FMO DATABASE

FMODB ID: M3M3Z

Calculation Name: 4DX9-u-Xray321

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: u

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	112
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-820677.049007
FMO2-HF: Nuclear repulsion	777885.436072
FMO2-HF: Total energy	-42791.612935
FMO2-MP2: Total energy	-42913.877608

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(u:59:ACE )

Summations of interaction energy for fragment #1(u: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.
2.095	3.366	0.607	-0.774	-1.102	-0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.008

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	u	61	ALA	0	-0.002	0.022	3.838	0.895	1.685	-0.005	-0.349	-0.437	-0.001
4	u	62	GLU	-1	-0.933	-0.967	6.583	-0.577	-0.577	0.000	0.000	0.000	0.000
5	u	63	PHE	0	0.002	-0.004	8.058	0.108	0.108	0.000	0.000	0.000	0.000
6	u	64	ARG	1	0.890	0.955	12.819	0.147	0.147	0.000	0.000	0.000	0.000
7	u	65	ILE	0	-0.003	-0.005	15.420	0.027	0.027	0.000	0.000	0.000	0.000
8	u	66	LYS	1	0.956	0.989	18.042	0.087	0.087	0.000	0.000	0.000	0.000
9	u	67	TYR	0	0.009	0.002	21.006	-0.001	-0.001	0.000	0.000	0.000	0.000
10	u	68	VAL	0	-0.001	0.006	22.408	0.008	0.008	0.000	0.000	0.000	0.000
11	u	69	GLY	0	0.043	0.013	24.260	0.007	0.007	0.000	0.000	0.000	0.000
12	u	70	ALA	0	-0.044	-0.032	24.069	-0.007	-0.007	0.000	0.000	0.000	0.000
13	u	71	ILE	0	-0.006	0.017	25.748	0.005	0.005	0.000	0.000	0.000	0.000
14	u	72	NME	0	0.044	0.028	26.664	-0.002	-0.002	0.000	0.000	0.000	0.000
15	u	88	ACE	0	-0.024	-0.022	22.700	0.000	0.000	0.000	0.000	0.000	0.000
16	u	89	ILE	0	0.036	-0.017	23.094	0.001	0.001	0.000	0.000	0.000	0.000
17	u	90	ASN	0	0.038	0.025	25.898	-0.002	-0.002	0.000	0.000	0.000	0.000
18	u	91	TYR	0	0.034	-0.001	28.507	0.000	0.000	0.000	0.000	0.000	0.000
19	u	92	ILE	0	-0.062	-0.012	23.537	-0.004	-0.004	0.000	0.000	0.000	0.000
20	u	93	ASP	-1	-0.832	-0.909	27.705	-0.024	-0.024	0.000	0.000	0.000	0.000
21	u	94	VAL	0	-0.055	-0.023	30.741	0.000	0.000	0.000	0.000	0.000	0.000
22	u	95	ALA	0	0.036	0.012	30.318	-0.001	-0.001	0.000	0.000	0.000	0.000
23	u	96	GLN	0	-0.027	-0.013	27.969	0.002	0.002	0.000	0.000	0.000	0.000
24	u	97	GLN	0	-0.039	-0.016	32.631	0.001	0.001	0.000	0.000	0.000	0.000
25	u	98	ASP	-1	-0.945	-0.959	35.495	-0.026	-0.026	0.000	0.000	0.000	0.000
26	u	99	GLY	0	-0.019	-0.002	35.410	0.000	0.000	0.000	0.000	0.000	0.000
27	u	100	LYS	1	0.878	0.939	32.629	0.033	0.033	0.000	0.000	0.000	0.000
28	u	101	LEU	0	-0.031	-0.013	26.704	-0.005	-0.005	0.000	0.000	0.000	0.000
29	u	102	PRO	0	0.033	0.018	29.055	0.005	0.005	0.000	0.000	0.000	0.000
30	u	103	PHE	0	0.025	0.007	29.406	-0.003	-0.003	0.000	0.000	0.000	0.000
31	u	104	VAL	0	-0.031	-0.018	29.044	-0.001	-0.001	0.000	0.000	0.000	0.000
32	u	105	PRO	0	-0.043	-0.013	25.143	-0.001	-0.001	0.000	0.000	0.000	0.000
33	u	106	PRO	0	0.034	0.009	26.858	0.004	0.004	0.000	0.000	0.000	0.000
34	u	107	GLU	-1	-0.888	-0.958	26.495	-0.079	-0.079	0.000	0.000	0.000	0.000
35	u	108	GLU	-1	-0.984	-0.973	25.152	-0.122	-0.122	0.000	0.000	0.000	0.000
36	u	109	GLU	-1	-0.937	-0.971	20.943	-0.134	-0.134	0.000	0.000	0.000	0.000
37	u	110	PHE	0	0.007	-0.010	18.625	-0.013	-0.013	0.000	0.000	0.000	0.000
38	u	111	ILE	0	0.010	0.004	13.765	0.002	0.002	0.000	0.000	0.000	0.000
39	u	112	MET	0	-0.027	-0.013	11.991	-0.016	-0.016	0.000	0.000	0.000	0.000
40	u	113	GLY	0	0.036	0.010	9.799	-0.043	-0.043	0.000	0.000	0.000	0.000
41	u	114	VAL	0	-0.023	-0.001	5.751	0.085	0.085	0.000	0.000	0.000	0.000
42	u	115	SER	0	0.016	-0.011	4.885	-0.615	-0.640	0.000	-0.020	0.046	0.000
43	u	116	LYS	1	0.999	0.987	4.228	0.776	0.923	0.000	-0.019	-0.128	0.000
44	u	117	TYR	0	0.016	0.012	6.106	0.257	0.257	0.000	0.000	0.000	0.000
45	u	118	GLY	0	0.026	0.019	8.713	0.165	0.165	0.000	0.000	0.000	0.000
46	u	119	ILE	0	-0.020	-0.004	9.210	-0.206	-0.206	0.000	0.000	0.000	0.000
47	u	120	LYS	1	0.906	0.952	11.463	0.568	0.568	0.000	0.000	0.000	0.000
48	u	121	VAL	0	0.025	0.021	13.427	-0.039	-0.039	0.000	0.000	0.000	0.000
49	u	122	NME	0	-0.011	0.015	16.158	0.027	0.027	0.000	0.000	0.000	0.000
50	u	129	ACE	0	-0.014	-0.015	21.312	-0.004	-0.004	0.000	0.000	0.000	0.000
51	u	130	LEU	0	0.023	0.013	21.522	0.014	0.014	0.000	0.000	0.000	0.000
52	u	131	HIS	0	0.067	0.056	18.344	-0.003	-0.003	0.000	0.000	0.000	0.000
53	u	132	ARG	1	0.947	0.970	14.145	0.326	0.326	0.000	0.000	0.000	0.000
54	u	133	HIS	1	0.924	0.983	14.380	0.273	0.273	0.000	0.000	0.000	0.000
55	u	134	ALA	0	0.042	0.020	13.384	-0.060	-0.060	0.000	0.000	0.000	0.000
56	u	135	LEU	0	0.042	-0.018	8.101	0.008	0.008	0.000	0.000	0.000	0.000
57	u	136	TYR	0	-0.021	-0.006	11.827	0.046	0.046	0.000	0.000	0.000	0.000
58	u	137	LEU	0	-0.015	0.013	14.788	0.016	0.016	0.000	0.000	0.000	0.000
59	u	138	ILE	0	-0.050	-0.018	12.288	0.006	0.006	0.000	0.000	0.000	0.000
60	u	139	ILE	0	0.011	0.029	15.691	0.023	0.023	0.000	0.000	0.000	0.000
61	u	140	ARG	1	0.942	0.956	16.794	0.000	0.000	0.000	0.000	0.000	0.000
62	u	141	MET	0	-0.045	-0.010	11.479	-0.036	-0.036	0.000	0.000	0.000	0.000
63	u	142	VAL	0	-0.029	-0.013	16.227	0.025	0.025	0.000	0.000	0.000	0.000
64	u	143	CYS	0	-0.034	-0.008	16.689	-0.015	-0.015	0.000	0.000	0.000	0.000
65	u	144	TYR	0	0.020	0.008	18.830	0.013	0.013	0.000	0.000	0.000	0.000
66	u	145	ASP	-1	-0.856	-0.945	22.162	-0.018	-0.018	0.000	0.000	0.000	0.000
67	u	146	ASP	-1	-0.864	-0.952	24.783	-0.034	-0.034	0.000	0.000	0.000	0.000
68	u	147	GLY	0	0.009	0.021	26.575	0.001	0.001	0.000	0.000	0.000	0.000
69	u	148	LEU	0	-0.070	-0.030	29.444	0.000	0.000	0.000	0.000	0.000	0.000
70	u	149	GLY	0	0.008	0.005	30.937	0.004	0.004	0.000	0.000	0.000	0.000
71	u	150	ALA	0	-0.058	-0.047	27.979	-0.001	-0.001	0.000	0.000	0.000	0.000
72	u	151	GLY	0	0.055	0.043	25.406	0.000	0.000	0.000	0.000	0.000	0.000
73	u	152	LYS	1	0.874	0.957	23.407	0.052	0.052	0.000	0.000	0.000	0.000
74	u	153	SER	0	0.051	0.024	20.045	0.009	0.009	0.000	0.000	0.000	0.000
75	u	154	LEU	0	0.017	0.020	21.265	-0.017	-0.017	0.000	0.000	0.000	0.000
76	u	155	LEU	0	-0.021	-0.035	14.244	0.006	0.006	0.000	0.000	0.000	0.000
77	u	156	ALA	0	0.019	0.022	18.785	-0.011	-0.011	0.000	0.000	0.000	0.000
78	u	157	LEU	0	-0.020	-0.033	13.948	0.002	0.002	0.000	0.000	0.000	0.000
79	u	158	LYS	1	0.962	1.000	18.081	0.027	0.027	0.000	0.000	0.000	0.000
80	u	159	THR	0	-0.017	-0.003	17.608	-0.009	-0.009	0.000	0.000	0.000	0.000
81	u	160	THR	0	-0.002	0.006	20.102	0.010	0.010	0.000	0.000	0.000	0.000
82	u	161	ASP	-1	-0.830	-0.929	21.629	-0.068	-0.068	0.000	0.000	0.000	0.000
83	u	162	ALA	0	-0.024	-0.031	23.651	0.004	0.004	0.000	0.000	0.000	0.000
84	u	163	SER	0	-0.046	-0.021	24.529	0.005	0.005	0.000	0.000	0.000	0.000
85	u	164	ASN	0	-0.071	-0.002	23.993	0.002	0.002	0.000	0.000	0.000	0.000
86	u	165	GLU	-1	-0.884	-0.945	26.786	-0.023	-0.023	0.000	0.000	0.000	0.000
87	u	166	GLU	-1	-0.954	-0.961	28.676	-0.037	-0.037	0.000	0.000	0.000	0.000
88	u	167	TYR	0	-0.034	-0.035	24.005	-0.002	-0.002	0.000	0.000	0.000	0.000
89	u	168	SER	0	-0.043	-0.018	23.085	-0.003	-0.003	0.000	0.000	0.000	0.000
90	u	169	LEU	0	-0.028	-0.018	22.450	0.000	0.000	0.000	0.000	0.000	0.000
91	u	170	TRP	0	-0.035	-0.048	19.301	-0.009	-0.009	0.000	0.000	0.000	0.000
92	u	171	VAL	0	0.035	0.025	20.327	0.001	0.001	0.000	0.000	0.000	0.000
93	u	172	TYR	0	-0.030	-0.058	17.719	-0.018	-0.018	0.000	0.000	0.000	0.000
94	u	173	GLN	0	0.053	0.018	20.230	0.011	0.011	0.000	0.000	0.000	0.000
95	u	174	CYS	0	-0.034	0.000	16.902	-0.025	-0.025	0.000	0.000	0.000	0.000
96	u	175	ASN	0	-0.039	-0.035	19.346	0.025	0.025	0.000	0.000	0.000	0.000
97	u	176	SER	0	0.060	0.021	19.242	0.010	0.010	0.000	0.000	0.000	0.000
98	u	177	LEU	0	0.097	0.051	19.286	-0.008	-0.008	0.000	0.000	0.000	0.000
99	u	178	GLU	-1	-0.938	-0.978	17.412	0.029	0.029	0.000	0.000	0.000	0.000
100	u	179	GLN	0	-0.038	-0.012	14.649	0.002	0.002	0.000	0.000	0.000	0.000
101	u	180	ALA	0	0.043	0.005	13.723	-0.026	-0.026	0.000	0.000	0.000	0.000
102	u	181	GLN	0	0.028	0.009	14.107	0.008	0.008	0.000	0.000	0.000	0.000
103	u	182	ALA	0	-0.018	-0.003	10.944	0.044	0.044	0.000	0.000	0.000	0.000
104	u	183	ILE	0	0.006	-0.002	9.192	0.011	0.011	0.000	0.000	0.000	0.000
105	u	184	CYS	0	-0.028	-0.017	9.143	-0.020	-0.020	0.000	0.000	0.000	0.000
106	u	185	LYS	1	0.970	0.999	8.476	-0.186	-0.186	0.000	0.000	0.000	0.000
107	u	186	VAL	0	0.005	0.000	3.611	0.080	0.216	0.005	-0.034	-0.107	0.000
108	u	187	LEU	0	0.024	-0.005	4.727	0.020	0.070	0.000	-0.004	-0.045	0.000
109	u	188	SER	0	-0.060	-0.025	7.482	0.057	0.057	0.000	0.000	0.000	0.000
110	u	189	THR	0	-0.085	-0.026	2.662	0.250	0.375	0.607	-0.337	-0.395	-0.002
111	u	190	ALA	0	-0.058	-0.024	4.745	0.128	0.176	0.000	-0.011	-0.036	0.000
112	u	191	NME	0	0.006	0.016	5.456	-0.109	-0.109	0.000	0.000	0.000	0.000

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