FMO DATABASE

FMODB ID: 52Z1Z

Calculation Name: 4ME7-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ME7

Chain ID: E

ChEMBL ID:

UniProt ID: P96621

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:

Apendix: None

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	78
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-388049.986388
FMO2-HF: Nuclear repulsion	355223.955552
FMO2-HF: Total energy	-32826.030836
FMO2-MP2: Total energy	-32917.509146

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(E:6:ALA)

Summations of interaction energy for fragment #1(E:6:ALA)

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.
-5.132	-2.145	-0.025	-1.526	-1.437	-0.001

Interaction energy analysis for fragmet #1(E:6:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.003

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	E	8	THR	0	0.004	0.006	3.429	-3.188	-0.570	-0.025	-1.430	-1.163	-0.001
4	E	9	GLU	-1	-0.866	-0.911	3.800	-0.635	-0.375	0.001	-0.092	-0.170	0.000
5	E	10	MET	0	-0.004	-0.004	6.171	0.276	0.276	0.000	0.000	0.000	0.000
6	E	11	LYS	1	0.869	0.917	9.162	0.108	0.108	0.000	0.000	0.000	0.000
7	E	12	ILE	0	0.006	0.004	11.396	0.056	0.056	0.000	0.000	0.000	0.000
8	E	13	SER	0	0.019	0.002	14.205	-0.038	-0.038	0.000	0.000	0.000	0.000
9	E	14	LEU	0	-0.014	0.000	14.267	0.017	0.017	0.000	0.000	0.000	0.000
10	E	15	PRO	0	0.034	0.010	18.107	-0.018	-0.018	0.000	0.000	0.000	0.000
11	E	16	GLU	-1	-0.902	-0.949	20.975	-0.007	-0.007	0.000	0.000	0.000	0.000
12	E	17	ASN	0	0.017	0.001	22.637	-0.006	-0.006	0.000	0.000	0.000	0.000
13	E	18	LEU	0	0.028	0.022	18.543	-0.001	-0.001	0.000	0.000	0.000	0.000
14	E	19	VAL	0	-0.016	-0.011	16.327	0.003	0.003	0.000	0.000	0.000	0.000
15	E	20	ALA	0	0.051	0.031	18.578	-0.013	-0.013	0.000	0.000	0.000	0.000
16	E	21	GLU	-1	-0.937	-0.967	21.338	0.056	0.056	0.000	0.000	0.000	0.000
17	E	22	LEU	0	-0.054	-0.029	13.396	0.003	0.003	0.000	0.000	0.000	0.000
18	E	23	ASP	-1	-0.759	-0.859	16.647	-0.084	-0.084	0.000	0.000	0.000	0.000
19	E	24	GLY	0	0.016	0.021	18.335	-0.010	-0.010	0.000	0.000	0.000	0.000
20	E	25	VAL	0	-0.059	-0.037	17.075	-0.002	-0.002	0.000	0.000	0.000	0.000
21	E	26	ALA	0	0.001	0.007	15.405	-0.001	-0.001	0.000	0.000	0.000	0.000
22	E	27	MET	0	0.008	0.002	16.916	-0.012	-0.012	0.000	0.000	0.000	0.000
23	E	28	ARG	1	0.866	0.931	19.957	-0.042	-0.042	0.000	0.000	0.000	0.000
24	E	29	GLU	-1	-0.854	-0.926	17.480	0.061	0.061	0.000	0.000	0.000	0.000
25	E	30	LYS	1	0.854	0.940	18.090	0.034	0.034	0.000	0.000	0.000	0.000
26	E	31	ARG	1	0.806	0.905	12.628	-0.072	-0.072	0.000	0.000	0.000	0.000
27	E	32	SER	0	0.016	-0.004	9.916	-0.041	-0.041	0.000	0.000	0.000	0.000
28	E	33	ARG	1	0.872	0.882	11.216	0.132	0.132	0.000	0.000	0.000	0.000
29	E	34	ASN	0	-0.019	-0.008	4.689	-0.225	-0.116	-0.001	-0.004	-0.104	0.000
30	E	35	GLU	-1	-0.754	-0.868	7.213	0.093	0.093	0.000	0.000	0.000	0.000
31	E	36	LEU	0	0.047	0.027	8.107	0.185	0.185	0.000	0.000	0.000	0.000
32	E	37	ILE	0	0.011	0.008	9.089	0.085	0.085	0.000	0.000	0.000	0.000
33	E	38	SER	0	0.008	0.010	4.998	0.456	0.456	0.000	0.000	0.000	0.000
34	E	39	GLN	0	0.000	-0.002	7.513	0.120	0.120	0.000	0.000	0.000	0.000
35	E	40	ALA	0	0.026	0.014	10.581	0.021	0.021	0.000	0.000	0.000	0.000
36	E	41	VAL	0	0.006	-0.002	9.764	-0.019	-0.019	0.000	0.000	0.000	0.000
37	E	42	ARG	1	0.923	0.963	5.942	-1.577	-1.577	0.000	0.000	0.000	0.000
38	E	43	ALA	0	0.028	0.031	11.510	-0.064	-0.064	0.000	0.000	0.000	0.000
39	E	44	TYR	0	0.041	0.024	14.888	-0.057	-0.057	0.000	0.000	0.000	0.000
40	E	45	VAL	0	0.033	0.007	12.864	-0.048	-0.048	0.000	0.000	0.000	0.000
41	E	46	SER	0	-0.002	0.001	14.360	-0.043	-0.043	0.000	0.000	0.000	0.000
42	E	47	GLU	-1	-0.821	-0.873	16.662	0.183	0.183	0.000	0.000	0.000	0.000
43	E	48	ARG	1	0.870	0.929	18.867	-0.292	-0.292	0.000	0.000	0.000	0.000
44	E	49	THR	0	0.006	-0.012	17.292	-0.028	-0.028	0.000	0.000	0.000	0.000
45	E	50	THR	0	-0.036	-0.025	19.917	-0.034	-0.034	0.000	0.000	0.000	0.000
46	E	51	ARG	1	0.844	0.883	22.104	-0.223	-0.223	0.000	0.000	0.000	0.000
47	E	52	HIS	0	0.008	0.020	22.804	-0.020	-0.020	0.000	0.000	0.000	0.000
48	E	53	ASN	0	0.062	0.013	21.205	-0.024	-0.024	0.000	0.000	0.000	0.000
49	E	54	ARG	1	0.897	0.941	24.788	-0.201	-0.201	0.000	0.000	0.000	0.000
50	E	55	ASP	-1	-0.787	-0.849	27.961	0.123	0.123	0.000	0.000	0.000	0.000
51	E	56	LEU	0	0.007	0.001	25.667	-0.011	-0.011	0.000	0.000	0.000	0.000
52	E	57	MET	0	-0.002	0.011	28.349	-0.003	-0.003	0.000	0.000	0.000	0.000
53	E	58	ARG	1	0.840	0.903	30.843	-0.126	-0.126	0.000	0.000	0.000	0.000
54	E	59	ARG	1	0.867	0.925	31.727	-0.137	-0.137	0.000	0.000	0.000	0.000
55	E	60	GLY	0	0.082	0.043	33.135	-0.006	-0.006	0.000	0.000	0.000	0.000
56	E	61	TYR	0	-0.009	-0.019	33.001	-0.004	-0.004	0.000	0.000	0.000	0.000
57	E	62	MET	0	-0.052	-0.024	36.830	-0.004	-0.004	0.000	0.000	0.000	0.000
58	E	63	GLU	-1	-0.943	-0.972	36.032	0.100	0.100	0.000	0.000	0.000	0.000
59	E	64	MET	0	-0.013	-0.005	37.249	-0.005	-0.005	0.000	0.000	0.000	0.000
60	E	65	ALA	0	0.014	0.024	40.081	-0.004	-0.004	0.000	0.000	0.000	0.000
61	E	66	LYS	1	0.964	0.973	42.558	-0.057	-0.057	0.000	0.000	0.000	0.000
62	E	67	ILE	0	0.008	0.002	41.528	-0.003	-0.003	0.000	0.000	0.000	0.000
63	E	68	ASN	0	0.000	-0.012	40.031	0.000	0.000	0.000	0.000	0.000	0.000
64	E	69	LEU	0	0.037	0.023	43.709	-0.002	-0.002	0.000	0.000	0.000	0.000
65	E	70	ASN	0	-0.071	-0.016	46.984	-0.003	-0.003	0.000	0.000	0.000	0.000
66	E	71	ILE	0	0.034	0.004	42.988	-0.001	-0.001	0.000	0.000	0.000	0.000
67	E	72	SER	0	-0.041	0.000	45.973	-0.001	-0.001	0.000	0.000	0.000	0.000
68	E	73	SER	0	-0.008	-0.030	47.778	-0.002	-0.002	0.000	0.000	0.000	0.000
69	E	74	GLU	-1	-0.968	-0.986	50.362	0.045	0.045	0.000	0.000	0.000	0.000
70	E	75	ALA	0	-0.004	-0.003	48.976	-0.002	-0.002	0.000	0.000	0.000	0.000
71	E	76	HIS	0	-0.061	-0.030	50.999	-0.003	-0.003	0.000	0.000	0.000	0.000
72	E	77	PHE	0	-0.012	-0.010	52.360	-0.001	-0.001	0.000	0.000	0.000	0.000
73	E	78	ALA	0	-0.009	-0.008	51.989	-0.001	-0.001	0.000	0.000	0.000	0.000
74	E	79	GLU	-1	-0.919	-0.947	47.839	0.050	0.050	0.000	0.000	0.000	0.000
75	E	80	CYS	0	-0.042	-0.024	51.650	-0.001	-0.001	0.000	0.000	0.000	0.000
76	E	81	GLU	-1	-0.967	-0.977	55.036	0.030	0.030	0.000	0.000	0.000	0.000
77	E	82	ALA	0	-0.055	-0.023	52.192	-0.001	-0.001	0.000	0.000	0.000	0.000
78	E	83	GLU	-1	-1.023	-0.997	52.756	0.034	0.034	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:6:ALA)