0.118	-0.028	12.102	0.003	0.003	0.000	0.000	0.000	0.000
14	E	28	TYR	0	-0.081	0.069	16.433	0.001	0.001	0.000	0.000	0.000	0.000
15	E	29	ARG	0	0.068	-0.136	15.203	0.063	0.063	0.000	0.000	0.000	0.000
16	E	29	ARG	1	0.792	1.032	15.647	-0.209	-0.209	0.000	0.000	0.000	0.000
17	E	30	PRO	0	-0.028	-0.093	17.538	-0.036	-0.036	0.000	0.000	0.000	0.000
18	E	31	ASP	0	0.177	0.001	20.575	0.032	0.032	0.000	0.000	0.000	0.000
19	E	31	ASP	-1	-0.948	-0.806	22.829	0.027	0.027	0.000	0.000	0.000	0.000
20	E	32	ILE	0	0.028	-0.124	22.496	-0.004	-0.004	0.000	0.000	0.000	0.000
21	E	32	ILE	0	-0.119	0.099	19.940	0.007	0.007	0.000	0.000	0.000	0.000
22	E	33	ASN	0	0.079	-0.088	23.602	0.007	0.007	0.000	0.000	0.000	0.000
23	E	33	ASN	0	-0.077	0.090	27.074	-0.003	-0.003	0.000	0.000	0.000	0.000
24	E	34	GLN	0	0.056	-0.142	26.742	-0.001	-0.001	0.000	0.000	0.000	0.000
25	E	34	GLN	0	-0.115	0.103	25.117	0.014	0.014	0.000	0.000	0.000	0.000
26	E	35	GLY	0	0.061	-0.078	27.854	0.003	0.003	0.000	0.000	0.000	0.000
27	E	36	ASN	0	0.062	0.023	30.993	-0.004	-0.004	0.000	0.000	0.000	0.000
28	E	36	ASN	0	-0.091	0.080	35.079	0.006	0.006	0.000	0.000	0.000	0.000
29	E	37	TYR	0	0.169	-0.079	33.359	0.003	0.003	0.000	0.000	0.000	0.000
30	E	37	TYR	0	-0.090	0.109	32.633	-0.001	-0.001	0.000	0.000	0.000	0.000
31	E	38	LEU	0	0.065	-0.093	34.536	-0.004	-0.004	0.000	0.000	0.000	0.000
32	E	38	LEU	0	-0.091	0.107	33.896	0.000	0.000	0.000	0.000	0.000	0.000
33	E	39	THR	0	-0.035	-0.130	35.126	0.002	0.002	0.000	0.000	0.000	0.000
34	E	39	THR	0	-0.033	0.040	37.895	0.000	0.000	0.000	0.000	0.000	0.000
35	E	40	ALA	0	0.232	-0.014	36.841	-0.004	-0.004	0.000	0.000	0.000	0.000
36	E	40	ALA	0	-0.093	0.096	36.393	-0.001	-0.001	0.000	0.000	0.000	0.000
37	E	41	ASN	0	0.081	-0.096	37.896	0.004	0.004	0.000	0.000	0.000	0.000
38	E	41	ASN	0	-0.106	0.076	41.543	-0.002	-0.002	0.000	0.000	0.000	0.000
39	E	42	ASP	0	0.109	-0.102	40.880	-0.002	-0.002	0.000	0.000	0.000	0.000
40	E	42	ASP	-1	-0.889	-0.781	40.566	0.035	0.035	0.000	0.000	0.000	0.000
41	E	43	VAL	0	0.109	-0.100	39.482	0.001	0.001	0.000	0.000	0.000	0.000
42	E	43	VAL	0	-0.060	0.106	37.383	0.001	0.001	0.000	0.000	0.000	0.000
43	E	44	SER	0	-0.022	-0.098	40.831	0.003	0.003	0.000	0.000	0.000	0.000
44	E	44	SER	0	-0.041	0.079	42.684	-0.002	-0.002	0.000	0.000	0.000	0.000
45	E	45	LYS	0	0.003	-0.132	43.474	-0.003	-0.003	0.000	0.000	0.000	0.000
46	E	45	LYS	1	0.815	1.052	44.806	-0.035	-0.035	0.000	0.000	0.000	0.000
47	E	46	ILE	0	0.010	-0.127	44.527	-0.002	-0.002	0.000	0.000	0.000	0.000
48	E	46	ILE	0	-0.033	0.133	42.563	0.001	0.001	0.000	0.000	0.000	0.000
49	E	47	ARG	0	0.052	-0.123	45.788	-0.001	-0.001	0.000	0.000	0.000	0.000
50	E	47	ARG	1	0.879	1.068	48.326	-0.033	-0.033	0.000	0.000	0.000	0.000
51	E	48	VAL	0	0.088	-0.108	48.372	0.002	0.002	0.000	0.000	0.000	0.000
52	E	48	VAL	0	-0.051	0.133	47.612	0.000	0.000	0.000	0.000	0.000	0.000
53	E	49	GLY	0	0.003	-0.099	49.602	-0.003	-0.003	0.000	0.000	0.000	0.000
54	E	50	MET	0	0.083	-0.002	49.372	-0.002	-0.002	0.000	0.000	0.000	0.000
55	E	50	MET	0	-0.115	0.101	48.067	0.000	0.000	0.000	0.000	0.000	0.000
56	E	51	THR	0	0.094	-0.052	50.797	0.002	0.002	0.000	0.000	0.000	0.000
57	E	51	THR	0	-0.072	0.069	52.303	-0.001	-0.001	0.000	0.000	0.000	0.000
58	E	52	GLN	0	0.075	-0.098	47.766	0.000	0.000	0.000	0.000	0.000	0.000
59	E	52	GLN	0	0.008	0.137	46.509	0.001	0.001	0.000	0.000	0.000	0.000
60	E	53	GLN	0	0.093	-0.111	47.907	0.003	0.003	0.000	0.000	0.000	0.000
61	E	53	GLN	0	-0.062	0.111	51.466	-0.001	-0.001	0.000	0.000	0.000	0.000
62	E	54	GLN	0	0.064	-0.131	49.495	0.000	0.000	0.000	0.000	0.000	0.000
63	E	54	GLN	0	-0.061	0.089	50.787	-0.001	-0.001	0.000	0.000	0.000	0.000
64	E	55	VAL	0	0.078	-0.097	45.876	-0.003	-0.003	0.000	0.000	0.000	0.000
65	E	55	VAL	0	-0.062	0.109	43.825	0.000	0.000	0.000	0.000	0.000	0.000
66	E	56	ALA	0	0.053	-0.088	44.560	0.000	0.000	0.000	0.000	0.000	0.000
67	E	56	ALA	0	-0.039	0.105	45.605	0.001	0.001	0.000	0.000	0.000	0.000
68	E	57	TYR	0	0.016	-0.055	45.647	0.001	0.001	0.000	0.000	0.000	0.000
69	E	57	TYR	0	-0.131	0.048	49.001	-0.001	-0.001	0.000	0.000	0.000	0.000
70	E	58	ALA	0	0.118	-0.073	45.114	0.000	0.000	0.000	0.000	0.000	0.000
71	E	58	ALA	0	-0.131	0.061	45.302	-0.001	-0.001	0.000	0.000	0.000	0.000
72	E	59	LEU	0	-0.015	-0.140	41.768	-0.003	-0.003	0.000	0.000	0.000	0.000
73	E	59	LEU	0	-0.058	0.098	40.339	0.001	0.001	0.000	0.000	0.000	0.000
74	E	60	GLY	0	0.065	-0.069	40.639	0.000	0.000	0.000	0.000	0.000	0.000
75	E	61	THR	0	0.054	0.005	41.652	0.000	0.000	0.000	0.000	0.000	0.000
76	E	61	THR	0	-0.032	0.101	40.772	-0.002	-0.002	0.000	0.000	0.000	0.000
77	E	62	PRO	0	-0.028	-0.084	38.326	0.002	0.002	0.000	0.000	0.000	0.000
78	E	63	LEU	0	0.104	-0.003	35.277	-0.001	-0.001	0.000	0.000	0.000	0.000
79	E	63	LEU	0	-0.111	0.081	33.786	0.000	0.000	0.000	0.000	0.000	0.000
80	E	64	MET	0	0.058	-0.086	34.346	0.008	0.008	0.000	0.000	0.000	0.000
81	E	64	MET	0	-0.103	0.084	30.717	0.004	0.004	0.000	0.000	0.000	0.000
82	E	65	SER	0	0.077	-0.043	35.672	-0.005	-0.005	0.000	0.000	0.000	0.000
83	E	65	SER	0	-0.026	0.062	40.028	-0.001	-0.001	0.000	0.000	0.000	0.000
84	E	66	ASP	0	0.162	-0.135	37.533	0.010	0.010	0.000	0.000	0.000	0.000
85	E	66	ASP	-1	-0.968	-0.752	39.619	0.115	0.115	0.000	0.000	0.000	0.000
86	E	67	PRO	0	-0.093	-0.091	37.471	-0.005	-0.005	0.000	0.000	0.000	0.000
87	E	68	PHE	0	0.118	-0.008	37.931	0.005	0.005	0.000	0.000	0.000	0.000
88	E	68	PHE	0	-0.104	0.092	35.524	0.000	0.000	0.000	0.000	0.000	0.000
89	E	69	GLY	0	0.020	-0.099	40.608	-0.001	-0.001	0.000	0.000	0.000	0.000
90	E	70	THR	0	-0.010	0.030	42.680	-0.007	-0.007	0.000	0.000	0.000	0.000
91	E	70	THR	0	-0.067	0.022	41.329	0.001	0.001	0.000	0.000	0.000	0.000
92	E	71	ASN	0	0.173	-0.065	43.501	0.003	0.003	0.000	0.000	0.000	0.000
93	E	71	ASN	0	-0.182	0.045	44.816	0.002	0.002	0.000	0.000	0.000	0.000
94	E	72	THR	0	-0.018	-0.126	40.349	-0.006	-0.006	0.000	0.000	0.000	0.000
95	E	72	THR	0	-0.027	0.072	39.422	0.002	0.002	0.000	0.000	0.000	0.000
96	E	73	TRP	0	0.128	-0.080	39.800	0.006	0.006	0.000	0.000	0.000	0.000
97	E	73	TRP	0	-0.122	0.074	40.480	-0.002	-0.002	0.000	0.000	0.000	0.000
98	E	74	PHE	0	0.075	-0.104	35.229	-0.007	-0.007	0.000	0.000	0.000	0.000
99	E	74	PHE	0	-0.096	0.099	34.244	0.003	0.003	0.000	0.000	0.000	0.000
100	E	75	TYR	0	0.100	-0.088	35.609	0.005	0.005	0.000	0.000	0.000	0.000
101	E	75	TYR	0	-0.110	0.067	36.332	-0.002	-0.002	0.000	0.000	0.000	0.000
102	E	76	VAL	0	0.120	-0.092	30.984	-0.006	-0.006	0.000	0.000	0.000	0.000
103	E	76	VAL	0	-0.080	0.105	28.984	0.002	0.002	0.000	0.000	0.000	0.000
104	E	77	PHE	0	0.151	-0.084	30.497	0.003	0.003	0.000	0.000	0.000	0.000
105	E	77	PHE	0	-0.146	0.093	29.240	-0.001	-0.001	0.000	0.000	0.000	0.000
106	E	78	ARG	0	0.168	-0.036	26.178	-0.005	-0.005	0.000	0.000	0.000	0.000
107	E	78	ARG	1	0.812	1.005	20.619	-0.252	-0.252	0.000	0.000	0.000	0.000
108	E	79	GLN	0	0.037	-0.111	24.958	0.006	0.006	0.000	0.000	0.000	0.000
109	E	79	GLN	0	-0.065	0.105	25.448	-0.010	-0.010	0.000	0.000	0.000	0.000
110	E	80	GLN	0	0.123	-0.070	20.699	-0.005	-0.005	0.000	0.000	0.000	0.000
111	E	80	GLN	0	-0.142	0.070	17.542	0.010	0.010	0.000	0.000	0.000	0.000
112	E	81	PRO	0	0.069	-0.070	21.016	0.023	0.023	0.000	0.000	0.000	0.000
113	E	82	GLY	0	0.081	0.026	19.036	0.004	0.004	0.000	0.000	0.000	0.000
114	E	83	HIS	0	-0.084	-0.047	14.819	-0.026	-0.026	0.000	0.000	0.000	0.000
115	E	83	HIS	0	-0.024	0.098	12.498	-0.035	-0.035	0.000	0.000	0.000	0.000
116	E	84	GLU	0	0.070	-0.095	15.290	-0.006	-0.006	0.000	0.000	0.000	0.000
117	E	84	GLU	-1	-1.027	-0.859	19.437	-0.056	-0.056	0.000	0.000	0.000	0.000
118	E	85	GLY	0	0.033	-0.098	16.995	0.005	0.005	0.000	0.000	0.000	0.000
119	E	86	VAL	0	0.047	-0.006	18.509	-0.014	-0.014	0.000	0.000	0.000	0.000
120	E	86	VAL	0	-0.117	0.065	18.714	0.009	0.009	0.000	0.000	0.000	0.000
121	E	87	THR	0	0.022	-0.102	20.830	0.002	0.002	0.000	0.000	0.000	0.000
122	E	87	THR	0	-0.027	0.110	23.258	-0.007	-0.007	0.000	0.000	0.000	0.000
123	E	88	GLN	0	0.164	-0.079	24.403	-0.004	-0.004	0.000	0.000	0.000	0.000
124	E	88	GLN	0	-0.103	0.092	25.513	0.019	0.019	0.000	0.000	0.000	0.000
125	E	89	GLN	0	0.087	-0.094	26.821	0.003	0.003	0.000	0.000	0.000	0.000
126	E	89	GLN	0	-0.078	0.096	30.740	-0.001	-0.001	0.000	0.000	0.000	0.000
127	E	90	THR	0	-0.028	-0.073	30.231	-0.001	-0.001	0.000	0.000	0.000	0.000
128	E	90	THR	0	-0.075	0.021	29.427	0.007	0.007	0.000	0.000	0.000	0.000
129	E	91	LEU	0	0.211	-0.044	32.020	-0.001	-0.001	0.000	0.000	0.000	0.000
130	E	91	LEU	0	-0.152	0.086	36.134	-0.002	-0.002	0.000	0.000	0.000	0.000
131	E	92	THR	0	0.013	-0.075	35.831	0.000	0.000	0.000	0.000	0.000	0.000
132	E	92	THR	0	-0.067	0.072	34.777	0.002	0.002	0.000	0.000	0.000	0.000
133	E	93	LEU	0	0.062	-0.103	37.405	-0.004	-0.004	0.000	0.000	0.000	0.000
134	E	93	LEU	0	-0.071	0.097	39.838	-0.001	-0.001	0.000	0.000	0.000	0.000
135	E	94	THR	0	0.113	-0.065	41.204	0.005	0.005	0.000	0.000	0.000	0.000
136	E	94	THR	0	-0.023	0.089	41.678	0.001	0.001	0.000	0.000	0.000	0.000
137	E	95	PHE	0	-0.013	-0.109	43.389	-0.005	-0.005	0.000	0.000	0.000	0.000
138	E	95	PHE	0	-0.024	0.143	43.184	-0.001	-0.001	0.000	0.000	0.000	0.000
139	E	96	ASN	0	0.125	-0.010	46.763	0.004	0.004	0.000	0.000	0.000	0.000
140	E	96	ASN	0	-0.087	0.030	50.661	0.000	0.000	0.000	0.000	0.000	0.000
141	E	97	SER	0	0.083	-0.081	49.772	0.002	0.002	0.000	0.000	0.000	0.000
142	E	97	SER	0	-0.033	0.071	52.208	-0.001	-0.001	0.000	0.000	0.000	0.000
143	E	98	SER	0	-0.023	-0.095	51.928	0.001	0.001	0.000	0.000	0.000	0.000
144	E	98	SER	0	-0.061	0.065	54.577	-0.001	-0.001	0.000	0.000	0.000	0.000
145	E	99	GLY	0	0.014	-0.073	50.399	-0.002	-0.002	0.000	0.000	0.000	0.000
146	E	100	VAL	0	0.114	0.001	50.820	0.000	0.000	0.000	0.000	0.000	0.000
147	E	100	VAL	0	-0.119	0.101	51.539	0.000	0.000	0.000	0.000	0.000	0.000
148	E	101	LEU	0	0.096	-0.110	46.868	0.002	0.002	0.000	0.000	0.000	0.000
149	E	101	LEU	0	-0.104	0.108	45.336	0.000	0.000	0.000	0.000	0.000	0.000
150	E	102	THR	0	0.056	-0.098	47.234	-0.004	-0.004	0.000	0.000	0.000	0.000
151	E	102	THR	0	-0.062	0.054	47.022	0.001	0.001	0.000	0.000	0.000	0.000
152	E	103	ASN	0	0.069	-0.039	43.991	-0.004	-0.004	0.000	0.000	0.000	0.000
153	E	103	ASN	0	-0.103	0.052	41.665	0.004	0.004	0.000	0.000	0.000	0.000
154	E	104	ILE	0	0.051	-0.137	41.682	0.003	0.003	0.000	0.000	0.000	0.000
155	E	104	ILE	0	-0.071	0.097	40.882	-0.001	-0.001	0.000	0.000	0.000	0.000
156	E	105	ASP	0	0.105	-0.082	37.985	-0.006	-0.006	0.000	0.000	0.000	0.000
157	E	105	ASP	-1	-0.961	-0.831	35.863	0.102	0.102	0.000	0.000	0.000	0.000
158	E	106	ASN	0	0.120	-0.072	35.797	0.006	0.006	0.000	0.000	0.000	0.000
159	E	106	ASN	0	-0.134	0.051	35.290	-0.004	-0.004	0.000	0.000	0.000	0.000
160	E	107	LYS	0	0.116	-0.079	32.213	-0.007	-0.007	0.000	0.000	0.000	0.000
161	E	107	LYS	1	0.809	1.052	30.819	-0.130	-0.130	0.000	0.000	0.000	0.000
162	E	108	PRO	0	-0.027	-0.125	30.834	0.009	0.009	0.000	0.000	0.000	0.000
163	E	109	ALA	0	0.163	0.078	26.652	0.002	0.002	0.000	0.000	0.000	0.000
164	E	109	ALA	0	-0.097	0.072	25.995	-0.003	-0.003	0.000	0.000	0.000	0.000
165	E	110	LEU	0	-0.023	-0.154	24.297	0.003	0.003	0.000	0.000	0.000	0.000
166	E	110	LEU	0	-0.039	0.074	22.636	0.006	0.006	0.000	0.000	0.000	0.000
167	E	111	SER	0	-0.126	-0.136	22.865	-0.005	-0.005	0.000	0.000	0.000	0.000
168	E	111	SER	0	0.114	0.085	24.111	-0.011	-0.011	0.000	0.000	0.000	0.000

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