FMO DATABASE

FMODB ID: YVJK2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-448369.684115
FMO2-HF: Nuclear repulsion	419601.163539
FMO2-HF: Total energy	-28768.520576
FMO2-MP2: Total energy	-28852.836448

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.
26.163	31.61	3.172	-4.071	-4.548	-0.029

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 : -0.935 / q_NPA : -0.972

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	0.027	0.000	3.550	-6.317	-4.240	-0.005	-0.947	-1.125	0.004
4	A	12	ASP	-1	-0.828	-0.910	2.342	34.651	37.806	3.178	-3.105	-3.228	-0.033
5	A	13	LEU	0	-0.006	0.009	4.721	-3.515	-3.300	-0.001	-0.019	-0.195	0.000
6	A	14	VAL	0	0.009	0.015	7.526	-3.244	-3.244	0.000	0.000	0.000	0.000
7	A	15	ARG	1	0.885	0.936	5.461	-34.143	-34.143	0.000	0.000	0.000	0.000
8	A	16	LEU	0	-0.038	-0.029	6.898	-1.969	-1.969	0.000	0.000	0.000	0.000
9	A	17	SER	0	-0.034	-0.027	10.305	-1.760	-1.760	0.000	0.000	0.000	0.000
10	A	18	LEU	0	-0.034	-0.013	11.873	-1.493	-1.493	0.000	0.000	0.000	0.000
11	A	19	ASP	-1	-0.900	-0.964	14.545	14.594	14.594	0.000	0.000	0.000	0.000
12	A	20	GLU	-1	-0.922	-0.946	15.743	15.890	15.890	0.000	0.000	0.000	0.000
13	A	21	ILE	0	-0.072	-0.042	17.999	-0.346	-0.346	0.000	0.000	0.000	0.000
14	A	22	VAL	0	-0.005	-0.001	14.798	0.567	0.567	0.000	0.000	0.000	0.000
15	A	23	TYR	0	-0.037	-0.020	17.496	-0.751	-0.751	0.000	0.000	0.000	0.000
16	A	24	VAL	0	0.013	-0.008	16.834	1.162	1.162	0.000	0.000	0.000	0.000
17	A	25	LYS	1	0.830	0.934	18.225	-13.755	-13.755	0.000	0.000	0.000	0.000
18	A	26	LEU	0	0.020	-0.007	19.303	0.567	0.567	0.000	0.000	0.000	0.000
19	A	27	ARG	1	0.870	0.910	18.831	-14.609	-14.609	0.000	0.000	0.000	0.000
20	A	28	GLY	0	-0.043	-0.009	23.468	-0.279	-0.279	0.000	0.000	0.000	0.000
21	A	29	ASP	-1	-0.919	-0.956	26.403	10.451	10.451	0.000	0.000	0.000	0.000
22	A	30	ARG	1	0.896	0.933	25.466	-11.011	-11.011	0.000	0.000	0.000	0.000
23	A	31	GLU	-1	-0.833	-0.901	23.174	13.249	13.249	0.000	0.000	0.000	0.000
24	A	32	LEU	0	0.005	0.000	20.985	-0.600	-0.600	0.000	0.000	0.000	0.000
25	A	33	ASN	0	-0.016	0.000	21.885	1.081	1.081	0.000	0.000	0.000	0.000
26	A	34	GLY	0	0.072	0.036	21.355	-0.707	-0.707	0.000	0.000	0.000	0.000
27	A	35	ARG	1	0.849	0.941	20.326	-12.884	-12.884	0.000	0.000	0.000	0.000
28	A	36	LEU	0	-0.013	0.008	13.078	-0.496	-0.496	0.000	0.000	0.000	0.000
29	A	37	HIS	0	0.052	0.015	17.503	0.178	0.178	0.000	0.000	0.000	0.000
30	A	38	ALA	0	-0.011	-0.009	15.966	0.049	0.049	0.000	0.000	0.000	0.000
31	A	39	TYR	0	0.003	-0.009	7.649	0.056	0.056	0.000	0.000	0.000	0.000
32	A	40	ASP	-1	-0.778	-0.868	12.800	16.299	16.299	0.000	0.000	0.000	0.000
33	A	41	GLU	-1	-0.859	-0.941	10.391	18.333	18.333	0.000	0.000	0.000	0.000
34	A	42	HIS	0	-0.112	-0.049	11.381	0.757	0.757	0.000	0.000	0.000	0.000
35	A	43	LEU	0	-0.015	-0.007	10.349	-0.162	-0.162	0.000	0.000	0.000	0.000
36	A	44	ASN	0	-0.060	-0.045	13.227	-1.031	-1.031	0.000	0.000	0.000	0.000
37	A	45	MET	0	-0.015	-0.003	14.856	0.993	0.993	0.000	0.000	0.000	0.000
38	A	46	VAL	0	-0.017	-0.003	17.234	-0.897	-0.897	0.000	0.000	0.000	0.000
39	A	47	LEU	0	-0.015	-0.008	18.073	0.548	0.548	0.000	0.000	0.000	0.000
40	A	48	GLY	0	0.012	-0.005	21.249	-0.661	-0.661	0.000	0.000	0.000	0.000
41	A	49	ASP	-1	-0.935	-0.964	23.987	10.887	10.887	0.000	0.000	0.000	0.000
42	A	50	ALA	0	-0.001	0.004	24.337	0.239	0.239	0.000	0.000	0.000	0.000
43	A	51	GLU	-1	-0.811	-0.891	25.703	10.273	10.273	0.000	0.000	0.000	0.000
44	A	52	GLU	-1	-0.825	-0.894	25.900	10.918	10.918	0.000	0.000	0.000	0.000
45	A	53	ILE	0	-0.054	-0.042	26.355	-0.525	-0.525	0.000	0.000	0.000	0.000
46	A	54	VAL	0	-0.002	0.007	28.105	0.279	0.279	0.000	0.000	0.000	0.000
47	A	55	THR	0	0.011	0.010	28.568	-0.524	-0.524	0.000	0.000	0.000	0.000
48	A	70	THR	0	-0.025	-0.035	32.281	0.081	0.081	0.000	0.000	0.000	0.000
49	A	71	ILE	0	-0.035	-0.006	33.434	-0.282	-0.282	0.000	0.000	0.000	0.000
50	A	72	ARG	1	0.835	0.891	29.027	-10.060	-10.060	0.000	0.000	0.000	0.000
51	A	73	LYS	1	0.883	0.946	31.139	-9.750	-9.750	0.000	0.000	0.000	0.000
52	A	74	HIS	0	-0.027	-0.017	29.624	0.075	0.075	0.000	0.000	0.000	0.000
53	A	75	TYR	0	-0.051	-0.048	27.572	-0.488	-0.488	0.000	0.000	0.000	0.000
54	A	76	GLU	-1	-0.879	-0.925	28.250	9.780	9.780	0.000	0.000	0.000	0.000
55	A	77	MET	0	-0.013	-0.001	23.547	0.546	0.546	0.000	0.000	0.000	0.000
56	A	78	LEU	0	-0.032	-0.004	23.741	-0.376	-0.376	0.000	0.000	0.000	0.000
57	A	79	PHE	0	-0.003	0.012	20.249	0.493	0.493	0.000	0.000	0.000	0.000
58	A	80	VAL	0	-0.012	-0.014	19.255	-0.442	-0.442	0.000	0.000	0.000	0.000
59	A	81	ARG	1	0.864	0.911	19.416	-12.043	-12.043	0.000	0.000	0.000	0.000
60	A	82	GLY	0	0.099	0.042	16.410	0.019	0.019	0.000	0.000	0.000	0.000
61	A	83	ASP	-1	-0.814	-0.890	17.020	14.052	14.052	0.000	0.000	0.000	0.000
62	A	84	SER	0	-0.129	-0.062	18.868	-0.188	-0.188	0.000	0.000	0.000	0.000
63	A	85	VAL	0	0.031	0.012	15.019	-0.446	-0.446	0.000	0.000	0.000	0.000
64	A	86	ILE	0	-0.063	-0.024	16.466	0.348	0.348	0.000	0.000	0.000	0.000
65	A	87	LEU	0	-0.037	-0.022	14.443	1.074	1.074	0.000	0.000	0.000	0.000
66	A	88	ILE	0	0.052	0.017	11.829	-0.930	-0.930	0.000	0.000	0.000	0.000
67	A	89	ALA	0	-0.054	-0.016	12.685	1.557	1.557	0.000	0.000	0.000	0.000
68	A	90	PRO	0	0.040	0.034	11.327	-1.219	-1.219	0.000	0.000	0.000	0.000
69	A	91	PRO	0	0.032	0.025	14.388	-0.598	-0.598	0.000	0.000	0.000	0.000
70	A	92	ARG	1	0.915	0.941	15.638	-15.243	-15.243	0.000	0.000	0.000	0.000
71	A	93	ASN	0	0.008	0.018	15.353	-0.139	-0.139	0.000	0.000	0.000	0.000

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