FMO DATABASE

FMODB ID: 7G8RK

Calculation Name: 3B09-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B09

Chain ID: A

ChEMBL ID:

UniProt ID: Q765B0

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	65
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-284899.64965
FMO2-HF: Nuclear repulsion	259956.550841
FMO2-HF: Total energy	-24943.09881
FMO2-MP2: Total energy	-25014.103134

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:3:ASP)

Summations of interaction energy for fragment #1(A:3:ASP)

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.
22.877	26.845	2.841	-1.953	-4.857	0.014

Interaction energy analysis for fragmet #1(A:3:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.955 / q_NPA : -0.989

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

Sort

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	5	PHE	0	-0.043	-0.003	2.336	-19.408	-16.689	2.540	-1.453	-3.805	0.019
4	A	6	SER	0	0.055	0.024	3.156	1.929	2.873	0.300	-0.431	-0.814	-0.005
5	A	7	THR	0	0.015	0.001	4.000	-4.039	-3.734	0.001	-0.069	-0.238	0.000
6	A	8	MET	0	-0.003	-0.004	5.249	-5.220	-5.220	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.831	-0.924	5.826	35.915	35.915	0.000	0.000	0.000	0.000
8	A	10	GLN	0	-0.027	-0.008	8.258	-4.280	-4.280	0.000	0.000	0.000	0.000
9	A	11	HIS	0	0.008	-0.003	9.480	-2.350	-2.350	0.000	0.000	0.000	0.000
10	A	12	ALA	0	0.013	0.013	11.208	-1.845	-1.845	0.000	0.000	0.000	0.000
11	A	13	SER	0	-0.017	-0.018	12.379	-1.686	-1.686	0.000	0.000	0.000	0.000
12	A	14	TYR	0	-0.008	-0.006	14.114	-1.593	-1.593	0.000	0.000	0.000	0.000
13	A	15	GLY	0	-0.010	-0.009	15.621	-1.051	-1.051	0.000	0.000	0.000	0.000
14	A	16	VAL	0	0.016	0.012	17.143	-0.871	-0.871	0.000	0.000	0.000	0.000
15	A	17	GLY	0	0.014	0.008	18.679	-0.799	-0.799	0.000	0.000	0.000	0.000
16	A	18	ARG	1	0.907	0.944	19.757	-13.435	-13.435	0.000	0.000	0.000	0.000
17	A	19	GLN	0	0.044	0.040	21.790	-0.300	-0.300	0.000	0.000	0.000	0.000
18	A	20	MET	0	-0.017	-0.013	22.400	-0.532	-0.532	0.000	0.000	0.000	0.000
19	A	21	GLY	0	0.000	0.000	24.647	-0.457	-0.457	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.952	-0.984	24.647	11.174	11.174	0.000	0.000	0.000	0.000
21	A	23	GLN	0	-0.047	-0.027	27.632	-0.276	-0.276	0.000	0.000	0.000	0.000
22	A	24	LEU	0	0.012	-0.002	28.859	-0.385	-0.385	0.000	0.000	0.000	0.000
23	A	25	ALA	0	-0.038	-0.017	30.459	-0.314	-0.314	0.000	0.000	0.000	0.000
24	A	26	ALA	0	-0.053	-0.012	32.209	-0.299	-0.299	0.000	0.000	0.000	0.000
25	A	27	ASN	0	-0.087	-0.047	33.938	-0.429	-0.429	0.000	0.000	0.000	0.000
26	A	28	SER	0	0.006	0.034	34.028	0.033	0.033	0.000	0.000	0.000	0.000
27	A	29	PHE	0	-0.031	-0.029	35.877	-0.197	-0.197	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.915	-0.964	38.050	7.269	7.269	0.000	0.000	0.000	0.000
29	A	31	GLY	0	0.020	0.000	39.061	-0.085	-0.085	0.000	0.000	0.000	0.000
30	A	32	ILE	0	-0.064	-0.009	32.857	0.101	0.101	0.000	0.000	0.000	0.000
31	A	33	ASP	-1	-0.810	-0.911	33.172	9.224	9.224	0.000	0.000	0.000	0.000
32	A	34	ILE	0	-0.010	-0.017	27.580	0.214	0.214	0.000	0.000	0.000	0.000
33	A	35	PRO	0	0.014	0.000	28.456	0.344	0.344	0.000	0.000	0.000	0.000
34	A	36	ALA	0	0.028	0.024	29.052	0.262	0.262	0.000	0.000	0.000	0.000
35	A	37	VAL	0	-0.020	-0.010	27.665	0.120	0.120	0.000	0.000	0.000	0.000
36	A	38	GLN	0	-0.051	-0.040	23.814	0.103	0.103	0.000	0.000	0.000	0.000
37	A	39	ALA	0	0.001	0.004	25.413	0.424	0.424	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.047	0.029	27.545	0.090	0.090	0.000	0.000	0.000	0.000
39	A	41	LEU	0	-0.042	-0.014	21.775	0.135	0.135	0.000	0.000	0.000	0.000
40	A	42	ALA	0	-0.011	-0.016	22.900	0.359	0.359	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.871	-0.938	23.863	11.223	11.223	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.011	-0.005	26.785	0.032	0.032	0.000	0.000	0.000	0.000
43	A	45	PHE	0	-0.065	-0.022	18.174	0.184	0.184	0.000	0.000	0.000	0.000
44	A	46	ALA	0	-0.047	-0.028	22.907	0.288	0.288	0.000	0.000	0.000	0.000
45	A	47	GLY	0	-0.026	0.000	23.800	-0.077	-0.077	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.819	0.923	26.886	-11.387	-11.387	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.979	-0.992	29.007	8.682	8.682	0.000	0.000	0.000	0.000
48	A	50	SER	0	-0.028	-0.039	32.319	0.188	0.188	0.000	0.000	0.000	0.000
49	A	51	ALA	0	0.019	0.003	33.189	-0.196	-0.196	0.000	0.000	0.000	0.000
50	A	52	VAL	0	-0.001	0.015	34.860	-0.221	-0.221	0.000	0.000	0.000	0.000
51	A	53	SER	0	0.038	0.047	37.359	0.100	0.100	0.000	0.000	0.000	0.000
52	A	54	MET	0	0.023	-0.018	35.688	0.003	0.003	0.000	0.000	0.000	0.000
53	A	55	GLU	-1	-0.956	-0.971	40.140	6.642	6.642	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.861	-0.943	41.278	7.441	7.441	0.000	0.000	0.000	0.000
55	A	57	LEU	0	-0.021	-0.006	35.883	-0.027	-0.027	0.000	0.000	0.000	0.000
56	A	58	GLN	0	0.011	0.006	40.054	-0.087	-0.087	0.000	0.000	0.000	0.000
57	A	59	VAL	0	0.024	0.015	42.689	-0.111	-0.111	0.000	0.000	0.000	0.000
58	A	60	ALA	0	0.039	0.026	40.601	-0.099	-0.099	0.000	0.000	0.000	0.000
59	A	61	PHE	0	0.002	-0.008	36.224	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	62	THR	0	-0.050	-0.018	41.674	-0.126	-0.126	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.981	-1.002	45.368	6.481	6.481	0.000	0.000	0.000	0.000
62	A	64	ILE	0	-0.024	0.004	40.374	-0.063	-0.063	0.000	0.000	0.000	0.000
63	A	65	SER	0	-0.082	-0.050	43.183	-0.028	-0.028	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.839	0.926	44.314	-6.378	-6.378	0.000	0.000	0.000	0.000
65	A	67	ARG	1	1.000	1.016	40.303	-7.426	-7.426	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ASP)