FMO DATABASE

FMODB ID: 82Y1Y

Calculation Name: 4DX9-E-Xray372

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: 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	123
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1014467.798625
FMO2-HF: Nuclear repulsion	965831.534754
FMO2-HF: Total energy	-48636.263871
FMO2-MP2: Total energy	-48775.988792

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:60:CYM)

Summations of interaction energy for fragment #1(E:60:CYM)

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.
12.315	8.953	22.054	-9.998	-8.695	0.06

Interaction energy analysis for fragmet #1(E:60:CYM)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.895 / q_NPA : -0.913

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	62	GLU	-1	-0.918	-0.953	3.832	35.026	37.002	-0.021	-1.039	-0.916	0.002
4	E	63	PHE	0	-0.021	-0.013	6.460	-2.707	-2.707	0.000	0.000	0.000	0.000
5	E	64	ARG	1	0.958	0.996	10.073	-16.654	-16.654	0.000	0.000	0.000	0.000
6	E	65	ILE	0	-0.048	-0.030	13.195	-0.578	-0.578	0.000	0.000	0.000	0.000
7	E	66	LYS	1	0.872	0.953	15.536	-13.401	-13.401	0.000	0.000	0.000	0.000
8	E	67	TYR	0	-0.008	-0.019	17.748	0.606	0.606	0.000	0.000	0.000	0.000
9	E	68	VAL	0	-0.016	0.001	20.238	-0.580	-0.580	0.000	0.000	0.000	0.000
10	E	69	GLY	0	0.036	0.005	22.492	-0.620	-0.620	0.000	0.000	0.000	0.000
11	E	70	ALA	0	0.004	0.008	21.657	0.510	0.510	0.000	0.000	0.000	0.000
12	E	71	ILE	0	0.006	0.028	23.518	-0.528	-0.528	0.000	0.000	0.000	0.000
13	E	84	GLY	0	0.046	0.009	26.517	0.153	0.153	0.000	0.000	0.000	0.000
14	E	85	PRO	0	-0.028	-0.033	22.169	-0.032	-0.032	0.000	0.000	0.000	0.000
15	E	86	LEU	0	0.061	0.018	24.088	0.185	0.185	0.000	0.000	0.000	0.000
16	E	87	ASP	-1	-0.876	-0.933	26.966	10.171	10.171	0.000	0.000	0.000	0.000
17	E	88	LEU	0	-0.085	-0.043	21.745	-0.015	-0.015	0.000	0.000	0.000	0.000
18	E	89	ILE	0	-0.013	0.010	24.481	0.079	0.079	0.000	0.000	0.000	0.000
19	E	90	ASN	0	0.057	0.025	26.469	0.003	0.003	0.000	0.000	0.000	0.000
20	E	91	TYR	0	-0.061	-0.021	26.510	-0.357	-0.357	0.000	0.000	0.000	0.000
21	E	92	ILE	0	-0.036	-0.024	23.380	-0.031	-0.031	0.000	0.000	0.000	0.000
22	E	93	ASP	-1	-0.839	-0.932	27.649	10.423	10.423	0.000	0.000	0.000	0.000
23	E	94	VAL	0	-0.064	-0.013	30.519	-0.315	-0.315	0.000	0.000	0.000	0.000
24	E	95	ALA	0	0.003	-0.004	29.537	-0.174	-0.174	0.000	0.000	0.000	0.000
25	E	96	GLN	0	-0.011	-0.021	26.853	-0.249	-0.249	0.000	0.000	0.000	0.000
26	E	97	GLN	0	-0.058	-0.015	31.519	-0.270	-0.270	0.000	0.000	0.000	0.000
27	E	98	ASP	-1	-0.927	-0.958	34.882	8.518	8.518	0.000	0.000	0.000	0.000
28	E	99	GLY	0	0.000	-0.001	34.437	-0.234	-0.234	0.000	0.000	0.000	0.000
29	E	100	LYS	1	0.846	0.935	30.408	-10.048	-10.048	0.000	0.000	0.000	0.000
30	E	101	LEU	0	-0.025	-0.017	25.716	0.354	0.354	0.000	0.000	0.000	0.000
31	E	102	PRO	0	-0.002	0.020	27.176	-0.320	-0.320	0.000	0.000	0.000	0.000
32	E	103	PHE	0	0.047	0.005	28.142	0.311	0.311	0.000	0.000	0.000	0.000
33	E	104	VAL	0	-0.033	-0.015	27.950	0.256	0.256	0.000	0.000	0.000	0.000
34	E	105	PRO	0	-0.021	-0.014	23.392	-0.071	-0.071	0.000	0.000	0.000	0.000
35	E	106	PRO	0	0.011	-0.001	24.569	-0.221	-0.221	0.000	0.000	0.000	0.000
36	E	107	GLU	-1	-0.897	-0.967	24.034	12.206	12.206	0.000	0.000	0.000	0.000
37	E	108	GLU	-1	-0.921	-0.950	20.459	14.039	14.039	0.000	0.000	0.000	0.000
38	E	109	GLU	-1	-0.948	-0.978	17.801	15.083	15.083	0.000	0.000	0.000	0.000
39	E	110	PHE	0	-0.035	-0.028	14.986	0.207	0.207	0.000	0.000	0.000	0.000
40	E	111	ILE	0	0.029	0.016	9.342	-0.130	-0.130	0.000	0.000	0.000	0.000
41	E	112	MET	0	-0.046	-0.027	9.351	0.278	0.278	0.000	0.000	0.000	0.000
42	E	113	GLY	0	0.011	0.007	6.003	0.795	0.795	0.000	0.000	0.000	0.000
43	E	114	VAL	0	-0.044	-0.040	4.311	-3.712	-3.375	-0.001	-0.109	-0.227	0.000
44	E	115	SER	0	0.049	-0.021	2.192	-7.027	-13.051	22.064	-9.125	-6.916	0.051
45	E	116	LYS	1	0.875	0.922	3.769	-65.983	-65.760	0.012	0.301	-0.536	0.007
46	E	117	TYR	0	0.017	0.046	6.380	-5.762	-5.762	0.000	0.000	0.000	0.000
47	E	118	GLY	0	0.042	0.007	7.971	-3.527	-3.527	0.000	0.000	0.000	0.000
48	E	119	ILE	0	-0.031	-0.009	6.936	5.956	5.956	0.000	0.000	0.000	0.000
49	E	120	LYS	1	0.875	0.945	8.276	-30.272	-30.272	0.000	0.000	0.000	0.000
50	E	121	VAL	0	0.042	0.042	9.743	0.410	0.410	0.000	0.000	0.000	0.000
51	E	122	SER	0	0.001	-0.016	12.057	-0.677	-0.677	0.000	0.000	0.000	0.000
52	E	123	THR	0	0.050	0.035	13.917	0.192	0.192	0.000	0.000	0.000	0.000
53	E	124	SER	0	0.061	0.020	15.919	0.075	0.075	0.000	0.000	0.000	0.000
54	E	125	ASP	-1	-0.922	-0.953	13.172	19.527	19.527	0.000	0.000	0.000	0.000
55	E	126	GLN	0	-0.082	-0.036	13.393	-0.239	-0.239	0.000	0.000	0.000	0.000
56	E	127	TYR	0	-0.029	-0.021	12.477	2.016	2.016	0.000	0.000	0.000	0.000
57	E	128	ASP	-1	-0.881	-0.940	13.978	17.514	17.514	0.000	0.000	0.000	0.000
58	E	129	VAL	0	-0.098	-0.052	13.175	1.985	1.985	0.000	0.000	0.000	0.000
59	E	130	LEU	0	-0.013	0.003	14.872	-1.226	-1.226	0.000	0.000	0.000	0.000
60	E	131	HIS	0	0.018	0.019	14.930	-0.606	-0.606	0.000	0.000	0.000	0.000
61	E	132	ARG	1	0.940	0.950	12.041	-22.277	-22.277	0.000	0.000	0.000	0.000
62	E	133	HIS	0	0.034	0.035	12.688	-0.949	-0.949	0.000	0.000	0.000	0.000
63	E	134	ALA	0	0.003	-0.011	10.908	3.040	3.040	0.000	0.000	0.000	0.000
64	E	135	LEU	0	-0.003	-0.021	9.523	-2.158	-2.158	0.000	0.000	0.000	0.000
65	E	136	TYR	0	0.005	-0.004	11.628	-0.748	-0.748	0.000	0.000	0.000	0.000
66	E	137	LEU	0	-0.017	-0.003	14.862	-1.154	-1.154	0.000	0.000	0.000	0.000
67	E	138	ILE	0	-0.036	-0.013	10.913	-1.147	-1.147	0.000	0.000	0.000	0.000
68	E	139	ILE	0	-0.001	0.014	15.004	-0.210	-0.210	0.000	0.000	0.000	0.000
69	E	140	ARG	1	0.888	0.934	17.632	-13.701	-13.701	0.000	0.000	0.000	0.000
70	E	141	MET	0	0.054	0.049	11.362	0.351	0.351	0.000	0.000	0.000	0.000
71	E	142	VAL	0	-0.054	-0.019	16.298	-0.379	-0.379	0.000	0.000	0.000	0.000
72	E	143	CYS	0	-0.022	0.004	16.678	-0.109	-0.109	0.000	0.000	0.000	0.000
73	E	144	TYR	0	-0.010	-0.006	18.576	-0.192	-0.192	0.000	0.000	0.000	0.000
74	E	145	ASP	-1	-0.836	-0.918	22.042	11.501	11.501	0.000	0.000	0.000	0.000
75	E	146	ASP	-1	-0.836	-0.932	24.661	11.114	11.114	0.000	0.000	0.000	0.000
76	E	147	GLY	0	-0.035	-0.011	26.150	-0.273	-0.273	0.000	0.000	0.000	0.000
77	E	148	LEU	0	-0.079	-0.033	28.977	-0.421	-0.421	0.000	0.000	0.000	0.000
78	E	149	GLY	0	0.048	0.011	29.815	-0.361	-0.361	0.000	0.000	0.000	0.000
79	E	150	ALA	0	-0.081	-0.035	28.124	0.013	0.013	0.000	0.000	0.000	0.000
80	E	151	GLY	0	0.025	0.023	26.430	0.126	0.126	0.000	0.000	0.000	0.000
81	E	152	LYS	1	0.867	0.950	22.210	-12.253	-12.253	0.000	0.000	0.000	0.000
82	E	153	SER	0	-0.035	-0.013	19.562	0.127	0.127	0.000	0.000	0.000	0.000
83	E	154	LEU	0	0.031	0.019	20.804	0.295	0.295	0.000	0.000	0.000	0.000
84	E	155	LEU	0	0.015	-0.009	13.238	0.122	0.122	0.000	0.000	0.000	0.000
85	E	156	ALA	0	0.017	0.023	17.605	0.269	0.269	0.000	0.000	0.000	0.000
86	E	157	LEU	0	0.010	-0.006	13.555	0.790	0.790	0.000	0.000	0.000	0.000
87	E	158	LYS	1	0.936	0.966	17.267	-13.388	-13.388	0.000	0.000	0.000	0.000
88	E	159	THR	0	-0.007	-0.008	15.935	0.784	0.784	0.000	0.000	0.000	0.000
89	E	160	THR	0	0.022	0.015	18.901	-0.798	-0.798	0.000	0.000	0.000	0.000
90	E	161	ASP	-1	-0.698	-0.838	21.622	13.201	13.201	0.000	0.000	0.000	0.000
91	E	162	ALA	0	-0.094	-0.055	21.410	0.482	0.482	0.000	0.000	0.000	0.000
92	E	163	SER	0	-0.155	-0.086	22.535	-0.299	-0.299	0.000	0.000	0.000	0.000
93	E	164	ASN	0	-0.026	-0.013	26.247	-0.462	-0.462	0.000	0.000	0.000	0.000
94	E	165	GLU	-1	-0.957	-0.983	26.287	10.865	10.865	0.000	0.000	0.000	0.000
95	E	166	GLU	-1	-0.927	-0.956	27.190	10.849	10.849	0.000	0.000	0.000	0.000
96	E	167	TYR	0	-0.057	-0.033	22.733	0.793	0.793	0.000	0.000	0.000	0.000
97	E	168	SER	0	-0.019	-0.006	21.450	-0.511	-0.511	0.000	0.000	0.000	0.000
98	E	169	LEU	0	-0.046	-0.026	20.698	0.730	0.730	0.000	0.000	0.000	0.000
99	E	170	TRP	0	0.013	0.000	17.450	-0.563	-0.563	0.000	0.000	0.000	0.000
100	E	171	VAL	0	0.022	0.015	18.495	0.602	0.602	0.000	0.000	0.000	0.000
101	E	172	TYR	0	0.013	-0.007	15.295	0.066	0.066	0.000	0.000	0.000	0.000
102	E	173	GLN	0	0.007	0.003	18.454	-0.609	-0.609	0.000	0.000	0.000	0.000
103	E	174	CYS	0	-0.005	0.000	16.103	1.161	1.161	0.000	0.000	0.000	0.000
104	E	175	ASN	0	-0.019	-0.025	17.572	-0.252	-0.252	0.000	0.000	0.000	0.000
105	E	176	SER	0	0.064	0.032	18.915	-0.364	-0.364	0.000	0.000	0.000	0.000
106	E	177	LEU	0	0.119	0.053	18.600	0.715	0.715	0.000	0.000	0.000	0.000
107	E	178	GLU	-1	-0.902	-0.959	18.118	14.706	14.706	0.000	0.000	0.000	0.000
108	E	179	GLN	0	-0.084	-0.045	13.853	0.589	0.589	0.000	0.000	0.000	0.000
109	E	180	ALA	0	0.064	0.021	13.801	1.388	1.388	0.000	0.000	0.000	0.000
110	E	181	GLN	0	0.006	-0.020	14.046	1.174	1.174	0.000	0.000	0.000	0.000
111	E	182	ALA	0	-0.030	-0.016	11.372	0.985	0.985	0.000	0.000	0.000	0.000
112	E	183	ILE	0	0.023	0.017	8.915	2.258	2.258	0.000	0.000	0.000	0.000
113	E	184	CYS	0	-0.026	-0.020	9.234	1.668	1.668	0.000	0.000	0.000	0.000
114	E	185	LYS	1	0.911	0.963	10.768	-19.012	-19.012	0.000	0.000	0.000	0.000
115	E	186	VAL	0	0.043	0.018	4.257	0.171	0.297	0.000	-0.026	-0.100	0.000
116	E	187	LEU	0	0.006	-0.001	6.441	3.988	3.988	0.000	0.000	0.000	0.000
117	E	188	SER	0	-0.014	-0.019	8.221	-0.336	-0.336	0.000	0.000	0.000	0.000
118	E	189	THR	0	0.013	0.022	6.097	-0.847	-0.847	0.000	0.000	0.000	0.000
119	E	190	ALA	0	-0.038	-0.018	6.069	1.096	1.096	0.000	0.000	0.000	0.000
120	E	191	PHE	0	-0.036	-0.033	7.740	-1.379	-1.379	0.000	0.000	0.000	0.000
121	E	192	ASP	-1	-0.918	-0.933	10.603	20.358	20.358	0.000	0.000	0.000	0.000
122	E	193	SER	0	-0.070	-0.018	7.665	2.578	2.578	0.000	0.000	0.000	0.000
123	E	194	VAL	0	-0.052	-0.017	9.693	-1.800	-1.800	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:60:CYM)