FMO DATABASE

FMODB ID: Z626N

Calculation Name: 5J2Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5J2Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X7H4

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:

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-447452.101725
FMO2-HF: Nuclear repulsion	418899.872803
FMO2-HF: Total energy	-28552.228922
FMO2-MP2: Total energy	-28635.824763

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:7:THR)

Summations of interaction energy for fragment #1(A:7:THR)

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.
-2.348	1.026	0.289	-1.301	-2.362	-0.002

Interaction energy analysis for fragmet #1(A:7:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.006

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	9	PRO	0	0.000	0.001	2.757	-3.137	-0.579	0.215	-1.102	-1.671	-0.001
4	A	10	GLN	0	0.023	0.012	4.101	-0.708	-0.428	0.001	-0.061	-0.220	0.000
5	A	11	ASN	0	0.039	0.016	3.039	0.190	0.726	0.073	-0.138	-0.471	-0.001
6	A	12	MET	0	-0.024	0.003	6.463	0.213	0.213	0.000	0.000	0.000	0.000
7	A	13	ALA	0	0.044	0.031	9.071	0.103	0.103	0.000	0.000	0.000	0.000
8	A	14	PHE	0	0.043	0.017	8.986	0.078	0.078	0.000	0.000	0.000	0.000
9	A	15	ARG	1	0.962	0.986	9.096	0.188	0.188	0.000	0.000	0.000	0.000
10	A	16	ALA	0	0.024	0.006	11.743	0.049	0.049	0.000	0.000	0.000	0.000
11	A	17	LYS	1	0.971	0.995	14.372	0.307	0.307	0.000	0.000	0.000	0.000
12	A	18	ALA	0	0.006	0.001	14.771	0.029	0.029	0.000	0.000	0.000	0.000
13	A	19	THR	0	-0.008	0.002	15.709	0.034	0.034	0.000	0.000	0.000	0.000
14	A	20	ARG	1	0.795	0.869	18.038	0.146	0.146	0.000	0.000	0.000	0.000
15	A	21	THR	0	-0.034	-0.024	19.402	0.011	0.011	0.000	0.000	0.000	0.000
16	A	22	ALA	0	-0.038	-0.015	20.360	0.011	0.011	0.000	0.000	0.000	0.000
17	A	23	ARG	1	0.825	0.900	21.784	0.015	0.015	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.856	0.938	24.168	0.115	0.115	0.000	0.000	0.000	0.000
19	A	25	GLU	-1	-0.750	-0.849	23.800	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	26	SER	0	0.046	0.014	24.120	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	27	GLN	0	-0.003	-0.010	20.497	0.021	0.021	0.000	0.000	0.000	0.000
22	A	28	GLU	-1	-0.865	-0.929	23.477	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	29	THR	0	-0.035	0.009	26.393	0.014	0.014	0.000	0.000	0.000	0.000
24	A	30	PHE	0	0.006	-0.005	17.677	0.009	0.009	0.000	0.000	0.000	0.000
25	A	31	TRP	0	-0.014	-0.023	15.605	0.023	0.023	0.000	0.000	0.000	0.000
26	A	32	SER	0	0.004	-0.018	22.242	0.022	0.022	0.000	0.000	0.000	0.000
27	A	33	ARG	1	0.779	0.880	23.371	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	34	PHE	0	0.008	0.000	19.373	0.017	0.017	0.000	0.000	0.000	0.000
29	A	35	GLY	0	-0.004	0.010	22.269	0.011	0.011	0.000	0.000	0.000	0.000
30	A	36	ILE	0	-0.059	-0.019	18.219	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	37	SER	0	0.048	0.014	22.547	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	38	GLN	0	0.067	0.013	23.070	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	39	SER	0	-0.007	0.001	23.041	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	40	CYS	0	0.004	0.002	19.019	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	41	GLY	0	0.071	0.045	19.070	-0.016	-0.016	0.000	0.000	0.000	0.000
36	A	42	SER	0	-0.112	-0.057	18.356	-0.042	-0.042	0.000	0.000	0.000	0.000
37	A	43	ARG	1	0.982	0.977	18.487	0.073	0.073	0.000	0.000	0.000	0.000
38	A	44	PHE	0	0.054	0.022	14.674	-0.025	-0.025	0.000	0.000	0.000	0.000
39	A	45	GLU	-1	-0.756	-0.850	13.734	-0.241	-0.241	0.000	0.000	0.000	0.000
40	A	46	ASN	0	-0.121	-0.060	14.777	-0.060	-0.060	0.000	0.000	0.000	0.000
41	A	47	GLY	0	0.006	0.011	11.952	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	48	GLU	-1	-0.942	-0.961	12.590	-0.132	-0.132	0.000	0.000	0.000	0.000
43	A	49	ASN	0	-0.031	-0.026	10.172	-0.128	-0.128	0.000	0.000	0.000	0.000
44	A	50	LEU	0	0.005	0.014	9.856	0.074	0.074	0.000	0.000	0.000	0.000
45	A	51	PRO	0	0.012	0.008	10.460	0.072	0.072	0.000	0.000	0.000	0.000
46	A	52	PHE	0	0.051	0.011	7.539	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	53	PRO	0	0.040	0.013	11.116	0.061	0.061	0.000	0.000	0.000	0.000
48	A	54	ILE	0	0.043	0.022	13.996	0.003	0.003	0.000	0.000	0.000	0.000
49	A	55	TYR	0	0.010	0.010	6.437	0.084	0.084	0.000	0.000	0.000	0.000
50	A	56	LEU	0	-0.021	-0.009	10.865	0.056	0.056	0.000	0.000	0.000	0.000
51	A	57	LEU	0	0.026	0.009	12.649	-0.024	-0.024	0.000	0.000	0.000	0.000
52	A	58	LEU	0	-0.025	-0.014	12.986	-0.046	-0.046	0.000	0.000	0.000	0.000
53	A	59	HIS	0	-0.024	-0.012	10.951	0.011	0.011	0.000	0.000	0.000	0.000
54	A	60	PHE	0	0.026	0.003	12.867	-0.033	-0.033	0.000	0.000	0.000	0.000
55	A	61	TYR	0	-0.087	-0.054	16.157	-0.064	-0.064	0.000	0.000	0.000	0.000
56	A	62	ILE	0	-0.053	-0.033	13.219	-0.052	-0.052	0.000	0.000	0.000	0.000
57	A	63	GLU	-1	-0.962	-0.978	14.358	0.450	0.450	0.000	0.000	0.000	0.000
58	A	64	GLY	0	-0.007	-0.002	16.256	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	65	GLN	0	-0.094	-0.037	18.120	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	66	ILE	0	0.013	0.018	18.929	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	67	THR	0	0.010	-0.008	21.864	-0.021	-0.021	0.000	0.000	0.000	0.000
62	A	68	ASP	-1	-0.732	-0.853	24.622	0.045	0.045	0.000	0.000	0.000	0.000
63	A	69	ARG	1	0.940	0.973	26.274	-0.060	-0.060	0.000	0.000	0.000	0.000
64	A	70	GLN	0	0.073	0.044	24.947	0.002	0.002	0.000	0.000	0.000	0.000
65	A	71	LEU	0	-0.009	0.005	22.186	0.001	0.001	0.000	0.000	0.000	0.000
66	A	72	ALA	0	-0.049	-0.033	26.464	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	73	ASP	-1	-0.930	-0.971	29.942	0.073	0.073	0.000	0.000	0.000	0.000
68	A	74	LEU	0	-0.054	-0.028	25.970	0.001	0.001	0.000	0.000	0.000	0.000
69	A	75	ARG	1	0.875	0.952	28.188	-0.037	-0.037	0.000	0.000	0.000	0.000
70	A	76	GLY	0	0.002	0.019	30.315	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:THR)