FMO DATABASE

FMODB ID: YZL32

Calculation Name: 2J8B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J8B

Chain ID: A

ChEMBL ID:

UniProt ID: P13987

Base Structure: X-ray

Registration Date: 2023-09-20

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	OptHSide
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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-543305.69972
FMO2-HF: Nuclear repulsion	508807.094671
FMO2-HF: Total energy	-34498.605049
FMO2-MP2: Total energy	-34590.175163

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:0:MET)

Summations of interaction energy for fragment #1(A:0:MET)

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.
-15.184	-15.093	15.538	-6.523	-9.104	0.007

Interaction energy analysis for fragmet #1(A:0:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : 0.015

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	2	GLN	0	0.002	-0.006	3.791	-0.321	1.995	-0.005	-1.073	-1.238	0.004
4	A	3	CYS	0	-0.038	-0.001	5.520	-0.091	-0.091	0.000	0.000	0.000	0.000
5	A	4	TYR	0	0.050	0.020	8.805	0.244	0.244	0.000	0.000	0.000	0.000
6	A	5	ASN	0	0.020	0.002	10.147	-0.167	-0.167	0.000	0.000	0.000	0.000
7	A	6	CYS	0	-0.062	0.011	12.133	0.145	0.145	0.000	0.000	0.000	0.000
8	A	7	PRO	0	0.010	0.009	15.088	-0.042	-0.042	0.000	0.000	0.000	0.000
9	A	8	ASN	0	0.008	-0.005	16.579	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	9	PRO	0	0.033	0.030	19.622	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	10	THR	0	-0.058	-0.038	20.024	0.042	0.042	0.000	0.000	0.000	0.000
12	A	11	ALA	0	0.006	0.006	22.033	-0.023	-0.023	0.000	0.000	0.000	0.000
13	A	12	ASP	-1	-0.834	-0.916	20.999	-0.287	-0.287	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.912	0.927	16.197	0.163	0.163	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.032	-0.013	12.237	0.045	0.045	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.024	0.028	9.410	-0.140	-0.140	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.016	-0.015	6.634	0.289	0.289	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.010	-0.019	2.323	-6.763	-11.899	13.870	-3.733	-5.000	0.023
19	A	19	CYS	0	-0.020	0.005	3.448	-1.526	-0.543	0.086	-0.301	-0.768	-0.002
20	A	20	SER	0	0.010	-0.030	2.450	-5.131	-3.365	1.588	-1.420	-1.933	-0.018
21	A	21	SER	0	0.020	-0.008	4.174	-0.048	0.114	-0.001	0.004	-0.165	0.000
22	A	22	ASP	-1	-0.898	-0.904	5.685	-0.582	-0.582	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.079	-0.032	6.998	0.276	0.276	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.809	-0.912	7.155	-1.359	-1.359	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.026	-0.019	8.619	-0.068	-0.068	0.000	0.000	0.000	0.000
26	A	27	LEU	0	0.029	0.008	11.266	0.098	0.098	0.000	0.000	0.000	0.000
27	A	28	ILE	0	-0.018	-0.001	14.816	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	29	THR	0	-0.018	-0.020	17.572	0.015	0.015	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.836	0.928	20.937	0.340	0.340	0.000	0.000	0.000	0.000
30	A	31	ALA	0	0.064	0.027	24.261	0.001	0.001	0.000	0.000	0.000	0.000
31	A	32	GLY	0	0.033	0.024	26.986	0.014	0.014	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.025	-0.022	28.590	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	34	GLN	0	-0.069	-0.017	24.934	0.007	0.007	0.000	0.000	0.000	0.000
34	A	35	VAL	0	0.013	0.008	20.349	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	36	TYR	0	-0.079	-0.071	18.873	0.008	0.008	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.003	-0.014	14.781	0.019	0.019	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.843	0.921	12.795	0.480	0.480	0.000	0.000	0.000	0.000
38	A	40	TRP	0	-0.012	-0.036	10.031	0.210	0.210	0.000	0.000	0.000	0.000
39	A	41	LYS	1	0.892	0.929	11.057	0.451	0.451	0.000	0.000	0.000	0.000
40	A	42	PHE	0	0.039	-0.013	11.770	0.090	0.090	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.857	-0.901	15.065	-0.470	-0.470	0.000	0.000	0.000	0.000
42	A	44	HIS	0	-0.017	-0.015	16.912	0.065	0.065	0.000	0.000	0.000	0.000
43	A	45	CYS	0	-0.079	-0.010	14.774	-0.044	-0.044	0.000	0.000	0.000	0.000
44	A	46	ASN	0	-0.024	-0.022	18.693	0.041	0.041	0.000	0.000	0.000	0.000
45	A	47	PHE	0	0.074	0.036	22.488	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	48	ASN	0	0.037	0.028	25.308	0.020	0.020	0.000	0.000	0.000	0.000
47	A	49	ASP	-1	-0.766	-0.874	21.146	-0.343	-0.343	0.000	0.000	0.000	0.000
48	A	50	VAL	0	-0.007	-0.002	19.661	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	51	THR	0	0.001	-0.002	22.047	0.015	0.015	0.000	0.000	0.000	0.000
50	A	52	THR	0	-0.040	-0.031	24.659	0.011	0.011	0.000	0.000	0.000	0.000
51	A	53	ARG	1	0.751	0.885	18.501	0.390	0.390	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.057	-0.038	18.734	0.006	0.006	0.000	0.000	0.000	0.000
53	A	55	ARG	1	0.875	0.952	22.492	0.241	0.241	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.778	-0.851	25.212	-0.205	-0.205	0.000	0.000	0.000	0.000
55	A	57	ASN	0	-0.021	-0.023	27.514	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.947	-0.971	30.026	-0.191	-0.191	0.000	0.000	0.000	0.000
57	A	59	LEU	0	-0.027	-0.014	23.844	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	60	THR	0	-0.011	-0.009	25.439	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	61	TYR	0	0.009	-0.012	20.040	0.005	0.005	0.000	0.000	0.000	0.000
60	A	62	TYR	0	0.047	0.023	16.478	-0.023	-0.023	0.000	0.000	0.000	0.000
61	A	64	CYS	0	-0.020	0.038	11.056	0.213	0.213	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.935	0.966	8.849	1.281	1.281	0.000	0.000	0.000	0.000
63	A	66	LYS	1	0.856	0.916	8.279	1.720	1.720	0.000	0.000	0.000	0.000
64	A	67	ASP	-1	-0.729	-0.875	5.963	-4.166	-4.166	0.000	0.000	0.000	0.000
65	A	68	LEU	0	-0.064	-0.032	8.785	0.394	0.394	0.000	0.000	0.000	0.000
66	A	70	ASN	0	-0.013	-0.020	12.353	0.045	0.045	0.000	0.000	0.000	0.000
67	A	71	PHE	0	0.038	0.015	14.772	0.054	0.054	0.000	0.000	0.000	0.000
68	A	72	ASN	0	0.050	0.003	17.579	0.003	0.003	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.851	-0.949	21.202	-0.353	-0.353	0.000	0.000	0.000	0.000
70	A	74	GLN	0	-0.090	-0.022	16.552	0.057	0.057	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.069	-0.025	21.264	0.003	0.003	0.000	0.000	0.000	0.000
72	A	76	GLU	-1	-0.915	-0.941	23.640	-0.265	-0.265	0.000	0.000	0.000	0.000
73	A	77	ASN	0	-0.007	0.007	26.478	0.015	0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:MET)