FMO DATABASE

FMODB ID: 988Q2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-281037.722378
FMO2-HF: Nuclear repulsion	257243.431195
FMO2-HF: Total energy	-23794.291183
FMO2-MP2: Total energy	-23857.658309

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.
1.406	2.803	-0.006	-0.698	-0.694	0.004

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 : 0.061 / q_NPA : 0.031

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	-0.040	-0.015	3.857	0.368	1.700	-0.005	-0.693	-0.635	0.004
4	A	6	ALA	0	0.012	0.007	6.332	0.249	0.249	0.000	0.000	0.000	0.000
5	A	7	CYS	0	-0.026	-0.004	10.067	0.038	0.038	0.000	0.000	0.000	0.000
6	A	8	PRO	0	0.039	0.019	13.404	0.031	0.031	0.000	0.000	0.000	0.000
7	A	9	ARG	1	0.943	0.981	17.000	0.394	0.394	0.000	0.000	0.000	0.000
8	A	10	ILE	0	0.003	-0.003	18.685	0.046	0.046	0.000	0.000	0.000	0.000
9	A	11	TYR	0	-0.007	0.002	20.239	-0.038	-0.038	0.000	0.000	0.000	0.000
10	A	12	MET	0	-0.013	-0.017	21.669	0.031	0.031	0.000	0.000	0.000	0.000
11	A	13	PRO	0	0.011	0.004	21.310	-0.022	-0.022	0.000	0.000	0.000	0.000
12	A	14	VAL	0	-0.023	0.014	17.776	0.025	0.025	0.000	0.000	0.000	0.000
13	A	15	CYS	0	-0.035	0.003	20.215	-0.015	-0.015	0.000	0.000	0.000	0.000
14	A	16	GLY	0	0.049	0.016	17.543	0.007	0.007	0.000	0.000	0.000	0.000
15	A	17	SER	0	0.022	-0.016	18.239	0.011	0.011	0.000	0.000	0.000	0.000
16	A	18	ASN	0	-0.002	-0.007	15.649	0.055	0.055	0.000	0.000	0.000	0.000
17	A	19	LEU	0	0.037	0.017	19.320	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.875	0.941	17.116	0.360	0.360	0.000	0.000	0.000	0.000
19	A	21	THR	0	0.047	0.015	19.459	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	22	TYR	0	-0.046	-0.040	13.635	0.003	0.003	0.000	0.000	0.000	0.000
21	A	23	ASN	0	0.030	-0.007	17.965	0.068	0.068	0.000	0.000	0.000	0.000
22	A	24	ASN	0	-0.012	-0.015	16.172	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	25	ASP	-1	-0.660	-0.818	16.318	-0.437	-0.437	0.000	0.000	0.000	0.000
24	A	27	LEU	0	0.017	-0.003	11.777	-0.159	-0.159	0.000	0.000	0.000	0.000
25	A	28	LEU	0	0.029	0.027	11.623	-0.141	-0.141	0.000	0.000	0.000	0.000
26	A	29	ARG	1	0.838	0.899	11.059	0.353	0.353	0.000	0.000	0.000	0.000
27	A	31	GLU	-1	-0.825	-0.876	6.960	-1.303	-1.303	0.000	0.000	0.000	0.000
28	A	32	ILE	0	-0.017	-0.002	8.961	0.040	0.040	0.000	0.000	0.000	0.000
29	A	33	ASN	0	-0.060	-0.040	5.573	0.472	0.472	0.000	0.000	0.000	0.000
30	A	34	SER	0	-0.034	-0.016	4.776	0.088	0.153	-0.001	-0.005	-0.059	0.000
31	A	35	ASP	-1	-0.826	-0.923	5.768	0.922	0.922	0.000	0.000	0.000	0.000
32	A	36	LEU	0	-0.014	0.016	7.917	0.198	0.198	0.000	0.000	0.000	0.000
33	A	37	GLY	0	0.054	0.024	9.461	0.162	0.162	0.000	0.000	0.000	0.000
34	A	38	ARG	1	0.879	0.922	7.130	-0.359	-0.359	0.000	0.000	0.000	0.000
35	A	39	ALA	0	-0.014	-0.001	11.013	0.076	0.076	0.000	0.000	0.000	0.000
36	A	40	ASN	0	-0.090	-0.056	13.495	0.062	0.062	0.000	0.000	0.000	0.000
37	A	41	ASN	0	-0.065	-0.024	14.542	0.039	0.039	0.000	0.000	0.000	0.000
38	A	42	LEU	0	-0.065	-0.006	12.207	0.014	0.014	0.000	0.000	0.000	0.000
39	A	43	ARG	1	0.982	0.984	14.176	0.153	0.153	0.000	0.000	0.000	0.000
40	A	44	LYS	1	0.820	0.894	16.352	0.273	0.273	0.000	0.000	0.000	0.000
41	A	45	ILE	0	-0.053	-0.036	18.546	0.037	0.037	0.000	0.000	0.000	0.000
42	A	46	ALA	0	0.032	0.027	22.049	0.024	0.024	0.000	0.000	0.000	0.000
43	A	47	ASP	-1	-0.909	-0.953	22.274	-0.266	-0.266	0.000	0.000	0.000	0.000
44	A	48	GLN	0	0.024	0.018	23.944	0.010	0.010	0.000	0.000	0.000	0.000
45	A	49	ALA	0	-0.006	-0.011	23.512	-0.016	-0.016	0.000	0.000	0.000	0.000
46	A	51	ASP	-1	-0.806	-0.903	24.974	-0.231	-0.231	0.000	0.000	0.000	0.000
47	A	52	ASN	0	-0.083	-0.032	27.800	0.023	0.023	0.000	0.000	0.000	0.000
48	A	53	LEU	0	-0.071	-0.037	25.503	0.009	0.009	0.000	0.000	0.000	0.000
49	A	54	THR	0	-0.043	-0.039	29.627	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	55	ASP	-1	-0.829	-0.920	29.123	-0.133	-0.133	0.000	0.000	0.000	0.000
51	A	56	ASN	0	-0.011	-0.006	31.263	0.007	0.007	0.000	0.000	0.000	0.000
52	A	57	VAL	0	-0.068	-0.022	29.534	0.007	0.007	0.000	0.000	0.000	0.000
53	A	58	ASN	0	-0.073	-0.041	29.593	0.001	0.001	0.000	0.000	0.000	0.000
54	A	59	ASP	-1	-0.925	-0.933	33.574	-0.099	-0.099	0.000	0.000	0.000	0.000

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