FMO DATABASE

FMODB ID: 4J5RN

Calculation Name: 4HJG-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HJG

Chain ID: E

ChEMBL ID:

UniProt ID: P0A015

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	62
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-327130.072705
FMO2-HF: Nuclear repulsion	303608.436401
FMO2-HF: Total energy	-23521.636304
FMO2-MP2: Total energy	-23590.940825

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:20:GLU)

Summations of interaction energy for fragment #1(E:20: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.
31.798	40.827	4.067	-5.505	-7.593	-0.008

Interaction energy analysis for fragmet #1(E:20:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -1.012 / q_NPA : -1.010

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	22	THR	0	-0.050	-0.042	3.273	4.912	7.402	0.121	-1.131	-1.480	0.002
4	E	23	ILE	0	0.024	0.030	5.341	-3.435	-3.366	-0.001	-0.003	-0.064	0.000
5	E	24	LYS	1	0.881	0.947	8.728	-25.006	-25.006	0.000	0.000	0.000	0.000
6	E	25	VAL	0	0.034	0.016	11.416	-1.205	-1.205	0.000	0.000	0.000	0.000
7	E	26	ASN	0	-0.017	-0.014	14.602	0.382	0.382	0.000	0.000	0.000	0.000
8	E	27	LEU	0	-0.026	-0.021	17.131	-0.292	-0.292	0.000	0.000	0.000	0.000
9	E	28	ILE	0	0.029	0.005	20.196	-0.452	-0.452	0.000	0.000	0.000	0.000
10	E	29	PHE	0	0.016	0.000	22.120	-0.163	-0.163	0.000	0.000	0.000	0.000
11	E	30	ALA	0	0.009	0.006	26.470	-0.246	-0.246	0.000	0.000	0.000	0.000
12	E	31	ASP	-1	-0.911	-0.956	29.665	10.445	10.445	0.000	0.000	0.000	0.000
13	E	32	GLY	0	-0.018	-0.014	29.027	-0.213	-0.213	0.000	0.000	0.000	0.000
14	E	33	LYS	1	0.894	0.953	26.730	-10.425	-10.425	0.000	0.000	0.000	0.000
15	E	34	ILE	0	0.010	0.007	21.525	0.197	0.197	0.000	0.000	0.000	0.000
16	E	35	GLN	0	-0.051	-0.020	19.828	0.499	0.499	0.000	0.000	0.000	0.000
17	E	36	THR	0	-0.005	0.006	15.793	-0.067	-0.067	0.000	0.000	0.000	0.000
18	E	37	ALA	0	-0.015	-0.001	13.616	-0.006	-0.006	0.000	0.000	0.000	0.000
19	E	38	GLU	-1	-0.918	-0.969	8.425	30.116	30.116	0.000	0.000	0.000	0.000
20	E	39	PHE	0	-0.007	0.002	7.941	-0.015	-0.015	0.000	0.000	0.000	0.000
21	E	40	LYS	1	0.929	0.958	3.030	-57.112	-54.476	0.392	-1.346	-1.683	0.013
22	E	41	GLY	0	0.098	0.062	2.236	-3.133	-1.169	1.303	-1.176	-2.091	0.003
23	E	42	THR	0	0.007	0.005	2.552	-3.418	-1.579	2.253	-1.853	-2.240	-0.026
24	E	43	PHE	0	0.034	0.020	3.978	-1.270	-1.239	-0.001	0.004	-0.035	0.000
25	E	44	GLU	-1	-0.887	-0.951	6.334	25.378	25.378	0.000	0.000	0.000	0.000
26	E	45	GLU	-1	-0.916	-0.960	6.423	39.865	39.865	0.000	0.000	0.000	0.000
27	E	46	ALA	0	0.016	0.013	5.436	-1.982	-1.982	0.000	0.000	0.000	0.000
28	E	47	THR	0	0.017	-0.009	7.470	-3.236	-3.236	0.000	0.000	0.000	0.000
29	E	48	ALA	0	-0.048	-0.025	10.841	-1.908	-1.908	0.000	0.000	0.000	0.000
30	E	49	GLU	-1	-0.957	-0.985	9.409	23.480	23.480	0.000	0.000	0.000	0.000
31	E	50	ALA	0	0.016	0.023	11.339	-1.699	-1.699	0.000	0.000	0.000	0.000
32	E	51	TYR	0	0.013	-0.012	12.941	-1.933	-1.933	0.000	0.000	0.000	0.000
33	E	52	ARG	1	0.923	0.974	15.036	-19.749	-19.749	0.000	0.000	0.000	0.000
34	E	53	TYR	0	-0.014	-0.011	14.814	-1.197	-1.197	0.000	0.000	0.000	0.000
35	E	54	ALA	0	0.035	0.020	16.734	-1.025	-1.025	0.000	0.000	0.000	0.000
36	E	55	ALA	0	0.018	0.002	19.006	-0.971	-0.971	0.000	0.000	0.000	0.000
37	E	56	LEU	0	-0.062	-0.032	19.737	-0.892	-0.892	0.000	0.000	0.000	0.000
38	E	57	LEU	0	0.010	0.000	19.775	-0.788	-0.788	0.000	0.000	0.000	0.000
39	E	58	ALA	0	0.057	0.035	22.536	-0.651	-0.651	0.000	0.000	0.000	0.000
40	E	59	LYS	1	0.836	0.935	23.853	-13.522	-13.522	0.000	0.000	0.000	0.000
41	E	60	VAL	0	-0.037	-0.012	26.363	-0.457	-0.457	0.000	0.000	0.000	0.000
42	E	61	ASN	0	-0.067	-0.049	24.812	-0.598	-0.598	0.000	0.000	0.000	0.000
43	E	62	GLY	0	0.038	0.034	27.634	-0.168	-0.168	0.000	0.000	0.000	0.000
44	E	63	GLU	-1	-0.940	-0.980	26.669	11.013	11.013	0.000	0.000	0.000	0.000
45	E	64	TYR	0	-0.003	-0.004	20.416	0.097	0.097	0.000	0.000	0.000	0.000
46	E	65	THR	0	0.028	0.012	23.858	-0.307	-0.307	0.000	0.000	0.000	0.000
47	E	66	ALA	0	-0.034	-0.026	18.485	0.251	0.251	0.000	0.000	0.000	0.000
48	E	67	ASP	-1	-0.912	-0.931	20.589	12.556	12.556	0.000	0.000	0.000	0.000
49	E	68	LEU	0	-0.046	-0.037	15.515	0.802	0.802	0.000	0.000	0.000	0.000
50	E	69	GLU	-1	-0.906	-0.965	16.820	13.657	13.657	0.000	0.000	0.000	0.000
51	E	70	ASP	-1	-0.908	-0.968	13.358	20.608	20.608	0.000	0.000	0.000	0.000
52	E	71	GLY	0	-0.009	-0.008	13.743	1.135	1.135	0.000	0.000	0.000	0.000
53	E	72	GLY	0	-0.012	-0.007	13.198	0.601	0.601	0.000	0.000	0.000	0.000
54	E	73	ASN	0	-0.054	-0.022	9.002	3.721	3.721	0.000	0.000	0.000	0.000
55	E	74	HIS	0	-0.022	-0.005	11.173	2.145	2.145	0.000	0.000	0.000	0.000
56	E	75	MET	0	-0.015	-0.003	12.763	-1.023	-1.023	0.000	0.000	0.000	0.000
57	E	76	ASN	0	0.036	0.031	16.106	0.564	0.564	0.000	0.000	0.000	0.000
58	E	77	ILE	0	0.036	0.011	16.133	-0.370	-0.370	0.000	0.000	0.000	0.000
59	E	78	LYS	1	0.909	0.967	20.338	-11.024	-11.024	0.000	0.000	0.000	0.000
60	E	79	PHE	0	0.000	-0.006	20.474	0.039	0.039	0.000	0.000	0.000	0.000
61	E	80	ALA	0	-0.062	-0.027	25.969	-0.319	-0.319	0.000	0.000	0.000	0.000
62	E	81	GLY	0	-0.021	-0.004	29.313	-0.388	-0.388	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:20:GLU)