FMO DATABASE

FMODB ID: 39L6L

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:

Apendix: None

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	101
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-819774.403271
FMO2-HF: Nuclear repulsion	775587.409577
FMO2-HF: Total energy	-44186.993694
FMO2-MP2: Total energy	-44308.883956

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.
-38.978	-21.276	28.202	-15.193	-30.713	-0.077

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 : -0.041 / q_NPA : 0.012

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	0.939	0.982	3.755	-1.027	1.885	-0.033	-1.461	-1.418	0.009
4	A	46	ILE	0	0.030	0.016	5.981	0.644	0.644	0.000	0.000	0.000	0.000
5	A	47	TRP	0	-0.033	-0.022	8.203	-0.294	-0.294	0.000	0.000	0.000	0.000
6	A	48	GLN	0	0.038	0.017	11.861	0.027	0.027	0.000	0.000	0.000	0.000
7	A	49	SER	0	-0.055	0.004	14.520	-0.048	-0.048	0.000	0.000	0.000	0.000
8	A	50	PRO	0	0.060	0.013	18.021	0.047	0.047	0.000	0.000	0.000	0.000
9	A	51	ARG	1	1.043	0.987	19.707	0.508	0.508	0.000	0.000	0.000	0.000
10	A	52	PHE	0	0.013	0.011	21.149	-0.032	-0.032	0.000	0.000	0.000	0.000
11	A	53	ILE	0	-0.044	-0.008	22.840	0.041	0.041	0.000	0.000	0.000	0.000
12	A	54	ALA	0	0.054	0.032	26.538	-0.015	-0.015	0.000	0.000	0.000	0.000
13	A	55	ARG	1	0.914	0.951	27.160	0.097	0.097	0.000	0.000	0.000	0.000
14	A	56	LYS	1	0.958	0.999	31.286	0.076	0.076	0.000	0.000	0.000	0.000
15	A	57	ARG	1	1.008	0.999	32.194	0.134	0.134	0.000	0.000	0.000	0.000
16	A	58	GLY	0	-0.006	-0.019	32.116	0.013	0.013	0.000	0.000	0.000	0.000
17	A	59	PHE	0	-0.015	0.015	31.097	0.015	0.015	0.000	0.000	0.000	0.000
18	A	60	THR	0	-0.024	-0.001	27.359	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	61	VAL	0	-0.019	-0.035	23.205	0.006	0.006	0.000	0.000	0.000	0.000
20	A	62	LYS	1	0.943	0.982	21.304	-0.156	-0.156	0.000	0.000	0.000	0.000
21	A	63	MET	0	-0.036	-0.001	18.097	-0.041	-0.041	0.000	0.000	0.000	0.000
22	A	64	HIS	0	0.026	0.006	16.414	0.107	0.107	0.000	0.000	0.000	0.000
23	A	65	CYS	0	-0.033	0.004	10.360	-0.083	-0.083	0.000	0.000	0.000	0.000
24	A	66	TYR	0	-0.016	0.008	11.287	0.256	0.256	0.000	0.000	0.000	0.000
25	A	67	MET	0	-0.018	-0.001	6.322	-0.076	-0.076	0.000	0.000	0.000	0.000
26	A	68	ASN	0	0.041	-0.004	3.052	-1.218	0.256	0.165	-0.636	-1.004	-0.006
27	A	69	SER	0	0.030	0.008	5.948	0.238	0.238	0.000	0.000	0.000	0.000
28	A	70	ALA	0	0.046	0.050	3.519	-0.389	-0.041	0.032	-0.104	-0.275	0.000
29	A	71	SER	0	-0.038	-0.050	3.232	2.696	5.323	0.318	-1.024	-1.921	0.003
30	A	72	GLY	0	-0.060	-0.036	2.792	2.307	2.912	2.192	-0.714	-2.083	0.001
31	A	73	ASN	0	-0.101	-0.037	4.260	-2.625	-2.633	-0.002	-0.016	0.025	0.000
32	A	74	VAL	0	0.024	0.006	6.336	-0.616	-0.616	0.000	0.000	0.000	0.000
33	A	75	SER	0	-0.008	0.025	7.018	-0.305	-0.305	0.000	0.000	0.000	0.000
34	A	76	TRP	0	0.020	-0.014	9.336	-0.208	-0.208	0.000	0.000	0.000	0.000
35	A	77	LEU	0	-0.044	-0.020	10.364	-0.046	-0.046	0.000	0.000	0.000	0.000
36	A	78	TRP	0	-0.051	-0.031	13.633	0.110	0.110	0.000	0.000	0.000	0.000
37	A	79	LYS	1	0.876	0.954	17.297	0.773	0.773	0.000	0.000	0.000	0.000
38	A	80	GLN	0	-0.040	-0.011	19.759	0.061	0.061	0.000	0.000	0.000	0.000
39	A	81	GLU	-1	-0.905	-0.950	23.050	-0.428	-0.428	0.000	0.000	0.000	0.000
40	A	82	MET	0	-0.057	-0.050	22.591	-0.078	-0.078	0.000	0.000	0.000	0.000
41	A	83	ASP	-1	-0.907	-0.954	22.714	-0.571	-0.571	0.000	0.000	0.000	0.000
42	A	84	GLU	-1	-0.788	-0.876	21.318	-0.741	-0.741	0.000	0.000	0.000	0.000
43	A	85	ASN	0	-0.013	-0.023	16.092	-0.059	-0.059	0.000	0.000	0.000	0.000
44	A	86	PRO	0	-0.041	-0.038	13.942	0.059	0.059	0.000	0.000	0.000	0.000
45	A	87	GLN	0	-0.024	0.008	14.782	-0.147	-0.147	0.000	0.000	0.000	0.000
46	A	88	GLN	0	-0.008	-0.029	10.787	0.234	0.234	0.000	0.000	0.000	0.000
47	A	89	LEU	0	0.035	0.042	14.763	0.110	0.110	0.000	0.000	0.000	0.000
48	A	90	LYS	1	0.960	0.985	16.505	0.455	0.455	0.000	0.000	0.000	0.000
49	A	91	LEU	0	0.004	0.008	17.160	0.026	0.026	0.000	0.000	0.000	0.000
50	A	92	GLU	-1	-0.721	-0.846	20.532	-0.203	-0.203	0.000	0.000	0.000	0.000
51	A	93	LYS	1	0.923	0.948	24.332	0.142	0.142	0.000	0.000	0.000	0.000
52	A	94	GLY	0	0.057	0.022	25.840	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	95	ARG	1	0.706	0.827	25.257	0.193	0.193	0.000	0.000	0.000	0.000
54	A	96	MET	0	-0.047	-0.021	20.545	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	97	GLU	-1	-0.921	-0.942	20.043	0.157	0.157	0.000	0.000	0.000	0.000
56	A	98	GLU	-1	-0.891	-0.947	13.097	-0.173	-0.173	0.000	0.000	0.000	0.000
57	A	99	SER	0	-0.010	0.000	16.408	0.059	0.059	0.000	0.000	0.000	0.000
58	A	100	GLN	0	0.029	-0.010	9.052	-0.051	-0.051	0.000	0.000	0.000	0.000
59	A	101	ASN	0	-0.021	0.000	13.252	0.049	0.049	0.000	0.000	0.000	0.000
60	A	102	GLU	-1	-0.895	-0.948	11.540	1.681	1.681	0.000	0.000	0.000	0.000
61	A	103	SER	0	0.028	0.016	10.074	0.379	0.379	0.000	0.000	0.000	0.000
62	A	104	LEU	0	-0.032	-0.012	11.125	-0.199	-0.199	0.000	0.000	0.000	0.000
63	A	105	ALA	0	0.028	0.019	10.728	0.017	0.017	0.000	0.000	0.000	0.000
64	A	106	THR	0	-0.032	-0.048	12.797	-0.191	-0.191	0.000	0.000	0.000	0.000
65	A	107	LEU	0	0.023	0.035	15.973	0.033	0.033	0.000	0.000	0.000	0.000
66	A	108	THR	0	-0.050	-0.035	17.670	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	109	ILE	0	0.042	0.032	20.932	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	110	GLN	0	-0.017	-0.030	23.886	0.017	0.017	0.000	0.000	0.000	0.000
69	A	111	GLY	0	0.010	-0.010	27.542	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	112	ILE	0	-0.084	-0.014	26.581	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	113	ARG	1	0.829	0.879	27.650	0.206	0.206	0.000	0.000	0.000	0.000
72	A	114	PHE	0	-0.006	-0.008	28.907	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	115	GLU	-1	-0.850	-0.942	28.232	-0.227	-0.227	0.000	0.000	0.000	0.000
74	A	116	ASP	-1	-0.721	-0.821	24.879	-0.246	-0.246	0.000	0.000	0.000	0.000
75	A	117	ASN	0	0.002	0.012	24.245	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	118	GLY	0	0.086	0.054	22.969	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	119	ILE	0	-0.061	-0.033	18.166	0.039	0.039	0.000	0.000	0.000	0.000
78	A	120	TYR	0	0.024	0.002	16.676	-0.052	-0.052	0.000	0.000	0.000	0.000
79	A	121	PHE	0	-0.024	-0.005	12.367	0.018	0.018	0.000	0.000	0.000	0.000
80	A	123	GLN	0	0.025	-0.019	5.646	-0.716	-0.716	0.000	0.000	0.000	0.000
81	A	124	GLN	0	0.047	0.007	2.360	-7.335	-4.378	2.478	-2.198	-3.237	0.014
84	A	128	ASN	0	0.017	-0.011	2.814	-5.611	-3.299	1.699	-0.191	-3.821	0.002
85	A	129	THR	0	0.023	-0.002	2.904	-1.428	-0.731	4.812	-1.619	-3.890	-0.017
86	A	130	SER	0	-0.010	0.032	2.966	-3.204	-2.003	0.195	-0.121	-1.275	-0.006
87	A	131	GLU	-1	-0.863	-0.921	2.082	-4.791	-2.592	1.758	-1.184	-2.773	-0.008
88	A	132	VAL	0	-0.028	-0.037	1.891	-12.821	-15.759	9.462	-3.105	-3.419	-0.043
89	A	133	TYR	0	-0.040	-0.011	2.439	-4.216	-0.900	5.126	-2.820	-5.622	-0.026
90	A	134	GLN	0	0.037	0.002	5.408	-0.359	-0.359	0.000	0.000	0.000	0.000
91	A	135	GLY	0	-0.002	0.015	8.738	0.157	0.157	0.000	0.000	0.000	0.000
92	A	136	CYS	0	-0.091	-0.065	11.670	-0.100	-0.100	0.000	0.000	0.000	0.000
93	A	137	GLY	0	0.025	0.006	14.452	0.067	0.067	0.000	0.000	0.000	0.000
94	A	138	THR	0	-0.067	-0.005	16.154	0.058	0.058	0.000	0.000	0.000	0.000
95	A	139	GLU	-1	-0.900	-0.949	19.237	-0.415	-0.415	0.000	0.000	0.000	0.000
96	A	140	LEU	0	-0.019	-0.016	22.137	0.056	0.056	0.000	0.000	0.000	0.000
97	A	141	ARG	1	0.907	0.944	24.647	0.282	0.282	0.000	0.000	0.000	0.000
98	A	142	VAL	0	0.001	0.001	28.306	0.027	0.027	0.000	0.000	0.000	0.000
99	A	143	MET	0	-0.046	-0.035	30.667	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	144	GLY	0	0.011	-0.012	34.353	0.004	0.004	0.000	0.000	0.000	0.000
101	A	145	PHE	0	-0.007	0.016	37.770	0.006	0.006	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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