FMO DATABASE

FMODB ID: MRNYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-562066.415678
FMO2-HF: Nuclear repulsion	527058.485403
FMO2-HF: Total energy	-35007.930274
FMO2-MP2: Total energy	-35110.157914

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.
-2.692	0.976	0.769	-1.956	-2.482	-0.007

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 : 0.064 / q_NPA : 0.033

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	-0.085	0.097	3.234	-0.399	0.342	0.097	-0.324	-0.515	0.002
5	E	24	GLU	0	0.031	-0.109	3.870	-0.471	1.441	-0.014	-1.105	-0.792	0.001
6	E	24	GLU	-1	-0.915	-0.853	2.749	-2.434	-1.419	0.686	-0.527	-1.175	-0.010
7	E	25	ARG	0	0.024	-0.121	5.829	0.591	0.591	0.000	0.000	0.000	0.000
8	E	25	ARG	1	0.892	1.059	8.528	0.819	0.819	0.000	0.000	0.000	0.000
9	E	26	VAL	0	-0.002	-0.095	7.611	-0.606	-0.606	0.000	0.000	0.000	0.000
10	E	26	VAL	0	-0.023	0.111	7.064	0.069	0.069	0.000	0.000	0.000	0.000
11	E	27	VAL	0	0.049	-0.090	9.668	0.094	0.094	0.000	0.000	0.000	0.000
12	E	27	VAL	0	-0.048	0.095	12.840	0.005	0.005	0.000	0.000	0.000	0.000
13	E	28	TYR	0	0.135	-0.063	12.720	-0.037	-0.037	0.000	0.000	0.000	0.000
14	E	28	TYR	0	-0.059	0.083	16.894	0.001	0.001	0.000	0.000	0.000	0.000
15	E	29	ARG	0	0.077	-0.108	15.741	0.041	0.041	0.000	0.000	0.000	0.000
16	E	29	ARG	1	0.709	0.992	15.489	-0.159	-0.159	0.000	0.000	0.000	0.000
17	E	30	PRO	0	-0.032	-0.096	17.457	-0.025	-0.025	0.000	0.000	0.000	0.000
18	E	31	ASP	0	0.163	0.006	20.750	0.037	0.037	0.000	0.000	0.000	0.000
19	E	31	ASP	-1	-0.941	-0.814	22.807	0.010	0.010	0.000	0.000	0.000	0.000
20	E	32	ILE	0	0.048	-0.102	22.599	-0.006	-0.006	0.000	0.000	0.000	0.000
21	E	32	ILE	0	-0.099	0.100	20.066	0.008	0.008	0.000	0.000	0.000	0.000
22	E	33	ASN	0	0.054	-0.096	23.683	0.006	0.006	0.000	0.000	0.000	0.000
23	E	33	ASN	0	-0.062	0.096	26.864	-0.003	-0.003	0.000	0.000	0.000	0.000
24	E	34	GLN	0	0.063	-0.119	26.778	-0.004	-0.004	0.000	0.000	0.000	0.000
25	E	34	GLN	0	-0.113	0.083	25.573	0.015	0.015	0.000	0.000	0.000	0.000
26	E	35	GLY	0	0.045	-0.074	28.264	0.002	0.002	0.000	0.000	0.000	0.000
27	E	36	ASN	0	0.091	0.021	31.428	-0.006	-0.006	0.000	0.000	0.000	0.000
28	E	36	ASN	0	-0.090	0.081	35.361	0.007	0.007	0.000	0.000	0.000	0.000
29	E	37	TYR	0	0.171	-0.076	33.675	0.004	0.004	0.000	0.000	0.000	0.000
30	E	37	TYR	0	-0.085	0.107	32.718	-0.001	-0.001	0.000	0.000	0.000	0.000
31	E	38	LEU	0	-0.001	-0.104	34.373	-0.003	-0.003	0.000	0.000	0.000	0.000
32	E	38	LEU	0	-0.071	0.098	33.858	0.000	0.000	0.000	0.000	0.000	0.000
33	E	39	THR	0	0.004	-0.102	34.856	0.003	0.003	0.000	0.000	0.000	0.000
34	E	39	THR	0	-0.039	0.040	37.874	0.001	0.001	0.000	0.000	0.000	0.000
35	E	40	ALA	0	0.153	-0.053	36.554	-0.005	-0.005	0.000	0.000	0.000	0.000
36	E	40	ALA	0	-0.064	0.115	35.722	-0.001	-0.001	0.000	0.000	0.000	0.000
37	E	41	ASN	0	0.109	-0.085	37.459	0.003	0.003	0.000	0.000	0.000	0.000
38	E	41	ASN	0	-0.135	0.051	40.959	-0.002	-0.002	0.000	0.000	0.000	0.000
39	E	42	ASP	0	0.077	-0.120	40.626	-0.001	-0.001	0.000	0.000	0.000	0.000
40	E	42	ASP	-1	-0.849	-0.757	40.663	0.037	0.037	0.000	0.000	0.000	0.000
41	E	43	VAL	0	0.088	-0.099	39.486	0.001	0.001	0.000	0.000	0.000	0.000
42	E	43	VAL	0	-0.061	0.112	37.384	0.001	0.001	0.000	0.000	0.000	0.000
43	E	44	SER	0	0.018	-0.098	40.816	0.003	0.003	0.000	0.000	0.000	0.000
44	E	44	SER	0	-0.022	0.090	42.714	-0.001	-0.001	0.000	0.000	0.000	0.000
45	E	45	LYS	0	0.029	-0.129	43.599	-0.003	-0.003	0.000	0.000	0.000	0.000
46	E	45	LYS	1	0.746	1.029	44.468	-0.041	-0.041	0.000	0.000	0.000	0.000
47	E	46	ILE	0	-0.002	-0.099	44.590	-0.003	-0.003	0.000	0.000	0.000	0.000
48	E	46	ILE	0	-0.040	0.119	42.673	0.001	0.001	0.000	0.000	0.000	0.000
49	E	47	ARG	0	0.052	-0.118	45.838	-0.001	-0.001	0.000	0.000	0.000	0.000
50	E	47	ARG	1	0.850	1.045	48.719	-0.039	-0.039	0.000	0.000	0.000	0.000
51	E	48	VAL	0	0.120	-0.102	48.264	0.002	0.002	0.000	0.000	0.000	0.000
52	E	48	VAL	0	-0.054	0.126	47.366	0.000	0.000	0.000	0.000	0.000	0.000
53	E	49	GLY	0	-0.003	-0.103	49.262	-0.003	-0.003	0.000	0.000	0.000	0.000
54	E	50	MET	0	0.074	-0.012	49.163	-0.002	-0.002	0.000	0.000	0.000	0.000
55	E	50	MET	0	-0.116	0.111	48.028	0.000	0.000	0.000	0.000	0.000	0.000
56	E	51	THR	0	0.083	-0.050	50.145	0.004	0.004	0.000	0.000	0.000	0.000
57	E	51	THR	0	-0.059	0.073	52.897	-0.001	-0.001	0.000	0.000	0.000	0.000
58	E	52	GLN	0	0.104	-0.073	47.813	-0.001	-0.001	0.000	0.000	0.000	0.000
59	E	52	GLN	0	-0.030	0.125	46.687	0.001	0.001	0.000	0.000	0.000	0.000
60	E	53	GLN	0	0.127	-0.110	47.676	0.003	0.003	0.000	0.000	0.000	0.000
61	E	53	GLN	0	-0.072	0.101	51.121	-0.001	-0.001	0.000	0.000	0.000	0.000
62	E	54	GLN	0	0.053	-0.120	48.994	0.000	0.000	0.000	0.000	0.000	0.000
63	E	54	GLN	0	-0.045	0.095	50.656	0.000	0.000	0.000	0.000	0.000	0.000
64	E	55	VAL	0	0.043	-0.113	45.556	-0.004	-0.004	0.000	0.000	0.000	0.000
65	E	55	VAL	0	-0.055	0.112	43.529	0.000	0.000	0.000	0.000	0.000	0.000
66	E	56	ALA	0	0.125	-0.070	44.375	0.000	0.000	0.000	0.000	0.000	0.000
67	E	56	ALA	0	-0.057	0.103	45.590	0.000	0.000	0.000	0.000	0.000	0.000
68	E	57	TYR	0	0.015	-0.101	45.309	0.000	0.000	0.000	0.000	0.000	0.000
69	E	57	TYR	0	-0.108	0.077	49.078	-0.001	-0.001	0.000	0.000	0.000	0.000
70	E	58	ALA	0	0.070	-0.097	45.714	-0.002	-0.002	0.000	0.000	0.000	0.000
71	E	58	ALA	0	-0.110	0.084	46.173	-0.001	-0.001	0.000	0.000	0.000	0.000
72	E	59	LEU	0	-0.002	-0.141	41.496	-0.004	-0.004	0.000	0.000	0.000	0.000
73	E	59	LEU	0	-0.006	0.123	39.875	0.001	0.001	0.000	0.000	0.000	0.000
74	E	60	GLY	0	0.043	-0.056	40.353	0.003	0.003	0.000	0.000	0.000	0.000
75	E	61	THR	0	0.056	-0.009	42.025	0.002	0.002	0.000	0.000	0.000	0.000
76	E	61	THR	0	-0.022	0.102	40.955	-0.002	-0.002	0.000	0.000	0.000	0.000
77	E	62	PRO	0	-0.038	-0.082	38.248	0.000	0.000	0.000	0.000	0.000	0.000
78	E	63	LEU	0	0.106	0.007	35.121	-0.002	-0.002	0.000	0.000	0.000	0.000
79	E	63	LEU	0	-0.113	0.082	33.632	0.001	0.001	0.000	0.000	0.000	0.000
80	E	64	MET	0	0.050	-0.099	34.527	0.006	0.006	0.000	0.000	0.000	0.000
81	E	64	MET	0	-0.083	0.081	30.950	0.005	0.005	0.000	0.000	0.000	0.000
82	E	65	SER	0	-0.006	-0.082	35.900	-0.005	-0.005	0.000	0.000	0.000	0.000
83	E	65	SER	0	-0.001	0.066	40.020	-0.002	-0.002	0.000	0.000	0.000	0.000
84	E	66	ASP	0	0.127	-0.073	37.676	0.010	0.010	0.000	0.000	0.000	0.000
85	E	66	ASP	-1	-0.874	-0.741	41.231	0.118	0.118	0.000	0.000	0.000	0.000
86	E	67	PRO	0	-0.043	-0.110	37.838	-0.005	-0.005	0.000	0.000	0.000	0.000
87	E	68	PHE	0	0.013	0.016	38.287	0.004	0.004	0.000	0.000	0.000	0.000
88	E	68	PHE	0	-0.069	0.080	35.281	0.001	0.001	0.000	0.000	0.000	0.000
89	E	69	GLY	0	0.035	-0.123	40.646	-0.001	-0.001	0.000	0.000	0.000	0.000
90	E	70	THR	0	-0.020	0.046	43.006	-0.006	-0.006	0.000	0.000	0.000	0.000
91	E	70	THR	0	-0.094	0.006	41.814	0.001	0.001	0.000	0.000	0.000	0.000
92	E	71	ASN	0	0.182	-0.066	44.243	0.002	0.002	0.000	0.000	0.000	0.000
93	E	71	ASN	0	-0.195	0.049	45.466	0.002	0.002	0.000	0.000	0.000	0.000
94	E	72	THR	0	0.003	-0.124	40.398	-0.007	-0.007	0.000	0.000	0.000	0.000
95	E	72	THR	0	-0.035	0.075	39.685	0.003	0.003	0.000	0.000	0.000	0.000
96	E	73	TRP	0	0.115	-0.088	39.676	0.004	0.004	0.000	0.000	0.000	0.000
97	E	73	TRP	0	-0.101	0.070	40.399	-0.003	-0.003	0.000	0.000	0.000	0.000
98	E	74	PHE	0	0.088	-0.082	35.217	-0.006	-0.006	0.000	0.000	0.000	0.000
99	E	74	PHE	0	-0.122	0.097	34.198	0.003	0.003	0.000	0.000	0.000	0.000
100	E	75	TYR	0	0.155	-0.059	35.120	0.006	0.006	0.000	0.000	0.000	0.000
101	E	75	TYR	0	-0.138	0.050	36.477	-0.001	-0.001	0.000	0.000	0.000	0.000
102	E	76	VAL	0	0.120	-0.103	31.014	-0.006	-0.006	0.000	0.000	0.000	0.000
103	E	76	VAL	0	-0.081	0.094	28.932	0.003	0.003	0.000	0.000	0.000	0.000
104	E	77	PHE	0	0.109	-0.098	30.633	-0.001	-0.001	0.000	0.000	0.000	0.000
105	E	77	PHE	0	-0.140	0.092	29.201	-0.001	-0.001	0.000	0.000	0.000	0.000
106	E	78	ARG	0	0.158	-0.072	26.340	-0.002	-0.002	0.000	0.000	0.000	0.000
107	E	78	ARG	1	0.801	1.022	20.695	-0.266	-0.266	0.000	0.000	0.000	0.000
108	E	79	GLN	0	0.045	-0.103	24.902	0.003	0.003	0.000	0.000	0.000	0.000
109	E	79	GLN	0	-0.073	0.088	25.285	-0.008	-0.008	0.000	0.000	0.000	0.000
110	E	80	GLN	0	0.108	-0.079	20.588	0.006	0.006	0.000	0.000	0.000	0.000
111	E	80	GLN	0	-0.150	0.060	17.830	0.010	0.010	0.000	0.000	0.000	0.000
112	E	81	PRO	0	0.082	-0.051	20.979	0.011	0.011	0.000	0.000	0.000	0.000
113	E	82	GLY	0	0.044	0.007	18.998	0.027	0.027	0.000	0.000	0.000	0.000
114	E	83	HIS	0	-0.024	-0.018	14.772	-0.028	-0.028	0.000	0.000	0.000	0.000
115	E	83	HIS	0	-0.047	0.095	12.652	-0.047	-0.047	0.000	0.000	0.000	0.000
116	E	84	GLU	0	0.068	-0.127	15.101	0.025	0.025	0.000	0.000	0.000	0.000
117	E	84	GLU	-1	-0.976	-0.838	19.035	-0.045	-0.045	0.000	0.000	0.000	0.000
118	E	85	GLY	0	0.025	-0.083	16.814	0.005	0.005	0.000	0.000	0.000	0.000
119	E	86	VAL	0	0.019	-0.010	17.779	-0.006	-0.006	0.000	0.000	0.000	0.000
120	E	86	VAL	0	-0.096	0.076	18.375	0.008	0.008	0.000	0.000	0.000	0.000
121	E	87	THR	0	0.028	-0.109	20.343	0.004	0.004	0.000	0.000	0.000	0.000
122	E	87	THR	0	-0.021	0.114	22.698	-0.008	-0.008	0.000	0.000	0.000	0.000
123	E	88	GLN	0	0.151	-0.061	23.953	-0.004	-0.004	0.000	0.000	0.000	0.000
124	E	88	GLN	0	-0.095	0.090	25.167	0.018	0.018	0.000	0.000	0.000	0.000
125	E	89	GLN	0	0.071	-0.075	26.601	-0.004	-0.004	0.000	0.000	0.000	0.000
126	E	89	GLN	0	-0.057	0.101	30.692	-0.002	-0.002	0.000	0.000	0.000	0.000
127	E	90	THR	0	-0.010	-0.081	30.018	0.001	0.001	0.000	0.000	0.000	0.000
128	E	90	THR	0	-0.075	0.023	29.455	0.006	0.006	0.000	0.000	0.000	0.000
129	E	91	LEU	0	0.210	-0.043	32.062	0.001	0.001	0.000	0.000	0.000	0.000
130	E	91	LEU	0	-0.125	0.095	36.295	-0.002	-0.002	0.000	0.000	0.000	0.000
131	E	92	THR	0	-0.073	-0.107	35.818	0.002	0.002	0.000	0.000	0.000	0.000
132	E	92	THR	0	-0.063	0.035	34.726	0.000	0.000	0.000	0.000	0.000	0.000
133	E	93	LEU	0	0.058	-0.101	37.396	-0.004	-0.004	0.000	0.000	0.000	0.000
134	E	93	LEU	0	-0.055	0.093	40.086	-0.001	-0.001	0.000	0.000	0.000	0.000
135	E	94	THR	0	0.095	-0.053	41.169	0.004	0.004	0.000	0.000	0.000	0.000
136	E	94	THR	0	-0.041	0.070	41.790	0.002	0.002	0.000	0.000	0.000	0.000
137	E	95	PHE	0	0.036	-0.122	43.452	-0.005	-0.005	0.000	0.000	0.000	0.000
138	E	95	PHE	0	-0.040	0.133	43.190	-0.001	-0.001	0.000	0.000	0.000	0.000
139	E	96	ASN	0	0.115	-0.016	46.910	0.004	0.004	0.000	0.000	0.000	0.000
140	E	96	ASN	0	-0.057	0.053	50.925	0.000	0.000	0.000	0.000	0.000	0.000
141	E	97	SER	0	0.083	-0.082	50.057	0.002	0.002	0.000	0.000	0.000	0.000
142	E	97	SER	0	-0.028	0.073	52.235	0.000	0.000	0.000	0.000	0.000	0.000
143	E	98	SER	0	-0.026	-0.090	52.040	0.000	0.000	0.000	0.000	0.000	0.000
144	E	98	SER	0	-0.056	0.066	54.573	-0.001	-0.001	0.000	0.000	0.000	0.000
145	E	99	GLY	0	0.015	-0.079	50.211	-0.002	-0.002	0.000	0.000	0.000	0.000
146	E	100	VAL	0	0.096	-0.007	51.093	-0.001	-0.001	0.000	0.000	0.000	0.000
147	E	100	VAL	0	-0.121	0.101	51.806	0.000	0.000	0.000	0.000	0.000	0.000
148	E	101	LEU	0	0.092	-0.093	47.016	0.002	0.002	0.000	0.000	0.000	0.000
149	E	101	LEU	0	-0.111	0.102	45.113	0.000	0.000	0.000	0.000	0.000	0.000
150	E	102	THR	0	0.020	-0.131	47.152	-0.005	-0.005	0.000	0.000	0.000	0.000
151	E	102	THR	0	-0.040	0.062	47.375	0.001	0.001	0.000	0.000	0.000	0.000
152	E	103	ASN	0	0.062	-0.050	44.304	-0.003	-0.003	0.000	0.000	0.000	0.000
153	E	103	ASN	0	-0.093	0.067	41.509	0.004	0.004	0.000	0.000	0.000	0.000
154	E	104	ILE	0	0.084	-0.104	41.534	0.002	0.002	0.000	0.000	0.000	0.000
155	E	104	ILE	0	-0.063	0.100	40.434	-0.001	-0.001	0.000	0.000	0.000	0.000
156	E	105	ASP	0	0.099	-0.070	37.703	-0.004	-0.004	0.000	0.000	0.000	0.000
157	E	105	ASP	-1	-0.861	-0.750	35.543	0.124	0.124	0.000	0.000	0.000	0.000
158	E	106	ASN	0	0.125	-0.078	35.426	0.003	0.003	0.000	0.000	0.000	0.000
159	E	106	ASN	0	-0.129	0.054	35.199	-0.003	-0.003	0.000	0.000	0.000	0.000
160	E	107	LYS	0	0.104	-0.080	31.760	-0.007	-0.007	0.000	0.000	0.000	0.000
161	E	107	LYS	1	0.719	0.991	30.316	-0.137	-0.137	0.000	0.000	0.000	0.000
162	E	108	PRO	0	0.008	-0.108	30.241	0.008	0.008	0.000	0.000	0.000	0.000
163	E	109	ALA	0	0.143	0.060	26.014	0.003	0.003	0.000	0.000	0.000	0.000
164	E	109	ALA	0	-0.098	0.079	25.346	-0.002	-0.002	0.000	0.000	0.000	0.000
165	E	110	LEU	0	-0.016	-0.138	23.460	-0.001	-0.001	0.000	0.000	0.000	0.000
166	E	110	LEU	0	-0.061	0.085	21.973	0.008	0.008	0.000	0.000	0.000	0.000
167	E	111	SER	0	-0.104	-0.158	22.701	0.000	0.000	0.000	0.000	0.000	0.000
168	E	111	SER	0	0.110	0.084	24.065	-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)