FMO DATABASE

FMODB ID: VQJ11

Calculation Name: 4EMG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EMG

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y7M4

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	71
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-447679.192206
FMO2-HF: Nuclear repulsion	418910.519381
FMO2-HF: Total energy	-28768.672826
FMO2-MP2: Total energy	-28853.011999

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:9:GLU)

Summations of interaction energy for fragment #1(A:9:GLU)

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.
20.336	20.02	11.385	-5.764	-5.305	-0.041

Interaction energy analysis for fragmet #1(A:9:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.945 / q_NPA : -0.980

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	11	LEU	0	0.028	0.008	3.273	-7.932	-5.649	0.034	-1.034	-1.283	0.005
4	A	12	ASP	-1	-0.813	-0.896	1.855	31.827	28.939	11.351	-4.683	-3.780	-0.046
5	A	13	LEU	0	0.011	0.021	4.197	-3.002	-2.713	0.000	-0.047	-0.242	0.000
6	A	14	VAL	0	0.007	0.012	6.806	-3.827	-3.827	0.000	0.000	0.000	0.000
7	A	15	ARG	1	0.863	0.925	5.262	-33.861	-33.861	0.000	0.000	0.000	0.000
8	A	16	LEU	0	-0.033	-0.027	6.563	-2.272	-2.272	0.000	0.000	0.000	0.000
9	A	17	SER	0	-0.042	-0.026	9.813	-1.845	-1.845	0.000	0.000	0.000	0.000
10	A	18	LEU	0	-0.033	-0.021	11.198	-1.558	-1.558	0.000	0.000	0.000	0.000
11	A	19	ASP	-1	-0.887	-0.948	13.871	14.450	14.450	0.000	0.000	0.000	0.000
12	A	20	GLU	-1	-0.842	-0.916	15.887	15.187	15.187	0.000	0.000	0.000	0.000
13	A	21	ILE	0	-0.091	-0.036	17.803	-0.068	-0.068	0.000	0.000	0.000	0.000
14	A	22	VAL	0	0.003	0.006	14.564	0.620	0.620	0.000	0.000	0.000	0.000
15	A	23	TYR	0	-0.044	-0.021	17.676	-0.741	-0.741	0.000	0.000	0.000	0.000
16	A	24	VAL	0	0.007	-0.015	16.542	1.264	1.264	0.000	0.000	0.000	0.000
17	A	25	LYS	1	0.826	0.924	18.135	-14.021	-14.021	0.000	0.000	0.000	0.000
18	A	26	LEU	0	0.032	-0.002	19.069	0.618	0.618	0.000	0.000	0.000	0.000
19	A	27	ARG	1	0.832	0.899	18.396	-15.074	-15.074	0.000	0.000	0.000	0.000
20	A	28	GLY	0	-0.035	-0.006	23.718	-0.277	-0.277	0.000	0.000	0.000	0.000
21	A	29	ASP	-1	-0.929	-0.970	26.635	10.822	10.822	0.000	0.000	0.000	0.000
22	A	30	ARG	1	0.908	0.950	25.284	-11.185	-11.185	0.000	0.000	0.000	0.000
23	A	31	GLU	-1	-0.828	-0.902	23.049	13.505	13.505	0.000	0.000	0.000	0.000
24	A	32	LEU	0	-0.006	-0.002	20.739	-0.616	-0.616	0.000	0.000	0.000	0.000
25	A	33	ASN	0	-0.028	-0.017	21.603	1.182	1.182	0.000	0.000	0.000	0.000
26	A	34	GLY	0	0.054	0.026	21.051	-0.744	-0.744	0.000	0.000	0.000	0.000
27	A	35	ARG	1	0.804	0.919	19.923	-13.281	-13.281	0.000	0.000	0.000	0.000
28	A	36	LEU	0	0.003	-0.001	12.774	-0.505	-0.505	0.000	0.000	0.000	0.000
29	A	37	HIS	0	0.026	0.006	16.497	0.521	0.521	0.000	0.000	0.000	0.000
30	A	38	ALA	0	-0.013	-0.005	15.537	0.041	0.041	0.000	0.000	0.000	0.000
31	A	39	TYR	0	-0.022	-0.015	7.035	0.002	0.002	0.000	0.000	0.000	0.000
32	A	40	ASP	-1	-0.769	-0.859	12.721	16.498	16.498	0.000	0.000	0.000	0.000
33	A	41	GLU	-1	-0.855	-0.938	10.222	18.681	18.681	0.000	0.000	0.000	0.000
34	A	42	HIS	0	-0.120	-0.054	11.275	0.716	0.716	0.000	0.000	0.000	0.000
35	A	43	LEU	0	-0.022	-0.012	10.150	-0.207	-0.207	0.000	0.000	0.000	0.000
36	A	44	ASN	0	-0.047	-0.040	12.848	-1.089	-1.089	0.000	0.000	0.000	0.000
37	A	45	MET	0	-0.037	-0.021	14.320	1.145	1.145	0.000	0.000	0.000	0.000
38	A	46	VAL	0	-0.024	-0.015	16.728	-0.945	-0.945	0.000	0.000	0.000	0.000
39	A	47	LEU	0	0.009	0.010	17.783	0.493	0.493	0.000	0.000	0.000	0.000
40	A	48	GLY	0	0.011	-0.018	20.688	-0.632	-0.632	0.000	0.000	0.000	0.000
41	A	49	ASP	-1	-0.933	-0.956	23.658	11.072	11.072	0.000	0.000	0.000	0.000
42	A	50	ALA	0	-0.010	0.004	23.922	0.327	0.327	0.000	0.000	0.000	0.000
43	A	51	GLU	-1	-0.793	-0.880	25.474	10.527	10.527	0.000	0.000	0.000	0.000
44	A	52	GLU	-1	-0.827	-0.892	25.367	11.153	11.153	0.000	0.000	0.000	0.000
45	A	53	ILE	0	-0.046	-0.025	26.397	-0.537	-0.537	0.000	0.000	0.000	0.000
46	A	54	VAL	0	0.009	0.005	27.765	0.322	0.322	0.000	0.000	0.000	0.000
47	A	55	THR	0	-0.004	0.004	28.468	-0.537	-0.537	0.000	0.000	0.000	0.000
48	A	70	THR	0	-0.031	-0.031	31.746	0.073	0.073	0.000	0.000	0.000	0.000
49	A	71	ILE	0	-0.026	0.003	33.385	-0.284	-0.284	0.000	0.000	0.000	0.000
50	A	72	ARG	1	0.848	0.888	28.795	-10.181	-10.181	0.000	0.000	0.000	0.000
51	A	73	LYS	1	0.864	0.942	30.880	-9.975	-9.975	0.000	0.000	0.000	0.000
52	A	74	HIS	0	-0.007	-0.012	29.357	0.071	0.071	0.000	0.000	0.000	0.000
53	A	75	TYR	0	-0.049	-0.045	27.169	-0.486	-0.486	0.000	0.000	0.000	0.000
54	A	76	GLU	-1	-0.897	-0.936	27.954	9.840	9.840	0.000	0.000	0.000	0.000
55	A	77	MET	0	-0.010	0.000	22.982	0.514	0.514	0.000	0.000	0.000	0.000
56	A	78	LEU	0	-0.030	-0.011	23.280	-0.417	-0.417	0.000	0.000	0.000	0.000
57	A	79	PHE	0	0.000	0.010	19.845	0.508	0.508	0.000	0.000	0.000	0.000
58	A	80	VAL	0	-0.001	-0.003	18.802	-0.416	-0.416	0.000	0.000	0.000	0.000
59	A	81	ARG	1	0.864	0.916	18.911	-12.222	-12.222	0.000	0.000	0.000	0.000
60	A	82	GLY	0	0.094	0.054	16.133	-0.056	-0.056	0.000	0.000	0.000	0.000
61	A	83	ASP	-1	-0.814	-0.891	16.831	14.111	14.111	0.000	0.000	0.000	0.000
62	A	84	SER	0	-0.113	-0.069	18.996	-0.257	-0.257	0.000	0.000	0.000	0.000
63	A	85	VAL	0	0.041	0.021	14.749	-0.405	-0.405	0.000	0.000	0.000	0.000
64	A	86	ILE	0	-0.075	-0.033	16.810	-0.091	-0.091	0.000	0.000	0.000	0.000
65	A	87	LEU	0	-0.019	-0.012	14.244	1.030	1.030	0.000	0.000	0.000	0.000
66	A	88	ILE	0	0.050	0.020	11.737	-1.019	-1.019	0.000	0.000	0.000	0.000
67	A	89	ALA	0	-0.040	-0.013	12.966	1.463	1.463	0.000	0.000	0.000	0.000
68	A	90	PRO	0	0.050	0.039	11.237	-1.174	-1.174	0.000	0.000	0.000	0.000
69	A	91	PRO	0	0.039	0.028	14.206	-0.731	-0.731	0.000	0.000	0.000	0.000
70	A	92	ARG	1	0.930	0.952	15.638	-15.354	-15.354	0.000	0.000	0.000	0.000
71	A	93	ASN	0	-0.013	0.005	14.957	-0.423	-0.423	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:GLU)