FMO DATABASE

FMODB ID: 49GYN

Calculation Name: 2EBB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EBB

Chain ID: A

ChEMBL ID:

UniProt ID: Q5KYG7

Base Structure: X-ray

Registration Date: 2023-06-26

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	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	96
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-766358.238788
FMO2-HF: Nuclear repulsion	726708.741327
FMO2-HF: Total energy	-39649.497461
FMO2-MP2: Total energy	-39767.084037

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:MET)

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

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.
-12.804	-8.497	1.156	-2.064	-3.399	-0.012

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.015

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

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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	LEU	0	-0.029	-0.005	2.512	-6.566	-3.368	1.140	-1.803	-2.536	-0.012
4	A	6	THR	0	-0.015	-0.015	3.837	1.514	1.808	0.001	-0.030	-0.265	0.000
5	A	7	GLU	-1	-0.906	-0.955	5.730	-0.539	-0.539	0.000	0.000	0.000	0.000
6	A	8	GLU	-1	-0.857	-0.942	9.302	-1.382	-1.382	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.889	-0.947	4.348	-6.435	-6.331	-0.001	-0.019	-0.084	0.000
8	A	10	VAL	0	-0.044	-0.025	8.149	0.251	0.251	0.000	0.000	0.000	0.000
9	A	11	GLN	0	-0.011	-0.004	10.240	0.207	0.207	0.000	0.000	0.000	0.000
10	A	12	ALA	0	0.021	0.019	11.780	0.131	0.131	0.000	0.000	0.000	0.000
11	A	13	LEU	0	-0.095	-0.055	8.779	0.135	0.135	0.000	0.000	0.000	0.000
12	A	14	LEU	0	-0.014	-0.024	12.963	0.159	0.159	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.975	-0.959	15.468	-0.513	-0.513	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.902	0.954	15.447	0.958	0.958	0.000	0.000	0.000	0.000
15	A	17	ALA	0	-0.029	-0.008	16.356	0.029	0.029	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.835	-0.909	18.400	-0.348	-0.348	0.000	0.000	0.000	0.000
17	A	19	GLY	0	-0.088	-0.063	21.926	0.022	0.022	0.000	0.000	0.000	0.000
18	A	20	TRP	0	-0.018	-0.015	17.282	0.047	0.047	0.000	0.000	0.000	0.000
19	A	21	LYS	1	0.913	0.952	19.489	0.277	0.277	0.000	0.000	0.000	0.000
20	A	22	LEU	0	0.043	0.033	14.023	0.027	0.027	0.000	0.000	0.000	0.000
21	A	23	ALA	0	-0.027	-0.021	17.325	0.031	0.031	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.894	-0.959	17.487	0.050	0.050	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.943	-0.971	15.388	0.087	0.087	0.000	0.000	0.000	0.000
24	A	26	ARG	1	0.870	0.940	11.795	-0.407	-0.407	0.000	0.000	0.000	0.000
25	A	27	TRP	0	0.013	0.021	12.482	0.106	0.106	0.000	0.000	0.000	0.000
26	A	28	ILE	0	0.021	0.035	12.964	-0.075	-0.075	0.000	0.000	0.000	0.000
27	A	29	VAL	0	-0.039	-0.039	15.785	0.083	0.083	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.862	0.951	19.124	0.228	0.228	0.000	0.000	0.000	0.000
29	A	31	LYS	1	0.873	0.936	21.540	0.098	0.098	0.000	0.000	0.000	0.000
30	A	32	TYR	0	0.012	-0.021	20.885	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	33	ARG	1	0.977	0.988	26.580	0.088	0.088	0.000	0.000	0.000	0.000
32	A	34	PHE	0	0.030	0.032	27.294	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	35	GLN	0	0.053	0.015	32.617	0.004	0.004	0.000	0.000	0.000	0.000
34	A	36	ASP	-1	-0.824	-0.921	35.279	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	37	TYR	0	-0.006	-0.016	33.480	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	38	LEU	0	0.052	0.018	33.473	0.004	0.004	0.000	0.000	0.000	0.000
37	A	39	GLN	0	-0.022	-0.005	32.713	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.027	0.018	29.753	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	41	ILE	0	-0.001	-0.005	28.562	0.004	0.004	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.746	-0.820	28.761	0.001	0.001	0.000	0.000	0.000	0.000
41	A	43	PHE	0	-0.010	-0.015	22.639	0.003	0.003	0.000	0.000	0.000	0.000
42	A	44	VAL	0	0.005	-0.001	24.405	0.000	0.000	0.000	0.000	0.000	0.000
43	A	45	ARG	1	0.831	0.884	24.101	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	46	ARG	1	0.876	0.913	24.648	0.057	0.057	0.000	0.000	0.000	0.000
45	A	47	ILE	0	0.029	0.014	19.954	0.000	0.000	0.000	0.000	0.000	0.000
46	A	48	ALA	0	-0.002	0.028	19.489	0.016	0.016	0.000	0.000	0.000	0.000
47	A	49	ALA	0	-0.011	0.002	20.083	0.028	0.028	0.000	0.000	0.000	0.000
48	A	50	ILE	0	-0.024	-0.014	16.746	0.010	0.010	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.014	-0.030	15.667	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.893	-0.924	15.570	0.362	0.362	0.000	0.000	0.000	0.000
51	A	53	ASN	0	-0.022	-0.003	16.968	0.048	0.048	0.000	0.000	0.000	0.000
52	A	54	ALA	0	-0.046	-0.018	12.370	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	55	ASN	0	-0.065	-0.022	11.948	0.079	0.079	0.000	0.000	0.000	0.000
54	A	56	HIS	0	-0.058	-0.048	8.176	0.311	0.311	0.000	0.000	0.000	0.000
55	A	57	HIS	0	-0.041	-0.041	12.391	-0.080	-0.080	0.000	0.000	0.000	0.000
56	A	58	PRO	0	-0.022	0.011	14.846	0.054	0.054	0.000	0.000	0.000	0.000
57	A	59	PHE	0	-0.007	-0.002	16.265	0.011	0.011	0.000	0.000	0.000	0.000
58	A	60	ILE	0	0.009	-0.017	19.209	-0.048	-0.048	0.000	0.000	0.000	0.000
59	A	61	SER	0	0.002	0.001	22.287	0.013	0.013	0.000	0.000	0.000	0.000
60	A	62	ILE	0	-0.017	-0.022	25.740	-0.020	-0.020	0.000	0.000	0.000	0.000
61	A	63	ASP	-1	-0.908	-0.930	28.913	0.009	0.009	0.000	0.000	0.000	0.000
62	A	64	TYR	0	0.059	0.009	31.553	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	65	LYS	1	0.878	0.940	32.664	0.034	0.034	0.000	0.000	0.000	0.000
64	A	66	LEU	0	-0.072	-0.030	28.316	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.043	0.033	24.480	0.013	0.013	0.000	0.000	0.000	0.000
66	A	68	THR	0	-0.075	-0.033	22.519	-0.031	-0.031	0.000	0.000	0.000	0.000
67	A	69	VAL	0	0.023	0.017	18.006	0.030	0.030	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.944	0.967	17.689	-0.094	-0.094	0.000	0.000	0.000	0.000
69	A	71	LEU	0	0.010	0.016	12.482	0.080	0.080	0.000	0.000	0.000	0.000
70	A	72	SER	0	0.028	-0.008	10.647	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	73	SER	0	0.024	0.035	6.587	0.099	0.099	0.000	0.000	0.000	0.000
72	A	74	TRP	0	0.047	0.006	8.448	0.589	0.589	0.000	0.000	0.000	0.000
73	A	75	ARG	1	0.921	0.957	7.445	-1.658	-1.658	0.000	0.000	0.000	0.000
74	A	76	ALA	0	0.011	0.017	4.210	0.416	0.682	0.005	-0.074	-0.197	0.000
75	A	77	LYS	1	0.913	0.949	5.804	-2.641	-2.609	-0.001	-0.001	-0.029	0.000
76	A	78	GLY	0	0.000	-0.009	8.500	-0.406	-0.406	0.000	0.000	0.000	0.000
77	A	79	LEU	0	0.023	0.035	8.009	0.359	0.359	0.000	0.000	0.000	0.000
78	A	80	THR	0	0.005	-0.019	3.426	-0.994	-0.581	0.012	-0.137	-0.288	0.000
79	A	81	LYS	1	0.936	0.962	4.962	2.010	2.010	0.000	0.000	0.000	0.000
80	A	82	LEU	0	0.063	0.040	6.025	0.349	0.349	0.000	0.000	0.000	0.000
81	A	83	ASP	-1	-0.719	-0.837	7.838	0.277	0.277	0.000	0.000	0.000	0.000
82	A	84	PHE	0	0.027	-0.010	9.622	0.109	0.109	0.000	0.000	0.000	0.000
83	A	85	ASP	-1	-0.872	-0.934	9.976	-1.034	-1.034	0.000	0.000	0.000	0.000
84	A	86	LEU	0	0.012	-0.005	11.467	0.104	0.104	0.000	0.000	0.000	0.000
85	A	87	ALA	0	0.000	0.006	13.706	0.055	0.055	0.000	0.000	0.000	0.000
86	A	88	LYS	1	0.975	0.987	15.405	0.706	0.706	0.000	0.000	0.000	0.000
87	A	89	GLN	0	0.004	0.007	14.514	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	90	TYR	0	0.002	-0.027	15.941	0.036	0.036	0.000	0.000	0.000	0.000
89	A	91	ASP	-1	-0.802	-0.883	19.638	-0.286	-0.286	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.911	-0.950	21.087	-0.212	-0.212	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.027	-0.012	22.054	0.025	0.025	0.000	0.000	0.000	0.000
92	A	94	TYR	0	-0.071	-0.057	24.069	0.010	0.010	0.000	0.000	0.000	0.000
93	A	95	ASN	0	-0.048	-0.040	24.629	0.021	0.021	0.000	0.000	0.000	0.000
94	A	96	GLN	0	-0.044	-0.001	26.667	0.021	0.021	0.000	0.000	0.000	0.000
95	A	97	MET	0	-0.102	-0.035	28.390	0.012	0.012	0.000	0.000	0.000	0.000
96	A	98	LYS	1	0.936	0.988	29.559	0.164	0.164	0.000	0.000	0.000	0.000

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