FMO DATABASE

FMODB ID: JLN19

Calculation Name: 3KG5-A-Xray372

Preferred Name: B-cell antigen receptor complex-associated protein beta chain

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3KG5

Chain ID: A

ChEMBL ID: CHEMBL3712852

UniProt ID: P40259

Base Structure: X-ray

Registration Date: 2023-09-19

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-819982.285092
FMO2-HF: Nuclear repulsion	775796.265418
FMO2-HF: Total energy	-44186.019674
FMO2-MP2: Total energy	-44308.047343

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:43:CYS)

Summations of interaction energy for fragment #1(A:43:CYS)

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.
-41.274	-27.224	34.68	-17.649	-31.082	-0.083

Interaction energy analysis for fragmet #1(A:43:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.040 / q_NPA : 0.007

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

Sort

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	45	ARG	1	0.957	0.987	3.675	-0.819	1.930	-0.028	-1.322	-1.399	0.008
4	A	46	ILE	0	0.023	0.021	5.843	0.637	0.637	0.000	0.000	0.000	0.000
5	A	47	TRP	0	-0.047	-0.029	7.932	-0.281	-0.281	0.000	0.000	0.000	0.000
6	A	48	GLN	0	0.033	0.023	11.585	0.009	0.009	0.000	0.000	0.000	0.000
7	A	49	SER	0	-0.070	-0.004	14.260	-0.040	-0.040	0.000	0.000	0.000	0.000
8	A	50	PRO	0	0.056	0.007	17.757	0.041	0.041	0.000	0.000	0.000	0.000
9	A	51	ARG	1	1.050	0.995	19.650	0.498	0.498	0.000	0.000	0.000	0.000
10	A	52	PHE	0	0.006	0.013	20.888	-0.027	-0.027	0.000	0.000	0.000	0.000
11	A	53	ILE	0	-0.032	-0.003	23.120	0.043	0.043	0.000	0.000	0.000	0.000
12	A	54	ALA	0	0.055	0.035	26.538	-0.014	-0.014	0.000	0.000	0.000	0.000
13	A	55	ARG	1	0.925	0.955	26.723	0.110	0.110	0.000	0.000	0.000	0.000
14	A	56	LYS	1	0.949	1.000	31.286	0.077	0.077	0.000	0.000	0.000	0.000
15	A	57	ARG	1	1.013	0.996	32.220	0.134	0.134	0.000	0.000	0.000	0.000
16	A	58	GLY	0	-0.009	-0.020	32.118	0.012	0.012	0.000	0.000	0.000	0.000
17	A	59	PHE	0	-0.005	0.017	31.086	0.013	0.013	0.000	0.000	0.000	0.000
18	A	60	THR	0	-0.036	-0.003	27.305	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	61	VAL	0	-0.021	-0.042	23.182	0.006	0.006	0.000	0.000	0.000	0.000
20	A	62	LYS	1	0.942	0.984	21.367	-0.136	-0.136	0.000	0.000	0.000	0.000
21	A	63	MET	0	-0.035	0.003	18.065	-0.040	-0.040	0.000	0.000	0.000	0.000
22	A	64	HIS	0	0.015	-0.003	16.425	0.099	0.099	0.000	0.000	0.000	0.000
23	A	65	CYS	0	-0.016	0.016	10.112	-0.084	-0.084	0.000	0.000	0.000	0.000
24	A	66	TYR	0	-0.010	0.010	11.105	0.264	0.264	0.000	0.000	0.000	0.000
25	A	67	MET	0	-0.008	0.010	6.163	-0.092	-0.092	0.000	0.000	0.000	0.000
26	A	68	ASN	0	0.011	-0.020	2.488	-3.903	-2.019	1.103	-1.235	-1.751	-0.019
27	A	69	SER	0	0.026	0.012	5.812	0.271	0.271	0.000	0.000	0.000	0.000
28	A	70	ALA	0	0.063	0.047	3.552	-0.920	-0.540	0.033	-0.099	-0.314	0.000
29	A	71	SER	0	-0.026	-0.040	3.026	1.631	4.451	0.668	-1.162	-2.326	0.006
30	A	72	GLY	0	-0.075	-0.048	2.792	2.783	3.295	2.181	-0.667	-2.025	0.002
31	A	73	ASN	0	-0.089	-0.033	4.260	-2.614	-2.628	-0.002	-0.017	0.031	0.000
32	A	74	VAL	0	0.027	0.010	6.336	-0.540	-0.540	0.000	0.000	0.000	0.000
33	A	75	SER	0	0.020	0.035	6.972	-0.431	-0.431	0.000	0.000	0.000	0.000
34	A	76	TRP	0	0.006	-0.021	9.336	-0.223	-0.223	0.000	0.000	0.000	0.000
35	A	77	LEU	0	-0.043	-0.018	10.171	-0.060	-0.060	0.000	0.000	0.000	0.000
36	A	78	TRP	0	-0.049	-0.029	13.633	0.100	0.100	0.000	0.000	0.000	0.000
37	A	79	LYS	1	0.868	0.951	17.297	0.771	0.771	0.000	0.000	0.000	0.000
38	A	80	GLN	0	0.015	0.025	19.759	0.038	0.038	0.000	0.000	0.000	0.000
39	A	81	GLU	-1	-0.890	-0.942	23.104	-0.438	-0.438	0.000	0.000	0.000	0.000
40	A	82	MET	0	-0.085	-0.063	22.591	-0.080	-0.080	0.000	0.000	0.000	0.000
41	A	83	ASP	-1	-0.888	-0.954	22.714	-0.558	-0.558	0.000	0.000	0.000	0.000
42	A	84	GLU	-1	-0.865	-0.921	20.985	-0.704	-0.704	0.000	0.000	0.000	0.000
43	A	85	ASN	0	-0.015	-0.023	16.535	-0.044	-0.044	0.000	0.000	0.000	0.000
44	A	86	PRO	0	-0.045	-0.043	13.976	0.054	0.054	0.000	0.000	0.000	0.000
45	A	87	GLN	0	0.016	0.036	14.782	-0.135	-0.135	0.000	0.000	0.000	0.000
46	A	88	GLN	0	-0.023	-0.036	10.951	0.216	0.216	0.000	0.000	0.000	0.000
47	A	89	LEU	0	0.038	0.039	14.775	0.103	0.103	0.000	0.000	0.000	0.000
48	A	90	LYS	1	0.961	0.986	16.505	0.422	0.422	0.000	0.000	0.000	0.000
49	A	91	LEU	0	0.014	0.014	17.133	0.024	0.024	0.000	0.000	0.000	0.000
50	A	92	GLU	-1	-0.883	-0.964	20.532	-0.240	-0.240	0.000	0.000	0.000	0.000
51	A	93	LYS	1	0.921	0.951	24.332	0.136	0.136	0.000	0.000	0.000	0.000
52	A	94	GLY	0	0.064	0.024	25.840	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	95	ARG	1	0.746	0.873	25.285	0.180	0.180	0.000	0.000	0.000	0.000
54	A	96	MET	0	-0.025	-0.015	20.250	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	97	GLU	-1	-0.911	-0.934	19.879	0.165	0.165	0.000	0.000	0.000	0.000
56	A	98	GLU	-1	-0.915	-0.951	13.297	-0.109	-0.109	0.000	0.000	0.000	0.000
57	A	99	SER	0	-0.004	0.008	16.440	0.069	0.069	0.000	0.000	0.000	0.000
58	A	100	GLN	0	0.057	-0.004	8.681	-0.220	-0.220	0.000	0.000	0.000	0.000
59	A	101	ASN	0	-0.029	0.003	13.251	0.057	0.057	0.000	0.000	0.000	0.000
60	A	102	GLU	-1	-0.925	-0.971	11.416	1.633	1.633	0.000	0.000	0.000	0.000
61	A	103	SER	0	0.008	-0.002	9.927	0.375	0.375	0.000	0.000	0.000	0.000
62	A	104	LEU	0	-0.006	-0.006	10.988	-0.202	-0.202	0.000	0.000	0.000	0.000
63	A	105	ALA	0	0.027	0.018	10.756	0.033	0.033	0.000	0.000	0.000	0.000
64	A	106	THR	0	-0.090	-0.064	12.797	-0.172	-0.172	0.000	0.000	0.000	0.000
65	A	107	LEU	0	0.057	0.043	16.042	0.033	0.033	0.000	0.000	0.000	0.000
66	A	108	THR	0	-0.057	-0.038	17.670	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	109	ILE	0	0.067	0.047	21.318	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	110	GLN	0	-0.037	-0.037	23.886	0.018	0.018	0.000	0.000	0.000	0.000
69	A	111	GLY	0	0.007	-0.010	27.542	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	112	ILE	0	-0.107	-0.019	26.627	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	113	ARG	1	0.947	0.955	28.165	0.196	0.196	0.000	0.000	0.000	0.000
72	A	114	PHE	0	0.010	0.005	28.907	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	115	GLU	-1	-0.865	-0.947	28.048	-0.230	-0.230	0.000	0.000	0.000	0.000
74	A	116	ASP	-1	-0.729	-0.855	24.981	-0.247	-0.247	0.000	0.000	0.000	0.000
75	A	117	ASN	0	-0.004	0.031	24.245	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	118	GLY	0	0.094	0.060	22.971	-0.013	-0.013	0.000	0.000	0.000	0.000
77	A	119	ILE	0	-0.047	-0.026	18.217	0.033	0.033	0.000	0.000	0.000	0.000
78	A	120	TYR	0	0.026	-0.015	16.681	-0.053	-0.053	0.000	0.000	0.000	0.000
79	A	121	PHE	0	-0.001	-0.003	12.288	0.009	0.009	0.000	0.000	0.000	0.000
80	A	123	GLN	0	0.022	-0.014	5.720	-0.946	-0.946	0.000	0.000	0.000	0.000
81	A	124	GLN	0	0.081	0.034	2.502	-5.636	-2.809	2.416	-2.061	-3.181	0.011
84	A	128	ASN	0	-0.018	-0.023	3.512	-5.383	-2.717	0.364	-0.523	-2.507	0.006
85	A	129	THR	0	0.029	0.010	2.580	-1.723	-1.723	6.560	-2.087	-4.474	-0.016
86	A	130	SER	0	0.004	0.040	2.865	-3.431	-1.871	0.219	-0.529	-1.250	-0.007
87	A	131	GLU	-1	-0.908	-0.964	2.004	-5.517	-3.726	1.941	-1.189	-2.544	-0.006
88	A	132	VAL	0	-0.022	-0.026	1.878	-13.050	-16.087	9.637	-3.205	-3.395	-0.044
89	A	133	TYR	0	-0.047	0.003	2.274	-2.775	-2.901	9.590	-3.553	-5.911	-0.024
90	A	134	GLN	0	0.040	-0.007	5.324	-0.452	-0.414	-0.002	0.000	-0.036	0.000
91	A	135	GLY	0	-0.008	0.011	8.738	0.159	0.159	0.000	0.000	0.000	0.000
92	A	136	CYS	0	-0.087	-0.067	11.444	-0.086	-0.086	0.000	0.000	0.000	0.000
93	A	137	GLY	0	0.002	-0.001	14.444	0.076	0.076	0.000	0.000	0.000	0.000
94	A	138	THR	0	-0.076	-0.008	16.154	0.067	0.067	0.000	0.000	0.000	0.000
95	A	139	GLU	-1	-0.925	-0.984	19.237	-0.440	-0.440	0.000	0.000	0.000	0.000
96	A	140	LEU	0	-0.031	-0.012	22.137	0.056	0.056	0.000	0.000	0.000	0.000
97	A	141	ARG	1	0.982	0.992	24.647	0.256	0.256	0.000	0.000	0.000	0.000
98	A	142	VAL	0	-0.020	-0.023	28.331	0.027	0.027	0.000	0.000	0.000	0.000
99	A	143	MET	0	-0.049	-0.038	30.667	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	144	GLY	0	0.019	-0.015	34.353	0.004	0.004	0.000	0.000	0.000	0.000
101	A	145	PHE	0	-0.018	0.013	37.770	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:43:CYS)