FMO DATABASE

FMODB ID: J3169

Calculation Name: 4DX9-y-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: y

ChEMBL ID: CHEMBL1905

UniProt ID: P05556

Base Structure: X-ray

Registration Date: 2023-06-20

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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-723137.208569
FMO2-HF: Nuclear repulsion	683088.606149
FMO2-HF: Total energy	-40048.602419
FMO2-MP2: Total energy	-40162.423619

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(y:60:CYS)

Summations of interaction energy for fragment #1(y: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.
-5.458	-0.659	4.377	-4.241	-4.937	-0.032

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.077 / q_NPA : -0.055

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	y	62	GLU	-1	-0.923	-0.962	3.815	0.815	2.602	-0.029	-0.761	-0.998	0.000
4	y	63	PHE	0	-0.012	-0.010	6.737	-0.309	-0.309	0.000	0.000	0.000	0.000
5	y	64	ARG	1	0.894	0.957	10.177	0.177	0.177	0.000	0.000	0.000	0.000
6	y	65	ILE	0	-0.005	-0.006	12.863	-0.020	-0.020	0.000	0.000	0.000	0.000
7	y	66	LYS	1	0.963	0.991	15.386	-0.082	-0.082	0.000	0.000	0.000	0.000
8	y	67	TYR	0	0.012	0.008	18.524	0.021	0.021	0.000	0.000	0.000	0.000
9	y	68	VAL	0	-0.020	-0.005	19.637	-0.028	-0.028	0.000	0.000	0.000	0.000
10	y	69	GLY	0	0.025	0.002	21.949	-0.022	-0.022	0.000	0.000	0.000	0.000
11	y	70	ALA	0	-0.012	-0.011	21.770	0.028	0.028	0.000	0.000	0.000	0.000
12	y	71	ILE	0	-0.005	0.023	23.617	-0.015	-0.015	0.000	0.000	0.000	0.000
13	y	86	LEU	0	-0.009	-0.015	24.441	0.009	0.009	0.000	0.000	0.000	0.000
14	y	87	ASP	-1	-0.867	-0.950	25.893	0.168	0.168	0.000	0.000	0.000	0.000
15	y	88	LEU	0	-0.044	-0.031	20.937	-0.003	-0.003	0.000	0.000	0.000	0.000
16	y	89	ILE	0	-0.014	-0.005	24.150	0.002	0.002	0.000	0.000	0.000	0.000
17	y	90	ASN	0	-0.054	-0.027	26.107	-0.009	-0.009	0.000	0.000	0.000	0.000
18	y	91	TYR	0	0.007	0.021	27.462	-0.010	-0.010	0.000	0.000	0.000	0.000
19	y	92	ILE	0	-0.023	0.005	23.222	-0.006	-0.006	0.000	0.000	0.000	0.000
20	y	100	LYS	1	0.969	0.958	30.765	-0.142	-0.142	0.000	0.000	0.000	0.000
21	y	101	LEU	0	0.023	0.024	24.768	0.007	0.007	0.000	0.000	0.000	0.000
22	y	102	PRO	0	-0.005	0.010	26.849	-0.011	-0.011	0.000	0.000	0.000	0.000
23	y	103	PHE	0	0.007	-0.001	27.483	0.008	0.008	0.000	0.000	0.000	0.000
24	y	104	VAL	0	-0.026	-0.016	27.235	0.003	0.003	0.000	0.000	0.000	0.000
25	y	105	PRO	0	-0.026	-0.005	22.921	0.003	0.003	0.000	0.000	0.000	0.000
26	y	106	PRO	0	0.026	0.006	24.027	-0.016	-0.016	0.000	0.000	0.000	0.000
27	y	107	GLU	-1	-0.887	-0.959	23.557	0.078	0.078	0.000	0.000	0.000	0.000
28	y	108	GLU	-1	-0.989	-0.973	21.482	0.156	0.156	0.000	0.000	0.000	0.000
29	y	109	GLU	-1	-0.912	-0.959	17.701	0.041	0.041	0.000	0.000	0.000	0.000
30	y	110	PHE	0	-0.013	-0.004	14.973	0.009	0.009	0.000	0.000	0.000	0.000
31	y	111	ILE	0	0.011	0.014	9.266	-0.038	-0.038	0.000	0.000	0.000	0.000
32	y	112	MET	0	-0.024	-0.016	9.219	0.142	0.142	0.000	0.000	0.000	0.000
33	y	113	GLY	0	0.037	0.010	5.949	-0.197	-0.197	0.000	0.000	0.000	0.000
34	y	114	VAL	0	-0.014	0.006	4.167	0.000	0.327	-0.001	-0.104	-0.223	0.000
35	y	115	SER	0	0.013	-0.019	2.294	-3.552	-1.132	4.384	-3.441	-3.363	-0.032
36	y	116	LYS	1	0.987	0.982	3.756	-1.444	-1.424	0.018	0.140	-0.178	0.000
37	y	117	TYR	0	0.024	0.014	6.656	-0.473	-0.473	0.000	0.000	0.000	0.000
38	y	118	GLY	0	0.044	0.025	7.511	-0.425	-0.425	0.000	0.000	0.000	0.000
39	y	119	ILE	0	-0.013	0.001	6.964	0.595	0.595	0.000	0.000	0.000	0.000
40	y	120	LYS	1	0.959	0.989	7.778	-1.251	-1.251	0.000	0.000	0.000	0.000
41	y	121	VAL	0	0.028	0.026	9.588	0.012	0.012	0.000	0.000	0.000	0.000
42	y	122	SER	0	-0.057	-0.022	11.342	-0.057	-0.057	0.000	0.000	0.000	0.000
43	y	123	THR	0	0.062	0.019	13.512	-0.033	-0.033	0.000	0.000	0.000	0.000
44	y	124	SER	0	-0.047	-0.024	15.330	-0.014	-0.014	0.000	0.000	0.000	0.000
45	y	134	ALA	0	0.006	-0.012	12.180	0.043	0.043	0.000	0.000	0.000	0.000
46	y	135	LEU	0	0.013	-0.027	8.305	-0.051	-0.051	0.000	0.000	0.000	0.000
47	y	136	TYR	0	-0.024	-0.009	11.821	-0.089	-0.089	0.000	0.000	0.000	0.000
48	y	137	LEU	0	-0.018	0.013	15.396	-0.052	-0.052	0.000	0.000	0.000	0.000
49	y	138	ILE	0	-0.029	-0.004	11.668	-0.045	-0.045	0.000	0.000	0.000	0.000
50	y	139	ILE	0	0.009	0.021	15.606	-0.011	-0.011	0.000	0.000	0.000	0.000
51	y	140	ARG	1	0.944	0.957	17.531	-0.301	-0.301	0.000	0.000	0.000	0.000
52	y	141	MET	0	-0.025	0.004	11.385	0.032	0.032	0.000	0.000	0.000	0.000
53	y	142	VAL	0	-0.032	-0.021	16.392	-0.032	-0.032	0.000	0.000	0.000	0.000
54	y	143	CYS	0	-0.024	0.000	16.725	0.005	0.005	0.000	0.000	0.000	0.000
55	y	144	TYR	0	0.015	0.008	18.841	-0.011	-0.011	0.000	0.000	0.000	0.000
56	y	145	ASP	-1	-0.883	-0.941	22.193	0.089	0.089	0.000	0.000	0.000	0.000
57	y	153	SER	0	0.043	0.024	19.269	-0.008	-0.008	0.000	0.000	0.000	0.000
58	y	154	LEU	0	-0.052	-0.024	20.019	0.011	0.011	0.000	0.000	0.000	0.000
59	y	155	LEU	0	-0.010	-0.031	13.095	0.006	0.006	0.000	0.000	0.000	0.000
60	y	156	ALA	0	0.009	0.015	17.768	0.007	0.007	0.000	0.000	0.000	0.000
61	y	157	LEU	0	-0.002	-0.020	12.779	0.032	0.032	0.000	0.000	0.000	0.000
62	y	158	LYS	1	0.953	0.995	17.129	-0.337	-0.337	0.000	0.000	0.000	0.000
63	y	159	THR	0	0.006	0.015	16.500	0.051	0.051	0.000	0.000	0.000	0.000
64	y	160	THR	0	-0.010	0.009	19.179	-0.044	-0.044	0.000	0.000	0.000	0.000
65	y	161	ASP	-1	-0.788	-0.873	20.916	0.414	0.414	0.000	0.000	0.000	0.000
66	y	162	ALA	0	0.052	0.024	23.276	-0.026	-0.026	0.000	0.000	0.000	0.000
67	y	163	SER	0	-0.061	-0.039	25.390	-0.007	-0.007	0.000	0.000	0.000	0.000
68	y	164	ASN	0	-0.106	-0.064	27.238	-0.008	-0.008	0.000	0.000	0.000	0.000
69	y	165	GLU	-1	-0.924	-0.951	27.124	0.237	0.237	0.000	0.000	0.000	0.000
70	y	166	GLU	-1	-0.885	-0.930	27.348	0.196	0.196	0.000	0.000	0.000	0.000
71	y	167	TYR	0	-0.096	-0.061	23.597	0.033	0.033	0.000	0.000	0.000	0.000
72	y	168	SER	0	-0.026	-0.027	21.575	-0.029	-0.029	0.000	0.000	0.000	0.000
73	y	169	LEU	0	-0.060	-0.039	21.255	0.026	0.026	0.000	0.000	0.000	0.000
74	y	170	TRP	0	-0.014	-0.035	17.514	-0.023	-0.023	0.000	0.000	0.000	0.000
75	y	171	VAL	0	0.009	0.011	18.823	0.017	0.017	0.000	0.000	0.000	0.000
76	y	172	TYR	0	0.019	-0.008	15.672	0.017	0.017	0.000	0.000	0.000	0.000
77	y	173	GLN	0	0.034	0.008	18.220	-0.020	-0.020	0.000	0.000	0.000	0.000
78	y	174	CYS	0	-0.032	0.001	15.495	0.019	0.019	0.000	0.000	0.000	0.000
79	y	175	ASN	0	-0.008	-0.006	17.732	-0.019	-0.019	0.000	0.000	0.000	0.000
80	y	176	SER	0	0.051	0.015	18.293	-0.021	-0.021	0.000	0.000	0.000	0.000
81	y	177	LEU	0	0.062	0.028	18.570	0.022	0.022	0.000	0.000	0.000	0.000
82	y	178	GLU	-1	-0.937	-0.977	17.779	0.004	0.004	0.000	0.000	0.000	0.000
83	y	179	GLN	0	-0.028	-0.006	13.423	0.036	0.036	0.000	0.000	0.000	0.000
84	y	180	ALA	0	0.044	0.007	13.176	0.052	0.052	0.000	0.000	0.000	0.000
85	y	181	GLN	0	0.020	0.003	14.100	0.062	0.062	0.000	0.000	0.000	0.000
86	y	182	ALA	0	-0.021	-0.004	10.929	0.052	0.052	0.000	0.000	0.000	0.000
87	y	183	ILE	0	0.017	0.004	8.630	0.142	0.142	0.000	0.000	0.000	0.000
88	y	184	CYS	0	-0.024	-0.016	9.439	0.251	0.251	0.000	0.000	0.000	0.000
89	y	185	LYS	1	0.960	0.995	9.726	-0.105	-0.105	0.000	0.000	0.000	0.000
90	y	186	VAL	0	0.018	0.008	4.097	-0.155	0.090	0.005	-0.075	-0.175	0.000
91	y	187	LEU	0	0.026	-0.002	6.332	0.736	0.736	0.000	0.000	0.000	0.000
92	y	188	SER	0	-0.029	-0.017	8.736	-0.104	-0.104	0.000	0.000	0.000	0.000
93	y	189	THR	0	-0.025	0.008	5.168	-0.216	-0.216	0.000	0.000	0.000	0.000
94	y	190	ALA	0	-0.028	-0.019	6.048	-0.240	-0.240	0.000	0.000	0.000	0.000
95	y	191	PHE	0	-0.029	-0.033	7.306	-0.218	-0.218	0.000	0.000	0.000	0.000
96	y	192	ASP	-1	-0.889	-0.931	10.379	0.365	0.365	0.000	0.000	0.000	0.000
97	y	193	SER	0	-0.127	-0.053	7.327	-0.152	-0.152	0.000	0.000	0.000	0.000
98	y	194	VAL	0	-0.075	-0.040	9.433	-0.108	-0.108	0.000	0.000	0.000	0.000
99	y	195	LEU	0	0.001	0.022	12.023	-0.100	-0.100	0.000	0.000	0.000	0.000

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