FMO DATABASE

FMODB ID: 6Y8JZ

Calculation Name: 4EMK-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EMK

Chain ID: B

ChEMBL ID:

UniProt ID: O42978

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	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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-436226.908865
FMO2-HF: Nuclear repulsion	407618.061985
FMO2-HF: Total energy	-28608.84688
FMO2-MP2: Total energy	-28691.526855

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(B:1:MET)

Summations of interaction energy for fragment #1(B:1: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.
0.132	1.694	-0.011	-0.741	-0.81	0.002

Interaction energy analysis for fragmet #1(B:1: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 : -0.030

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	B	3	SER	0	-0.012	-0.018	3.794	-0.312	1.250	-0.011	-0.741	-0.810	0.002
4	B	4	SER	0	0.023	-0.012	5.902	0.477	0.477	0.000	0.000	0.000	0.000
5	B	5	PRO	0	-0.022	-0.007	6.261	0.103	0.103	0.000	0.000	0.000	0.000
6	B	6	ASN	0	0.056	0.011	9.157	0.090	0.090	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.937	-0.940	10.484	-0.259	-0.259	0.000	0.000	0.000	0.000
8	B	8	PHE	0	-0.067	-0.033	11.593	0.055	0.055	0.000	0.000	0.000	0.000
9	B	9	LEU	0	0.000	-0.011	13.276	0.017	0.017	0.000	0.000	0.000	0.000
10	B	10	ASN	0	0.012	-0.024	14.070	0.024	0.024	0.000	0.000	0.000	0.000
11	B	11	LYS	1	0.928	0.986	15.535	-0.012	-0.012	0.000	0.000	0.000	0.000
12	B	12	VAL	0	-0.064	-0.049	17.987	0.012	0.012	0.000	0.000	0.000	0.000
13	B	13	ILE	0	0.029	0.023	18.737	0.007	0.007	0.000	0.000	0.000	0.000
14	B	14	GLY	0	-0.022	-0.010	21.716	-0.001	-0.001	0.000	0.000	0.000	0.000
15	B	15	LYS	1	0.879	0.953	22.504	0.004	0.004	0.000	0.000	0.000	0.000
16	B	16	LYS	1	0.935	0.966	24.755	-0.019	-0.019	0.000	0.000	0.000	0.000
17	B	17	VAL	0	-0.001	0.009	20.403	0.003	0.003	0.000	0.000	0.000	0.000
18	B	18	LEU	0	-0.059	-0.037	22.531	-0.003	-0.003	0.000	0.000	0.000	0.000
19	B	19	ILE	0	0.024	0.011	20.392	0.006	0.006	0.000	0.000	0.000	0.000
20	B	20	ARG	1	0.843	0.890	21.217	-0.053	-0.053	0.000	0.000	0.000	0.000
21	B	21	LEU	0	0.043	0.022	21.178	0.001	0.001	0.000	0.000	0.000	0.000
22	B	22	SER	0	0.037	0.003	21.011	0.002	0.002	0.000	0.000	0.000	0.000
23	B	23	SER	0	-0.027	-0.011	22.788	0.001	0.001	0.000	0.000	0.000	0.000
24	B	24	GLY	0	0.018	0.010	25.647	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	25	VAL	0	-0.052	-0.010	27.217	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	26	ASP	-1	-0.793	-0.843	25.875	0.045	0.045	0.000	0.000	0.000	0.000
27	B	27	TYR	0	0.010	-0.010	25.035	-0.003	-0.003	0.000	0.000	0.000	0.000
28	B	28	LYS	1	0.898	0.947	25.573	-0.030	-0.030	0.000	0.000	0.000	0.000
29	B	29	GLY	0	0.047	0.031	26.193	-0.002	-0.002	0.000	0.000	0.000	0.000
30	B	30	ILE	0	-0.025	-0.006	25.831	0.002	0.002	0.000	0.000	0.000	0.000
31	B	31	LEU	0	0.017	0.031	18.864	0.001	0.001	0.000	0.000	0.000	0.000
32	B	32	SER	0	0.025	0.026	23.373	-0.003	-0.003	0.000	0.000	0.000	0.000
33	B	33	CYS	0	-0.028	-0.029	21.384	-0.004	-0.004	0.000	0.000	0.000	0.000
34	B	34	LEU	0	0.022	0.018	14.834	0.005	0.005	0.000	0.000	0.000	0.000
35	B	35	ASP	-1	-0.755	-0.856	16.188	0.026	0.026	0.000	0.000	0.000	0.000
36	B	36	GLY	0	0.004	-0.016	12.985	-0.014	-0.014	0.000	0.000	0.000	0.000
37	B	37	TYR	0	-0.073	-0.043	11.499	0.023	0.023	0.000	0.000	0.000	0.000
38	B	38	MET	0	-0.010	0.004	10.518	-0.010	-0.010	0.000	0.000	0.000	0.000
39	B	39	ASN	0	-0.061	-0.029	14.359	0.005	0.005	0.000	0.000	0.000	0.000
40	B	40	LEU	0	-0.017	-0.011	16.698	-0.007	-0.007	0.000	0.000	0.000	0.000
41	B	41	ALA	0	0.024	0.021	20.106	0.004	0.004	0.000	0.000	0.000	0.000
42	B	42	LEU	0	-0.048	-0.041	22.436	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	43	GLU	-1	-0.779	-0.886	25.666	0.001	0.001	0.000	0.000	0.000	0.000
44	B	44	ARG	1	0.750	0.848	29.014	-0.013	-0.013	0.000	0.000	0.000	0.000
45	B	45	THR	0	0.010	-0.006	27.548	0.002	0.002	0.000	0.000	0.000	0.000
46	B	46	GLU	-1	-0.893	-0.927	30.042	0.017	0.017	0.000	0.000	0.000	0.000
47	B	47	GLU	-1	-0.787	-0.893	29.871	0.022	0.022	0.000	0.000	0.000	0.000
48	B	48	TYR	0	-0.051	-0.028	30.324	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	49	VAL	0	0.094	0.052	30.818	0.002	0.002	0.000	0.000	0.000	0.000
50	B	50	ASN	0	0.015	0.004	32.853	0.000	0.000	0.000	0.000	0.000	0.000
51	B	51	GLY	0	0.005	0.006	33.235	-0.001	-0.001	0.000	0.000	0.000	0.000
52	B	52	LYS	1	0.922	0.957	34.566	-0.019	-0.019	0.000	0.000	0.000	0.000
53	B	53	LYS	1	0.906	0.953	34.903	-0.016	-0.016	0.000	0.000	0.000	0.000
54	B	54	THR	0	-0.036	-0.023	34.461	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	55	ASN	0	0.034	0.018	33.868	-0.002	-0.002	0.000	0.000	0.000	0.000
56	B	56	VAL	0	-0.063	-0.033	33.669	0.001	0.001	0.000	0.000	0.000	0.000
57	B	57	TYR	0	-0.030	-0.014	30.775	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	58	GLY	0	-0.024	-0.007	32.184	0.000	0.000	0.000	0.000	0.000	0.000
59	B	59	ASP	-1	-0.825	-0.925	29.903	0.006	0.006	0.000	0.000	0.000	0.000
60	B	60	ALA	0	-0.041	-0.018	27.403	0.001	0.001	0.000	0.000	0.000	0.000
61	B	61	PHE	0	-0.002	0.010	20.876	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	62	ILE	0	0.024	-0.002	20.328	0.002	0.002	0.000	0.000	0.000	0.000
63	B	63	ARG	1	0.916	0.956	15.941	-0.048	-0.048	0.000	0.000	0.000	0.000
64	B	64	GLY	0	0.070	0.031	16.094	0.002	0.002	0.000	0.000	0.000	0.000
65	B	65	ASN	0	-0.036	-0.027	12.061	-0.002	-0.002	0.000	0.000	0.000	0.000
66	B	66	ASN	0	-0.045	-0.018	14.725	-0.002	-0.002	0.000	0.000	0.000	0.000
67	B	67	VAL	0	-0.055	-0.010	17.230	0.000	0.000	0.000	0.000	0.000	0.000
68	B	68	LEU	0	-0.043	-0.013	16.929	0.000	0.000	0.000	0.000	0.000	0.000
69	B	69	TYR	0	-0.010	-0.023	16.453	0.012	0.012	0.000	0.000	0.000	0.000
70	B	70	VAL	0	0.043	0.020	16.432	-0.011	-0.011	0.000	0.000	0.000	0.000
71	B	71	SER	0	-0.032	-0.011	16.929	0.014	0.014	0.000	0.000	0.000	0.000
72	B	72	ALA	0	0.039	0.014	19.294	-0.012	-0.012	0.000	0.000	0.000	0.000
73	B	73	LEU	0	-0.048	-0.019	20.813	0.004	0.004	0.000	0.000	0.000	0.000

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