FMO DATABASE

FMODB ID: 5393Z

Calculation Name: 4DX9-3-Xray321

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: 3

ChEMBL ID: CHEMBL1905

UniProt ID: P05556

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	123
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-978712.290167
FMO2-HF: Nuclear repulsion	931021.36078
FMO2-HF: Total energy	-47690.929387
FMO2-MP2: Total energy	-47827.721807

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(3:59:ACE )

Summations of interaction energy for fragment #1(3:59:ACE )

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.
0.312	2.205	1.011	-1.209	-1.695	-0.002

Interaction energy analysis for fragmet #1(3:59:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : -0.003

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	3	61	ALA	0	0.017	0.016	3.856	0.901	1.646	-0.005	-0.327	-0.414	-0.001
4	3	62	GLU	-1	-0.906	-0.948	6.750	-0.593	-0.593	0.000	0.000	0.000	0.000
5	3	63	PHE	0	-0.034	-0.029	7.383	0.109	0.109	0.000	0.000	0.000	0.000
6	3	64	ARG	1	0.958	1.000	12.504	0.134	0.134	0.000	0.000	0.000	0.000
7	3	65	ILE	0	0.006	-0.010	14.748	0.024	0.024	0.000	0.000	0.000	0.000
8	3	66	LYS	1	0.920	0.974	17.584	0.098	0.098	0.000	0.000	0.000	0.000
9	3	67	TYR	0	0.019	0.008	20.443	0.005	0.005	0.000	0.000	0.000	0.000
10	3	68	VAL	0	0.002	0.007	22.258	0.010	0.010	0.000	0.000	0.000	0.000
11	3	69	GLY	0	0.017	0.003	23.648	0.007	0.007	0.000	0.000	0.000	0.000
12	3	70	ALA	0	-0.019	-0.014	23.613	-0.004	-0.004	0.000	0.000	0.000	0.000
13	3	71	ILE	0	-0.033	-0.017	25.341	0.004	0.004	0.000	0.000	0.000	0.000
14	3	72	GLU	-1	-0.914	-0.965	26.973	-0.051	-0.051	0.000	0.000	0.000	0.000
15	3	73	NME	0	0.006	0.019	28.410	0.004	0.004	0.000	0.000	0.000	0.000
16	3	84	ACE	0	0.077	0.026	24.229	0.001	0.001	0.000	0.000	0.000	0.000
17	3	85	PRO	0	-0.071	-0.048	20.378	-0.005	-0.005	0.000	0.000	0.000	0.000
18	3	86	LEU	0	0.067	0.012	22.059	-0.007	-0.007	0.000	0.000	0.000	0.000
19	3	87	ASP	-1	-0.884	-0.927	25.101	0.003	0.003	0.000	0.000	0.000	0.000
20	3	88	LEU	0	-0.043	-0.024	20.111	-0.004	-0.004	0.000	0.000	0.000	0.000
21	3	89	ILE	0	-0.050	-0.016	22.708	-0.006	-0.006	0.000	0.000	0.000	0.000
22	3	90	ASN	0	0.021	-0.001	25.123	-0.005	-0.005	0.000	0.000	0.000	0.000
23	3	91	TYR	0	0.004	-0.003	27.695	0.000	0.000	0.000	0.000	0.000	0.000
24	3	92	ILE	0	-0.028	0.002	23.262	-0.004	-0.004	0.000	0.000	0.000	0.000
25	3	93	ASP	-1	-0.799	-0.898	27.179	-0.028	-0.028	0.000	0.000	0.000	0.000
26	3	94	VAL	0	-0.029	-0.014	29.454	0.000	0.000	0.000	0.000	0.000	0.000
27	3	95	ALA	0	0.042	0.028	30.283	-0.001	-0.001	0.000	0.000	0.000	0.000
28	3	96	GLN	0	-0.049	-0.037	26.848	0.002	0.002	0.000	0.000	0.000	0.000
29	3	97	GLN	0	-0.030	-0.017	32.031	-0.001	-0.001	0.000	0.000	0.000	0.000
30	3	98	ASP	-1	-0.946	-0.958	35.079	-0.024	-0.024	0.000	0.000	0.000	0.000
31	3	99	GLY	0	-0.063	-0.023	35.335	0.001	0.001	0.000	0.000	0.000	0.000
32	3	100	LYS	1	0.873	0.943	31.780	0.037	0.037	0.000	0.000	0.000	0.000
33	3	101	LEU	0	-0.023	-0.002	26.426	-0.002	-0.002	0.000	0.000	0.000	0.000
34	3	102	PRO	0	0.006	0.008	29.573	0.004	0.004	0.000	0.000	0.000	0.000
35	3	103	PHE	0	0.048	0.013	28.878	-0.005	-0.005	0.000	0.000	0.000	0.000
36	3	104	VAL	0	-0.068	-0.029	27.830	-0.002	-0.002	0.000	0.000	0.000	0.000
37	3	105	PRO	0	-0.012	0.006	24.084	0.000	0.000	0.000	0.000	0.000	0.000
38	3	106	PRO	0	0.039	0.005	26.356	0.004	0.004	0.000	0.000	0.000	0.000
39	3	107	GLU	-1	-0.999	-1.010	26.026	-0.077	-0.077	0.000	0.000	0.000	0.000
40	3	108	GLU	-1	-0.941	-0.962	25.329	-0.120	-0.120	0.000	0.000	0.000	0.000
41	3	109	GLU	-1	-0.938	-0.967	20.875	-0.135	-0.135	0.000	0.000	0.000	0.000
42	3	110	PHE	0	0.038	0.021	18.915	-0.009	-0.009	0.000	0.000	0.000	0.000
43	3	111	ILE	0	-0.019	0.000	14.177	-0.010	-0.010	0.000	0.000	0.000	0.000
44	3	112	MET	0	-0.023	-0.005	12.256	-0.007	-0.007	0.000	0.000	0.000	0.000
45	3	113	GLY	0	-0.010	0.003	9.793	-0.041	-0.041	0.000	0.000	0.000	0.000
46	3	114	VAL	0	-0.021	-0.012	4.683	-0.004	0.078	0.000	-0.012	-0.070	0.000
47	3	115	SER	0	-0.058	-0.055	6.119	-0.609	-0.609	0.000	0.000	0.000	0.000
48	3	116	LYS	1	0.975	0.965	2.883	0.111	0.488	0.045	-0.157	-0.264	0.001
49	3	117	TYR	0	-0.009	0.008	6.654	0.195	0.195	0.000	0.000	0.000	0.000
50	3	118	GLY	0	0.082	0.025	9.896	0.123	0.123	0.000	0.000	0.000	0.000
51	3	119	ILE	0	0.010	0.029	9.457	-0.184	-0.184	0.000	0.000	0.000	0.000
52	3	120	LYS	1	0.843	0.927	11.257	0.559	0.559	0.000	0.000	0.000	0.000
53	3	121	VAL	0	0.042	0.031	12.975	-0.024	-0.024	0.000	0.000	0.000	0.000
54	3	122	SER	0	0.002	-0.007	15.935	0.007	0.007	0.000	0.000	0.000	0.000
55	3	123	THR	0	0.018	-0.040	18.051	-0.002	-0.002	0.000	0.000	0.000	0.000
56	3	124	SER	0	-0.066	-0.037	20.614	-0.010	-0.010	0.000	0.000	0.000	0.000
57	3	125	ASP	-1	-0.800	-0.879	20.742	-0.221	-0.221	0.000	0.000	0.000	0.000
58	3	126	GLN	0	-0.078	-0.035	16.903	-0.034	-0.034	0.000	0.000	0.000	0.000
59	3	127	TYR	0	-0.075	-0.069	21.494	-0.001	-0.001	0.000	0.000	0.000	0.000
60	3	128	ASP	-1	-0.839	-0.873	23.271	-0.164	-0.164	0.000	0.000	0.000	0.000
61	3	129	VAL	0	-0.073	-0.047	18.902	-0.011	-0.011	0.000	0.000	0.000	0.000
62	3	130	LEU	0	0.013	0.025	20.642	0.015	0.015	0.000	0.000	0.000	0.000
63	3	131	HIS	0	0.057	0.016	20.003	0.006	0.006	0.000	0.000	0.000	0.000
64	3	132	ARG	1	0.924	0.964	12.220	0.420	0.420	0.000	0.000	0.000	0.000
65	3	133	HIS	0	0.019	0.012	16.484	0.020	0.020	0.000	0.000	0.000	0.000
66	3	134	ALA	0	-0.018	-0.026	13.486	-0.051	-0.051	0.000	0.000	0.000	0.000
67	3	135	LEU	0	0.092	0.087	10.973	0.031	0.031	0.000	0.000	0.000	0.000
68	3	136	TYR	0	-0.164	-0.100	15.052	0.029	0.029	0.000	0.000	0.000	0.000
69	3	137	LEU	0	0.008	-0.012	17.627	0.004	0.004	0.000	0.000	0.000	0.000
70	3	138	ILE	0	-0.004	-0.001	15.214	-0.020	-0.020	0.000	0.000	0.000	0.000
71	3	139	ILE	0	0.019	0.018	11.814	0.014	0.014	0.000	0.000	0.000	0.000
72	3	140	ARG	1	0.954	0.988	14.929	-0.023	-0.023	0.000	0.000	0.000	0.000
73	3	141	MET	0	-0.003	0.006	11.309	-0.005	-0.005	0.000	0.000	0.000	0.000
74	3	142	VAL	0	-0.061	-0.034	15.621	0.031	0.031	0.000	0.000	0.000	0.000
75	3	143	CYS	0	-0.051	-0.022	14.509	-0.013	-0.013	0.000	0.000	0.000	0.000
76	3	144	TYR	0	-0.044	-0.033	17.813	0.020	0.020	0.000	0.000	0.000	0.000
77	3	145	ASP	-1	-0.898	-0.972	20.954	-0.016	-0.016	0.000	0.000	0.000	0.000
78	3	146	ASP	-1	-0.859	-0.939	23.387	-0.033	-0.033	0.000	0.000	0.000	0.000
79	3	147	GLY	0	0.023	0.032	26.053	0.003	0.003	0.000	0.000	0.000	0.000
80	3	148	LEU	0	-0.025	-0.020	27.223	-0.001	-0.001	0.000	0.000	0.000	0.000
81	3	149	GLY	0	-0.023	-0.014	29.696	-0.003	-0.003	0.000	0.000	0.000	0.000
82	3	150	ALA	0	-0.079	-0.050	26.435	0.003	0.003	0.000	0.000	0.000	0.000
83	3	151	GLY	0	0.023	0.033	25.259	0.002	0.002	0.000	0.000	0.000	0.000
84	3	152	LYS	1	0.853	0.935	22.411	0.063	0.063	0.000	0.000	0.000	0.000
85	3	153	SER	0	0.046	0.029	18.379	0.000	0.000	0.000	0.000	0.000	0.000
86	3	154	LEU	0	0.006	0.002	20.500	-0.017	-0.017	0.000	0.000	0.000	0.000
87	3	155	LEU	0	-0.065	-0.042	13.781	0.007	0.007	0.000	0.000	0.000	0.000
88	3	156	ALA	0	0.054	0.039	17.656	-0.008	-0.008	0.000	0.000	0.000	0.000
89	3	157	LEU	0	-0.047	-0.041	13.480	-0.002	-0.002	0.000	0.000	0.000	0.000
90	3	158	LYN	0	0.030	0.046	17.832	-0.001	-0.001	0.000	0.000	0.000	0.000
91	3	159	THR	0	-0.003	-0.005	17.980	-0.006	-0.006	0.000	0.000	0.000	0.000
92	3	160	THR	0	0.027	-0.015	20.320	0.012	0.012	0.000	0.000	0.000	0.000
93	3	161	ASP	-1	-0.915	-0.965	21.797	-0.092	-0.092	0.000	0.000	0.000	0.000
94	3	162	ALA	0	-0.017	-0.023	24.597	0.001	0.001	0.000	0.000	0.000	0.000
95	3	163	SER	0	-0.021	-0.012	23.919	0.004	0.004	0.000	0.000	0.000	0.000
96	3	164	ASN	0	-0.064	-0.043	24.696	0.001	0.001	0.000	0.000	0.000	0.000
97	3	165	GLU	-1	-0.848	-0.895	27.156	-0.012	-0.012	0.000	0.000	0.000	0.000
98	3	166	GLH	0	-0.075	-0.041	21.025	-0.008	-0.008	0.000	0.000	0.000	0.000
99	3	167	TYR	0	-0.007	0.022	24.381	0.005	0.005	0.000	0.000	0.000	0.000
100	3	168	SER	0	0.046	0.025	23.201	0.000	0.000	0.000	0.000	0.000	0.000
101	3	169	LEU	0	-0.028	-0.016	22.783	-0.001	-0.001	0.000	0.000	0.000	0.000
102	3	170	TRP	0	-0.067	-0.035	19.369	-0.010	-0.010	0.000	0.000	0.000	0.000
103	3	171	VAL	0	0.048	0.017	20.836	0.006	0.006	0.000	0.000	0.000	0.000
104	3	172	TYR	0	-0.007	-0.021	17.648	-0.021	-0.021	0.000	0.000	0.000	0.000
105	3	173	GLN	0	0.045	0.028	19.752	0.010	0.010	0.000	0.000	0.000	0.000
106	3	174	CYS	0	-0.016	-0.006	16.191	-0.030	-0.030	0.000	0.000	0.000	0.000
107	3	175	ASN	0	-0.011	-0.021	18.852	0.018	0.018	0.000	0.000	0.000	0.000
108	3	176	SER	0	0.079	0.031	18.941	0.014	0.014	0.000	0.000	0.000	0.000
109	3	177	LEU	0	0.078	0.040	17.850	-0.012	-0.012	0.000	0.000	0.000	0.000
110	3	178	GLU	-1	-0.892	-0.943	16.461	0.053	0.053	0.000	0.000	0.000	0.000
111	3	179	GLN	0	-0.051	-0.029	13.731	0.032	0.032	0.000	0.000	0.000	0.000
112	3	180	ALA	0	0.026	0.011	12.691	-0.026	-0.026	0.000	0.000	0.000	0.000
113	3	181	GLN	0	-0.007	-0.012	12.999	0.015	0.015	0.000	0.000	0.000	0.000
114	3	182	ALA	0	-0.035	-0.017	9.899	0.063	0.063	0.000	0.000	0.000	0.000
115	3	183	ILE	0	-0.003	0.003	8.176	0.014	0.014	0.000	0.000	0.000	0.000
116	3	184	CYS	0	0.042	0.012	8.308	-0.036	-0.036	0.000	0.000	0.000	0.000
117	3	185	LYS	1	0.895	0.959	7.873	-0.197	-0.197	0.000	0.000	0.000	0.000
118	3	186	VAL	0	-0.007	-0.005	2.350	-0.094	0.100	0.948	-0.551	-0.591	-0.002
119	3	187	LEU	0	0.028	0.002	4.097	0.209	0.399	0.001	-0.050	-0.141	0.000
120	3	188	SER	0	-0.020	0.000	6.523	0.011	0.011	0.000	0.000	0.000	0.000
121	3	189	THR	0	-0.049	-0.016	4.045	-0.031	0.012	0.002	-0.031	-0.014	0.000
122	3	190	ALA	0	-0.096	-0.026	3.345	0.001	0.204	0.019	-0.070	-0.151	0.000
123	3	191	NME	0	0.020	0.017	4.301	0.006	0.065	0.001	-0.011	-0.050	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(3:59:ACE )