FMO DATABASE

FMODB ID: R56L8

Calculation Name: 3FXD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FXD

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZYC9

Base Structure: X-ray

Registration Date: 2023-06-19

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	49
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-230066.419913
FMO2-HF: Nuclear repulsion	210908.731068
FMO2-HF: Total energy	-19157.688846
FMO2-MP2: Total energy	-19215.501777

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:4:GLN)

Summations of interaction energy for fragment #1(A:4:GLN)

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.
-0.514	1.149	-0.012	-0.8	-0.85	0.001

Interaction energy analysis for fragmet #1(A:4:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.023

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	6	SER	0	0.044	0.025	3.782	-0.629	1.034	-0.012	-0.800	-0.850	0.001
4	A	7	ASP	-1	-0.868	-0.957	5.994	0.248	0.248	0.000	0.000	0.000	0.000
5	A	8	GLU	-1	-0.900	-0.941	9.103	0.393	0.393	0.000	0.000	0.000	0.000
6	A	9	GLN	0	0.020	-0.012	5.639	-0.489	-0.489	0.000	0.000	0.000	0.000
7	A	10	LYS	1	0.906	0.942	5.795	-0.923	-0.923	0.000	0.000	0.000	0.000
8	A	11	GLU	-1	-0.928	-0.957	9.658	0.106	0.106	0.000	0.000	0.000	0.000
9	A	12	THR	0	-0.036	0.010	11.957	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	13	ILE	0	-0.011	-0.013	8.982	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	14	LEU	0	-0.009	-0.007	13.024	-0.023	-0.023	0.000	0.000	0.000	0.000
12	A	15	LYS	1	1.004	1.000	14.748	-0.134	-0.134	0.000	0.000	0.000	0.000
13	A	16	ALA	0	0.039	0.033	16.090	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.001	-0.010	14.065	-0.016	-0.016	0.000	0.000	0.000	0.000
15	A	18	ASN	0	0.003	-0.008	18.112	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	19	ASP	-1	-0.827	-0.897	20.611	0.110	0.110	0.000	0.000	0.000	0.000
17	A	20	ALA	0	-0.002	0.005	21.211	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	21	ILE	0	-0.067	-0.033	20.554	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	22	GLU	-1	-0.970	-0.984	23.980	0.062	0.062	0.000	0.000	0.000	0.000
20	A	23	LYS	1	0.894	0.949	24.650	-0.120	-0.120	0.000	0.000	0.000	0.000
21	A	24	GLY	0	-0.024	-0.005	26.853	0.001	0.001	0.000	0.000	0.000	0.000
22	A	25	PRO	0	-0.028	-0.026	28.100	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	26	TRP	0	-0.055	-0.052	25.323	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	27	ASP	-1	-0.850	-0.914	30.310	0.017	0.017	0.000	0.000	0.000	0.000
25	A	28	LYS	1	0.870	0.933	33.705	-0.043	-0.043	0.000	0.000	0.000	0.000
26	A	29	SER	0	0.046	0.020	34.804	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	30	ASN	0	0.077	0.027	34.347	0.000	0.000	0.000	0.000	0.000	0.000
28	A	31	PHE	0	0.026	0.017	30.209	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	32	LEU	0	0.047	0.014	29.885	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	33	ARG	1	0.964	1.004	29.505	0.002	0.002	0.000	0.000	0.000	0.000
31	A	34	VAL	0	-0.052	-0.026	28.104	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	35	ILE	0	0.005	0.008	25.095	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	36	GLY	0	0.081	0.034	24.719	0.001	0.001	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.911	0.952	24.402	0.009	0.009	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.954	0.993	19.237	0.058	0.058	0.000	0.000	0.000	0.000
36	A	39	LEU	0	0.064	0.020	20.195	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	40	ILE	0	0.039	0.029	19.512	0.001	0.001	0.000	0.000	0.000	0.000
38	A	41	ALA	0	-0.002	0.010	19.824	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	42	ILE	0	-0.076	-0.041	15.138	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	43	ARG	1	0.849	0.907	15.162	-0.022	-0.022	0.000	0.000	0.000	0.000
41	A	44	ASP	-1	-0.813	-0.907	15.693	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	45	ARG	1	0.847	0.924	11.614	0.281	0.281	0.000	0.000	0.000	0.000
43	A	46	PHE	0	-0.016	-0.010	7.933	-0.025	-0.025	0.000	0.000	0.000	0.000
44	A	47	LEU	0	0.073	0.033	11.297	0.035	0.035	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.960	0.983	13.374	0.160	0.160	0.000	0.000	0.000	0.000
46	A	49	ARG	1	0.893	0.940	7.844	0.488	0.488	0.000	0.000	0.000	0.000
47	A	50	ILE	0	-0.029	-0.004	7.973	0.082	0.082	0.000	0.000	0.000	0.000
48	A	51	GLY	0	0.026	0.030	9.852	0.013	0.013	0.000	0.000	0.000	0.000
49	A	52	ALA	0	-0.058	-0.016	10.864	-0.011	-0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLN)