FMO DATABASE

FMODB ID: 661JZ

Calculation Name: 4DX9-0-Xray372

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: 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	117
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-924570.808935
FMO2-HF: Nuclear repulsion	878402.13704
FMO2-HF: Total energy	-46168.671895
FMO2-MP2: Total energy	-46301.102994

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(0:60:CYS)

Summations of interaction energy for fragment #1(0:60: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.
-10.847	-6.378	6.32	-5.507	-5.28	-0.02

Interaction energy analysis for fragmet #1(0:60:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.019

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	62	GLU	-1	-0.908	-0.950	3.818	0.296	2.777	-0.012	-1.128	-1.341	0.003
4	63	PHE	0	-0.015	-0.019	6.346	-0.591	-0.576	-0.001	-0.002	-0.011	0.000
5	64	ARG	1	0.976	0.990	10.027	0.369	0.369	0.000	0.000	0.000	0.000
6	65	ILE	0	-0.056	-0.025	12.496	-0.058	-0.058	0.000	0.000	0.000	0.000
7	66	LYS	1	1.018	1.007	15.167	0.034	0.034	0.000	0.000	0.000	0.000
8	67	TYR	0	0.025	0.020	17.882	0.015	0.015	0.000	0.000	0.000	0.000
9	68	VAL	0	0.031	0.007	19.204	-0.023	-0.023	0.000	0.000	0.000	0.000
10	69	GLY	0	0.021	0.011	22.427	0.006	0.006	0.000	0.000	0.000	0.000
11	70	ALA	0	-0.037	-0.027	22.488	0.016	0.016	0.000	0.000	0.000	0.000
12	71	ILE	0	0.028	0.026	24.219	-0.009	-0.009	0.000	0.000	0.000	0.000
13	84	GLY	0	0.009	-0.013	25.691	-0.001	-0.001	0.000	0.000	0.000	0.000
14	85	PRO	0	-0.045	-0.029	22.869	0.011	0.011	0.000	0.000	0.000	0.000
15	86	LEU	0	0.102	0.023	23.791	-0.003	-0.003	0.000	0.000	0.000	0.000
16	87	ASP	-1	-0.932	-0.959	26.583	0.039	0.039	0.000	0.000	0.000	0.000
17	88	LEU	0	-0.047	-0.024	21.298	0.011	0.011	0.000	0.000	0.000	0.000
18	89	ILE	0	-0.033	0.000	23.856	0.009	0.009	0.000	0.000	0.000	0.000
19	90	ASN	0	0.049	0.026	25.878	0.002	0.002	0.000	0.000	0.000	0.000
20	91	TYR	0	-0.055	-0.018	26.788	0.003	0.003	0.000	0.000	0.000	0.000
21	92	ILE	0	-0.019	-0.024	23.188	0.010	0.010	0.000	0.000	0.000	0.000
22	93	ASP	-1	-0.805	-0.912	27.548	0.011	0.011	0.000	0.000	0.000	0.000
23	94	VAL	0	-0.024	-0.010	30.099	-0.004	-0.004	0.000	0.000	0.000	0.000
24	95	ALA	0	-0.015	-0.004	29.004	0.002	0.002	0.000	0.000	0.000	0.000
25	96	GLN	0	-0.033	-0.032	26.991	-0.002	-0.002	0.000	0.000	0.000	0.000
26	97	GLN	0	-0.024	-0.010	31.267	-0.001	-0.001	0.000	0.000	0.000	0.000
27	98	ASP	-1	-0.927	-0.944	34.683	0.047	0.047	0.000	0.000	0.000	0.000
28	99	GLY	0	-0.019	-0.010	34.129	-0.001	-0.001	0.000	0.000	0.000	0.000
29	100	LYS	1	0.865	0.934	31.484	-0.061	-0.061	0.000	0.000	0.000	0.000
30	101	LEU	0	-0.012	0.002	25.467	0.010	0.010	0.000	0.000	0.000	0.000
31	102	PRO	0	-0.003	0.012	26.414	-0.009	-0.009	0.000	0.000	0.000	0.000
32	103	PHE	0	0.033	0.007	27.265	0.001	0.001	0.000	0.000	0.000	0.000
33	104	VAL	0	-0.022	-0.015	27.025	-0.007	-0.007	0.000	0.000	0.000	0.000
34	105	PRO	0	-0.050	-0.012	22.877	0.007	0.007	0.000	0.000	0.000	0.000
35	106	PRO	0	0.030	0.006	23.252	-0.013	-0.013	0.000	0.000	0.000	0.000
36	107	GLU	-1	-0.976	-0.990	22.842	0.000	0.000	0.000	0.000	0.000	0.000
37	108	GLU	-1	-0.952	-0.965	20.118	0.153	0.153	0.000	0.000	0.000	0.000
38	109	GLU	-1	-0.998	-0.997	17.180	-0.010	-0.010	0.000	0.000	0.000	0.000
39	110	PHE	0	-0.030	-0.022	13.526	0.048	0.048	0.000	0.000	0.000	0.000
40	111	ILE	0	-0.016	-0.014	8.568	-0.108	-0.108	0.000	0.000	0.000	0.000
41	112	MET	0	-0.039	-0.002	8.447	0.165	0.165	0.000	0.000	0.000	0.000
42	113	GLY	0	0.061	0.022	4.460	-0.296	-0.219	0.006	-0.036	-0.047	0.000
43	114	VAL	0	-0.036	-0.013	4.251	0.299	0.682	0.000	-0.102	-0.281	0.000
44	115	SER	0	0.036	-0.002	2.013	-6.381	-4.143	6.309	-5.459	-3.088	-0.022
45	116	LYS	1	0.972	0.977	3.005	-2.828	-3.760	0.015	1.268	-0.350	-0.001
46	117	TYR	0	-0.002	0.000	6.341	-0.856	-0.856	0.000	0.000	0.000	0.000
47	118	GLY	0	-0.004	-0.008	7.368	-0.547	-0.547	0.000	0.000	0.000	0.000
48	119	ILE	0	-0.016	0.006	6.939	0.509	0.509	0.000	0.000	0.000	0.000
49	120	LYS	1	0.871	0.941	7.645	-1.241	-1.241	0.000	0.000	0.000	0.000
50	121	VAL	0	0.011	0.007	8.882	0.078	0.078	0.000	0.000	0.000	0.000
51	122	SER	0	0.035	0.013	10.952	-0.003	-0.003	0.000	0.000	0.000	0.000
52	123	THR	0	0.072	0.055	12.326	0.016	0.016	0.000	0.000	0.000	0.000
53	124	SER	0	-0.038	-0.054	13.176	0.029	0.029	0.000	0.000	0.000	0.000
54	125	ASP	-1	-0.876	-0.907	15.105	0.144	0.144	0.000	0.000	0.000	0.000
55	126	GLN	0	-0.018	0.000	16.785	-0.021	-0.021	0.000	0.000	0.000	0.000
56	127	TYR	0	-0.044	-0.036	17.164	0.038	0.038	0.000	0.000	0.000	0.000
57	128	ASP	-1	-0.858	-0.921	17.133	0.290	0.290	0.000	0.000	0.000	0.000
58	129	VAL	0	-0.055	-0.039	14.051	0.072	0.072	0.000	0.000	0.000	0.000
59	130	LEU	0	-0.037	-0.003	12.778	0.142	0.142	0.000	0.000	0.000	0.000
60	131	HIS	0	0.009	-0.001	14.304	0.009	0.009	0.000	0.000	0.000	0.000
61	132	ARG	1	0.941	0.955	12.754	-0.719	-0.719	0.000	0.000	0.000	0.000
62	133	HIS	0	0.031	0.027	12.523	-0.052	-0.052	0.000	0.000	0.000	0.000
63	134	ALA	0	0.025	0.005	11.601	0.174	0.174	0.000	0.000	0.000	0.000
64	135	LEU	0	0.055	0.007	8.594	-0.102	-0.102	0.000	0.000	0.000	0.000
65	136	TYR	0	-0.021	-0.009	11.878	-0.137	-0.137	0.000	0.000	0.000	0.000
66	137	LEU	0	-0.038	-0.016	15.147	-0.077	-0.077	0.000	0.000	0.000	0.000
67	138	ILE	0	-0.027	0.012	11.063	-0.066	-0.066	0.000	0.000	0.000	0.000
68	139	ILE	0	-0.006	0.000	15.067	-0.023	-0.023	0.000	0.000	0.000	0.000
69	140	ARG	1	0.937	0.962	16.961	-0.080	-0.080	0.000	0.000	0.000	0.000
70	141	MET	0	-0.030	0.018	10.693	0.067	0.067	0.000	0.000	0.000	0.000
71	142	VAL	0	-0.006	0.003	16.018	-0.048	-0.048	0.000	0.000	0.000	0.000
72	143	CYS	0	-0.037	0.000	16.592	0.002	0.002	0.000	0.000	0.000	0.000
73	144	TYR	0	0.011	0.004	18.639	-0.021	-0.021	0.000	0.000	0.000	0.000
74	145	ASP	-1	-0.859	-0.950	22.050	-0.113	-0.113	0.000	0.000	0.000	0.000
75	146	ASP	-1	-0.932	-0.972	24.286	-0.011	-0.011	0.000	0.000	0.000	0.000
76	147	GLY	0	0.003	0.012	26.060	0.007	0.007	0.000	0.000	0.000	0.000
77	148	LEU	0	-0.044	-0.006	28.607	0.005	0.005	0.000	0.000	0.000	0.000
78	149	GLY	0	-0.003	-0.014	29.852	0.004	0.004	0.000	0.000	0.000	0.000
79	150	ALA	0	-0.058	-0.049	28.602	-0.006	-0.006	0.000	0.000	0.000	0.000
80	151	GLY	0	0.005	0.005	25.380	0.001	0.001	0.000	0.000	0.000	0.000
81	152	LYS	1	0.966	0.993	22.607	0.092	0.092	0.000	0.000	0.000	0.000
82	153	SER	0	-0.004	0.021	18.701	0.006	0.006	0.000	0.000	0.000	0.000
83	154	LEU	0	0.021	0.010	20.687	0.020	0.020	0.000	0.000	0.000	0.000
84	155	LEU	0	-0.033	-0.027	13.248	-0.003	-0.003	0.000	0.000	0.000	0.000
85	156	ALA	0	0.040	0.012	17.582	0.038	0.038	0.000	0.000	0.000	0.000
86	157	LEU	0	-0.026	-0.015	13.274	-0.020	-0.020	0.000	0.000	0.000	0.000
87	158	LYS	1	0.980	0.991	16.579	-0.140	-0.140	0.000	0.000	0.000	0.000
88	159	THR	0	-0.003	0.004	16.344	0.027	0.027	0.000	0.000	0.000	0.000
89	168	SER	0	-0.038	-0.029	22.484	0.002	0.002	0.000	0.000	0.000	0.000
90	169	LEU	0	-0.043	-0.026	20.686	0.018	0.018	0.000	0.000	0.000	0.000
91	170	TRP	0	-0.002	0.003	17.726	0.001	0.001	0.000	0.000	0.000	0.000
92	171	VAL	0	0.040	0.021	19.150	-0.017	-0.017	0.000	0.000	0.000	0.000
93	172	TYR	0	-0.004	-0.007	15.584	0.046	0.046	0.000	0.000	0.000	0.000
94	173	GLN	0	0.043	0.036	17.764	-0.038	-0.038	0.000	0.000	0.000	0.000
95	174	CYS	0	-0.015	-0.006	15.691	-0.003	-0.003	0.000	0.000	0.000	0.000
96	175	ASN	0	0.016	-0.013	16.249	-0.021	-0.021	0.000	0.000	0.000	0.000
97	176	SER	0	-0.023	-0.018	18.075	-0.012	-0.012	0.000	0.000	0.000	0.000
98	177	LEU	0	0.063	0.027	19.160	0.027	0.027	0.000	0.000	0.000	0.000
99	178	GLU	-1	-0.858	-0.942	17.229	-0.383	-0.383	0.000	0.000	0.000	0.000
100	179	GLN	0	-0.019	-0.011	13.955	-0.099	-0.099	0.000	0.000	0.000	0.000
101	180	ALA	0	0.039	0.022	12.758	-0.056	-0.056	0.000	0.000	0.000	0.000
102	181	GLN	0	0.040	0.015	13.433	-0.041	-0.041	0.000	0.000	0.000	0.000
103	182	ALA	0	-0.020	0.004	10.366	-0.075	-0.075	0.000	0.000	0.000	0.000
104	183	ILE	0	0.009	0.009	8.644	-0.284	-0.284	0.000	0.000	0.000	0.000
105	184	CYS	0	-0.019	-0.017	9.072	0.044	0.044	0.000	0.000	0.000	0.000
106	185	LYS	1	0.969	0.978	9.707	0.699	0.699	0.000	0.000	0.000	0.000
107	186	VAL	0	-0.004	-0.007	3.655	-0.243	-0.036	0.003	-0.048	-0.162	0.000
108	187	LEU	0	0.005	-0.003	5.854	0.175	0.175	0.000	0.000	0.000	0.000
109	188	SER	0	-0.038	-0.015	8.229	0.234	0.234	0.000	0.000	0.000	0.000
110	189	THR	0	0.026	0.020	5.673	0.090	0.090	0.000	0.000	0.000	0.000
111	190	ALA	0	-0.012	-0.003	5.863	0.283	0.283	0.000	0.000	0.000	0.000
112	191	PHE	0	-0.009	-0.033	7.221	0.267	0.267	0.000	0.000	0.000	0.000
113	192	ASP	-1	-0.919	-0.957	10.737	-0.100	-0.100	0.000	0.000	0.000	0.000
114	193	SER	0	-0.099	-0.034	8.743	0.032	0.032	0.000	0.000	0.000	0.000
115	194	VAL	0	-0.079	-0.040	9.635	0.037	0.037	0.000	0.000	0.000	0.000
116	195	LEU	0	-0.024	0.003	12.126	-0.010	-0.010	0.000	0.000	0.000	0.000
117	196	THR	0	-0.029	-0.001	14.575	-0.062	-0.062	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(0:60:CYS)