FMO DATABASE

FMODB ID: N1YRQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1014821.313818
FMO2-HF: Nuclear repulsion	966184.58982
FMO2-HF: Total energy	-48636.723997
FMO2-MP2: Total energy	-48776.455677

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.
8.292	-11.085	46.507	-15.427	-11.705	0.091

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 : -0.885 / q_NPA : -0.871

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

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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	-0.932	-0.959	3.832	33.117	35.239	-0.024	-1.135	-0.964	0.003
4	E	63	PHE	0	-0.019	-0.016	6.547	-2.500	-2.500	0.000	0.000	0.000	0.000
5	E	64	ARG	1	0.953	0.987	10.287	-16.197	-16.197	0.000	0.000	0.000	0.000
6	E	65	ILE	0	-0.061	-0.035	13.068	-0.508	-0.508	0.000	0.000	0.000	0.000
7	E	66	LYS	1	0.872	0.939	15.664	-13.457	-13.457	0.000	0.000	0.000	0.000
8	E	67	TYR	0	-0.021	-0.022	17.768	0.643	0.643	0.000	0.000	0.000	0.000
9	E	68	VAL	0	-0.013	-0.003	20.234	-0.578	-0.578	0.000	0.000	0.000	0.000
10	E	69	GLY	0	0.035	0.009	22.502	-0.627	-0.627	0.000	0.000	0.000	0.000
11	E	70	ALA	0	-0.008	-0.002	21.643	0.543	0.543	0.000	0.000	0.000	0.000
12	E	71	ILE	0	0.005	0.029	23.538	-0.529	-0.529	0.000	0.000	0.000	0.000
13	E	84	GLY	0	0.048	0.029	26.418	0.185	0.185	0.000	0.000	0.000	0.000
14	E	85	PRO	0	-0.018	-0.024	22.083	-0.056	-0.056	0.000	0.000	0.000	0.000
15	E	86	LEU	0	0.058	0.023	24.019	0.168	0.168	0.000	0.000	0.000	0.000
16	E	87	ASP	-1	-0.862	-0.937	26.895	10.380	10.380	0.000	0.000	0.000	0.000
17	E	88	LEU	0	-0.063	-0.040	21.708	-0.049	-0.049	0.000	0.000	0.000	0.000
18	E	89	ILE	0	-0.002	0.016	24.197	0.049	0.049	0.000	0.000	0.000	0.000
19	E	90	ASN	0	0.042	0.014	26.416	-0.170	-0.170	0.000	0.000	0.000	0.000
20	E	91	TYR	0	-0.059	-0.019	26.526	-0.373	-0.373	0.000	0.000	0.000	0.000
21	E	92	ILE	0	-0.021	-0.018	23.162	-0.042	-0.042	0.000	0.000	0.000	0.000
22	E	93	ASP	-1	-0.861	-0.941	27.621	10.442	10.442	0.000	0.000	0.000	0.000
23	E	94	VAL	0	-0.057	-0.013	30.483	-0.325	-0.325	0.000	0.000	0.000	0.000
24	E	95	ALA	0	0.003	-0.002	29.509	-0.181	-0.181	0.000	0.000	0.000	0.000
25	E	96	GLN	0	-0.038	-0.039	27.131	-0.154	-0.154	0.000	0.000	0.000	0.000
26	E	97	GLN	0	-0.061	-0.016	31.503	-0.342	-0.342	0.000	0.000	0.000	0.000
27	E	98	ASP	-1	-0.932	-0.954	34.828	8.612	8.612	0.000	0.000	0.000	0.000
28	E	99	GLY	0	0.004	-0.005	34.425	-0.242	-0.242	0.000	0.000	0.000	0.000
29	E	100	LYS	1	0.849	0.937	30.101	-10.167	-10.167	0.000	0.000	0.000	0.000
30	E	101	LEU	0	-0.034	-0.017	25.657	0.347	0.347	0.000	0.000	0.000	0.000
31	E	102	PRO	0	0.018	0.030	27.193	-0.319	-0.319	0.000	0.000	0.000	0.000
32	E	103	PHE	0	0.055	0.011	28.135	0.313	0.313	0.000	0.000	0.000	0.000
33	E	104	VAL	0	-0.036	-0.014	27.911	0.253	0.253	0.000	0.000	0.000	0.000
34	E	105	PRO	0	-0.010	0.002	23.382	-0.082	-0.082	0.000	0.000	0.000	0.000
35	E	106	PRO	0	0.008	-0.013	24.503	-0.232	-0.232	0.000	0.000	0.000	0.000
36	E	107	GLU	-1	-0.858	-0.931	24.135	12.272	12.272	0.000	0.000	0.000	0.000
37	E	108	GLU	-1	-0.892	-0.922	20.483	14.091	14.091	0.000	0.000	0.000	0.000
38	E	109	GLU	-1	-0.914	-0.964	17.954	15.167	15.167	0.000	0.000	0.000	0.000
39	E	110	PHE	0	-0.044	-0.029	15.108	0.180	0.180	0.000	0.000	0.000	0.000
40	E	111	ILE	0	0.026	0.012	9.616	-0.026	-0.026	0.000	0.000	0.000	0.000
41	E	112	MET	0	-0.028	-0.015	9.388	0.293	0.293	0.000	0.000	0.000	0.000
42	E	113	GLY	0	0.015	0.007	6.043	0.735	0.735	0.000	0.000	0.000	0.000
43	E	114	VAL	0	-0.053	-0.046	4.206	-3.406	-3.081	-0.001	-0.101	-0.224	0.000
44	E	115	SER	0	0.038	-0.069	1.913	-6.898	-26.872	46.529	-17.310	-9.244	0.076
45	E	116	LYS	1	0.880	0.919	3.735	-72.742	-74.728	0.003	3.172	-1.189	0.012
46	E	117	TYR	0	0.003	0.047	5.844	-7.124	-7.137	-0.001	-0.018	0.032	0.000
47	E	118	GLY	0	0.005	-0.036	7.701	-2.776	-2.776	0.000	0.000	0.000	0.000
48	E	119	ILE	0	-0.040	-0.009	6.879	5.986	5.986	0.000	0.000	0.000	0.000
49	E	120	LYS	1	0.845	0.931	8.077	-28.242	-28.242	0.000	0.000	0.000	0.000
50	E	121	VAL	0	0.034	0.033	9.557	0.369	0.369	0.000	0.000	0.000	0.000
51	E	122	SER	0	-0.022	-0.048	12.183	-0.310	-0.310	0.000	0.000	0.000	0.000
52	E	123	THR	0	0.000	-0.014	13.904	0.188	0.188	0.000	0.000	0.000	0.000
53	E	124	SER	0	0.028	0.008	16.001	0.044	0.044	0.000	0.000	0.000	0.000
54	E	125	ASP	-1	-0.912	-0.947	13.418	18.999	18.999	0.000	0.000	0.000	0.000
55	E	126	GLN	0	-0.076	-0.035	13.722	-0.138	-0.138	0.000	0.000	0.000	0.000
56	E	127	TYR	0	-0.016	-0.019	12.867	1.677	1.677	0.000	0.000	0.000	0.000
57	E	128	ASP	-1	-0.843	-0.914	13.850	17.268	17.268	0.000	0.000	0.000	0.000
58	E	129	VAL	0	-0.080	-0.025	13.115	2.033	2.033	0.000	0.000	0.000	0.000
59	E	130	LEU	0	0.002	0.013	14.743	-1.204	-1.204	0.000	0.000	0.000	0.000
60	E	131	HIS	0	0.017	0.023	14.767	-0.611	-0.611	0.000	0.000	0.000	0.000
61	E	132	ARG	1	0.936	0.950	12.196	-21.736	-21.736	0.000	0.000	0.000	0.000
62	E	133	HIS	0	0.047	0.037	12.518	-0.849	-0.849	0.000	0.000	0.000	0.000
63	E	134	ALA	0	0.022	-0.002	10.952	3.207	3.207	0.000	0.000	0.000	0.000
64	E	135	LEU	0	0.019	0.014	10.028	-2.386	-2.386	0.000	0.000	0.000	0.000
65	E	136	TYR	0	-0.004	-0.007	11.631	-0.719	-0.719	0.000	0.000	0.000	0.000
66	E	137	LEU	0	-0.020	0.003	14.899	-1.204	-1.204	0.000	0.000	0.000	0.000
67	E	138	ILE	0	-0.036	-0.020	10.941	-1.272	-1.272	0.000	0.000	0.000	0.000
68	E	139	ILE	0	0.011	0.015	14.995	-0.181	-0.181	0.000	0.000	0.000	0.000
69	E	140	ARG	1	0.858	0.907	17.605	-13.795	-13.795	0.000	0.000	0.000	0.000
70	E	141	MET	0	0.011	0.026	11.353	0.489	0.489	0.000	0.000	0.000	0.000
71	E	142	VAL	0	-0.044	-0.017	16.264	-0.348	-0.348	0.000	0.000	0.000	0.000
72	E	143	CYS	0	-0.021	0.012	16.455	-0.124	-0.124	0.000	0.000	0.000	0.000
73	E	144	TYR	0	0.000	-0.001	18.502	-0.188	-0.188	0.000	0.000	0.000	0.000
74	E	145	ASP	-1	-0.850	-0.922	21.967	11.601	11.601	0.000	0.000	0.000	0.000
75	E	146	ASP	-1	-0.786	-0.906	24.590	11.002	11.002	0.000	0.000	0.000	0.000
76	E	147	GLY	0	-0.008	0.004	26.096	-0.253	-0.253	0.000	0.000	0.000	0.000
77	E	148	LEU	0	-0.091	-0.035	29.135	-0.433	-0.433	0.000	0.000	0.000	0.000
78	E	149	GLY	0	0.028	0.001	29.759	-0.373	-0.373	0.000	0.000	0.000	0.000
79	E	150	ALA	0	-0.072	-0.029	28.106	0.019	0.019	0.000	0.000	0.000	0.000
80	E	151	GLY	0	0.027	0.022	26.370	0.143	0.143	0.000	0.000	0.000	0.000
81	E	152	LYS	1	0.779	0.896	23.084	-11.737	-11.737	0.000	0.000	0.000	0.000
82	E	153	SER	0	-0.038	-0.028	19.539	0.112	0.112	0.000	0.000	0.000	0.000
83	E	154	LEU	0	0.030	0.027	20.763	0.286	0.286	0.000	0.000	0.000	0.000
84	E	155	LEU	0	0.022	-0.010	13.172	0.184	0.184	0.000	0.000	0.000	0.000
85	E	156	ALA	0	0.012	0.021	17.580	0.266	0.266	0.000	0.000	0.000	0.000
86	E	157	LEU	0	0.010	-0.007	13.498	0.832	0.832	0.000	0.000	0.000	0.000
87	E	158	LYS	1	0.934	0.968	17.247	-13.533	-13.533	0.000	0.000	0.000	0.000
88	E	159	THR	0	0.020	0.011	16.184	0.798	0.798	0.000	0.000	0.000	0.000
89	E	160	THR	0	-0.018	-0.004	18.904	-0.691	-0.691	0.000	0.000	0.000	0.000
90	E	161	ASP	-1	-0.703	-0.843	21.635	13.405	13.405	0.000	0.000	0.000	0.000
91	E	162	ALA	0	-0.095	-0.049	20.879	0.511	0.511	0.000	0.000	0.000	0.000
92	E	163	SER	0	-0.157	-0.085	22.016	-0.298	-0.298	0.000	0.000	0.000	0.000
93	E	164	ASN	0	-0.050	-0.039	25.715	-0.475	-0.475	0.000	0.000	0.000	0.000
94	E	165	GLU	-1	-0.936	-0.980	25.927	11.103	11.103	0.000	0.000	0.000	0.000
95	E	166	GLU	-1	-0.891	-0.923	27.347	11.038	11.038	0.000	0.000	0.000	0.000
96	E	167	TYR	0	-0.053	-0.036	22.553	0.819	0.819	0.000	0.000	0.000	0.000
97	E	168	SER	0	-0.022	-0.009	21.459	-0.582	-0.582	0.000	0.000	0.000	0.000
98	E	169	LEU	0	-0.051	-0.025	20.725	0.698	0.698	0.000	0.000	0.000	0.000
99	E	170	TRP	0	0.005	-0.009	17.447	-0.546	-0.546	0.000	0.000	0.000	0.000
100	E	171	VAL	0	0.020	0.011	18.488	0.629	0.629	0.000	0.000	0.000	0.000
101	E	172	TYR	0	0.003	-0.005	15.312	-0.101	-0.101	0.000	0.000	0.000	0.000
102	E	173	GLN	0	0.020	0.000	18.446	-0.569	-0.569	0.000	0.000	0.000	0.000
103	E	174	CYS	0	-0.008	0.004	15.943	1.229	1.229	0.000	0.000	0.000	0.000
104	E	175	ASN	0	0.045	0.026	17.837	-0.303	-0.303	0.000	0.000	0.000	0.000
105	E	176	SER	0	0.010	-0.004	18.846	-0.457	-0.457	0.000	0.000	0.000	0.000
106	E	177	LEU	0	0.112	0.054	18.532	0.746	0.746	0.000	0.000	0.000	0.000
107	E	178	GLU	-1	-0.862	-0.950	18.029	14.933	14.933	0.000	0.000	0.000	0.000
108	E	179	GLN	0	-0.047	-0.026	13.775	0.230	0.230	0.000	0.000	0.000	0.000
109	E	180	ALA	0	0.059	0.024	13.729	1.422	1.422	0.000	0.000	0.000	0.000
110	E	181	GLN	0	-0.037	-0.028	13.966	1.387	1.387	0.000	0.000	0.000	0.000
111	E	182	ALA	0	-0.034	-0.020	11.337	1.060	1.060	0.000	0.000	0.000	0.000
112	E	183	ILE	0	0.018	0.011	9.000	2.311	2.311	0.000	0.000	0.000	0.000
113	E	184	CYS	0	-0.009	-0.009	9.151	1.773	1.773	0.000	0.000	0.000	0.000
114	E	185	LYS	1	0.923	0.970	10.782	-19.152	-19.152	0.000	0.000	0.000	0.000
115	E	186	VAL	0	0.048	0.023	4.033	0.096	0.245	0.001	-0.035	-0.116	0.000
116	E	187	LEU	0	0.013	0.005	6.331	4.245	4.245	0.000	0.000	0.000	0.000
117	E	188	SER	0	-0.018	-0.025	8.136	-0.311	-0.311	0.000	0.000	0.000	0.000
118	E	189	THR	0	0.008	0.011	6.291	-0.715	-0.715	0.000	0.000	0.000	0.000
119	E	190	ALA	0	-0.027	-0.011	5.960	1.121	1.121	0.000	0.000	0.000	0.000
120	E	191	PHE	0	-0.046	-0.036	7.673	-1.605	-1.605	0.000	0.000	0.000	0.000
121	E	192	ASP	-1	-0.925	-0.933	10.521	20.921	20.921	0.000	0.000	0.000	0.000
122	E	193	SER	0	-0.082	-0.026	7.461	2.841	2.841	0.000	0.000	0.000	0.000
123	E	194	VAL	0	-0.041	-0.012	9.483	-1.976	-1.976	0.000	0.000	0.000	0.000

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