FMO DATABASE

FMODB ID: LZY19

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

Total energy (hartree)

FMO2-HF: Electronic energy	-820571.010962
FMO2-HF: Nuclear repulsion	776383.132705
FMO2-HF: Total energy	-44187.878257
FMO2-MP2: Total energy	-44309.683988

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.
-59.947	-37.914	33.483	-20.425	-35.091	-0.051

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 : 0.009 / q_NPA : 0.044

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	0.902	0.970	3.885	-1.061	1.852	-0.019	-1.668	-1.226	0.006
4	A	46	ILE	0	0.031	0.029	5.769	0.374	0.374	0.000	0.000	0.000	0.000
5	A	47	TRP	0	-0.025	-0.020	8.389	-0.445	-0.445	0.000	0.000	0.000	0.000
6	A	48	GLN	0	0.040	0.014	12.111	0.024	0.024	0.000	0.000	0.000	0.000
7	A	49	SER	0	-0.033	0.005	14.952	-0.058	-0.058	0.000	0.000	0.000	0.000
8	A	50	PRO	0	0.044	0.016	18.442	0.037	0.037	0.000	0.000	0.000	0.000
9	A	51	ARG	1	1.003	0.978	19.565	0.327	0.327	0.000	0.000	0.000	0.000
10	A	52	PHE	0	-0.007	0.000	21.222	-0.037	-0.037	0.000	0.000	0.000	0.000
11	A	53	ILE	0	-0.018	0.006	22.509	0.037	0.037	0.000	0.000	0.000	0.000
12	A	54	ALA	0	0.062	0.035	26.265	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	55	ARG	1	0.887	0.930	27.598	0.038	0.038	0.000	0.000	0.000	0.000
14	A	56	LYS	1	0.919	0.970	31.400	0.046	0.046	0.000	0.000	0.000	0.000
15	A	57	ARG	1	0.996	0.997	32.425	0.109	0.109	0.000	0.000	0.000	0.000
16	A	58	GLY	0	-0.018	-0.007	32.335	0.011	0.011	0.000	0.000	0.000	0.000
17	A	59	PHE	0	-0.017	-0.004	30.901	0.012	0.012	0.000	0.000	0.000	0.000
18	A	60	THR	0	-0.003	0.008	27.255	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	61	VAL	0	-0.010	-0.009	22.715	0.005	0.005	0.000	0.000	0.000	0.000
20	A	62	LYS	1	0.898	0.944	20.739	-0.169	-0.169	0.000	0.000	0.000	0.000
21	A	63	MET	0	-0.034	0.003	18.074	-0.028	-0.028	0.000	0.000	0.000	0.000
22	A	64	HIS	0	0.010	0.009	16.210	0.079	0.079	0.000	0.000	0.000	0.000
23	A	65	CYS	0	-0.025	-0.001	10.218	-0.061	-0.061	0.000	0.000	0.000	0.000
24	A	66	TYR	0	0.022	0.023	11.572	0.246	0.246	0.000	0.000	0.000	0.000
25	A	67	MET	0	-0.072	-0.021	6.589	0.199	0.199	0.000	0.000	0.000	0.000
26	A	68	ASN	0	0.061	0.015	3.053	0.499	1.377	0.039	-0.278	-0.639	-0.002
27	A	69	SER	0	0.026	0.006	5.981	0.204	0.204	0.000	0.000	0.000	0.000
28	A	70	ALA	0	-0.002	0.016	3.936	-0.224	-0.005	0.006	-0.058	-0.167	0.000
29	A	71	SER	0	-0.008	-0.026	3.379	4.803	6.604	0.133	-0.589	-1.346	-0.002
30	A	72	GLY	0	-0.047	-0.023	2.583	-5.115	-2.728	1.121	-1.528	-1.979	0.013
31	A	73	ASN	0	-0.075	-0.056	3.606	-6.041	-6.114	0.006	0.216	-0.149	0.001
32	A	74	VAL	0	0.004	0.006	6.552	-0.994	-0.994	0.000	0.000	0.000	0.000
33	A	75	SER	0	0.000	0.024	7.200	-0.313	-0.313	0.000	0.000	0.000	0.000
34	A	76	TRP	0	-0.020	-0.031	9.342	-0.071	-0.071	0.000	0.000	0.000	0.000
35	A	77	LEU	0	-0.023	-0.006	10.636	-0.120	-0.120	0.000	0.000	0.000	0.000
36	A	78	TRP	0	-0.046	-0.022	13.788	0.130	0.130	0.000	0.000	0.000	0.000
37	A	79	LYS	1	0.810	0.915	17.437	0.602	0.602	0.000	0.000	0.000	0.000
38	A	80	GLN	0	-0.025	0.006	19.905	0.064	0.064	0.000	0.000	0.000	0.000
39	A	81	GLU	-1	-0.917	-0.955	23.272	-0.364	-0.364	0.000	0.000	0.000	0.000
40	A	82	MET	0	-0.035	-0.044	22.929	-0.059	-0.059	0.000	0.000	0.000	0.000
41	A	83	ASP	-1	-0.875	-0.934	23.153	-0.470	-0.470	0.000	0.000	0.000	0.000
42	A	84	GLU	-1	-0.774	-0.868	21.391	-0.667	-0.667	0.000	0.000	0.000	0.000
43	A	85	ASN	0	-0.020	-0.030	15.748	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	86	PRO	0	-0.062	-0.034	14.160	0.042	0.042	0.000	0.000	0.000	0.000
45	A	87	GLN	0	-0.009	0.007	15.359	-0.126	-0.126	0.000	0.000	0.000	0.000
46	A	88	GLN	0	0.005	-0.022	10.577	0.213	0.213	0.000	0.000	0.000	0.000
47	A	89	LEU	0	0.019	0.031	14.579	0.131	0.131	0.000	0.000	0.000	0.000
48	A	90	LYS	1	0.940	0.966	16.544	0.502	0.502	0.000	0.000	0.000	0.000
49	A	91	LEU	0	0.020	0.017	17.361	0.038	0.038	0.000	0.000	0.000	0.000
50	A	92	GLU	-1	-0.709	-0.839	20.540	-0.216	-0.216	0.000	0.000	0.000	0.000
51	A	93	LYS	1	0.877	0.920	24.361	0.187	0.187	0.000	0.000	0.000	0.000
52	A	94	GLY	0	0.015	0.004	26.536	0.002	0.002	0.000	0.000	0.000	0.000
53	A	95	ARG	1	0.730	0.848	25.612	0.201	0.201	0.000	0.000	0.000	0.000
54	A	96	MET	0	-0.042	-0.018	20.517	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	97	GLU	-1	-0.908	-0.948	19.719	0.095	0.095	0.000	0.000	0.000	0.000
56	A	98	GLU	-1	-0.874	-0.944	12.780	-0.360	-0.360	0.000	0.000	0.000	0.000
57	A	99	SER	0	0.025	0.017	15.898	0.027	0.027	0.000	0.000	0.000	0.000
58	A	100	GLN	0	-0.016	-0.034	8.661	-0.142	-0.142	0.000	0.000	0.000	0.000
59	A	101	ASN	0	0.029	0.021	13.260	0.030	0.030	0.000	0.000	0.000	0.000
60	A	102	GLU	-1	-0.847	-0.903	11.480	1.680	1.680	0.000	0.000	0.000	0.000
61	A	103	SER	0	0.006	0.000	10.026	0.502	0.502	0.000	0.000	0.000	0.000
62	A	104	LEU	0	-0.044	-0.023	11.112	-0.132	-0.132	0.000	0.000	0.000	0.000
63	A	105	ALA	0	0.022	0.008	10.958	0.020	0.020	0.000	0.000	0.000	0.000
64	A	106	THR	0	-0.020	-0.042	12.938	-0.130	-0.130	0.000	0.000	0.000	0.000
65	A	107	LEU	0	0.023	0.046	15.745	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	108	THR	0	-0.022	-0.009	17.303	0.030	0.030	0.000	0.000	0.000	0.000
67	A	109	ILE	0	0.026	0.021	20.882	-0.030	-0.030	0.000	0.000	0.000	0.000
68	A	110	GLN	0	0.001	-0.015	23.683	0.024	0.024	0.000	0.000	0.000	0.000
69	A	111	GLY	0	0.018	0.008	27.408	-0.019	-0.019	0.000	0.000	0.000	0.000
70	A	112	ILE	0	-0.065	-0.023	26.476	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	113	ARG	1	0.848	0.884	27.724	0.202	0.202	0.000	0.000	0.000	0.000
72	A	114	PHE	0	-0.016	-0.016	29.071	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	115	GLU	-1	-0.836	-0.939	28.598	-0.207	-0.207	0.000	0.000	0.000	0.000
74	A	116	ASP	-1	-0.735	-0.817	24.887	-0.225	-0.225	0.000	0.000	0.000	0.000
75	A	117	ASN	0	0.012	0.016	24.196	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	118	GLY	0	0.069	0.043	23.010	-0.022	-0.022	0.000	0.000	0.000	0.000
77	A	119	ILE	0	-0.067	-0.037	18.079	0.046	0.046	0.000	0.000	0.000	0.000
78	A	120	TYR	0	0.012	-0.004	16.815	-0.060	-0.060	0.000	0.000	0.000	0.000
79	A	121	PHE	0	-0.024	-0.017	12.582	0.053	0.053	0.000	0.000	0.000	0.000
80	A	123	GLN	0	0.024	-0.018	5.798	-0.534	-0.534	0.000	0.000	0.000	0.000
81	A	124	GLN	0	0.005	0.007	2.097	-14.852	-11.467	3.928	-3.512	-3.801	0.031
84	A	128	ASN	0	0.012	-0.015	2.541	-11.536	-8.308	9.677	-4.750	-8.155	-0.002
85	A	129	THR	0	0.011	-0.024	2.707	-1.987	-1.568	4.722	-1.574	-3.567	-0.011
86	A	130	SER	0	-0.036	-0.001	3.310	-3.157	-2.274	0.100	-0.027	-0.957	-0.002
87	A	131	GLU	-1	-0.827	-0.886	2.448	-4.692	-1.599	1.836	-1.534	-3.395	-0.015
88	A	132	VAL	0	-0.023	-0.021	2.221	-10.589	-10.624	4.282	-1.326	-2.921	-0.029
89	A	133	TYR	0	-0.030	-0.026	2.157	-6.140	-3.205	7.652	-3.797	-6.789	-0.039
90	A	134	GLN	0	0.041	0.006	5.483	-0.425	-0.425	0.000	0.000	0.000	0.000
91	A	135	GLY	0	0.007	0.018	8.836	0.195	0.195	0.000	0.000	0.000	0.000
92	A	136	CYS	0	-0.060	-0.052	11.779	-0.134	-0.134	0.000	0.000	0.000	0.000
93	A	137	GLY	0	0.017	0.014	14.829	0.011	0.011	0.000	0.000	0.000	0.000
94	A	138	THR	0	-0.074	-0.040	16.517	0.076	0.076	0.000	0.000	0.000	0.000
95	A	139	GLU	-1	-0.842	-0.896	19.247	-0.284	-0.284	0.000	0.000	0.000	0.000
96	A	140	LEU	0	-0.032	-0.014	22.337	0.051	0.051	0.000	0.000	0.000	0.000
97	A	141	ARG	1	0.860	0.903	24.623	0.199	0.199	0.000	0.000	0.000	0.000
98	A	142	VAL	0	0.014	0.002	28.058	0.026	0.026	0.000	0.000	0.000	0.000
99	A	143	MET	0	-0.003	0.000	30.490	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	144	GLY	0	0.022	0.000	34.214	0.006	0.006	0.000	0.000	0.000	0.000
101	A	145	PHE	0	0.002	0.002	37.397	0.008	0.008	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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