FMO DATABASE

FMODB ID: 76L4K

Calculation Name: 4DX9-A-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: A

ChEMBL ID: CHEMBL1905

UniProt ID: P05556

Base Structure: X-ray

Registration Date: 2023-09-24

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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-904460.485986
FMO2-HF: Nuclear repulsion	858684.567355
FMO2-HF: Total energy	-45775.918631
FMO2-MP2: Total energy	-45906.89571

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:60:CYS)

Summations of interaction energy for fragment #1(A:60: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.
-15.278	-11.461	7.235	-5.166	-5.886	-0.016

Interaction energy analysis for fragmet #1(A:60:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.019

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	62	GLU	-1	-0.939	-0.964	3.812	-2.403	-0.494	-0.027	-0.827	-1.055	0.002
4	A	63	PHE	0	-0.018	-0.008	6.181	0.103	0.103	0.000	0.000	0.000	0.000
5	A	64	ARG	1	0.833	0.897	9.815	0.784	0.784	0.000	0.000	0.000	0.000
6	A	65	ILE	0	-0.032	-0.012	13.064	0.013	0.013	0.000	0.000	0.000	0.000
7	A	66	LYS	1	0.973	0.993	15.446	0.308	0.308	0.000	0.000	0.000	0.000
8	A	67	TYR	0	0.029	0.004	17.192	0.012	0.012	0.000	0.000	0.000	0.000
9	A	68	VAL	0	-0.006	0.004	19.471	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	69	GLY	0	0.031	-0.005	21.625	0.009	0.009	0.000	0.000	0.000	0.000
11	A	70	ALA	0	-0.047	-0.023	21.294	0.006	0.006	0.000	0.000	0.000	0.000
12	A	71	ILE	0	-0.008	0.001	23.093	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	72	GLU	-1	-0.955	-0.963	24.930	0.171	0.171	0.000	0.000	0.000	0.000
14	A	83	GLU	-1	-0.856	-0.920	27.819	0.064	0.064	0.000	0.000	0.000	0.000
15	A	84	GLY	0	-0.085	-0.056	25.255	0.008	0.008	0.000	0.000	0.000	0.000
16	A	85	PRO	0	-0.044	-0.039	21.713	0.010	0.010	0.000	0.000	0.000	0.000
17	A	86	LEU	0	0.039	-0.001	23.642	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	87	ASP	-1	-0.819	-0.901	26.913	0.003	0.003	0.000	0.000	0.000	0.000
19	A	88	LEU	0	-0.069	-0.045	21.176	0.006	0.006	0.000	0.000	0.000	0.000
20	A	89	ILE	0	-0.018	0.002	24.067	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	90	ASN	0	0.065	0.043	25.948	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	91	TYR	0	-0.028	-0.017	26.658	0.002	0.002	0.000	0.000	0.000	0.000
23	A	92	ILE	0	-0.025	-0.012	22.789	0.008	0.008	0.000	0.000	0.000	0.000
24	A	93	ASP	-1	-0.843	-0.931	27.069	-0.080	-0.080	0.000	0.000	0.000	0.000
25	A	94	VAL	0	-0.058	-0.026	30.127	0.001	0.001	0.000	0.000	0.000	0.000
26	A	95	ALA	0	-0.018	-0.011	28.613	0.003	0.003	0.000	0.000	0.000	0.000
27	A	96	GLN	0	-0.012	-0.009	26.284	0.000	0.000	0.000	0.000	0.000	0.000
28	A	97	GLN	0	-0.048	-0.031	30.606	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	98	ASP	-1	-0.955	-0.944	33.746	0.001	0.001	0.000	0.000	0.000	0.000
30	A	99	GLY	0	-0.017	-0.021	32.800	0.000	0.000	0.000	0.000	0.000	0.000
31	A	100	LYS	1	0.860	0.941	29.857	-0.033	-0.033	0.000	0.000	0.000	0.000
32	A	101	LEU	0	-0.012	-0.009	24.397	0.008	0.008	0.000	0.000	0.000	0.000
33	A	102	PRO	0	0.006	0.021	26.202	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	103	PHE	0	0.043	0.008	26.692	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	104	VAL	0	-0.020	-0.014	26.197	-0.016	-0.016	0.000	0.000	0.000	0.000
36	A	105	PRO	0	-0.017	0.011	22.683	0.014	0.014	0.000	0.000	0.000	0.000
37	A	106	PRO	0	0.034	-0.002	24.461	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	107	GLU	-1	-1.004	-1.022	23.348	-0.237	-0.237	0.000	0.000	0.000	0.000
39	A	108	GLU	-1	-0.931	-0.953	20.650	-0.126	-0.126	0.000	0.000	0.000	0.000
40	A	109	GLU	-1	-0.852	-0.911	16.789	-0.460	-0.460	0.000	0.000	0.000	0.000
41	A	110	PHE	0	-0.022	-0.005	14.544	0.013	0.013	0.000	0.000	0.000	0.000
42	A	111	ILE	0	0.015	0.000	8.227	-0.088	-0.088	0.000	0.000	0.000	0.000
43	A	112	MET	0	-0.028	0.004	8.833	0.236	0.236	0.000	0.000	0.000	0.000
44	A	113	GLY	0	0.021	-0.001	5.554	-0.655	-0.655	0.000	0.000	0.000	0.000
45	A	114	VAL	0	-0.008	-0.010	4.237	1.048	1.389	-0.001	-0.081	-0.259	0.000
46	A	115	SER	0	-0.057	-0.046	2.008	-5.914	-3.656	7.151	-5.786	-3.624	-0.018
47	A	116	LYS	1	1.007	0.982	2.898	-4.401	-5.497	0.107	1.604	-0.615	0.000
48	A	117	TYR	0	-0.031	-0.012	4.305	-1.127	-0.868	0.007	-0.055	-0.210	0.000
49	A	118	GLY	0	0.073	0.041	6.653	-0.707	-0.707	0.000	0.000	0.000	0.000
50	A	119	ILE	0	-0.035	0.001	6.423	0.758	0.758	0.000	0.000	0.000	0.000
51	A	120	LYS	1	0.979	1.000	5.626	-3.217	-3.159	-0.001	-0.007	-0.051	0.000
52	A	131	HIS	0	0.013	0.009	14.078	0.072	0.072	0.000	0.000	0.000	0.000
53	A	132	ARG	1	0.901	0.938	10.601	-0.962	-0.962	0.000	0.000	0.000	0.000
54	A	133	HIS	0	0.032	0.034	11.305	-0.075	-0.075	0.000	0.000	0.000	0.000
55	A	134	ALA	0	0.002	-0.004	11.243	0.225	0.225	0.000	0.000	0.000	0.000
56	A	135	LEU	0	0.022	-0.002	8.762	-0.077	-0.077	0.000	0.000	0.000	0.000
57	A	136	TYR	0	-0.008	0.002	12.296	-0.094	-0.094	0.000	0.000	0.000	0.000
58	A	137	LEU	0	-0.025	-0.008	15.817	-0.062	-0.062	0.000	0.000	0.000	0.000
59	A	138	ILE	0	-0.038	0.003	12.458	-0.073	-0.073	0.000	0.000	0.000	0.000
60	A	139	ILE	0	0.009	0.012	15.904	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	140	ARG	1	0.876	0.922	17.274	-0.058	-0.058	0.000	0.000	0.000	0.000
62	A	141	MET	0	0.009	0.018	12.763	0.019	0.019	0.000	0.000	0.000	0.000
63	A	142	VAL	0	-0.041	-0.018	16.166	-0.014	-0.014	0.000	0.000	0.000	0.000
64	A	143	CYS	0	-0.062	-0.035	15.994	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	144	TYR	0	0.030	0.009	19.054	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	145	ASP	-1	-0.942	-0.988	22.196	-0.281	-0.281	0.000	0.000	0.000	0.000
67	A	146	ASP	-1	-0.695	-0.860	24.619	-0.180	-0.180	0.000	0.000	0.000	0.000
68	A	147	GLY	0	-0.045	-0.012	26.559	0.013	0.013	0.000	0.000	0.000	0.000
69	A	148	LEU	0	-0.130	-0.072	29.560	0.011	0.011	0.000	0.000	0.000	0.000
70	A	149	GLY	0	-0.010	0.006	27.382	0.003	0.003	0.000	0.000	0.000	0.000
71	A	150	ALA	0	-0.028	0.009	27.391	-0.023	-0.023	0.000	0.000	0.000	0.000
72	A	151	GLY	0	-0.064	-0.027	26.807	0.012	0.012	0.000	0.000	0.000	0.000
73	A	152	LYS	1	0.941	0.963	23.151	0.253	0.253	0.000	0.000	0.000	0.000
74	A	153	SER	0	0.037	0.010	19.967	-0.017	-0.017	0.000	0.000	0.000	0.000
75	A	154	LEU	0	-0.005	0.008	20.735	0.012	0.012	0.000	0.000	0.000	0.000
76	A	155	LEU	0	-0.037	-0.037	13.734	-0.050	-0.050	0.000	0.000	0.000	0.000
77	A	156	ALA	0	0.037	0.033	17.756	0.036	0.036	0.000	0.000	0.000	0.000
78	A	157	LEU	0	-0.027	-0.009	13.222	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	158	LYS	1	0.955	0.977	16.997	-0.139	-0.139	0.000	0.000	0.000	0.000
80	A	159	THR	0	0.029	0.012	15.649	0.031	0.031	0.000	0.000	0.000	0.000
81	A	160	THR	0	0.052	0.028	18.331	-0.036	-0.036	0.000	0.000	0.000	0.000
82	A	161	ASP	-1	-0.843	-0.928	20.507	0.429	0.429	0.000	0.000	0.000	0.000
83	A	162	ALA	0	-0.029	-0.009	22.499	-0.020	-0.020	0.000	0.000	0.000	0.000
84	A	163	SER	0	-0.037	-0.039	25.568	-0.032	-0.032	0.000	0.000	0.000	0.000
85	A	164	ASN	0	-0.065	-0.036	27.576	-0.026	-0.026	0.000	0.000	0.000	0.000
86	A	165	GLU	-1	-0.940	-0.969	28.348	0.146	0.146	0.000	0.000	0.000	0.000
87	A	166	GLU	-1	-0.942	-0.957	26.993	0.182	0.182	0.000	0.000	0.000	0.000
88	A	167	TYR	0	-0.021	-0.020	22.857	0.031	0.031	0.000	0.000	0.000	0.000
89	A	168	SER	0	-0.042	-0.013	20.544	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	169	LEU	0	-0.027	-0.028	20.829	0.001	0.001	0.000	0.000	0.000	0.000
91	A	170	TRP	0	0.013	0.011	17.001	-0.021	-0.021	0.000	0.000	0.000	0.000
92	A	171	VAL	0	0.064	0.032	18.432	-0.025	-0.025	0.000	0.000	0.000	0.000
93	A	172	TYR	0	-0.043	-0.027	14.429	0.010	0.010	0.000	0.000	0.000	0.000
94	A	173	GLN	0	0.028	0.007	17.860	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	174	CYS	0	-0.037	0.012	15.521	-0.072	-0.072	0.000	0.000	0.000	0.000
96	A	175	ASN	0	0.004	-0.001	17.451	0.092	0.092	0.000	0.000	0.000	0.000
97	A	176	SER	0	0.023	0.002	18.495	0.022	0.022	0.000	0.000	0.000	0.000
98	A	177	LEU	0	0.139	0.068	18.526	-0.033	-0.033	0.000	0.000	0.000	0.000
99	A	178	GLU	-1	-0.913	-0.957	17.563	-0.584	-0.584	0.000	0.000	0.000	0.000
100	A	179	GLN	0	0.001	-0.010	13.628	-0.041	-0.041	0.000	0.000	0.000	0.000
101	A	180	ALA	0	0.030	0.009	13.186	-0.115	-0.115	0.000	0.000	0.000	0.000
102	A	181	GLN	0	0.005	-0.008	14.348	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	182	ALA	0	-0.049	-0.026	11.436	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	183	ILE	0	0.020	0.010	9.004	-0.215	-0.215	0.000	0.000	0.000	0.000
105	A	184	CYS	0	0.015	-0.001	9.129	0.010	0.010	0.000	0.000	0.000	0.000
106	A	185	LYS	1	0.949	0.976	10.399	0.789	0.789	0.000	0.000	0.000	0.000
107	A	186	VAL	0	-0.023	-0.002	4.096	-0.166	-0.078	-0.001	-0.014	-0.072	0.000
108	A	187	LEU	0	0.013	-0.013	6.587	0.336	0.336	0.000	0.000	0.000	0.000
109	A	188	SER	0	-0.028	0.001	8.686	0.195	0.195	0.000	0.000	0.000	0.000
110	A	189	THR	0	-0.004	0.004	7.619	0.032	0.032	0.000	0.000	0.000	0.000
111	A	190	ALA	0	-0.031	-0.022	5.411	0.340	0.340	0.000	0.000	0.000	0.000
112	A	191	PHE	0	0.005	-0.004	7.204	0.312	0.312	0.000	0.000	0.000	0.000
113	A	192	ASP	-1	-0.885	-0.930	10.928	0.282	0.282	0.000	0.000	0.000	0.000
114	A	193	SER	0	-0.122	-0.048	7.917	0.273	0.273	0.000	0.000	0.000	0.000
115	A	194	VAL	0	-0.060	-0.016	9.971	0.043	0.043	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:60:CYS)