FMO DATABASE

FMODB ID: 3JJGL

Calculation Name: 5DAE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DAE

Chain ID: A

ChEMBL ID:

UniProt ID: Q1HRB8

Base Structure: X-ray

Registration Date: 2023-09-21

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	54
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-280866.384271
FMO2-HF: Nuclear repulsion	257072.452337
FMO2-HF: Total energy	-23793.931934
FMO2-MP2: Total energy	-23857.321811

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:GLY)

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

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.
2.318	3.333	-0.009	-0.432	-0.574	0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.012

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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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	CYS	0	-0.068	-0.024	3.797	0.912	1.927	-0.009	-0.432	-0.574	0.002
4	A	6	ALA	0	0.012	0.005	6.144	0.283	0.283	0.000	0.000	0.000	0.000
5	A	7	CYS	0	-0.082	-0.030	9.818	-0.013	-0.013	0.000	0.000	0.000	0.000
6	A	8	PRO	0	0.034	0.021	13.144	0.059	0.059	0.000	0.000	0.000	0.000
7	A	9	ARG	1	0.952	0.981	16.693	0.342	0.342	0.000	0.000	0.000	0.000
8	A	10	ILE	0	0.010	0.003	18.878	0.047	0.047	0.000	0.000	0.000	0.000
9	A	11	TYR	0	-0.007	0.000	20.101	-0.035	-0.035	0.000	0.000	0.000	0.000
10	A	12	MET	0	-0.010	-0.019	21.518	0.026	0.026	0.000	0.000	0.000	0.000
11	A	13	PRO	0	-0.002	-0.002	21.202	-0.028	-0.028	0.000	0.000	0.000	0.000
12	A	14	VAL	0	-0.013	0.012	18.091	0.019	0.019	0.000	0.000	0.000	0.000
13	A	15	CYS	0	-0.013	0.000	20.328	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	16	GLY	0	0.044	0.014	17.558	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	17	SER	0	0.020	-0.003	18.346	0.017	0.017	0.000	0.000	0.000	0.000
16	A	18	ASN	0	-0.003	-0.013	15.422	0.050	0.050	0.000	0.000	0.000	0.000
17	A	19	LEU	0	0.021	0.004	19.187	0.007	0.007	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.920	0.974	16.436	0.333	0.333	0.000	0.000	0.000	0.000
19	A	21	THR	0	0.071	0.026	19.150	-0.016	-0.016	0.000	0.000	0.000	0.000
20	A	22	TYR	0	-0.069	-0.064	12.931	0.007	0.007	0.000	0.000	0.000	0.000
21	A	23	ASN	0	0.031	0.000	17.422	0.060	0.060	0.000	0.000	0.000	0.000
22	A	24	ASN	0	0.001	0.001	15.840	-0.035	-0.035	0.000	0.000	0.000	0.000
23	A	25	ASP	-1	-0.721	-0.862	16.224	-0.488	-0.488	0.000	0.000	0.000	0.000
24	A	27	LEU	0	0.051	0.005	11.644	-0.172	-0.172	0.000	0.000	0.000	0.000
25	A	28	LEU	0	0.018	0.023	11.375	-0.138	-0.138	0.000	0.000	0.000	0.000
26	A	29	ARG	1	0.938	0.952	11.607	0.485	0.485	0.000	0.000	0.000	0.000
27	A	31	GLU	-1	-0.811	-0.862	7.073	-1.335	-1.335	0.000	0.000	0.000	0.000
28	A	32	ILE	0	-0.022	-0.010	9.171	0.089	0.089	0.000	0.000	0.000	0.000
29	A	33	ASN	0	-0.038	-0.025	6.167	0.366	0.366	0.000	0.000	0.000	0.000
30	A	34	SER	0	-0.026	0.009	5.082	-0.141	-0.141	0.000	0.000	0.000	0.000
31	A	35	ASP	-1	-0.885	-0.954	5.859	0.972	0.972	0.000	0.000	0.000	0.000
32	A	36	LEU	0	-0.013	0.002	7.809	0.161	0.161	0.000	0.000	0.000	0.000
33	A	37	GLY	0	0.032	0.023	9.197	0.122	0.122	0.000	0.000	0.000	0.000
34	A	38	ARG	1	0.959	0.965	7.677	0.303	0.303	0.000	0.000	0.000	0.000
35	A	39	ALA	0	-0.039	-0.007	11.419	0.075	0.075	0.000	0.000	0.000	0.000
36	A	40	ASN	0	-0.075	-0.044	13.649	0.077	0.077	0.000	0.000	0.000	0.000
37	A	41	ASN	0	-0.074	-0.036	14.902	0.003	0.003	0.000	0.000	0.000	0.000
38	A	42	LEU	0	-0.033	0.011	12.237	0.019	0.019	0.000	0.000	0.000	0.000
39	A	43	ARG	1	0.985	0.981	14.613	0.207	0.207	0.000	0.000	0.000	0.000
40	A	44	LYS	1	0.773	0.864	16.813	0.352	0.352	0.000	0.000	0.000	0.000
41	A	45	ILE	0	-0.069	-0.045	18.948	0.031	0.031	0.000	0.000	0.000	0.000
42	A	46	ALA	0	0.039	0.023	22.216	0.026	0.026	0.000	0.000	0.000	0.000
43	A	47	ASP	-1	-0.896	-0.945	22.535	-0.317	-0.317	0.000	0.000	0.000	0.000
44	A	48	GLN	0	0.042	0.023	24.050	0.017	0.017	0.000	0.000	0.000	0.000
45	A	49	ALA	0	0.014	0.003	23.599	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	51	ASP	-1	-0.918	-0.948	24.921	-0.204	-0.204	0.000	0.000	0.000	0.000
47	A	52	ASN	0	-0.048	-0.010	27.828	0.027	0.027	0.000	0.000	0.000	0.000
48	A	53	LEU	0	-0.084	-0.049	25.685	0.007	0.007	0.000	0.000	0.000	0.000
49	A	54	THR	0	-0.050	-0.019	29.597	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	55	ASP	-1	-0.877	-0.943	28.635	-0.146	-0.146	0.000	0.000	0.000	0.000
51	A	56	ASN	0	0.002	-0.019	31.118	0.007	0.007	0.000	0.000	0.000	0.000
52	A	57	VAL	0	-0.108	-0.043	29.763	0.008	0.008	0.000	0.000	0.000	0.000
53	A	58	ASN	0	-0.048	-0.026	30.046	0.012	0.012	0.000	0.000	0.000	0.000
54	A	59	ASP	-1	-0.870	-0.915	33.357	-0.109	-0.109	0.000	0.000	0.000	0.000

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