FMO DATABASE

FMODB ID: VR221

Calculation Name: 4DX9-0-Xray321

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: 0

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	-943881.492005
FMO2-HF: Nuclear repulsion	897199.893325
FMO2-HF: Total energy	-46681.59868
FMO2-MP2: Total energy	-46815.642224

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(0:59:ACE )

Summations of interaction energy for fragment #1(0:59: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.
-1.603	0.107	0.324	-0.877	-1.158	0

Interaction energy analysis for fragmet #1(0:59:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.010

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.	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].
3	61	ALA	0	-0.010	0.014	3.850	0.904	1.673	-0.005	-0.332	-0.432
4	62	GLU	-1	-0.902	-0.945	6.825	-0.674	-0.674	0.000	0.000	0.000
5	63	PHE	0	-0.016	-0.020	8.775	0.116	0.116	0.000	0.000	0.000
6	64	ARG	1	0.978	0.992	13.322	0.207	0.207	0.000	0.000	0.000
7	65	ILE	0	-0.056	-0.025	15.960	0.021	0.021	0.000	0.000	0.000
8	66	LYS	1	1.016	1.007	18.534	0.131	0.131	0.000	0.000	0.000
9	67	TYR	0	0.025	0.020	21.219	-0.005	-0.005	0.000	0.000	0.000
10	68	VAL	0	0.031	0.007	22.704	0.012	0.012	0.000	0.000	0.000
11	69	GLY	0	0.020	0.010	25.560	0.003	0.003	0.000	0.000	0.000
12	70	ALA	0	-0.054	-0.038	25.279	-0.009	-0.009	0.000	0.000	0.000
13	71	ILE	0	0.012	0.008	26.681	0.007	0.007	0.000	0.000	0.000
14	72	NME	0	0.010	0.033	26.478	0.003	0.003	0.000	0.000	0.000
15	83	ACE	0	0.082	0.031	28.049	-0.001	-0.001	0.000	0.000	0.000
16	84	GLY	0	-0.082	-0.060	25.471	0.007	0.007	0.000	0.000	0.000
17	85	PRO	0	-0.054	-0.025	22.726	-0.006	-0.006	0.000	0.000	0.000
18	86	LEU	0	0.101	0.023	23.823	-0.007	-0.007	0.000	0.000	0.000
19	87	ASP	-1	-0.920	-0.951	26.804	-0.022	-0.022	0.000	0.000	0.000
20	88	LEU	0	-0.049	-0.026	22.079	-0.002	-0.002	0.000	0.000	0.000
21	89	ILE	0	-0.027	0.003	24.447	-0.005	-0.005	0.000	0.000	0.000
22	90	ASN	0	0.047	0.025	26.846	-0.004	-0.004	0.000	0.000	0.000
23	91	TYR	0	-0.056	-0.018	28.262	0.000	0.000	0.000	0.000	0.000
24	92	ILE	0	-0.018	-0.023	24.716	-0.003	-0.003	0.000	0.000	0.000
25	93	ASP	-1	-0.805	-0.912	29.269	-0.049	-0.049	0.000	0.000	0.000
26	94	VAL	0	-0.028	-0.011	31.741	0.002	0.002	0.000	0.000	0.000
27	95	ALA	0	-0.010	-0.002	31.097	0.000	0.000	0.000	0.000	0.000
28	96	GLN	0	-0.033	-0.032	29.201	0.003	0.003	0.000	0.000	0.000
29	97	GLN	0	-0.026	-0.010	33.545	0.001	0.001	0.000	0.000	0.000
30	98	ASP	-1	-0.925	-0.943	36.850	-0.038	-0.038	0.000	0.000	0.000
31	99	GLY	0	-0.019	-0.009	36.577	0.001	0.001	0.000	0.000	0.000
32	100	LYS	1	0.866	0.934	34.174	0.045	0.045	0.000	0.000	0.000
33	101	LEU	0	-0.015	0.001	27.999	-0.006	-0.006	0.000	0.000	0.000
34	102	PRO	0	-0.001	0.012	29.482	0.004	0.004	0.000	0.000	0.000
35	103	PHE	0	0.031	0.006	30.068	-0.005	-0.005	0.000	0.000	0.000
36	104	VAL	0	-0.023	-0.016	29.786	-0.004	-0.004	0.000	0.000	0.000
37	105	PRO	0	-0.050	-0.011	25.985	0.002	0.002	0.000	0.000	0.000
38	106	PRO	0	0.030	0.006	26.997	0.004	0.004	0.000	0.000	0.000
39	107	GLU	-1	-0.973	-0.988	26.891	-0.131	-0.131	0.000	0.000	0.000
40	108	GLU	-1	-0.962	-0.972	25.105	-0.137	-0.137	0.000	0.000	0.000
41	109	GLU	-1	-1.007	-1.002	21.840	-0.172	-0.172	0.000	0.000	0.000
42	110	PHE	0	-0.021	-0.012	18.315	-0.011	-0.011	0.000	0.000	0.000
43	111	ILE	0	-0.019	-0.016	14.208	0.001	0.001	0.000	0.000	0.000
44	112	MET	0	-0.041	-0.002	11.664	-0.057	-0.057	0.000	0.000	0.000
45	113	GLY	0	0.063	0.022	9.355	-0.022	-0.022	0.000	0.000	0.000
46	114	VAL	0	-0.042	-0.018	5.981	0.085	0.085	0.000	0.000	0.000
47	115	SER	0	0.027	-0.002	4.269	-0.705	-0.609	0.000	-0.060	-0.037
48	116	LYS	1	0.975	0.977	2.542	-2.607	-1.959	0.329	-0.460	-0.518
49	117	TYR	0	-0.004	-0.001	5.185	0.303	0.379	0.000	-0.003	-0.073
50	118	GLY	0	-0.006	-0.009	8.488	0.173	0.173	0.000	0.000	0.000
51	119	ILE	0	-0.024	0.002	9.218	-0.211	-0.211	0.000	0.000	0.000
52	120	LYS	1	0.859	0.923	11.677	0.504	0.504	0.000	0.000	0.000
53	121	VAL	0	0.004	0.002	13.598	-0.048	-0.048	0.000	0.000	0.000
54	122	SER	0	0.017	0.016	16.189	0.027	0.027	0.000	0.000	0.000
55	123	THR	0	0.089	0.067	17.943	-0.027	-0.027	0.000	0.000	0.000
56	124	SER	0	-0.055	-0.044	19.216	-0.023	-0.023	0.000	0.000	0.000
57	125	ASP	-1	-0.872	-0.921	21.343	-0.146	-0.146	0.000	0.000	0.000
58	126	GLN	0	-0.036	-0.030	21.854	-0.035	-0.035	0.000	0.000	0.000
59	127	TYR	0	-0.063	-0.040	19.079	-0.001	-0.001	0.000	0.000	0.000
60	128	ASP	-1	-0.762	-0.854	20.152	-0.233	-0.233	0.000	0.000	0.000
61	129	VAL	0	-0.093	-0.060	18.616	-0.047	-0.047	0.000	0.000	0.000
62	130	LEU	0	-0.019	-0.018	18.925	0.000	0.000	0.000	0.000	0.000
63	131	HIS	0	0.017	0.021	18.093	0.013	0.013	0.000	0.000	0.000
64	132	ARG	1	0.942	0.953	16.046	0.231	0.231	0.000	0.000	0.000
65	133	HIS	0	0.044	0.033	14.876	0.043	0.043	0.000	0.000	0.000
66	134	ALA	0	0.028	0.006	13.137	-0.062	-0.062	0.000	0.000	0.000
67	135	LEU	0	0.055	0.007	7.937	0.009	0.009	0.000	0.000	0.000
68	136	TYR	0	-0.017	-0.006	11.937	0.055	0.055	0.000	0.000	0.000
69	137	LEU	0	-0.036	-0.013	14.800	0.019	0.019	0.000	0.000	0.000
70	138	ILE	0	-0.018	0.008	12.092	0.007	0.007	0.000	0.000	0.000
71	139	ILE	0	-0.005	0.002	15.453	0.027	0.027	0.000	0.000	0.000
72	140	ARG	1	0.937	0.963	16.622	0.024	0.024	0.000	0.000	0.000
73	141	MET	0	-0.028	0.018	11.794	-0.021	-0.021	0.000	0.000	0.000
74	142	VAL	0	-0.004	0.003	16.584	0.019	0.019	0.000	0.000	0.000
75	143	CYS	0	-0.032	0.002	17.168	-0.015	-0.015	0.000	0.000	0.000
76	144	TYR	0	0.008	0.004	19.665	0.011	0.011	0.000	0.000	0.000
77	145	ASP	-1	-0.869	-0.958	23.054	-0.063	-0.063	0.000	0.000	0.000
78	146	ASP	-1	-0.921	-0.972	25.565	-0.070	-0.070	0.000	0.000	0.000
79	147	GLY	0	0.000	0.007	27.811	0.005	0.005	0.000	0.000	0.000
80	148	LEU	0	-0.039	-0.003	30.562	0.003	0.003	0.000	0.000	0.000
81	149	GLY	0	-0.002	-0.011	31.951	0.004	0.004	0.000	0.000	0.000
82	150	ALA	0	-0.043	-0.038	30.541	0.004	0.004	0.000	0.000	0.000
83	151	GLY	0	0.017	0.007	27.027	-0.004	-0.004	0.000	0.000	0.000
84	152	LYS	1	0.925	0.980	24.706	0.082	0.082	0.000	0.000	0.000
85	153	SER	0	0.004	0.023	20.411	0.000	0.000	0.000	0.000	0.000
86	154	LEU	0	0.023	0.012	22.402	-0.009	-0.009	0.000	0.000	0.000
87	155	LEU	0	-0.031	-0.026	14.765	0.008	0.008	0.000	0.000	0.000
88	156	ALA	0	0.038	0.012	19.392	-0.011	-0.011	0.000	0.000	0.000
89	157	LEU	0	-0.026	-0.016	14.731	0.004	0.004	0.000	0.000	0.000
90	158	LYS	1	0.978	0.988	17.933	0.056	0.056	0.000	0.000	0.000
91	159	THR	0	-0.016	-0.017	17.625	-0.007	-0.007	0.000	0.000	0.000
92	160	NME	0	0.005	0.024	19.980	0.007	0.007	0.000	0.000	0.000
93	167	ACE	0	0.027	0.004	23.918	0.000	0.000	0.000	0.000	0.000
94	168	SER	0	-0.049	-0.043	23.578	0.009	0.009	0.000	0.000	0.000
95	169	LEU	0	-0.062	-0.029	22.044	-0.005	-0.005	0.000	0.000	0.000
96	170	TRP	0	0.012	0.004	20.050	-0.002	-0.002	0.000	0.000	0.000
97	171	VAL	0	0.044	0.022	21.294	-0.001	-0.001	0.000	0.000	0.000
98	172	TYR	0	-0.009	-0.009	18.647	-0.015	-0.015	0.000	0.000	0.000
99	173	GLN	0	0.037	0.033	20.248	-0.001	-0.001	0.000	0.000	0.000
100	174	CYS	0	-0.015	-0.007	18.018	-0.026	-0.026	0.000	0.000	0.000
101	175	ASN	0	0.005	-0.019	19.033	0.025	0.025	0.000	0.000	0.000
102	176	SER	0	0.001	0.001	20.018	0.015	0.015	0.000	0.000	0.000
103	177	LEU	0	0.050	0.018	20.353	-0.001	-0.001	0.000	0.000	0.000
104	178	GLU	-1	-0.857	-0.943	18.039	-0.041	-0.041	0.000	0.000	0.000
105	179	GLN	0	-0.018	-0.010	15.374	-0.033	-0.033	0.000	0.000	0.000
106	180	ALA	0	0.039	0.021	14.383	-0.042	-0.042	0.000	0.000	0.000
107	181	GLN	0	0.038	0.015	14.462	-0.007	-0.007	0.000	0.000	0.000
108	182	ALA	0	-0.016	0.005	11.370	0.022	0.022	0.000	0.000	0.000
109	183	ILE	0	0.008	0.009	9.814	-0.037	-0.037	0.000	0.000	0.000
110	184	CYS	0	-0.020	-0.018	9.839	-0.039	-0.039	0.000	0.000	0.000
111	185	LYS	1	0.970	0.979	9.650	-0.122	-0.122	0.000	0.000	0.000
112	186	VAL	0	-0.006	-0.008	4.039	0.100	0.169	0.000	-0.014	-0.054
113	187	LEU	0	0.008	-0.003	5.566	0.007	0.007	0.000	0.000	0.000
114	188	SER	0	-0.042	-0.016	8.181	0.098	0.098	0.000	0.000	0.000
115	189	THR	0	0.025	0.020	4.464	0.233	0.285	0.000	-0.008	-0.044
116	190	ALA	0	-0.010	-0.002	5.307	0.365	0.365	0.000	0.000	0.000
117	191	PHE	0	-0.012	-0.033	6.062	0.020	0.020	0.000	0.000	0.000
118	192	ASP	-1	-0.918	-0.957	9.227	0.382	0.382	0.000	0.000	0.000
119	193	SER	0	-0.101	-0.035	6.468	0.188	0.188	0.000	0.000	0.000
120	194	VAL	0	-0.076	-0.039	7.605	-0.094	-0.094	0.000	0.000	0.000
121	195	LEU	0	-0.028	0.002	9.836	-0.085	-0.085	0.000	0.000	0.000
122	196	THR	0	-0.006	-0.002	11.874	0.033	0.033	0.000	0.000	0.000
123	197	NME	0	-0.023	0.000	14.465	-0.031	-0.031	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(0:59:ACE )