FMO DATABASE

FMODB ID: 72GKK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-798613.795396
FMO2-HF: Nuclear repulsion	757711.917381
FMO2-HF: Total energy	-40901.878015
FMO2-MP2: Total energy	-41021.978934

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.
-39.606	-37.314	0.151	-0.968	-1.475	-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 : 0.977 / q_NPA : 0.977

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	-0.012	0.001	3.636	1.049	2.780	-0.008	-0.761	-0.962	-0.001
4	A	3	THR	0	0.015	0.001	5.692	0.732	0.732	0.000	0.000	0.000	0.000
5	A	4	PRO	0	-0.013	0.007	9.432	0.881	0.881	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.977	1.000	11.432	15.393	15.393	0.000	0.000	0.000	0.000
7	A	6	PHE	0	-0.002	-0.007	14.868	-0.134	-0.134	0.000	0.000	0.000	0.000
8	A	7	SER	0	-0.043	-0.018	17.479	0.509	0.509	0.000	0.000	0.000	0.000
9	A	8	ILE	0	0.030	0.004	21.047	-0.267	-0.267	0.000	0.000	0.000	0.000
10	A	9	THR	0	0.006	0.027	23.978	0.224	0.224	0.000	0.000	0.000	0.000
11	A	10	GLN	0	0.018	-0.016	27.546	-0.211	-0.211	0.000	0.000	0.000	0.000
12	A	11	ASP	-1	-0.830	-0.901	30.294	-8.902	-8.902	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.931	-0.970	33.751	-8.404	-8.404	0.000	0.000	0.000	0.000
14	A	13	GLU	-1	-0.887	-0.953	33.750	-8.552	-8.552	0.000	0.000	0.000	0.000
15	A	14	PHE	0	-0.008	-0.008	29.314	-0.264	-0.264	0.000	0.000	0.000	0.000
16	A	15	ILE	0	-0.016	0.000	23.969	0.117	0.117	0.000	0.000	0.000	0.000
17	A	16	PHE	0	-0.016	-0.017	25.583	-0.212	-0.212	0.000	0.000	0.000	0.000
18	A	17	LEU	0	0.006	0.003	18.298	-0.065	-0.065	0.000	0.000	0.000	0.000
19	A	18	LYS	1	0.894	0.970	20.284	11.780	11.780	0.000	0.000	0.000	0.000
20	A	19	ILE	0	0.001	-0.016	13.970	-0.363	-0.363	0.000	0.000	0.000	0.000
21	A	20	PHE	0	-0.038	-0.029	15.444	0.155	0.155	0.000	0.000	0.000	0.000
22	A	21	ILE	0	-0.055	-0.017	12.041	-1.235	-1.235	0.000	0.000	0.000	0.000
23	A	22	SER	0	0.047	0.022	11.729	0.846	0.846	0.000	0.000	0.000	0.000
24	A	23	ASN	0	-0.027	-0.023	11.147	-0.530	-0.530	0.000	0.000	0.000	0.000
25	A	24	ILE	0	0.029	0.030	8.796	-1.203	-1.203	0.000	0.000	0.000	0.000
26	A	25	ARG	1	0.933	0.961	11.478	19.802	19.802	0.000	0.000	0.000	0.000
27	A	26	PHE	0	0.045	0.024	13.012	-0.886	-0.886	0.000	0.000	0.000	0.000
28	A	27	SER	0	-0.031	-0.036	14.471	0.018	0.018	0.000	0.000	0.000	0.000
29	A	28	ALA	0	-0.002	-0.003	17.033	-0.037	-0.037	0.000	0.000	0.000	0.000
30	A	29	VAL	0	0.017	-0.001	14.726	0.271	0.271	0.000	0.000	0.000	0.000
31	A	30	GLY	0	-0.021	0.010	12.486	-0.790	-0.790	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.037	-0.012	11.978	-1.391	-1.391	0.000	0.000	0.000	0.000
33	A	32	GLU	-1	-0.923	-0.956	12.850	-21.014	-21.014	0.000	0.000	0.000	0.000
34	A	33	ILE	0	-0.005	-0.030	14.742	-0.691	-0.691	0.000	0.000	0.000	0.000
35	A	34	ILE	0	-0.010	0.013	16.029	0.610	0.610	0.000	0.000	0.000	0.000
36	A	35	ILE	0	0.028	0.005	19.005	-0.412	-0.412	0.000	0.000	0.000	0.000
37	A	36	GLN	0	-0.006	-0.006	21.984	-0.025	-0.025	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.835	-0.913	23.535	-12.462	-12.462	0.000	0.000	0.000	0.000
39	A	38	ASN	0	0.002	0.012	24.622	-0.133	-0.133	0.000	0.000	0.000	0.000
40	A	39	MET	0	-0.022	0.004	18.410	-0.952	-0.952	0.000	0.000	0.000	0.000
41	A	40	ILE	0	0.035	0.019	17.873	0.241	0.241	0.000	0.000	0.000	0.000
42	A	41	ILE	0	-0.052	-0.029	13.121	-0.998	-0.998	0.000	0.000	0.000	0.000
43	A	42	PHE	0	0.015	0.014	11.456	0.712	0.712	0.000	0.000	0.000	0.000
44	A	43	HIS	0	-0.033	-0.028	6.042	-3.441	-3.441	0.000	0.000	0.000	0.000
45	A	44	LEU	0	0.025	0.024	9.742	1.289	1.289	0.000	0.000	0.000	0.000
46	A	45	SER	0	-0.010	0.019	4.897	-2.362	-2.362	0.000	0.000	0.000	0.000
47	A	46	PRO	0	0.019	-0.006	2.905	1.198	1.778	0.160	-0.195	-0.545	-0.001
48	A	47	TYR	0	-0.017	-0.018	4.319	-2.699	-2.718	-0.001	-0.012	0.032	0.000
49	A	48	TYR	0	0.015	0.002	7.552	0.229	0.229	0.000	0.000	0.000	0.000
50	A	49	LEU	0	0.011	0.002	9.475	0.310	0.310	0.000	0.000	0.000	0.000
51	A	50	ARG	1	0.947	0.978	12.884	19.968	19.968	0.000	0.000	0.000	0.000
52	A	51	LEU	0	-0.032	-0.021	14.734	0.016	0.016	0.000	0.000	0.000	0.000
53	A	52	ARG	1	0.920	0.957	18.260	13.938	13.938	0.000	0.000	0.000	0.000
54	A	53	PHE	0	0.005	-0.006	21.405	0.177	0.177	0.000	0.000	0.000	0.000
55	A	54	PRO	0	-0.022	-0.005	24.698	-0.053	-0.053	0.000	0.000	0.000	0.000
56	A	55	HIS	1	0.891	0.952	27.999	10.037	10.037	0.000	0.000	0.000	0.000
57	A	56	GLU	-1	-0.922	-0.964	27.647	-10.850	-10.850	0.000	0.000	0.000	0.000
58	A	57	LEU	0	-0.045	-0.022	24.275	0.303	0.303	0.000	0.000	0.000	0.000
59	A	58	ILE	0	-0.030	-0.027	27.922	0.032	0.032	0.000	0.000	0.000	0.000
60	A	59	ASP	-1	-0.899	-0.941	24.256	-12.347	-12.347	0.000	0.000	0.000	0.000
61	A	60	ASP	-1	-0.788	-0.879	26.923	-9.493	-9.493	0.000	0.000	0.000	0.000
62	A	61	GLU	-1	-0.967	-0.978	28.568	-9.091	-9.091	0.000	0.000	0.000	0.000
63	A	62	ARG	1	0.760	0.853	29.950	9.288	9.288	0.000	0.000	0.000	0.000
64	A	63	SER	0	-0.036	-0.008	24.747	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	64	THR	0	-0.054	-0.023	25.193	0.220	0.220	0.000	0.000	0.000	0.000
66	A	65	ALA	0	0.005	-0.002	20.022	-0.307	-0.307	0.000	0.000	0.000	0.000
67	A	66	GLN	0	-0.030	-0.013	22.118	0.259	0.259	0.000	0.000	0.000	0.000
68	A	67	TYR	0	-0.030	-0.008	17.051	-0.064	-0.064	0.000	0.000	0.000	0.000
69	A	68	ASP	-1	-0.853	-0.924	20.487	-10.678	-10.678	0.000	0.000	0.000	0.000
70	A	69	SER	0	0.000	-0.020	20.835	-0.335	-0.335	0.000	0.000	0.000	0.000
71	A	70	LYS	1	0.928	0.972	21.983	9.438	9.438	0.000	0.000	0.000	0.000
72	A	71	ASP	-1	-0.865	-0.948	21.971	-11.298	-11.298	0.000	0.000	0.000	0.000
73	A	72	GLU	-1	-1.020	-0.995	17.382	-14.594	-14.594	0.000	0.000	0.000	0.000
74	A	73	CYS	0	-0.054	-0.020	17.225	-0.603	-0.603	0.000	0.000	0.000	0.000
75	A	74	ILE	0	0.006	0.006	15.248	0.437	0.437	0.000	0.000	0.000	0.000
76	A	75	ASN	0	-0.012	-0.014	18.568	-0.291	-0.291	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.005	-0.022	18.764	0.112	0.112	0.000	0.000	0.000	0.000
78	A	77	LYS	1	0.918	0.981	22.000	10.019	10.019	0.000	0.000	0.000	0.000
79	A	78	VAL	0	0.038	0.012	23.297	-0.047	-0.047	0.000	0.000	0.000	0.000
80	A	79	ALA	0	0.043	0.035	26.381	0.246	0.246	0.000	0.000	0.000	0.000
81	A	80	LYS	1	0.856	0.942	29.019	9.173	9.173	0.000	0.000	0.000	0.000
82	A	81	LEU	0	-0.035	-0.007	30.773	0.238	0.238	0.000	0.000	0.000	0.000
83	A	82	ASN	0	-0.048	-0.022	32.332	0.498	0.498	0.000	0.000	0.000	0.000
84	A	83	LYS	1	0.991	0.990	35.223	7.620	7.620	0.000	0.000	0.000	0.000
85	A	84	ASN	0	-0.056	-0.053	37.033	0.097	0.097	0.000	0.000	0.000	0.000
86	A	85	GLU	-1	-0.895	-0.933	33.941	-9.028	-9.028	0.000	0.000	0.000	0.000
87	A	86	TYR	0	-0.046	-0.030	33.506	-0.248	-0.248	0.000	0.000	0.000	0.000
88	A	87	PHE	0	-0.012	-0.007	27.557	-0.145	-0.145	0.000	0.000	0.000	0.000
89	A	88	GLU	-1	-0.837	-0.937	30.820	-9.585	-9.585	0.000	0.000	0.000	0.000
90	A	89	ASP	-1	-0.894	-0.961	27.718	-10.602	-10.602	0.000	0.000	0.000	0.000
91	A	90	LEU	0	-0.045	-0.026	25.494	-0.496	-0.496	0.000	0.000	0.000	0.000
92	A	91	ASP	-1	-0.899	-0.942	24.827	-10.768	-10.768	0.000	0.000	0.000	0.000
93	A	92	LEU	0	-0.051	-0.018	24.472	-0.230	-0.230	0.000	0.000	0.000	0.000
94	A	93	PRO	0	0.062	0.026	19.832	-0.387	-0.387	0.000	0.000	0.000	0.000
95	A	94	THR	0	-0.069	-0.062	18.766	-0.235	-0.235	0.000	0.000	0.000	0.000
96	A	95	LYS	1	0.929	0.955	19.845	12.710	12.710	0.000	0.000	0.000	0.000
97	A	96	LEU	0	0.050	0.045	20.781	-0.130	-0.130	0.000	0.000	0.000	0.000
98	A	97	LEU	0	-0.052	0.013	14.937	-0.533	-0.533	0.000	0.000	0.000	0.000
99	A	98	ALA	0	-0.018	-0.005	16.561	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)