FMO DATABASE

FMODB ID: Q181Y

Calculation Name: 4DX9-E-Xray321

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: E

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	127
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1028971.323464
FMO2-HF: Nuclear repulsion	979992.616857
FMO2-HF: Total energy	-48978.706607
FMO2-MP2: Total energy	-49119.547249

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(E:59:ACE )

Summations of interaction energy for fragment #1(E: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.
-0.81	-0.415	2.337	-1.436	-1.296	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / 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	E	61	ALA	0	0.013	0.021	3.869	0.784	1.523	-0.005	-0.326	-0.409	0.000
4	E	62	GLU	-1	-0.900	-0.942	7.075	-0.618	-0.618	0.000	0.000	0.000	0.000
5	E	63	PHE	0	-0.018	-0.012	9.606	0.102	0.102	0.000	0.000	0.000	0.000
6	E	64	ARG	1	0.965	1.000	13.872	0.175	0.175	0.000	0.000	0.000	0.000
7	E	65	ILE	0	-0.045	-0.029	16.940	0.018	0.018	0.000	0.000	0.000	0.000
8	E	66	LYS	1	0.872	0.955	19.636	0.131	0.131	0.000	0.000	0.000	0.000
9	E	67	TYR	0	-0.010	-0.019	21.847	-0.013	-0.013	0.000	0.000	0.000	0.000
10	E	68	VAL	0	-0.015	0.001	24.385	0.012	0.012	0.000	0.000	0.000	0.000
11	E	69	GLY	0	0.038	0.006	26.189	0.010	0.010	0.000	0.000	0.000	0.000
12	E	70	ALA	0	-0.013	0.000	25.361	-0.008	-0.008	0.000	0.000	0.000	0.000
13	E	71	ILE	0	-0.022	-0.008	27.099	0.009	0.009	0.000	0.000	0.000	0.000
14	E	72	NME	0	0.023	0.044	27.709	0.001	0.001	0.000	0.000	0.000	0.000
15	E	83	ACE	0	0.035	0.004	28.658	0.000	0.000	0.000	0.000	0.000	0.000
16	E	84	GLY	0	0.021	-0.002	27.163	0.004	0.004	0.000	0.000	0.000	0.000
17	E	85	PRO	0	-0.032	-0.026	23.176	-0.004	-0.004	0.000	0.000	0.000	0.000
18	E	86	LEU	0	0.062	0.019	25.242	-0.005	-0.005	0.000	0.000	0.000	0.000
19	E	87	ASP	-1	-0.880	-0.935	28.255	-0.043	-0.043	0.000	0.000	0.000	0.000
20	E	88	LEU	0	-0.091	-0.046	23.592	-0.002	-0.002	0.000	0.000	0.000	0.000
21	E	89	ILE	0	-0.012	0.010	26.119	-0.004	-0.004	0.000	0.000	0.000	0.000
22	E	90	ASN	0	0.059	0.027	28.543	-0.001	-0.001	0.000	0.000	0.000	0.000
23	E	91	TYR	0	-0.059	-0.021	29.097	0.003	0.003	0.000	0.000	0.000	0.000
24	E	92	ILE	0	-0.040	-0.026	25.912	-0.002	-0.002	0.000	0.000	0.000	0.000
25	E	93	ASP	-1	-0.837	-0.932	30.383	-0.063	-0.063	0.000	0.000	0.000	0.000
26	E	94	VAL	0	-0.063	-0.013	33.158	0.003	0.003	0.000	0.000	0.000	0.000
27	E	95	ALA	0	0.000	-0.006	32.598	0.001	0.001	0.000	0.000	0.000	0.000
28	E	96	GLN	0	-0.011	-0.021	29.864	0.003	0.003	0.000	0.000	0.000	0.000
29	E	97	GLN	0	-0.058	-0.015	34.712	0.003	0.003	0.000	0.000	0.000	0.000
30	E	98	ASP	-1	-0.924	-0.956	37.992	-0.049	-0.049	0.000	0.000	0.000	0.000
31	E	99	GLY	0	0.003	0.001	37.790	0.002	0.002	0.000	0.000	0.000	0.000
32	E	100	LYS	1	0.844	0.934	33.731	0.070	0.070	0.000	0.000	0.000	0.000
33	E	101	LEU	0	-0.030	-0.019	29.082	-0.006	-0.006	0.000	0.000	0.000	0.000
34	E	102	PRO	0	0.002	0.022	30.939	0.005	0.005	0.000	0.000	0.000	0.000
35	E	103	PHE	0	0.044	0.005	31.660	-0.004	-0.004	0.000	0.000	0.000	0.000
36	E	104	VAL	0	-0.032	-0.014	31.414	-0.003	-0.003	0.000	0.000	0.000	0.000
37	E	105	PRO	0	-0.022	-0.015	27.183	0.000	0.000	0.000	0.000	0.000	0.000
38	E	106	PRO	0	0.013	0.001	28.949	0.004	0.004	0.000	0.000	0.000	0.000
39	E	107	GLU	-1	-0.897	-0.967	28.547	-0.107	-0.107	0.000	0.000	0.000	0.000
40	E	108	GLU	-1	-0.918	-0.949	25.596	-0.147	-0.147	0.000	0.000	0.000	0.000
41	E	109	GLU	-1	-0.948	-0.978	22.518	-0.157	-0.157	0.000	0.000	0.000	0.000
42	E	110	PHE	0	-0.031	-0.026	19.947	-0.005	-0.005	0.000	0.000	0.000	0.000
43	E	111	ILE	0	0.027	0.015	14.342	0.000	0.000	0.000	0.000	0.000	0.000
44	E	112	MET	0	-0.038	-0.021	13.008	-0.001	-0.001	0.000	0.000	0.000	0.000
45	E	113	GLY	0	0.008	0.005	10.724	-0.044	-0.044	0.000	0.000	0.000	0.000
46	E	114	VAL	0	-0.031	-0.027	6.855	0.119	0.119	0.000	0.000	0.000	0.000
47	E	115	SER	0	0.022	-0.045	5.530	-0.741	-0.741	0.000	0.000	0.000	0.000
48	E	116	LYS	1	0.910	0.926	2.126	-1.227	-1.678	2.340	-1.078	-0.811	0.001
49	E	117	TYR	0	0.026	0.002	6.447	0.276	0.276	0.000	0.000	0.000	0.000
50	E	118	GLY	0	-0.027	0.007	10.122	0.113	0.113	0.000	0.000	0.000	0.000
51	E	119	ILE	0	-0.003	0.005	10.203	-0.191	-0.191	0.000	0.000	0.000	0.000
52	E	120	LYS	1	0.878	0.949	12.156	0.489	0.489	0.000	0.000	0.000	0.000
53	E	121	VAL	0	0.045	0.043	14.277	-0.024	-0.024	0.000	0.000	0.000	0.000
54	E	122	SER	0	0.003	-0.014	17.280	0.025	0.025	0.000	0.000	0.000	0.000
55	E	123	THR	0	0.055	0.037	19.217	-0.005	-0.005	0.000	0.000	0.000	0.000
56	E	124	SER	0	0.065	0.023	21.480	0.001	0.001	0.000	0.000	0.000	0.000
57	E	125	ASP	-1	-0.925	-0.955	18.386	-0.244	-0.244	0.000	0.000	0.000	0.000
58	E	126	GLN	0	-0.081	-0.035	18.888	0.016	0.016	0.000	0.000	0.000	0.000
59	E	127	TYR	0	-0.032	-0.024	17.834	-0.042	-0.042	0.000	0.000	0.000	0.000
60	E	128	ASP	-1	-0.879	-0.937	19.336	-0.196	-0.196	0.000	0.000	0.000	0.000
61	E	129	VAL	0	-0.097	-0.052	18.132	-0.041	-0.041	0.000	0.000	0.000	0.000
62	E	130	LEU	0	-0.013	0.003	19.846	0.024	0.024	0.000	0.000	0.000	0.000
63	E	131	HIS	0	0.019	0.019	19.144	0.015	0.015	0.000	0.000	0.000	0.000
64	E	132	ARG	1	0.935	0.947	16.325	0.268	0.268	0.000	0.000	0.000	0.000
65	E	133	HIS	0	0.054	0.045	16.122	0.025	0.025	0.000	0.000	0.000	0.000
66	E	134	ALA	0	0.045	0.009	13.406	-0.076	-0.076	0.000	0.000	0.000	0.000
67	E	135	LEU	0	-0.015	0.002	9.934	0.031	0.031	0.000	0.000	0.000	0.000
68	E	136	TYR	0	0.011	0.005	12.948	0.026	0.026	0.000	0.000	0.000	0.000
69	E	137	LEU	0	-0.007	0.005	16.362	0.021	0.021	0.000	0.000	0.000	0.000
70	E	138	ILE	0	-0.039	-0.015	13.099	0.012	0.012	0.000	0.000	0.000	0.000
71	E	139	ILE	0	-0.006	0.011	16.864	0.019	0.019	0.000	0.000	0.000	0.000
72	E	140	ARG	1	0.886	0.937	18.919	0.082	0.082	0.000	0.000	0.000	0.000
73	E	141	MET	0	0.056	0.050	14.120	-0.014	-0.014	0.000	0.000	0.000	0.000
74	E	142	VAL	0	-0.053	-0.019	18.122	0.020	0.020	0.000	0.000	0.000	0.000
75	E	143	CYS	0	-0.023	0.004	18.525	-0.006	-0.006	0.000	0.000	0.000	0.000
76	E	144	TYR	0	-0.011	-0.006	20.467	0.012	0.012	0.000	0.000	0.000	0.000
77	E	145	ASP	-1	-0.834	-0.918	23.905	-0.070	-0.070	0.000	0.000	0.000	0.000
78	E	146	ASP	-1	-0.839	-0.933	26.716	-0.073	-0.073	0.000	0.000	0.000	0.000
79	E	147	GLY	0	-0.031	-0.009	28.699	0.002	0.002	0.000	0.000	0.000	0.000
80	E	148	LEU	0	-0.079	-0.032	31.900	0.005	0.005	0.000	0.000	0.000	0.000
81	E	149	GLY	0	0.052	0.012	32.353	0.005	0.005	0.000	0.000	0.000	0.000
82	E	150	ALA	0	-0.082	-0.035	31.028	0.001	0.001	0.000	0.000	0.000	0.000
83	E	151	GLY	0	0.026	0.024	28.756	-0.002	-0.002	0.000	0.000	0.000	0.000
84	E	152	LYS	1	0.865	0.949	25.511	0.097	0.097	0.000	0.000	0.000	0.000
85	E	153	SER	0	-0.037	-0.015	22.174	0.000	0.000	0.000	0.000	0.000	0.000
86	E	154	LEU	0	0.036	0.021	23.772	-0.012	-0.012	0.000	0.000	0.000	0.000
87	E	155	LEU	0	0.012	-0.011	16.283	0.003	0.003	0.000	0.000	0.000	0.000
88	E	156	ALA	0	0.015	0.022	20.683	-0.012	-0.012	0.000	0.000	0.000	0.000
89	E	157	LEU	0	0.008	-0.008	16.149	-0.011	-0.011	0.000	0.000	0.000	0.000
90	E	158	LYS	1	0.936	0.965	19.949	0.089	0.089	0.000	0.000	0.000	0.000
91	E	159	THR	0	0.047	0.017	18.430	-0.010	-0.010	0.000	0.000	0.000	0.000
92	E	160	THR	0	-0.015	0.007	21.271	0.014	0.014	0.000	0.000	0.000	0.000
93	E	161	ASP	-1	-0.879	-0.948	22.768	-0.147	-0.147	0.000	0.000	0.000	0.000
94	E	162	ALA	0	0.029	0.011	24.463	0.002	0.002	0.000	0.000	0.000	0.000
95	E	163	SER	0	0.008	0.002	24.820	0.004	0.004	0.000	0.000	0.000	0.000
96	E	164	ASN	0	-0.111	-0.065	26.895	0.001	0.001	0.000	0.000	0.000	0.000
97	E	165	GLU	-1	-0.932	-0.959	29.709	-0.055	-0.055	0.000	0.000	0.000	0.000
98	E	166	GLU	-1	-0.948	-0.968	29.258	-0.072	-0.072	0.000	0.000	0.000	0.000
99	E	167	TYR	0	-0.085	-0.053	24.588	-0.008	-0.008	0.000	0.000	0.000	0.000
100	E	168	SER	0	0.024	0.010	24.524	0.004	0.004	0.000	0.000	0.000	0.000
101	E	169	LEU	0	-0.056	-0.033	23.326	-0.010	-0.010	0.000	0.000	0.000	0.000
102	E	170	TRP	0	0.023	0.005	20.821	0.004	0.004	0.000	0.000	0.000	0.000
103	E	171	VAL	0	0.018	0.014	21.708	-0.010	-0.010	0.000	0.000	0.000	0.000
104	E	172	TYR	0	0.012	-0.007	18.772	-0.006	-0.006	0.000	0.000	0.000	0.000
105	E	173	GLN	0	0.008	0.004	22.014	0.014	0.014	0.000	0.000	0.000	0.000
106	E	174	CYS	0	-0.009	-0.002	19.184	-0.027	-0.027	0.000	0.000	0.000	0.000
107	E	175	ASN	0	-0.024	-0.026	20.439	0.003	0.003	0.000	0.000	0.000	0.000
108	E	176	SER	0	0.068	0.034	21.256	0.009	0.009	0.000	0.000	0.000	0.000
109	E	177	LEU	0	0.122	0.053	20.875	-0.015	-0.015	0.000	0.000	0.000	0.000
110	E	178	GLU	-1	-0.900	-0.957	19.375	-0.056	-0.056	0.000	0.000	0.000	0.000
111	E	179	GLN	0	-0.084	-0.045	16.619	-0.002	-0.002	0.000	0.000	0.000	0.000
112	E	180	ALA	0	0.065	0.021	16.062	-0.037	-0.037	0.000	0.000	0.000	0.000
113	E	181	GLN	0	0.006	-0.020	16.022	-0.019	-0.019	0.000	0.000	0.000	0.000
114	E	182	ALA	0	-0.027	-0.014	12.683	-0.002	-0.002	0.000	0.000	0.000	0.000
115	E	183	ILE	0	0.015	0.013	11.114	-0.051	-0.051	0.000	0.000	0.000	0.000
116	E	184	CYS	0	-0.021	-0.019	11.121	-0.061	-0.061	0.000	0.000	0.000	0.000
117	E	185	LYS	1	0.918	0.968	10.756	0.016	0.016	0.000	0.000	0.000	0.000
118	E	186	VAL	0	0.027	0.009	5.219	0.062	0.062	0.000	0.000	0.000	0.000
119	E	187	LEU	0	0.009	-0.002	6.614	-0.152	-0.152	0.000	0.000	0.000	0.000
120	E	188	SER	0	-0.011	-0.015	9.200	0.033	0.033	0.000	0.000	0.000	0.000
121	E	189	THR	0	0.004	0.017	3.950	0.063	0.170	0.002	-0.032	-0.076	0.000
122	E	190	ALA	0	-0.057	-0.025	6.174	0.183	0.183	0.000	0.000	0.000	0.000
123	E	191	PHE	0	-0.020	-0.024	6.860	0.096	0.096	0.000	0.000	0.000	0.000
124	E	192	ASP	-1	-0.915	-0.932	8.735	0.210	0.210	0.000	0.000	0.000	0.000
125	E	193	SER	0	-0.102	-0.044	5.659	0.315	0.315	0.000	0.000	0.000	0.000
126	E	194	VAL	0	-0.075	-0.040	7.557	0.036	0.036	0.000	0.000	0.000	0.000
127	E	195	NME	0	0.022	0.029	10.903	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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