FMO DATABASE

FMODB ID: 397JL

Calculation Name: 3KXE-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KXE

Chain ID: C

ChEMBL ID:

UniProt ID: P58091

Base Structure: X-ray

Registration Date: 2023-06-22

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-332258.761761
FMO2-HF: Nuclear repulsion	303799.779502
FMO2-HF: Total energy	-28458.982258
FMO2-MP2: Total energy	-28543.738903

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(C:5:ASN)

Summations of interaction energy for fragment #1(C:5:ASN)

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.
-2.799	-0.992	-0.03	-0.877	-0.898	0.003

Interaction energy analysis for fragmet #1(C:5:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.028

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	C	7	SER	0	-0.024	-0.001	3.837	-0.794	0.972	-0.029	-0.878	-0.858	0.003
4	C	8	VAL	0	0.003	-0.007	6.872	0.453	0.453	0.000	0.000	0.000	0.000
5	C	9	VAL	0	0.011	0.014	10.012	-0.019	-0.019	0.000	0.000	0.000	0.000
6	C	10	LEU	0	0.003	0.001	11.590	0.143	0.143	0.000	0.000	0.000	0.000
7	C	11	GLY	0	0.024	0.016	14.858	-0.088	-0.088	0.000	0.000	0.000	0.000
8	C	12	ASP	-1	-0.852	-0.940	17.767	0.093	0.093	0.000	0.000	0.000	0.000
9	C	13	HIS	0	-0.022	-0.012	19.667	0.033	0.033	0.000	0.000	0.000	0.000
10	C	14	PHE	0	0.015	-0.012	16.429	0.033	0.033	0.000	0.000	0.000	0.000
11	C	15	GLN	0	0.001	0.019	14.503	0.137	0.137	0.000	0.000	0.000	0.000
12	C	16	ALA	0	0.041	0.029	16.420	0.060	0.060	0.000	0.000	0.000	0.000
13	C	17	PHE	0	-0.029	-0.016	17.688	0.037	0.037	0.000	0.000	0.000	0.000
14	C	18	ILE	0	-0.003	-0.022	12.225	0.086	0.086	0.000	0.000	0.000	0.000
15	C	19	ASP	-1	-0.852	-0.931	15.574	0.597	0.597	0.000	0.000	0.000	0.000
16	C	20	SER	0	-0.110	-0.051	17.526	-0.013	-0.013	0.000	0.000	0.000	0.000
17	C	21	GLN	0	-0.037	-0.025	17.163	0.045	0.045	0.000	0.000	0.000	0.000
18	C	22	VAL	0	-0.024	-0.018	13.629	0.036	0.036	0.000	0.000	0.000	0.000
19	C	23	ALA	0	-0.039	-0.002	16.919	-0.014	-0.014	0.000	0.000	0.000	0.000
20	C	24	ASP	-1	-0.915	-0.950	19.901	0.453	0.453	0.000	0.000	0.000	0.000
21	C	25	GLY	0	-0.018	-0.007	20.040	0.053	0.053	0.000	0.000	0.000	0.000
22	C	26	ARG	1	0.856	0.947	19.414	-0.742	-0.742	0.000	0.000	0.000	0.000
23	C	27	TYR	0	-0.041	-0.038	14.527	0.070	0.070	0.000	0.000	0.000	0.000
24	C	28	GLY	0	0.069	0.045	14.188	-0.082	-0.082	0.000	0.000	0.000	0.000
25	C	29	SER	0	-0.034	-0.026	9.313	0.308	0.308	0.000	0.000	0.000	0.000
26	C	30	ALA	0	0.117	0.048	8.782	-0.025	-0.025	0.000	0.000	0.000	0.000
27	C	31	SER	0	-0.008	-0.019	5.104	-0.673	-0.632	-0.001	0.001	-0.040	0.000
28	C	32	GLU	-1	-0.961	-0.972	8.126	1.479	1.479	0.000	0.000	0.000	0.000
29	C	33	VAL	0	0.045	0.034	11.308	-0.200	-0.200	0.000	0.000	0.000	0.000
30	C	34	ILE	0	0.023	0.005	9.088	-0.152	-0.152	0.000	0.000	0.000	0.000
31	C	35	ARG	1	0.919	0.959	7.416	-3.727	-3.727	0.000	0.000	0.000	0.000
32	C	36	ALA	0	-0.015	0.003	11.595	-0.191	-0.191	0.000	0.000	0.000	0.000
33	C	37	GLY	0	0.029	0.014	14.969	-0.128	-0.128	0.000	0.000	0.000	0.000
34	C	38	LEU	0	-0.007	-0.014	10.369	-0.081	-0.081	0.000	0.000	0.000	0.000
35	C	39	ARG	1	0.973	1.009	14.090	-1.340	-1.340	0.000	0.000	0.000	0.000
36	C	40	LEU	0	0.039	0.020	16.482	-0.096	-0.096	0.000	0.000	0.000	0.000
37	C	41	LEU	0	-0.033	-0.013	16.363	-0.076	-0.076	0.000	0.000	0.000	0.000
38	C	42	GLU	-1	-0.940	-0.981	16.738	0.829	0.829	0.000	0.000	0.000	0.000
39	C	43	GLU	-1	-0.945	-0.980	18.743	0.591	0.591	0.000	0.000	0.000	0.000
40	C	44	ASN	0	-0.054	-0.022	21.699	-0.079	-0.079	0.000	0.000	0.000	0.000
41	C	45	GLU	-1	-0.942	-0.969	21.160	0.354	0.354	0.000	0.000	0.000	0.000
42	C	46	ALA	0	0.012	-0.002	22.683	-0.044	-0.044	0.000	0.000	0.000	0.000
43	C	47	LYS	1	0.909	0.945	24.401	-0.439	-0.439	0.000	0.000	0.000	0.000
44	C	48	LEU	0	-0.015	0.001	26.633	-0.037	-0.037	0.000	0.000	0.000	0.000
45	C	49	ALA	0	0.000	-0.002	26.937	-0.029	-0.029	0.000	0.000	0.000	0.000
46	C	50	ALA	0	0.003	-0.002	28.472	-0.024	-0.024	0.000	0.000	0.000	0.000
47	C	51	LEU	0	-0.021	-0.003	30.387	-0.018	-0.018	0.000	0.000	0.000	0.000
48	C	52	ARG	1	0.953	0.971	29.101	-0.247	-0.247	0.000	0.000	0.000	0.000
49	C	53	ALA	0	0.020	0.013	32.654	-0.014	-0.014	0.000	0.000	0.000	0.000
50	C	54	ALA	0	-0.007	0.006	34.426	-0.012	-0.012	0.000	0.000	0.000	0.000
51	C	55	LEU	0	-0.009	-0.022	36.337	-0.008	-0.008	0.000	0.000	0.000	0.000
52	C	56	ILE	0	0.021	0.024	35.873	-0.008	-0.008	0.000	0.000	0.000	0.000
53	C	57	GLU	-1	-0.942	-0.955	38.122	0.165	0.165	0.000	0.000	0.000	0.000
54	C	58	GLY	0	-0.014	-0.014	40.343	-0.007	-0.007	0.000	0.000	0.000	0.000
55	C	59	GLU	-1	-0.992	-0.970	41.513	0.125	0.125	0.000	0.000	0.000	0.000
56	C	60	GLU	-1	-0.998	-1.015	41.175	0.117	0.117	0.000	0.000	0.000	0.000
57	C	61	SER	0	-0.150	-0.083	44.563	-0.006	-0.006	0.000	0.000	0.000	0.000
58	C	62	GLY	0	-0.018	0.006	46.182	-0.005	-0.005	0.000	0.000	0.000	0.000
59	C	63	PHE	0	-0.007	-0.017	47.479	0.004	0.004	0.000	0.000	0.000	0.000
60	C	64	ILE	0	-0.024	-0.010	51.682	-0.003	-0.003	0.000	0.000	0.000	0.000
61	C	65	GLU	-1	-0.939	-0.987	54.092	0.085	0.085	0.000	0.000	0.000	0.000
62	C	66	ASP	-1	-0.997	-0.988	56.650	0.080	0.080	0.000	0.000	0.000	0.000
63	C	67	PHE	0	-0.052	-0.027	53.315	0.000	0.000	0.000	0.000	0.000	0.000
64	C	68	ASP	-1	-0.820	-0.912	56.766	0.084	0.084	0.000	0.000	0.000	0.000
65	C	69	PHE	0	-0.028	-0.031	50.731	0.003	0.003	0.000	0.000	0.000	0.000
66	C	70	ASP	-1	-0.903	-0.945	56.615	0.093	0.093	0.000	0.000	0.000	0.000
67	C	71	ALA	0	0.056	0.034	59.525	0.001	0.001	0.000	0.000	0.000	0.000
68	C	72	PHE	0	-0.035	-0.014	50.411	0.003	0.003	0.000	0.000	0.000	0.000
69	C	73	ILE	0	-0.011	-0.012	54.425	0.003	0.003	0.000	0.000	0.000	0.000
70	C	74	GLU	-1	-0.902	-0.957	56.604	0.087	0.087	0.000	0.000	0.000	0.000
71	C	75	GLU	-1	-0.978	-0.985	57.601	0.089	0.089	0.000	0.000	0.000	0.000
72	C	76	ARG	1	0.867	0.923	49.425	-0.123	-0.123	0.000	0.000	0.000	0.000
73	C	77	SER	0	-0.044	-0.020	55.658	0.003	0.003	0.000	0.000	0.000	0.000
74	C	78	ARG	1	0.835	0.934	57.670	-0.086	-0.086	0.000	0.000	0.000	0.000
75	C	79	ALA	0	-0.033	0.003	55.668	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:5:ASN)