FMO DATABASE

FMODB ID: ZYJRN

Calculation Name: 4DX9-s-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: s

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	OptAll
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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-905049.336549
FMO2-HF: Nuclear repulsion	859490.638239
FMO2-HF: Total energy	-45558.69831
FMO2-MP2: Total energy	-45689.278949

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(s:60:CYS)

Summations of interaction energy for fragment #1(s: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.
-5.203	-3.123	6.381	-2.494	-5.967	-0.024

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : 0.000

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	s	62	GLU	-1	-0.824	-0.894	3.626	0.168	2.506	0.000	-1.021	-1.317	0.004
4	s	63	PHE	0	0.009	0.013	5.503	-0.011	-0.011	0.000	0.000	0.000	0.000
5	s	64	ARG	1	0.827	0.887	9.269	0.680	0.680	0.000	0.000	0.000	0.000
6	s	65	ILE	0	-0.022	-0.007	12.566	-0.034	-0.034	0.000	0.000	0.000	0.000
7	s	66	LYS	1	0.886	0.940	15.215	0.277	0.277	0.000	0.000	0.000	0.000
8	s	67	TYR	0	-0.060	-0.039	17.896	0.020	0.020	0.000	0.000	0.000	0.000
9	s	68	VAL	0	0.007	0.001	19.447	-0.007	-0.007	0.000	0.000	0.000	0.000
10	s	69	GLY	0	0.060	0.023	21.642	0.006	0.006	0.000	0.000	0.000	0.000
11	s	70	ALA	0	-0.042	-0.013	21.533	0.012	0.012	0.000	0.000	0.000	0.000
12	s	71	ILE	0	0.037	0.039	23.452	-0.007	-0.007	0.000	0.000	0.000	0.000
13	s	84	GLY	0	0.032	0.032	26.075	0.006	0.006	0.000	0.000	0.000	0.000
14	s	85	PRO	0	-0.017	-0.017	22.677	0.007	0.007	0.000	0.000	0.000	0.000
15	s	86	LEU	0	0.050	0.009	24.144	-0.008	-0.008	0.000	0.000	0.000	0.000
16	s	87	ASP	-1	-0.887	-0.943	27.214	0.015	0.015	0.000	0.000	0.000	0.000
17	s	88	LEU	0	0.004	-0.002	20.848	0.004	0.004	0.000	0.000	0.000	0.000
18	s	89	ILE	0	-0.003	0.004	23.702	-0.001	-0.001	0.000	0.000	0.000	0.000
19	s	90	ASN	0	0.010	-0.003	25.996	-0.007	-0.007	0.000	0.000	0.000	0.000
20	s	91	TYR	0	-0.015	-0.003	26.969	0.002	0.002	0.000	0.000	0.000	0.000
21	s	92	ILE	0	0.006	0.010	22.858	0.006	0.006	0.000	0.000	0.000	0.000
22	s	93	ASP	-1	-0.803	-0.890	27.218	-0.068	-0.068	0.000	0.000	0.000	0.000
23	s	94	VAL	0	-0.009	-0.006	30.036	0.000	0.000	0.000	0.000	0.000	0.000
24	s	95	ALA	0	-0.007	-0.005	28.933	0.002	0.002	0.000	0.000	0.000	0.000
25	s	96	GLN	0	-0.048	-0.034	27.197	0.000	0.000	0.000	0.000	0.000	0.000
26	s	97	GLN	0	-0.073	-0.033	31.377	-0.004	-0.004	0.000	0.000	0.000	0.000
27	s	98	ASP	-1	-0.899	-0.940	33.957	0.019	0.019	0.000	0.000	0.000	0.000
28	s	99	GLY	0	-0.031	-0.008	33.669	0.005	0.005	0.000	0.000	0.000	0.000
29	s	100	LYS	1	0.789	0.891	30.603	-0.031	-0.031	0.000	0.000	0.000	0.000
30	s	101	LEU	0	-0.018	0.003	25.377	0.007	0.007	0.000	0.000	0.000	0.000
31	s	102	PRO	0	0.008	0.015	26.789	-0.004	-0.004	0.000	0.000	0.000	0.000
32	s	103	PHE	0	0.033	0.005	27.711	-0.005	-0.005	0.000	0.000	0.000	0.000
33	s	104	VAL	0	-0.043	-0.018	27.188	-0.017	-0.017	0.000	0.000	0.000	0.000
34	s	105	PRO	0	-0.014	0.008	22.736	0.017	0.017	0.000	0.000	0.000	0.000
35	s	106	PRO	0	0.042	0.014	23.672	-0.006	-0.006	0.000	0.000	0.000	0.000
36	s	107	GLU	-1	-0.853	-0.899	23.749	-0.220	-0.220	0.000	0.000	0.000	0.000
37	s	108	GLU	-1	-0.954	-0.988	20.416	-0.035	-0.035	0.000	0.000	0.000	0.000
38	s	109	GLU	-1	-0.826	-0.904	17.474	-0.407	-0.407	0.000	0.000	0.000	0.000
39	s	110	PHE	0	-0.020	-0.012	14.531	0.032	0.032	0.000	0.000	0.000	0.000
40	s	111	ILE	0	-0.019	-0.019	8.471	-0.101	-0.101	0.000	0.000	0.000	0.000
41	s	112	MET	0	-0.027	0.006	8.904	0.209	0.209	0.000	0.000	0.000	0.000
42	s	113	GLY	0	0.047	0.010	5.033	-0.693	-0.693	0.000	0.000	0.000	0.000
43	s	114	VAL	0	-0.020	-0.001	4.624	0.998	1.330	-0.001	-0.092	-0.239	0.000
44	s	115	SER	0	0.013	-0.023	2.457	-1.488	-0.502	6.363	-3.666	-3.683	-0.028
45	s	116	LYS	1	0.983	0.963	3.467	-3.796	-5.527	0.018	2.313	-0.600	0.000
46	s	117	TYR	0	0.025	0.025	5.509	-0.978	-0.978	0.000	0.000	0.000	0.000
47	s	118	GLY	0	0.045	0.037	7.106	-0.548	-0.548	0.000	0.000	0.000	0.000
48	s	119	ILE	0	-0.020	0.005	6.721	0.919	0.919	0.000	0.000	0.000	0.000
49	s	120	LYS	1	0.843	0.903	5.626	-0.805	-0.805	0.000	0.000	0.000	0.000
50	s	130	LEU	0	0.038	0.014	15.585	0.026	0.026	0.000	0.000	0.000	0.000
51	s	131	HIS	1	0.859	0.918	14.568	-0.265	-0.265	0.000	0.000	0.000	0.000
52	s	132	ARG	1	0.951	0.979	11.547	-0.877	-0.877	0.000	0.000	0.000	0.000
53	s	133	HIS	0	0.039	0.032	11.686	-0.085	-0.085	0.000	0.000	0.000	0.000
54	s	134	ALA	0	0.041	0.023	11.420	0.224	0.224	0.000	0.000	0.000	0.000
55	s	135	LEU	0	0.013	-0.019	9.257	-0.140	-0.140	0.000	0.000	0.000	0.000
56	s	136	TYR	0	-0.046	-0.016	11.857	-0.115	-0.115	0.000	0.000	0.000	0.000
57	s	137	LEU	0	0.034	0.019	15.040	-0.068	-0.068	0.000	0.000	0.000	0.000
58	s	138	ILE	0	-0.060	-0.020	11.074	-0.071	-0.071	0.000	0.000	0.000	0.000
59	s	139	ILE	0	0.035	0.033	15.101	0.010	0.010	0.000	0.000	0.000	0.000
60	s	140	ARG	1	0.855	0.906	17.134	-0.120	-0.120	0.000	0.000	0.000	0.000
61	s	141	MET	0	-0.026	-0.003	11.694	0.014	0.014	0.000	0.000	0.000	0.000
62	s	142	VAL	0	-0.019	-0.009	16.029	-0.022	-0.022	0.000	0.000	0.000	0.000
63	s	143	CYS	0	-0.025	-0.016	16.812	-0.019	-0.019	0.000	0.000	0.000	0.000
64	s	144	TYR	0	-0.035	-0.031	18.832	0.001	0.001	0.000	0.000	0.000	0.000
65	s	145	ASP	-1	-0.871	-0.949	22.378	-0.247	-0.247	0.000	0.000	0.000	0.000
66	s	146	ASP	-1	-0.821	-0.923	24.512	-0.158	-0.158	0.000	0.000	0.000	0.000
67	s	147	GLY	0	0.010	0.013	26.750	0.018	0.018	0.000	0.000	0.000	0.000
68	s	148	LEU	0	-0.069	-0.027	29.710	0.010	0.010	0.000	0.000	0.000	0.000
69	s	149	GLY	0	-0.022	-0.013	31.089	0.002	0.002	0.000	0.000	0.000	0.000
70	s	150	ALA	0	-0.030	-0.004	28.209	-0.009	-0.009	0.000	0.000	0.000	0.000
71	s	151	GLY	0	0.098	0.063	25.332	-0.021	-0.021	0.000	0.000	0.000	0.000
72	s	152	LYS	1	0.669	0.811	22.836	0.260	0.260	0.000	0.000	0.000	0.000
73	s	153	SER	0	0.043	0.020	20.086	0.005	0.005	0.000	0.000	0.000	0.000
74	s	154	LEU	0	0.013	0.026	20.432	-0.023	-0.023	0.000	0.000	0.000	0.000
75	s	155	LEU	0	-0.023	-0.029	13.969	-0.026	-0.026	0.000	0.000	0.000	0.000
76	s	156	ALA	0	0.025	0.018	17.930	0.030	0.030	0.000	0.000	0.000	0.000
77	s	157	LEU	0	-0.044	-0.029	12.894	-0.008	-0.008	0.000	0.000	0.000	0.000
78	s	158	LYN	0	0.056	0.022	17.027	-0.006	-0.006	0.000	0.000	0.000	0.000
79	s	159	THR	0	-0.091	-0.087	17.061	0.042	0.042	0.000	0.000	0.000	0.000
80	s	160	THR	0	-0.013	0.005	19.725	0.020	0.020	0.000	0.000	0.000	0.000
81	s	161	ASP	-1	-0.815	-0.889	22.620	0.347	0.347	0.000	0.000	0.000	0.000
82	s	162	ALA	0	-0.054	-0.036	24.438	-0.026	-0.026	0.000	0.000	0.000	0.000
83	s	163	SER	0	-0.065	-0.038	27.263	-0.001	-0.001	0.000	0.000	0.000	0.000
84	s	164	ASN	0	-0.119	-0.083	25.953	-0.016	-0.016	0.000	0.000	0.000	0.000
85	s	165	GLU	-1	-0.889	-0.929	28.699	0.182	0.182	0.000	0.000	0.000	0.000
86	s	166	GLU	-1	-0.833	-0.871	24.261	0.254	0.254	0.000	0.000	0.000	0.000
87	s	167	TYR	-1	-0.922	-0.964	24.406	0.188	0.188	0.000	0.000	0.000	0.000
88	s	168	SER	0	-0.058	-0.047	22.223	-0.035	-0.035	0.000	0.000	0.000	0.000
89	s	169	LEU	0	-0.030	-0.009	20.684	0.019	0.019	0.000	0.000	0.000	0.000
90	s	170	TRP	0	-0.047	-0.019	17.783	-0.012	-0.012	0.000	0.000	0.000	0.000
91	s	171	VAL	0	0.034	0.009	18.972	-0.015	-0.015	0.000	0.000	0.000	0.000
92	s	172	TYR	0	-0.010	-0.016	14.992	0.020	0.020	0.000	0.000	0.000	0.000
93	s	173	GLN	0	0.041	0.013	18.394	-0.005	-0.005	0.000	0.000	0.000	0.000
94	s	174	CYS	0	-0.032	0.007	15.351	-0.042	-0.042	0.000	0.000	0.000	0.000
95	s	175	ASN	0	0.035	0.002	18.038	0.018	0.018	0.000	0.000	0.000	0.000
96	s	176	SER	0	0.020	0.015	19.234	0.051	0.051	0.000	0.000	0.000	0.000
97	s	177	LEU	0	0.084	0.050	18.821	-0.052	-0.052	0.000	0.000	0.000	0.000
98	s	178	GLU	-1	-0.821	-0.918	17.523	-0.531	-0.531	0.000	0.000	0.000	0.000
99	s	179	GLN	0	-0.032	-0.009	14.089	-0.032	-0.032	0.000	0.000	0.000	0.000
100	s	180	ALA	0	0.058	0.018	13.559	-0.107	-0.107	0.000	0.000	0.000	0.000
101	s	181	GLN	0	-0.031	-0.030	14.026	0.026	0.026	0.000	0.000	0.000	0.000
102	s	182	ALA	0	-0.037	-0.020	11.232	-0.043	-0.043	0.000	0.000	0.000	0.000
103	s	183	ILE	0	-0.007	-0.005	9.265	-0.240	-0.240	0.000	0.000	0.000	0.000
104	s	184	CYS	0	-0.007	-0.011	9.272	0.060	0.060	0.000	0.000	0.000	0.000
105	s	185	LYS	1	0.926	0.960	9.944	0.705	0.705	0.000	0.000	0.000	0.000
106	s	186	VAL	0	-0.006	0.006	3.976	-0.219	-0.064	0.001	-0.028	-0.128	0.000
107	s	187	LEU	0	0.056	0.018	6.521	0.514	0.514	0.000	0.000	0.000	0.000
108	s	188	SER	0	-0.068	-0.026	8.831	0.234	0.234	0.000	0.000	0.000	0.000
109	s	189	THR	0	-0.036	-0.011	5.972	-0.222	-0.222	0.000	0.000	0.000	0.000
110	s	190	ALA	0	-0.017	-0.004	5.721	0.442	0.442	0.000	0.000	0.000	0.000
111	s	191	PHE	0	0.052	0.035	7.005	0.223	0.223	0.000	0.000	0.000	0.000
112	s	192	ASP	-1	-0.881	-0.944	10.820	0.378	0.378	0.000	0.000	0.000	0.000
113	s	193	SER	0	-0.139	-0.083	8.112	0.222	0.222	0.000	0.000	0.000	0.000
114	s	194	VAL	0	-0.056	-0.029	10.107	0.113	0.113	0.000	0.000	0.000	0.000
115	s	195	LEU	0	-0.021	0.013	12.723	-0.113	-0.113	0.000	0.000	0.000	0.000

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