FMO DATABASE

FMODB ID: 3Q63L

Calculation Name: 4DX9-y-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: y

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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-724589.426186
FMO2-HF: Nuclear repulsion	684540.293102
FMO2-HF: Total energy	-40049.133083
FMO2-MP2: Total energy	-40163.040555

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(y:60:CYS)

Summations of interaction energy for fragment #1(y: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.
-13.804	-10.72	10.84	-7.041	-6.883	-0.057

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.069 / q_NPA : -0.034

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	y	62	GLU	-1	-0.870	-0.941	3.815	-0.330	2.166	-0.028	-1.195	-1.272	0.004
4	y	63	PHE	0	-0.007	-0.004	6.462	-0.102	-0.102	0.000	0.000	0.000	0.000
5	y	64	ARG	1	0.843	0.912	10.137	0.489	0.489	0.000	0.000	0.000	0.000
6	y	65	ILE	0	-0.007	-0.008	12.678	-0.024	-0.024	0.000	0.000	0.000	0.000
7	y	66	LYS	1	0.914	0.958	15.079	0.265	0.265	0.000	0.000	0.000	0.000
8	y	67	TYR	0	0.011	0.010	17.738	-0.019	-0.019	0.000	0.000	0.000	0.000
9	y	68	VAL	0	-0.022	-0.006	19.022	0.013	0.013	0.000	0.000	0.000	0.000
10	y	69	GLY	0	0.030	0.005	21.466	0.021	0.021	0.000	0.000	0.000	0.000
11	y	70	ALA	0	-0.017	-0.014	21.120	-0.017	-0.017	0.000	0.000	0.000	0.000
12	y	71	ILE	0	-0.001	0.025	23.063	0.009	0.009	0.000	0.000	0.000	0.000
13	y	86	LEU	0	-0.011	-0.014	24.068	-0.002	-0.002	0.000	0.000	0.000	0.000
14	y	87	ASP	-1	-0.822	-0.934	25.483	-0.090	-0.090	0.000	0.000	0.000	0.000
15	y	88	LEU	0	-0.023	-0.016	20.867	0.007	0.007	0.000	0.000	0.000	0.000
16	y	89	ILE	0	0.015	0.014	23.836	-0.001	-0.001	0.000	0.000	0.000	0.000
17	y	90	ASN	0	-0.057	-0.003	26.062	0.009	0.009	0.000	0.000	0.000	0.000
18	y	91	TYR	0	0.002	0.016	27.241	0.007	0.007	0.000	0.000	0.000	0.000
19	y	92	ILE	0	-0.059	-0.043	23.159	0.007	0.007	0.000	0.000	0.000	0.000
20	y	100	LYS	1	0.964	0.957	30.447	0.033	0.033	0.000	0.000	0.000	0.000
21	y	101	LEU	0	0.027	0.025	24.768	0.004	0.004	0.000	0.000	0.000	0.000
22	y	102	PRO	0	0.000	0.009	26.439	0.000	0.000	0.000	0.000	0.000	0.000
23	y	103	PHE	0	0.001	-0.003	27.246	-0.009	-0.009	0.000	0.000	0.000	0.000
24	y	104	VAL	0	-0.028	-0.015	27.041	-0.016	-0.016	0.000	0.000	0.000	0.000
25	y	105	PRO	0	-0.011	0.005	22.488	0.014	0.014	0.000	0.000	0.000	0.000
26	y	106	PRO	0	0.021	0.002	23.361	0.000	0.000	0.000	0.000	0.000	0.000
27	y	107	GLU	-1	-0.867	-0.932	22.916	-0.166	-0.166	0.000	0.000	0.000	0.000
28	y	108	GLU	-1	-0.961	-0.967	20.646	-0.060	-0.060	0.000	0.000	0.000	0.000
29	y	109	GLU	-1	-0.848	-0.909	16.973	-0.291	-0.291	0.000	0.000	0.000	0.000
30	y	110	PHE	0	-0.015	0.011	14.049	0.045	0.045	0.000	0.000	0.000	0.000
31	y	111	ILE	0	-0.010	0.005	8.670	-0.104	-0.104	0.000	0.000	0.000	0.000
32	y	112	MET	0	-0.012	-0.006	8.964	0.080	0.080	0.000	0.000	0.000	0.000
33	y	113	GLY	0	0.023	0.001	4.993	-0.264	-0.264	0.000	0.000	0.000	0.000
34	y	114	VAL	0	-0.012	0.007	4.100	0.032	0.560	-0.001	-0.228	-0.300	0.000
35	y	115	SER	0	0.023	-0.011	2.041	-9.892	-10.061	10.798	-5.836	-4.793	-0.060
36	y	116	LYS	1	1.007	0.993	3.386	-2.508	-2.626	0.046	0.311	-0.239	0.000
37	y	117	TYR	0	0.017	0.013	6.631	-0.398	-0.398	0.000	0.000	0.000	0.000
38	y	118	GLY	0	0.040	0.024	6.921	-0.215	-0.215	0.000	0.000	0.000	0.000
39	y	119	ILE	0	-0.020	-0.006	6.322	-0.171	-0.171	0.000	0.000	0.000	0.000
40	y	120	LYS	1	0.891	0.956	6.530	-0.648	-0.648	0.000	0.000	0.000	0.000
41	y	121	VAL	0	0.030	0.024	8.499	-0.144	-0.144	0.000	0.000	0.000	0.000
42	y	122	SER	0	-0.003	0.004	11.069	0.117	0.117	0.000	0.000	0.000	0.000
43	y	123	THR	0	0.029	0.005	12.808	-0.074	-0.074	0.000	0.000	0.000	0.000
44	y	124	SER	0	-0.059	-0.046	14.963	0.033	0.033	0.000	0.000	0.000	0.000
45	y	134	ALA	0	-0.006	-0.015	11.459	-0.001	-0.001	0.000	0.000	0.000	0.000
46	y	135	LEU	0	0.023	-0.019	8.779	-0.095	-0.095	0.000	0.000	0.000	0.000
47	y	136	TYR	0	-0.021	-0.010	11.750	-0.073	-0.073	0.000	0.000	0.000	0.000
48	y	137	LEU	0	-0.015	0.012	15.143	-0.032	-0.032	0.000	0.000	0.000	0.000
49	y	138	ILE	0	-0.038	-0.011	11.606	-0.050	-0.050	0.000	0.000	0.000	0.000
50	y	139	ILE	0	0.013	0.023	15.580	0.008	0.008	0.000	0.000	0.000	0.000
51	y	140	ARG	1	0.896	0.939	17.360	0.102	0.102	0.000	0.000	0.000	0.000
52	y	141	MET	0	-0.026	0.001	11.319	0.011	0.011	0.000	0.000	0.000	0.000
53	y	142	VAL	0	-0.031	-0.021	16.375	0.001	0.001	0.000	0.000	0.000	0.000
54	y	143	CYS	0	-0.008	-0.005	16.461	-0.029	-0.029	0.000	0.000	0.000	0.000
55	y	144	TYR	0	-0.002	0.010	18.573	0.009	0.009	0.000	0.000	0.000	0.000
56	y	145	ASP	-1	-0.876	-0.936	21.854	-0.282	-0.282	0.000	0.000	0.000	0.000
57	y	153	SER	0	0.032	0.017	19.224	-0.009	-0.009	0.000	0.000	0.000	0.000
58	y	154	LEU	0	-0.044	-0.018	19.987	-0.012	-0.012	0.000	0.000	0.000	0.000
59	y	155	LEU	0	-0.008	-0.033	13.209	-0.022	-0.022	0.000	0.000	0.000	0.000
60	y	156	ALA	0	0.004	0.011	17.733	0.032	0.032	0.000	0.000	0.000	0.000
61	y	157	LEU	0	0.000	-0.020	12.702	-0.023	-0.023	0.000	0.000	0.000	0.000
62	y	158	LYS	1	0.939	0.994	17.100	0.060	0.060	0.000	0.000	0.000	0.000
63	y	159	THR	0	-0.028	-0.014	16.237	-0.005	-0.005	0.000	0.000	0.000	0.000
64	y	160	THR	0	-0.014	-0.004	18.972	-0.008	-0.008	0.000	0.000	0.000	0.000
65	y	161	ASP	-1	-0.764	-0.861	20.477	0.085	0.085	0.000	0.000	0.000	0.000
66	y	162	ALA	0	0.054	0.023	22.695	-0.007	-0.007	0.000	0.000	0.000	0.000
67	y	163	SER	0	-0.063	-0.035	24.678	0.005	0.005	0.000	0.000	0.000	0.000
68	y	164	ASN	0	-0.099	-0.061	26.494	-0.001	-0.001	0.000	0.000	0.000	0.000
69	y	165	GLU	-1	-0.927	-0.949	26.913	0.089	0.089	0.000	0.000	0.000	0.000
70	y	166	GLU	-1	-0.880	-0.933	26.744	0.002	0.002	0.000	0.000	0.000	0.000
71	y	167	TYR	0	-0.074	-0.051	23.404	0.003	0.003	0.000	0.000	0.000	0.000
72	y	168	SER	0	-0.014	-0.021	21.101	-0.005	-0.005	0.000	0.000	0.000	0.000
73	y	169	LEU	0	-0.066	-0.041	21.102	-0.014	-0.014	0.000	0.000	0.000	0.000
74	y	170	TRP	0	-0.030	-0.032	17.228	0.002	0.002	0.000	0.000	0.000	0.000
75	y	171	VAL	0	0.020	0.013	18.700	-0.035	-0.035	0.000	0.000	0.000	0.000
76	y	172	TYR	0	0.020	-0.007	15.221	0.014	0.014	0.000	0.000	0.000	0.000
77	y	173	GLN	0	0.020	0.004	18.040	-0.004	-0.004	0.000	0.000	0.000	0.000
78	y	174	CYS	0	-0.039	-0.001	15.508	-0.055	-0.055	0.000	0.000	0.000	0.000
79	y	175	ASN	0	0.014	0.007	17.706	0.004	0.004	0.000	0.000	0.000	0.000
80	y	176	SER	0	0.037	0.004	18.251	0.002	0.002	0.000	0.000	0.000	0.000
81	y	177	LEU	0	0.056	0.028	18.353	-0.046	-0.046	0.000	0.000	0.000	0.000
82	y	178	GLU	-1	-0.932	-0.976	16.910	-0.530	-0.530	0.000	0.000	0.000	0.000
83	y	179	GLN	0	-0.004	0.003	13.581	-0.067	-0.067	0.000	0.000	0.000	0.000
84	y	180	ALA	0	0.040	0.006	12.824	-0.143	-0.143	0.000	0.000	0.000	0.000
85	y	181	GLN	0	0.028	0.009	13.648	-0.055	-0.055	0.000	0.000	0.000	0.000
86	y	182	ALA	0	-0.020	-0.004	10.272	-0.052	-0.052	0.000	0.000	0.000	0.000
87	y	183	ILE	0	0.011	0.005	8.547	-0.335	-0.335	0.000	0.000	0.000	0.000
88	y	184	CYS	0	-0.019	-0.014	8.923	0.003	0.003	0.000	0.000	0.000	0.000
89	y	185	LYS	1	0.957	0.993	8.643	0.897	0.897	0.000	0.000	0.000	0.000
90	y	186	VAL	0	0.015	0.004	3.067	-0.346	0.001	0.025	-0.093	-0.279	-0.001
91	y	187	LEU	0	0.023	0.002	5.458	0.445	0.445	0.000	0.000	0.000	0.000
92	y	188	SER	0	-0.035	-0.021	8.065	0.320	0.320	0.000	0.000	0.000	0.000
93	y	189	THR	0	-0.028	-0.001	4.801	-0.022	-0.022	0.000	0.000	0.000	0.000
94	y	190	ALA	0	-0.021	-0.014	5.874	0.472	0.472	0.000	0.000	0.000	0.000
95	y	191	PHE	0	-0.022	-0.031	7.269	0.121	0.121	0.000	0.000	0.000	0.000
96	y	192	ASP	-1	-0.886	-0.928	10.126	0.005	0.005	0.000	0.000	0.000	0.000
97	y	193	SER	0	-0.136	-0.057	7.858	0.250	0.250	0.000	0.000	0.000	0.000
98	y	194	VAL	0	-0.075	-0.042	10.004	0.036	0.036	0.000	0.000	0.000	0.000
99	y	195	LEU	0	0.005	0.027	12.733	-0.064	-0.064	0.000	0.000	0.000	0.000

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