FMO DATABASE

FMODB ID: LJK59

Calculation Name: 4DX9-3-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: 3

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	OptHSide
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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-964551.527849
FMO2-HF: Nuclear repulsion	917201.765299
FMO2-HF: Total energy	-47349.76255
FMO2-MP2: Total energy	-47485.470249

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(3:60:CYS)

Summations of interaction energy for fragment #1(3:60: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.
-14.062	-9.522	6.983	-5.457	-6.066	-0.042

Interaction energy analysis for fragmet #1(3:60:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.064 / q_NPA : -0.025

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	3	62	GLU	-1	-0.847	-0.921	3.819	-0.957	1.533	-0.029	-1.188	-1.273	0.005
4	3	63	PHE	0	-0.024	-0.015	5.975	-0.197	-0.197	0.000	0.000	0.000	0.000
5	3	64	ARG	1	0.843	0.904	9.976	0.445	0.445	0.000	0.000	0.000	0.000
6	3	65	ILE	0	-0.015	-0.014	12.334	-0.035	-0.035	0.000	0.000	0.000	0.000
7	3	66	LYS	1	0.891	0.963	15.138	0.235	0.235	0.000	0.000	0.000	0.000
8	3	67	TYR	0	0.015	-0.006	17.138	-0.016	-0.016	0.000	0.000	0.000	0.000
9	3	68	VAL	0	0.001	0.007	19.397	0.015	0.015	0.000	0.000	0.000	0.000
10	3	69	GLY	0	0.019	0.004	21.358	0.018	0.018	0.000	0.000	0.000	0.000
11	3	70	ALA	0	-0.021	-0.017	21.210	-0.014	-0.014	0.000	0.000	0.000	0.000
12	3	71	ILE	0	-0.026	-0.006	23.181	0.011	0.011	0.000	0.000	0.000	0.000
13	3	72	GLU	-1	-0.896	-0.947	25.632	-0.020	-0.020	0.000	0.000	0.000	0.000
14	3	85	PRO	0	0.021	-0.002	21.190	0.002	0.002	0.000	0.000	0.000	0.000
15	3	86	LEU	0	0.050	0.002	22.728	-0.010	-0.010	0.000	0.000	0.000	0.000
16	3	87	ASP	-1	-0.891	-0.941	25.606	-0.069	-0.069	0.000	0.000	0.000	0.000
17	3	88	LEU	0	-0.055	-0.029	20.270	0.008	0.008	0.000	0.000	0.000	0.000
18	3	89	ILE	0	-0.038	-0.013	22.793	-0.011	-0.011	0.000	0.000	0.000	0.000
19	3	90	ASN	0	0.012	-0.001	25.193	0.000	0.000	0.000	0.000	0.000	0.000
20	3	91	TYR	0	0.008	-0.003	27.532	0.006	0.006	0.000	0.000	0.000	0.000
21	3	92	ILE	0	-0.023	0.006	22.639	0.005	0.005	0.000	0.000	0.000	0.000
22	3	93	ASP	-1	-0.796	-0.881	26.642	-0.129	-0.129	0.000	0.000	0.000	0.000
23	3	94	VAL	0	-0.017	-0.013	28.936	0.004	0.004	0.000	0.000	0.000	0.000
24	3	95	ALA	0	0.036	0.025	29.283	0.004	0.004	0.000	0.000	0.000	0.000
25	3	96	GLN	0	-0.026	-0.029	25.831	0.004	0.004	0.000	0.000	0.000	0.000
26	3	97	GLN	0	-0.023	-0.013	30.878	0.004	0.004	0.000	0.000	0.000	0.000
27	3	98	ASP	-1	-0.908	-0.934	34.038	-0.046	-0.046	0.000	0.000	0.000	0.000
28	3	99	GLY	0	-0.056	-0.027	34.018	0.005	0.005	0.000	0.000	0.000	0.000
29	3	100	LYS	1	0.801	0.912	30.315	0.050	0.050	0.000	0.000	0.000	0.000
30	3	101	LEU	0	-0.015	0.005	24.663	0.001	0.001	0.000	0.000	0.000	0.000
31	3	102	PRO	0	0.004	0.006	27.415	-0.001	-0.001	0.000	0.000	0.000	0.000
32	3	103	PHE	0	0.032	0.004	27.151	-0.007	-0.007	0.000	0.000	0.000	0.000
33	3	104	VAL	0	-0.054	-0.022	26.280	-0.016	-0.016	0.000	0.000	0.000	0.000
34	3	105	PRO	0	-0.017	0.004	22.064	0.012	0.012	0.000	0.000	0.000	0.000
35	3	106	PRO	0	0.032	0.006	23.381	-0.002	-0.002	0.000	0.000	0.000	0.000
36	3	107	GLU	-1	-0.978	-0.992	23.172	-0.133	-0.133	0.000	0.000	0.000	0.000
37	3	108	GLU	-1	-0.905	-0.951	21.430	-0.094	-0.094	0.000	0.000	0.000	0.000
38	3	109	GLU	-1	-0.818	-0.879	17.540	-0.283	-0.283	0.000	0.000	0.000	0.000
39	3	110	PHE	0	0.041	0.027	14.853	0.025	0.025	0.000	0.000	0.000	0.000
40	3	111	ILE	0	-0.014	0.001	9.398	-0.069	-0.069	0.000	0.000	0.000	0.000
41	3	112	MET	0	-0.018	-0.006	9.072	0.040	0.040	0.000	0.000	0.000	0.000
42	3	113	GLY	0	0.016	0.009	5.473	-0.151	-0.151	0.000	0.000	0.000	0.000
43	3	114	VAL	0	-0.013	-0.009	2.819	-0.653	0.169	0.160	-0.330	-0.652	0.000
44	3	115	SER	0	-0.042	-0.046	2.070	-7.612	-7.217	6.541	-3.667	-3.269	-0.045
45	3	116	LYS	1	1.002	0.979	3.768	-4.456	-4.178	0.001	-0.038	-0.241	0.000
46	3	117	TYR	0	-0.010	0.007	6.843	-0.151	-0.151	0.000	0.000	0.000	0.000
47	3	118	GLY	0	0.089	0.027	8.044	-0.048	-0.048	0.000	0.000	0.000	0.000
48	3	119	ILE	0	0.019	0.031	7.524	-0.136	-0.136	0.000	0.000	0.000	0.000
49	3	120	LYS	1	0.831	0.926	6.096	-0.062	-0.062	0.000	0.000	0.000	0.000
50	3	121	VAL	0	0.027	0.023	8.350	-0.107	-0.107	0.000	0.000	0.000	0.000
51	3	122	SER	0	-0.009	-0.009	10.820	0.093	0.093	0.000	0.000	0.000	0.000
52	3	123	THR	0	0.041	-0.014	12.838	-0.059	-0.059	0.000	0.000	0.000	0.000
53	3	124	SER	0	-0.021	-0.017	15.314	0.020	0.020	0.000	0.000	0.000	0.000
54	3	125	ASP	-1	-0.898	-0.949	16.723	-0.001	-0.001	0.000	0.000	0.000	0.000
55	3	126	GLN	0	-0.061	-0.021	11.168	0.043	0.043	0.000	0.000	0.000	0.000
56	3	127	TYR	0	-0.119	-0.073	13.981	0.072	0.072	0.000	0.000	0.000	0.000
57	3	128	ASP	-1	-0.818	-0.881	16.551	0.045	0.045	0.000	0.000	0.000	0.000
58	3	129	VAL	0	-0.087	-0.048	13.219	0.003	0.003	0.000	0.000	0.000	0.000
59	3	130	LEU	0	0.017	0.025	15.599	-0.003	-0.003	0.000	0.000	0.000	0.000
60	3	131	HIS	0	0.052	0.026	15.449	0.000	0.000	0.000	0.000	0.000	0.000
61	3	132	ARG	1	0.870	0.928	7.977	-0.238	-0.238	0.000	0.000	0.000	0.000
62	3	133	HIS	0	0.048	0.026	13.075	0.046	0.046	0.000	0.000	0.000	0.000
63	3	134	ALA	0	-0.057	-0.048	11.749	-0.020	-0.020	0.000	0.000	0.000	0.000
64	3	135	LEU	0	0.082	0.070	12.261	-0.016	-0.016	0.000	0.000	0.000	0.000
65	3	136	TYR	0	-0.150	-0.088	15.079	0.030	0.030	0.000	0.000	0.000	0.000
66	3	137	LEU	0	-0.004	0.010	17.539	-0.030	-0.030	0.000	0.000	0.000	0.000
67	3	138	ILE	0	-0.004	0.004	17.427	0.012	0.012	0.000	0.000	0.000	0.000
68	3	139	ILE	0	0.039	0.018	13.394	-0.011	-0.011	0.000	0.000	0.000	0.000
69	3	140	ARG	1	0.871	0.934	15.476	0.098	0.098	0.000	0.000	0.000	0.000
70	3	141	MET	0	0.032	0.034	10.848	-0.027	-0.027	0.000	0.000	0.000	0.000
71	3	142	VAL	0	-0.061	-0.036	15.921	0.007	0.007	0.000	0.000	0.000	0.000
72	3	143	CYS	0	-0.054	-0.020	14.616	-0.008	-0.008	0.000	0.000	0.000	0.000
73	3	144	TYR	0	-0.033	-0.039	17.775	-0.011	-0.011	0.000	0.000	0.000	0.000
74	3	145	ASP	-1	-0.899	-0.970	20.926	-0.250	-0.250	0.000	0.000	0.000	0.000
75	3	146	ASP	-1	-0.855	-0.941	23.176	-0.187	-0.187	0.000	0.000	0.000	0.000
76	3	147	GLY	0	0.025	0.032	25.677	0.016	0.016	0.000	0.000	0.000	0.000
77	3	148	LEU	0	-0.025	-0.015	26.400	0.016	0.016	0.000	0.000	0.000	0.000
78	3	149	GLY	0	-0.022	-0.012	28.952	-0.001	-0.001	0.000	0.000	0.000	0.000
79	3	150	ALA	0	-0.079	-0.052	25.600	-0.005	-0.005	0.000	0.000	0.000	0.000
80	3	151	GLY	0	0.028	0.034	24.745	-0.014	-0.014	0.000	0.000	0.000	0.000
81	3	152	LYS	1	0.809	0.906	21.653	0.230	0.230	0.000	0.000	0.000	0.000
82	3	153	SER	0	0.047	0.016	17.778	0.003	0.003	0.000	0.000	0.000	0.000
83	3	154	LEU	0	0.021	0.009	19.629	-0.011	-0.011	0.000	0.000	0.000	0.000
84	3	155	LEU	0	-0.057	-0.040	12.844	-0.010	-0.010	0.000	0.000	0.000	0.000
85	3	156	ALA	0	0.039	0.035	16.930	0.027	0.027	0.000	0.000	0.000	0.000
86	3	157	LEU	0	-0.038	-0.036	12.470	-0.020	-0.020	0.000	0.000	0.000	0.000
87	3	158	LYS	1	0.885	0.966	17.139	0.042	0.042	0.000	0.000	0.000	0.000
88	3	159	THR	0	0.039	0.016	16.942	0.001	0.001	0.000	0.000	0.000	0.000
89	3	160	THR	0	-0.029	-0.032	19.603	-0.001	-0.001	0.000	0.000	0.000	0.000
90	3	161	ASP	-1	-0.816	-0.904	21.084	0.060	0.060	0.000	0.000	0.000	0.000
91	3	162	ALA	0	-0.010	-0.011	23.580	0.013	0.013	0.000	0.000	0.000	0.000
92	3	163	SER	0	-0.003	-0.006	25.104	-0.007	-0.007	0.000	0.000	0.000	0.000
93	3	164	ASN	0	-0.083	-0.040	27.100	0.002	0.002	0.000	0.000	0.000	0.000
94	3	165	GLU	-1	-0.926	-0.950	27.562	-0.006	-0.006	0.000	0.000	0.000	0.000
95	3	166	GLU	-1	-0.888	-0.971	22.368	0.028	0.028	0.000	0.000	0.000	0.000
96	3	167	TYR	0	-0.051	-0.005	23.906	-0.014	-0.014	0.000	0.000	0.000	0.000
97	3	168	SER	0	0.038	0.025	21.465	-0.003	-0.003	0.000	0.000	0.000	0.000
98	3	169	LEU	0	-0.019	-0.014	21.830	-0.007	-0.007	0.000	0.000	0.000	0.000
99	3	170	TRP	0	-0.063	-0.036	17.921	-0.008	-0.008	0.000	0.000	0.000	0.000
100	3	171	VAL	0	0.039	0.011	19.657	-0.018	-0.018	0.000	0.000	0.000	0.000
101	3	172	TYR	0	-0.009	-0.020	15.861	-0.003	-0.003	0.000	0.000	0.000	0.000
102	3	173	GLN	0	0.027	0.031	18.007	-0.007	-0.007	0.000	0.000	0.000	0.000
103	3	174	CYS	0	-0.031	-0.009	14.961	-0.061	-0.061	0.000	0.000	0.000	0.000
104	3	175	ASN	0	0.040	0.010	17.492	0.070	0.070	0.000	0.000	0.000	0.000
105	3	176	SER	0	0.070	0.025	18.011	0.027	0.027	0.000	0.000	0.000	0.000
106	3	177	LEU	0	0.090	0.050	17.213	-0.062	-0.062	0.000	0.000	0.000	0.000
107	3	178	GLU	-1	-0.838	-0.917	16.215	-0.482	-0.482	0.000	0.000	0.000	0.000
108	3	179	GLN	0	-0.032	-0.021	12.784	-0.034	-0.034	0.000	0.000	0.000	0.000
109	3	180	ALA	0	0.044	0.015	12.056	-0.146	-0.146	0.000	0.000	0.000	0.000
110	3	181	GLN	0	-0.034	-0.030	12.875	-0.037	-0.037	0.000	0.000	0.000	0.000
111	3	182	ALA	0	-0.039	-0.022	9.523	-0.028	-0.028	0.000	0.000	0.000	0.000
112	3	183	ILE	0	-0.009	0.003	8.083	-0.316	-0.316	0.000	0.000	0.000	0.000
113	3	184	CYS	0	0.011	0.002	8.252	-0.008	-0.008	0.000	0.000	0.000	0.000
114	3	185	LYS	1	0.884	0.950	8.600	0.732	0.732	0.000	0.000	0.000	0.000
115	3	186	VAL	0	-0.014	-0.006	2.672	-0.694	-0.139	0.310	-0.234	-0.631	-0.002
116	3	187	LEU	0	0.019	0.000	5.306	0.732	0.732	0.000	0.000	0.000	0.000
117	3	188	SER	0	-0.018	-0.005	7.147	0.304	0.304	0.000	0.000	0.000	0.000
118	3	189	THR	0	-0.043	-0.009	6.128	0.026	0.026	0.000	0.000	0.000	0.000
119	3	190	ALA	0	-0.075	-0.015	5.163	0.595	0.595	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(3:60:CYS)