FMO DATABASE

FMODB ID: J3589

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1018638.717533
FMO2-HF: Nuclear repulsion	970001.393242
FMO2-HF: Total energy	-48637.324292
FMO2-MP2: Total energy	-48777.068698

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.
-40.688	-93.554	96.691	-22.397	-21.428	0.101

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 : -0.907 / q_NPA : -0.816

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	-0.927	-0.966	3.898	28.877	30.486	-0.015	-0.856	-0.738	0.001
4	E	63	PHE	0	-0.016	-0.015	5.917	-1.852	-1.852	0.000	0.000	0.000	0.000
5	E	64	ARG	1	0.885	0.936	10.288	-15.363	-15.363	0.000	0.000	0.000	0.000
6	E	65	ILE	0	-0.046	-0.023	13.158	-0.016	-0.016	0.000	0.000	0.000	0.000
7	E	66	LYS	1	0.826	0.924	15.904	-13.060	-13.060	0.000	0.000	0.000	0.000
8	E	67	TYR	0	-0.003	-0.013	18.383	0.486	0.486	0.000	0.000	0.000	0.000
9	E	68	VAL	0	-0.007	-0.004	20.200	-0.572	-0.572	0.000	0.000	0.000	0.000
10	E	69	GLY	0	0.037	0.013	22.047	-0.685	-0.685	0.000	0.000	0.000	0.000
11	E	70	ALA	0	-0.013	-0.004	21.379	0.802	0.802	0.000	0.000	0.000	0.000
12	E	71	ILE	0	-0.031	0.010	23.233	-0.642	-0.642	0.000	0.000	0.000	0.000
13	E	84	GLY	0	0.041	0.023	25.395	0.187	0.187	0.000	0.000	0.000	0.000
14	E	85	PRO	0	-0.013	-0.021	21.048	-0.026	-0.026	0.000	0.000	0.000	0.000
15	E	86	LEU	0	0.056	0.021	22.966	0.111	0.111	0.000	0.000	0.000	0.000
16	E	87	ASP	-1	-0.841	-0.919	25.929	10.839	10.839	0.000	0.000	0.000	0.000
17	E	88	LEU	0	-0.061	-0.034	20.821	-0.080	-0.080	0.000	0.000	0.000	0.000
18	E	89	ILE	0	-0.010	0.013	23.419	-0.008	-0.008	0.000	0.000	0.000	0.000
19	E	90	ASN	0	0.000	-0.007	25.929	-0.309	-0.309	0.000	0.000	0.000	0.000
20	E	91	TYR	0	-0.038	-0.005	26.222	-0.426	-0.426	0.000	0.000	0.000	0.000
21	E	92	ILE	0	0.005	-0.005	22.552	-0.109	-0.109	0.000	0.000	0.000	0.000
22	E	93	ASP	-1	-0.805	-0.911	27.083	10.750	10.750	0.000	0.000	0.000	0.000
23	E	94	VAL	0	-0.049	-0.018	29.699	-0.350	-0.350	0.000	0.000	0.000	0.000
24	E	95	ALA	0	0.010	0.003	28.879	-0.204	-0.204	0.000	0.000	0.000	0.000
25	E	96	GLN	0	-0.056	-0.044	26.575	-0.116	-0.116	0.000	0.000	0.000	0.000
26	E	97	GLN	0	-0.052	-0.020	31.004	-0.443	-0.443	0.000	0.000	0.000	0.000
27	E	98	ASP	-1	-0.917	-0.958	34.055	8.774	8.774	0.000	0.000	0.000	0.000
28	E	99	GLY	0	-0.025	-0.004	34.191	-0.229	-0.229	0.000	0.000	0.000	0.000
29	E	100	LYS	1	0.821	0.915	29.372	-10.277	-10.277	0.000	0.000	0.000	0.000
30	E	101	LEU	0	0.005	-0.001	25.065	0.387	0.387	0.000	0.000	0.000	0.000
31	E	102	PRO	0	0.002	0.024	26.961	-0.315	-0.315	0.000	0.000	0.000	0.000
32	E	103	PHE	0	0.057	0.010	27.774	0.325	0.325	0.000	0.000	0.000	0.000
33	E	104	VAL	0	-0.036	-0.009	27.287	0.131	0.131	0.000	0.000	0.000	0.000
34	E	105	PRO	0	-0.008	0.007	23.086	-0.119	-0.119	0.000	0.000	0.000	0.000
35	E	106	PRO	0	0.011	-0.007	24.563	-0.349	-0.349	0.000	0.000	0.000	0.000
36	E	107	GLU	-1	-0.834	-0.917	24.509	11.964	11.964	0.000	0.000	0.000	0.000
37	E	108	GLU	-1	-0.888	-0.910	21.373	13.235	13.235	0.000	0.000	0.000	0.000
38	E	109	GLU	-1	-0.837	-0.911	19.131	14.601	14.601	0.000	0.000	0.000	0.000
39	E	110	PHE	0	-0.021	-0.020	15.983	0.013	0.013	0.000	0.000	0.000	0.000
40	E	111	ILE	0	0.009	0.011	10.624	0.173	0.173	0.000	0.000	0.000	0.000
41	E	112	MET	0	-0.013	-0.015	9.273	-0.518	-0.518	0.000	0.000	0.000	0.000
42	E	113	GLY	0	0.041	0.029	6.632	0.871	0.871	0.000	0.000	0.000	0.000
43	E	114	VAL	0	-0.042	-0.038	4.241	-2.033	-1.743	-0.001	-0.069	-0.220	0.000
44	E	115	SER	0	0.079	-0.069	1.922	-6.933	-34.264	56.101	-19.055	-9.716	0.002
45	E	116	LYS	1	0.888	0.895	2.044	-126.852	-154.937	40.505	-2.185	-10.235	0.095
46	E	117	TYR	0	-0.025	0.004	4.386	-11.298	-11.124	0.019	-0.064	-0.129	0.003
47	E	118	GLY	0	0.016	-0.003	6.520	-4.789	-4.789	0.000	0.000	0.000	0.000
48	E	119	ILE	0	-0.025	0.004	5.983	4.738	4.738	0.000	0.000	0.000	0.000
49	E	120	LYS	1	0.839	0.931	8.352	-25.148	-25.148	0.000	0.000	0.000	0.000
50	E	121	VAL	0	0.008	0.006	10.041	0.465	0.465	0.000	0.000	0.000	0.000
51	E	122	SER	0	-0.028	-0.052	12.952	-0.235	-0.235	0.000	0.000	0.000	0.000
52	E	123	THR	0	-0.013	-0.020	15.004	0.215	0.215	0.000	0.000	0.000	0.000
53	E	124	SER	0	0.019	-0.005	17.320	-0.042	-0.042	0.000	0.000	0.000	0.000
54	E	125	ASP	-1	-0.923	-0.949	14.447	17.537	17.537	0.000	0.000	0.000	0.000
55	E	126	GLN	0	-0.051	-0.021	14.801	-0.116	-0.116	0.000	0.000	0.000	0.000
56	E	127	TYR	0	-0.007	-0.020	13.824	1.435	1.435	0.000	0.000	0.000	0.000
57	E	128	ASP	-1	-0.856	-0.913	14.374	16.239	16.239	0.000	0.000	0.000	0.000
58	E	129	VAL	0	-0.061	-0.021	13.730	1.603	1.603	0.000	0.000	0.000	0.000
59	E	130	LEU	0	-0.018	0.012	15.576	-1.096	-1.096	0.000	0.000	0.000	0.000
60	E	131	HIS	0	0.025	0.016	14.972	-0.393	-0.393	0.000	0.000	0.000	0.000
61	E	132	ARG	1	0.945	0.956	12.318	-20.375	-20.375	0.000	0.000	0.000	0.000
62	E	133	HIS	0	0.021	0.016	11.887	-0.803	-0.803	0.000	0.000	0.000	0.000
63	E	134	ALA	0	-0.003	-0.007	10.666	3.090	3.090	0.000	0.000	0.000	0.000
64	E	135	LEU	0	0.016	0.001	8.814	-2.699	-2.699	0.000	0.000	0.000	0.000
65	E	136	TYR	0	0.013	0.005	11.315	-0.847	-0.847	0.000	0.000	0.000	0.000
66	E	137	LEU	0	-0.029	-0.003	14.529	-1.485	-1.485	0.000	0.000	0.000	0.000
67	E	138	ILE	0	-0.039	-0.020	10.854	-1.467	-1.467	0.000	0.000	0.000	0.000
68	E	139	ILE	0	0.007	0.010	14.870	-0.002	-0.002	0.000	0.000	0.000	0.000
69	E	140	ARG	1	0.831	0.897	16.948	-14.508	-14.508	0.000	0.000	0.000	0.000
70	E	141	MET	0	0.012	0.016	11.226	0.775	0.775	0.000	0.000	0.000	0.000
71	E	142	VAL	0	-0.046	-0.019	15.667	-0.389	-0.389	0.000	0.000	0.000	0.000
72	E	143	CYS	0	0.011	0.003	15.971	0.329	0.329	0.000	0.000	0.000	0.000
73	E	144	TYR	0	-0.040	-0.012	18.086	-0.067	-0.067	0.000	0.000	0.000	0.000
74	E	145	ASP	-1	-0.837	-0.915	21.532	11.729	11.729	0.000	0.000	0.000	0.000
75	E	146	ASP	-1	-0.769	-0.888	23.977	10.946	10.946	0.000	0.000	0.000	0.000
76	E	147	GLY	0	-0.016	-0.002	25.712	-0.212	-0.212	0.000	0.000	0.000	0.000
77	E	148	LEU	0	-0.064	-0.027	29.068	-0.428	-0.428	0.000	0.000	0.000	0.000
78	E	149	GLY	0	-0.003	-0.003	29.532	-0.355	-0.355	0.000	0.000	0.000	0.000
79	E	150	ALA	0	-0.063	-0.019	27.647	-0.107	-0.107	0.000	0.000	0.000	0.000
80	E	151	GLY	0	0.032	0.028	25.995	0.195	0.195	0.000	0.000	0.000	0.000
81	E	152	LYS	1	0.756	0.861	22.586	-11.486	-11.486	0.000	0.000	0.000	0.000
82	E	153	SER	0	-0.046	-0.036	19.103	0.184	0.184	0.000	0.000	0.000	0.000
83	E	154	LEU	0	0.034	0.038	20.203	0.327	0.327	0.000	0.000	0.000	0.000
84	E	155	LEU	0	0.017	-0.006	12.897	0.256	0.256	0.000	0.000	0.000	0.000
85	E	156	ALA	0	0.016	0.012	17.437	-0.001	-0.001	0.000	0.000	0.000	0.000
86	E	157	LEU	0	0.001	-0.018	13.047	0.842	0.842	0.000	0.000	0.000	0.000
87	E	158	LYS	1	0.918	0.975	16.632	-14.110	-14.110	0.000	0.000	0.000	0.000
88	E	159	THR	0	0.019	0.004	15.694	0.934	0.934	0.000	0.000	0.000	0.000
89	E	160	THR	0	-0.019	0.000	18.416	-0.914	-0.914	0.000	0.000	0.000	0.000
90	E	161	ASP	-1	-0.743	-0.864	20.760	14.130	14.130	0.000	0.000	0.000	0.000
91	E	162	ALA	0	-0.066	-0.041	20.329	0.529	0.529	0.000	0.000	0.000	0.000
92	E	163	SER	0	-0.154	-0.084	21.571	-0.243	-0.243	0.000	0.000	0.000	0.000
93	E	164	ASN	0	-0.050	-0.044	25.191	-0.479	-0.479	0.000	0.000	0.000	0.000
94	E	165	GLU	-1	-0.941	-0.977	25.456	11.518	11.518	0.000	0.000	0.000	0.000
95	E	166	GLU	-1	-0.864	-0.904	26.739	11.382	11.382	0.000	0.000	0.000	0.000
96	E	167	TYR	0	-0.029	-0.037	22.182	0.923	0.923	0.000	0.000	0.000	0.000
97	E	168	SER	0	-0.011	0.006	20.652	-0.812	-0.812	0.000	0.000	0.000	0.000
98	E	169	LEU	0	-0.022	-0.009	20.241	0.788	0.788	0.000	0.000	0.000	0.000
99	E	170	TRP	0	0.002	-0.008	17.258	-0.678	-0.678	0.000	0.000	0.000	0.000
100	E	171	VAL	0	0.006	0.001	18.695	0.477	0.477	0.000	0.000	0.000	0.000
101	E	172	TYR	0	0.018	0.001	15.433	-0.203	-0.203	0.000	0.000	0.000	0.000
102	E	173	GLN	0	-0.020	-0.019	18.345	-0.810	-0.810	0.000	0.000	0.000	0.000
103	E	174	CYS	0	-0.007	0.018	15.471	1.033	1.033	0.000	0.000	0.000	0.000
104	E	175	ASN	0	0.051	0.006	17.772	-0.494	-0.494	0.000	0.000	0.000	0.000
105	E	176	SER	0	0.001	0.001	18.832	-0.503	-0.503	0.000	0.000	0.000	0.000
106	E	177	LEU	0	0.072	0.030	18.252	0.775	0.775	0.000	0.000	0.000	0.000
107	E	178	GLU	-1	-0.830	-0.930	17.209	15.720	15.720	0.000	0.000	0.000	0.000
108	E	179	GLN	0	-0.033	-0.011	13.128	0.154	0.154	0.000	0.000	0.000	0.000
109	E	180	ALA	0	0.076	0.034	13.240	1.382	1.382	0.000	0.000	0.000	0.000
110	E	181	GLN	0	-0.036	-0.039	13.006	2.088	2.088	0.000	0.000	0.000	0.000
111	E	182	ALA	0	-0.042	-0.011	10.434	1.310	1.310	0.000	0.000	0.000	0.000
112	E	183	ILE	0	0.026	0.022	8.336	2.770	2.770	0.000	0.000	0.000	0.000
113	E	184	CYS	0	-0.007	-0.008	8.372	2.353	2.353	0.000	0.000	0.000	0.000
114	E	185	LYS	1	0.908	0.972	9.854	-19.142	-19.142	0.000	0.000	0.000	0.000
115	E	186	VAL	0	0.028	0.022	3.274	0.769	1.246	0.082	-0.168	-0.390	0.000
116	E	187	LEU	0	0.018	0.004	5.511	5.765	5.765	0.000	0.000	0.000	0.000
117	E	188	SER	0	-0.045	-0.037	7.400	-0.259	-0.259	0.000	0.000	0.000	0.000
118	E	189	THR	0	0.002	-0.009	5.247	-0.918	-0.918	0.000	0.000	0.000	0.000
119	E	190	ALA	0	-0.032	-0.015	5.127	3.794	3.794	0.000	0.000	0.000	0.000
120	E	191	PHE	0	-0.036	-0.025	6.625	-1.599	-1.599	0.000	0.000	0.000	0.000
121	E	192	ASP	-1	-0.903	-0.943	9.441	25.230	25.230	0.000	0.000	0.000	0.000
122	E	193	SER	0	-0.122	-0.057	5.955	4.242	4.242	0.000	0.000	0.000	0.000
123	E	194	VAL	0	-0.039	-0.001	7.984	-0.787	-0.787	0.000	0.000	0.000	0.000

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