FMO DATABASE

FMODB ID: Q1M2Y

Calculation Name: 2EJX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EJX

Chain ID: A

ChEMBL ID:

UniProt ID: Q973T5

Base Structure: X-ray

Registration Date: 2023-03-13

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	OptH
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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1264594.373085
FMO2-HF: Nuclear repulsion	1211377.569724
FMO2-HF: Total energy	-53216.80336
FMO2-MP2: Total energy	-53375.285817

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:LYS)

Summations of interaction energy for fragment #1(A:3:LYS)

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.
-77.843	-71.287	16.301	-10.348	-12.509	-0.096

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.915 / q_NPA : 0.966

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	GLU	-1	-0.881	-0.951	2.313	-86.244	-81.507	1.956	-2.992	-3.702	-0.035
4	A	6	LYS	1	0.845	0.926	5.648	25.214	25.214	0.000	0.000	0.000	0.000
5	A	7	GLU	-1	-0.853	-0.873	9.091	-24.524	-24.524	0.000	0.000	0.000	0.000
6	A	8	ILE	0	-0.005	-0.016	10.979	1.318	1.318	0.000	0.000	0.000	0.000
7	A	9	LYS	1	0.892	0.936	14.434	18.304	18.304	0.000	0.000	0.000	0.000
8	A	10	THR	0	-0.029	-0.039	17.532	0.527	0.527	0.000	0.000	0.000	0.000
9	A	11	ASN	0	0.010	-0.007	20.520	-0.222	-0.222	0.000	0.000	0.000	0.000
10	A	12	GLN	0	-0.049	-0.010	23.074	0.775	0.775	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.856	-0.926	23.385	-12.676	-12.676	0.000	0.000	0.000	0.000
12	A	14	ILE	0	0.049	0.010	17.174	-0.237	-0.237	0.000	0.000	0.000	0.000
13	A	15	ASP	-1	-0.845	-0.920	20.194	-14.760	-14.760	0.000	0.000	0.000	0.000
14	A	16	VAL	0	-0.068	-0.038	22.073	-0.082	-0.082	0.000	0.000	0.000	0.000
15	A	17	VAL	0	0.004	-0.007	17.942	-0.123	-0.123	0.000	0.000	0.000	0.000
16	A	18	MET	0	-0.014	0.000	14.280	-0.747	-0.747	0.000	0.000	0.000	0.000
17	A	19	THR	0	-0.018	-0.012	18.244	-0.219	-0.219	0.000	0.000	0.000	0.000
18	A	20	ILE	0	-0.039	0.005	19.934	0.218	0.218	0.000	0.000	0.000	0.000
19	A	21	PHE	0	0.029	0.012	14.092	-0.184	-0.184	0.000	0.000	0.000	0.000
20	A	22	SER	0	-0.099	-0.035	16.058	-0.423	-0.423	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.741	-0.868	17.912	-12.298	-12.298	0.000	0.000	0.000	0.000
22	A	24	PRO	0	0.021	0.018	17.289	-0.453	-0.453	0.000	0.000	0.000	0.000
23	A	25	ALA	0	0.009	-0.026	18.316	-0.149	-0.149	0.000	0.000	0.000	0.000
24	A	26	PHE	0	-0.054	-0.019	17.060	0.414	0.414	0.000	0.000	0.000	0.000
25	A	27	THR	0	0.008	-0.056	13.275	-0.077	-0.077	0.000	0.000	0.000	0.000
26	A	28	ILE	0	0.000	0.007	13.667	-0.822	-0.822	0.000	0.000	0.000	0.000
27	A	29	PRO	0	-0.019	-0.020	15.215	-0.335	-0.335	0.000	0.000	0.000	0.000
28	A	30	GLN	0	0.030	0.033	16.107	-0.390	-0.390	0.000	0.000	0.000	0.000
29	A	31	ILE	0	0.009	0.010	9.903	-0.544	-0.544	0.000	0.000	0.000	0.000
30	A	32	PHE	0	-0.012	0.000	10.325	-0.735	-0.735	0.000	0.000	0.000	0.000
31	A	33	PRO	0	-0.003	-0.005	11.279	0.730	0.730	0.000	0.000	0.000	0.000
32	A	34	GLY	0	0.024	0.041	14.333	0.421	0.421	0.000	0.000	0.000	0.000
33	A	35	ILE	0	-0.035	-0.007	15.770	0.476	0.476	0.000	0.000	0.000	0.000
34	A	36	ALA	0	0.015	-0.001	18.877	0.285	0.285	0.000	0.000	0.000	0.000
35	A	37	SER	0	-0.072	-0.030	21.807	0.632	0.632	0.000	0.000	0.000	0.000
36	A	38	ILE	0	0.032	0.003	19.304	-0.537	-0.537	0.000	0.000	0.000	0.000
37	A	39	LYS	1	0.897	0.973	22.530	10.763	10.763	0.000	0.000	0.000	0.000
38	A	40	CYS	0	-0.020	-0.020	21.991	-0.470	-0.470	0.000	0.000	0.000	0.000
39	A	41	ILE	0	-0.007	-0.011	24.609	0.218	0.218	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.839	-0.913	25.718	-10.819	-10.819	0.000	0.000	0.000	0.000
41	A	43	PRO	0	0.009	0.003	24.668	-0.325	-0.325	0.000	0.000	0.000	0.000
42	A	44	GLU	-1	-0.902	-0.946	20.969	-14.020	-14.020	0.000	0.000	0.000	0.000
43	A	45	ILE	0	-0.043	-0.011	20.326	-0.632	-0.632	0.000	0.000	0.000	0.000
44	A	46	PHE	0	0.008	0.000	14.756	0.249	0.249	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.922	-0.975	19.937	-11.343	-11.343	0.000	0.000	0.000	0.000
46	A	48	ALA	0	-0.009	-0.014	17.796	0.254	0.254	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.919	-0.947	19.325	-11.011	-11.011	0.000	0.000	0.000	0.000
48	A	50	GLY	0	0.058	0.033	17.957	0.006	0.006	0.000	0.000	0.000	0.000
49	A	51	LYS	1	0.892	0.958	18.770	11.097	11.097	0.000	0.000	0.000	0.000
50	A	52	PHE	0	0.022	0.020	13.383	-0.248	-0.248	0.000	0.000	0.000	0.000
51	A	53	LEU	0	0.028	0.015	16.720	0.111	0.111	0.000	0.000	0.000	0.000
52	A	54	ALA	0	-0.013	-0.012	19.749	0.333	0.333	0.000	0.000	0.000	0.000
53	A	55	PHE	0	-0.045	-0.031	17.311	0.403	0.403	0.000	0.000	0.000	0.000
54	A	56	SER	0	0.038	0.015	18.417	-0.389	-0.389	0.000	0.000	0.000	0.000
55	A	57	TYR	0	-0.047	-0.049	14.984	-0.284	-0.284	0.000	0.000	0.000	0.000
56	A	58	LYS	1	0.974	0.988	18.277	11.620	11.620	0.000	0.000	0.000	0.000
57	A	59	VAL	0	-0.028	-0.018	13.491	-0.326	-0.326	0.000	0.000	0.000	0.000
58	A	60	LYS	1	0.875	0.941	16.764	13.548	13.548	0.000	0.000	0.000	0.000
59	A	61	GLY	0	0.027	0.006	16.134	-0.767	-0.767	0.000	0.000	0.000	0.000
60	A	62	ARG	1	0.883	0.960	16.479	13.664	13.664	0.000	0.000	0.000	0.000
61	A	63	VAL	0	-0.016	-0.004	15.936	-1.164	-1.164	0.000	0.000	0.000	0.000
62	A	64	TYR	0	0.003	-0.001	15.611	1.128	1.128	0.000	0.000	0.000	0.000
63	A	65	LYS	1	0.897	0.941	15.920	12.689	12.689	0.000	0.000	0.000	0.000
64	A	66	GLY	0	0.008	0.004	16.804	0.450	0.450	0.000	0.000	0.000	0.000
65	A	67	VAL	0	0.003	-0.009	17.685	0.308	0.308	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.879	-0.930	15.566	-17.705	-17.705	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.834	-0.907	10.835	-28.367	-28.367	0.000	0.000	0.000	0.000
68	A	70	VAL	0	-0.019	0.006	12.940	1.609	1.609	0.000	0.000	0.000	0.000
69	A	71	ARG	1	0.849	0.901	10.418	22.744	22.744	0.000	0.000	0.000	0.000
70	A	72	ILE	0	0.002	-0.003	11.256	1.749	1.749	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.007	0.000	11.220	-1.595	-1.595	0.000	0.000	0.000	0.000
72	A	74	TYR	0	-0.036	-0.046	7.905	0.856	0.856	0.000	0.000	0.000	0.000
73	A	75	ASP	-1	-0.854	-0.921	12.814	-15.127	-15.127	0.000	0.000	0.000	0.000
74	A	76	SER	0	0.035	-0.006	13.485	0.536	0.536	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.830	-0.912	15.753	-13.214	-13.214	0.000	0.000	0.000	0.000
76	A	78	ARG	1	0.826	0.908	13.805	13.333	13.333	0.000	0.000	0.000	0.000
77	A	79	GLY	0	0.011	0.022	11.516	-0.803	-0.803	0.000	0.000	0.000	0.000
78	A	80	ASN	0	0.040	0.026	11.356	0.903	0.903	0.000	0.000	0.000	0.000
79	A	81	GLY	0	0.028	0.012	8.128	-1.243	-1.243	0.000	0.000	0.000	0.000
80	A	82	ILE	0	-0.032	0.000	7.339	2.023	2.023	0.000	0.000	0.000	0.000
81	A	83	LEU	0	-0.009	-0.003	6.526	-3.361	-3.361	0.000	0.000	0.000	0.000
82	A	84	TYR	0	-0.023	-0.020	5.572	3.462	3.462	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.008	0.000	8.378	-1.475	-1.475	0.000	0.000	0.000	0.000
84	A	86	ARG	1	0.931	0.970	4.544	42.026	42.086	-0.001	0.000	-0.058	0.000
85	A	87	LYS	1	0.968	0.994	11.324	15.116	15.116	0.000	0.000	0.000	0.000
86	A	88	LYS	1	0.722	0.833	9.647	27.555	27.555	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.789	-0.878	13.681	-17.372	-17.372	0.000	0.000	0.000	0.000
88	A	90	ASN	0	-0.036	-0.036	17.447	-0.106	-0.106	0.000	0.000	0.000	0.000
89	A	91	ASN	0	-0.039	-0.005	19.177	0.641	0.641	0.000	0.000	0.000	0.000
90	A	92	THR	0	-0.003	-0.006	13.615	-0.065	-0.065	0.000	0.000	0.000	0.000
91	A	93	LEU	0	0.019	0.015	12.842	-0.054	-0.054	0.000	0.000	0.000	0.000
92	A	94	GLN	0	0.001	-0.007	5.849	4.635	4.635	0.000	0.000	0.000	0.000
93	A	95	ILE	0	0.025	0.019	7.640	0.703	0.703	0.000	0.000	0.000	0.000
94	A	96	ILE	0	-0.008	-0.005	2.353	-5.072	-4.532	2.136	-0.692	-1.984	-0.003
95	A	97	LEU	0	-0.006	0.001	3.742	3.684	4.089	0.002	-0.125	-0.282	0.000
96	A	98	GLU	-1	-0.918	-0.982	1.832	-69.502	-68.765	12.195	-6.569	-6.363	-0.058
97	A	99	HIS	0	-0.029	0.014	3.561	2.296	2.373	0.013	0.030	-0.120	0.000
98	A	100	ASP	-1	-0.838	-0.923	5.824	-20.474	-20.474	0.000	0.000	0.000	0.000
99	A	101	ASN	0	0.010	0.018	8.520	0.878	0.878	0.000	0.000	0.000	0.000
100	A	102	LYS	1	1.015	0.986	8.135	20.383	20.383	0.000	0.000	0.000	0.000
101	A	103	LEU	0	0.003	0.009	9.215	-0.221	-0.221	0.000	0.000	0.000	0.000
102	A	104	THR	0	-0.004	-0.038	10.238	0.371	0.371	0.000	0.000	0.000	0.000
103	A	105	ALA	0	0.019	0.010	5.851	-0.050	-0.050	0.000	0.000	0.000	0.000
104	A	106	PHE	0	-0.080	-0.037	7.789	-0.541	-0.541	0.000	0.000	0.000	0.000
105	A	107	LEU	0	-0.013	-0.003	9.992	0.247	0.247	0.000	0.000	0.000	0.000
106	A	108	GLY	0	0.046	0.021	10.452	0.526	0.526	0.000	0.000	0.000	0.000
107	A	109	LYS	1	0.947	0.978	5.709	31.106	31.106	0.000	0.000	0.000	0.000
108	A	110	PRO	0	0.018	0.006	9.014	-0.853	-0.853	0.000	0.000	0.000	0.000
109	A	111	TYR	0	0.000	0.004	12.260	0.736	0.736	0.000	0.000	0.000	0.000
110	A	112	VAL	0	0.023	0.014	7.230	0.073	0.073	0.000	0.000	0.000	0.000
111	A	113	SER	0	-0.047	-0.029	9.583	-0.175	-0.175	0.000	0.000	0.000	0.000
112	A	114	SER	0	0.043	0.030	10.728	0.305	0.305	0.000	0.000	0.000	0.000
113	A	115	ASN	0	-0.020	-0.016	12.710	1.397	1.397	0.000	0.000	0.000	0.000
114	A	116	LEU	0	-0.027	-0.023	7.895	0.113	0.113	0.000	0.000	0.000	0.000
115	A	117	ASP	-1	-0.856	-0.917	12.454	-20.984	-20.984	0.000	0.000	0.000	0.000
116	A	118	ARG	1	0.900	0.963	15.050	15.846	15.846	0.000	0.000	0.000	0.000
117	A	119	LEU	0	-0.042	-0.034	13.497	0.638	0.638	0.000	0.000	0.000	0.000
118	A	120	ALA	0	-0.032	-0.038	14.527	0.422	0.422	0.000	0.000	0.000	0.000
119	A	121	GLU	-1	-0.973	-0.977	16.443	-15.024	-15.024	0.000	0.000	0.000	0.000
120	A	122	ASN	0	-0.045	-0.010	19.650	1.228	1.228	0.000	0.000	0.000	0.000
121	A	123	ILE	0	-0.001	0.024	17.335	0.492	0.492	0.000	0.000	0.000	0.000
122	A	124	ASP	-1	-0.699	-0.846	20.202	-13.345	-13.345	0.000	0.000	0.000	0.000
123	A	125	GLU	-1	-0.948	-0.984	23.511	-11.768	-11.768	0.000	0.000	0.000	0.000
124	A	126	ILE	0	-0.001	-0.001	19.921	0.403	0.403	0.000	0.000	0.000	0.000
125	A	127	ILE	0	0.009	0.000	19.648	0.441	0.441	0.000	0.000	0.000	0.000
126	A	128	ARG	1	0.956	0.984	23.564	10.534	10.534	0.000	0.000	0.000	0.000
127	A	129	LEU	0	-0.017	-0.015	26.702	0.470	0.470	0.000	0.000	0.000	0.000
128	A	130	GLU	-1	-0.826	-0.907	22.600	-11.651	-11.651	0.000	0.000	0.000	0.000
129	A	131	ARG	1	0.861	0.912	25.936	11.509	11.509	0.000	0.000	0.000	0.000
130	A	132	ILE	0	-0.042	-0.007	28.061	0.339	0.339	0.000	0.000	0.000	0.000
131	A	133	LYS	1	0.890	0.955	25.506	11.373	11.373	0.000	0.000	0.000	0.000
132	A	134	ARG	1	0.740	0.842	22.946	12.394	12.394	0.000	0.000	0.000	0.000
133	A	135	LYS	1	0.928	0.976	29.529	8.729	8.729	0.000	0.000	0.000	0.000
134	A	136	ILE	0	0.039	0.052	25.465	-0.096	-0.096	0.000	0.000	0.000	0.000

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