FMO DATABASE

FMODB ID: K3JV3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-230636.976168
FMO2-HF: Nuclear repulsion	211478.641238
FMO2-HF: Total energy	-19158.33493
FMO2-MP2: Total energy	-19216.084976

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.
-0.067	1.492	-0.015	-0.729	-0.815	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 : -0.005 / q_NPA : -0.019

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	6	SER	0	0.017	-0.012	3.872	0.013	1.572	-0.015	-0.729	-0.815	0.001
4	A	7	ASP	-1	-0.816	-0.917	6.420	1.046	1.046	0.000	0.000	0.000	0.000
5	A	8	GLU	-1	-0.796	-0.872	9.026	0.198	0.198	0.000	0.000	0.000	0.000
6	A	9	GLN	0	0.023	0.009	5.900	-0.425	-0.425	0.000	0.000	0.000	0.000
7	A	10	LYS	1	0.796	0.881	5.519	-1.908	-1.908	0.000	0.000	0.000	0.000
8	A	11	GLU	-1	-0.916	-0.953	9.688	0.181	0.181	0.000	0.000	0.000	0.000
9	A	12	THR	0	0.004	0.003	11.991	-0.053	-0.053	0.000	0.000	0.000	0.000
10	A	13	ILE	0	-0.020	-0.008	8.750	-0.048	-0.048	0.000	0.000	0.000	0.000
11	A	14	LEU	0	-0.008	-0.001	12.801	-0.029	-0.029	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.911	0.946	14.535	-0.060	-0.060	0.000	0.000	0.000	0.000
13	A	16	ALA	0	0.019	0.010	15.556	-0.015	-0.015	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.019	-0.020	13.403	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	18	ASN	0	0.022	0.001	17.540	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	19	ASP	-1	-0.840	-0.880	20.166	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	20	ALA	0	0.058	0.028	20.677	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	21	ILE	0	-0.076	-0.037	20.172	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	22	GLU	-1	-0.923	-0.951	23.729	0.019	0.019	0.000	0.000	0.000	0.000
20	A	23	LYS	1	0.832	0.896	25.157	0.004	0.004	0.000	0.000	0.000	0.000
21	A	24	GLY	0	0.023	0.031	26.771	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	25	PRO	0	-0.005	-0.013	27.743	0.006	0.006	0.000	0.000	0.000	0.000
23	A	26	TRP	0	-0.070	-0.055	24.537	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	27	ASP	-1	-0.804	-0.885	29.909	-0.025	-0.025	0.000	0.000	0.000	0.000
25	A	28	LYS	1	0.832	0.902	33.245	0.024	0.024	0.000	0.000	0.000	0.000
26	A	29	SER	0	0.038	0.011	34.327	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	30	ASN	0	0.051	0.019	33.956	0.001	0.001	0.000	0.000	0.000	0.000
28	A	31	PHE	0	0.032	0.030	29.853	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	32	LEU	0	0.041	0.016	29.673	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	33	ARG	1	0.953	0.982	28.993	0.038	0.038	0.000	0.000	0.000	0.000
31	A	34	VAL	0	-0.025	-0.011	27.681	0.001	0.001	0.000	0.000	0.000	0.000
32	A	35	ILE	0	-0.006	0.006	24.868	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	36	GLY	0	0.085	0.038	24.282	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.918	0.956	24.072	0.037	0.037	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.941	0.980	19.527	0.204	0.204	0.000	0.000	0.000	0.000
36	A	39	LEU	0	0.026	0.009	18.938	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	40	ILE	0	0.022	0.007	19.198	0.006	0.006	0.000	0.000	0.000	0.000
38	A	41	ALA	0	0.005	0.006	19.424	0.014	0.014	0.000	0.000	0.000	0.000
39	A	42	ILE	0	-0.046	-0.022	14.704	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	43	ARG	1	0.844	0.904	14.855	-0.036	-0.036	0.000	0.000	0.000	0.000
41	A	44	ASP	-1	-0.778	-0.879	15.376	0.095	0.095	0.000	0.000	0.000	0.000
42	A	45	ARG	1	0.868	0.933	12.521	0.125	0.125	0.000	0.000	0.000	0.000
43	A	46	PHE	0	-0.011	-0.007	8.067	0.056	0.056	0.000	0.000	0.000	0.000
44	A	47	LEU	0	0.053	0.028	11.127	0.148	0.148	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.921	0.961	13.144	0.007	0.007	0.000	0.000	0.000	0.000
46	A	49	ARG	1	0.888	0.943	7.410	0.109	0.109	0.000	0.000	0.000	0.000
47	A	50	ILE	0	0.009	-0.004	7.783	0.252	0.252	0.000	0.000	0.000	0.000
48	A	51	GLY	0	0.020	0.029	9.798	0.050	0.050	0.000	0.000	0.000	0.000
49	A	52	ALA	0	-0.067	-0.018	10.341	-0.007	-0.007	0.000	0.000	0.000	0.000

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