FMO DATABASE

FMODB ID: 2J2MR

Calculation Name: 3EUD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EUD

Chain ID: A

ChEMBL ID:

UniProt ID: P40486

Base Structure: X-ray

Registration Date: 2023-06-21

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	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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-799875.125473
FMO2-HF: Nuclear repulsion	758972.543261
FMO2-HF: Total energy	-40902.582212
FMO2-MP2: Total energy	-41022.705896

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:0:LYS)

Summations of interaction energy for fragment #1(A:0: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.
-40.352	-38.047	0.306	-1.031	-1.581	-0.002

Interaction energy analysis for fragmet #1(A:0:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.972 / q_NPA : 0.974

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	2	ILE	0	-0.013	0.002	3.620	1.071	2.793	-0.007	-0.743	-0.973	-0.001
4	A	3	THR	0	0.024	0.008	5.679	0.089	0.089	0.000	0.000	0.000	0.000
5	A	4	PRO	0	-0.015	0.001	9.418	0.996	0.996	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.930	0.983	11.422	15.543	15.543	0.000	0.000	0.000	0.000
7	A	6	PHE	0	0.000	-0.010	14.859	-0.127	-0.127	0.000	0.000	0.000	0.000
8	A	7	SER	0	-0.011	-0.002	17.469	0.349	0.349	0.000	0.000	0.000	0.000
9	A	8	ILE	0	-0.007	-0.011	20.975	-0.254	-0.254	0.000	0.000	0.000	0.000
10	A	9	THR	0	-0.003	0.022	23.966	0.415	0.415	0.000	0.000	0.000	0.000
11	A	10	GLN	0	0.049	0.006	27.535	-0.227	-0.227	0.000	0.000	0.000	0.000
12	A	11	ASP	-1	-0.802	-0.887	30.283	-9.023	-9.023	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.859	-0.932	33.741	-8.427	-8.427	0.000	0.000	0.000	0.000
14	A	13	GLU	-1	-0.818	-0.893	33.803	-8.553	-8.553	0.000	0.000	0.000	0.000
15	A	14	PHE	0	0.006	0.003	29.383	-0.259	-0.259	0.000	0.000	0.000	0.000
16	A	15	ILE	0	-0.008	0.002	24.018	0.113	0.113	0.000	0.000	0.000	0.000
17	A	16	PHE	0	-0.020	-0.018	25.577	-0.237	-0.237	0.000	0.000	0.000	0.000
18	A	17	LEU	0	-0.003	-0.001	18.365	-0.059	-0.059	0.000	0.000	0.000	0.000
19	A	18	LYS	1	0.833	0.911	20.228	11.999	11.999	0.000	0.000	0.000	0.000
20	A	19	ILE	0	0.001	-0.012	14.065	-0.381	-0.381	0.000	0.000	0.000	0.000
21	A	20	PHE	0	0.002	-0.013	15.530	0.156	0.156	0.000	0.000	0.000	0.000
22	A	21	ILE	0	-0.056	-0.022	11.826	-1.255	-1.255	0.000	0.000	0.000	0.000
23	A	22	SER	0	0.028	0.013	11.726	0.887	0.887	0.000	0.000	0.000	0.000
24	A	23	ASN	0	-0.059	-0.027	11.147	-0.708	-0.708	0.000	0.000	0.000	0.000
25	A	24	ILE	0	0.020	0.032	8.856	-1.228	-1.228	0.000	0.000	0.000	0.000
26	A	25	ARG	1	0.937	0.961	11.385	19.852	19.852	0.000	0.000	0.000	0.000
27	A	26	PHE	0	0.056	0.027	13.026	-0.920	-0.920	0.000	0.000	0.000	0.000
28	A	27	SER	0	-0.024	-0.030	14.426	0.250	0.250	0.000	0.000	0.000	0.000
29	A	28	ALA	0	0.007	-0.002	17.051	-0.033	-0.033	0.000	0.000	0.000	0.000
30	A	29	VAL	0	0.016	-0.003	14.925	0.274	0.274	0.000	0.000	0.000	0.000
31	A	30	GLY	0	-0.036	0.001	12.554	-0.817	-0.817	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.040	-0.013	12.062	-1.395	-1.395	0.000	0.000	0.000	0.000
33	A	32	GLU	-1	-0.919	-0.949	12.663	-21.653	-21.653	0.000	0.000	0.000	0.000
34	A	33	ILE	0	-0.011	-0.036	14.844	-0.721	-0.721	0.000	0.000	0.000	0.000
35	A	34	ILE	0	-0.006	0.015	16.007	0.628	0.628	0.000	0.000	0.000	0.000
36	A	35	ILE	0	0.014	0.003	18.860	-0.429	-0.429	0.000	0.000	0.000	0.000
37	A	36	GLN	0	-0.058	-0.036	21.573	-0.086	-0.086	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.786	-0.886	23.433	-12.668	-12.668	0.000	0.000	0.000	0.000
39	A	38	ASN	0	-0.004	0.013	24.483	-0.186	-0.186	0.000	0.000	0.000	0.000
40	A	39	MET	0	-0.006	0.019	18.363	-0.976	-0.976	0.000	0.000	0.000	0.000
41	A	40	ILE	0	0.027	0.017	17.848	0.272	0.272	0.000	0.000	0.000	0.000
42	A	41	ILE	0	-0.050	-0.029	12.989	-1.011	-1.011	0.000	0.000	0.000	0.000
43	A	42	PHE	0	0.029	0.018	11.585	0.749	0.749	0.000	0.000	0.000	0.000
44	A	43	HIS	0	-0.039	-0.043	6.133	-3.744	-3.744	0.000	0.000	0.000	0.000
45	A	44	LEU	0	0.038	0.026	9.772	1.399	1.399	0.000	0.000	0.000	0.000
46	A	45	SER	0	-0.003	0.025	4.844	-2.099	-2.099	0.000	0.000	0.000	0.000
47	A	46	PRO	0	0.014	-0.010	2.705	1.334	1.933	0.314	-0.274	-0.639	-0.001
48	A	47	TYR	0	-0.031	-0.030	4.336	-3.226	-3.242	-0.001	-0.014	0.031	0.000
49	A	48	TYR	0	0.009	0.004	7.461	0.080	0.080	0.000	0.000	0.000	0.000
50	A	49	LEU	0	-0.008	0.001	9.419	0.261	0.261	0.000	0.000	0.000	0.000
51	A	50	ARG	1	0.933	0.959	12.827	20.242	20.242	0.000	0.000	0.000	0.000
52	A	51	LEU	0	-0.036	-0.018	14.678	0.008	0.008	0.000	0.000	0.000	0.000
53	A	52	ARG	1	0.923	0.958	18.216	14.456	14.456	0.000	0.000	0.000	0.000
54	A	53	PHE	0	0.004	-0.009	21.070	0.166	0.166	0.000	0.000	0.000	0.000
55	A	54	PRO	0	-0.049	-0.009	24.655	-0.044	-0.044	0.000	0.000	0.000	0.000
56	A	55	HIS	1	0.879	0.947	27.960	10.160	10.160	0.000	0.000	0.000	0.000
57	A	56	GLU	-1	-0.903	-0.958	27.581	-11.015	-11.015	0.000	0.000	0.000	0.000
58	A	57	LEU	0	-0.059	-0.025	24.057	0.316	0.316	0.000	0.000	0.000	0.000
59	A	58	ILE	0	-0.023	-0.021	27.822	0.028	0.028	0.000	0.000	0.000	0.000
60	A	59	ASP	-1	-0.874	-0.908	24.144	-12.528	-12.528	0.000	0.000	0.000	0.000
61	A	60	ASP	-1	-0.783	-0.877	26.781	-9.515	-9.515	0.000	0.000	0.000	0.000
62	A	61	GLU	-1	-0.967	-0.978	28.620	-9.167	-9.167	0.000	0.000	0.000	0.000
63	A	62	ARG	1	0.775	0.851	29.972	9.333	9.333	0.000	0.000	0.000	0.000
64	A	63	SER	0	-0.045	-0.045	24.767	0.017	0.017	0.000	0.000	0.000	0.000
65	A	64	THR	0	-0.028	-0.018	25.201	0.216	0.216	0.000	0.000	0.000	0.000
66	A	65	ALA	0	-0.001	0.001	20.026	-0.312	-0.312	0.000	0.000	0.000	0.000
67	A	66	GLN	0	-0.026	-0.012	22.126	0.265	0.265	0.000	0.000	0.000	0.000
68	A	67	TYR	0	-0.021	-0.011	16.973	-0.082	-0.082	0.000	0.000	0.000	0.000
69	A	68	ASP	-1	-0.854	-0.929	20.495	-10.693	-10.693	0.000	0.000	0.000	0.000
70	A	69	SER	0	0.003	-0.011	20.842	-0.354	-0.354	0.000	0.000	0.000	0.000
71	A	70	LYS	1	0.928	0.971	21.987	9.459	9.459	0.000	0.000	0.000	0.000
72	A	71	ASP	-1	-0.827	-0.909	21.867	-11.522	-11.522	0.000	0.000	0.000	0.000
73	A	72	GLU	-1	-0.933	-0.953	16.562	-15.269	-15.269	0.000	0.000	0.000	0.000
74	A	73	CYS	0	-0.064	-0.020	17.232	-0.601	-0.601	0.000	0.000	0.000	0.000
75	A	74	ILE	0	0.025	0.013	15.000	0.469	0.469	0.000	0.000	0.000	0.000
76	A	75	ASN	0	-0.017	-0.008	18.581	-0.161	-0.161	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.019	-0.014	18.735	0.126	0.126	0.000	0.000	0.000	0.000
78	A	77	LYS	1	0.854	0.955	22.017	10.544	10.544	0.000	0.000	0.000	0.000
79	A	78	VAL	0	0.029	0.006	23.219	-0.037	-0.037	0.000	0.000	0.000	0.000
80	A	79	ALA	0	0.042	0.032	26.401	0.248	0.248	0.000	0.000	0.000	0.000
81	A	80	LYS	1	0.778	0.877	28.911	9.279	9.279	0.000	0.000	0.000	0.000
82	A	81	LEU	0	-0.030	-0.009	30.666	0.241	0.241	0.000	0.000	0.000	0.000
83	A	82	ASN	0	-0.067	-0.043	32.230	0.468	0.468	0.000	0.000	0.000	0.000
84	A	83	LYS	1	0.840	0.903	35.139	8.066	8.066	0.000	0.000	0.000	0.000
85	A	84	ASN	0	-0.063	-0.055	36.944	0.142	0.142	0.000	0.000	0.000	0.000
86	A	85	GLU	-1	-0.862	-0.903	33.724	-9.161	-9.161	0.000	0.000	0.000	0.000
87	A	86	TYR	0	-0.025	-0.012	33.288	-0.227	-0.227	0.000	0.000	0.000	0.000
88	A	87	PHE	0	-0.005	-0.008	27.363	-0.147	-0.147	0.000	0.000	0.000	0.000
89	A	88	GLU	-1	-0.810	-0.924	30.771	-9.764	-9.764	0.000	0.000	0.000	0.000
90	A	89	ASP	-1	-0.892	-0.957	27.795	-10.765	-10.765	0.000	0.000	0.000	0.000
91	A	90	LEU	0	-0.042	-0.025	25.440	-0.519	-0.519	0.000	0.000	0.000	0.000
92	A	91	ASP	-1	-0.914	-0.948	24.814	-10.874	-10.874	0.000	0.000	0.000	0.000
93	A	92	LEU	0	-0.042	-0.015	24.449	-0.207	-0.207	0.000	0.000	0.000	0.000
94	A	93	PRO	0	0.084	0.037	19.749	-0.400	-0.400	0.000	0.000	0.000	0.000
95	A	94	THR	0	-0.044	-0.037	18.741	-0.296	-0.296	0.000	0.000	0.000	0.000
96	A	95	LYS	1	0.851	0.917	19.829	13.457	13.457	0.000	0.000	0.000	0.000
97	A	96	LEU	0	0.091	0.056	20.711	-0.145	-0.145	0.000	0.000	0.000	0.000
98	A	97	LEU	0	-0.051	0.005	14.603	-0.555	-0.555	0.000	0.000	0.000	0.000
99	A	98	ALA	0	-0.019	-0.004	16.469	0.287	0.287	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:LYS)