FMO DATABASE

FMODB ID: 3QNQL

Calculation Name: 4DX9-y-Xray321

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	109
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-755316.192994
FMO2-HF: Nuclear repulsion	714412.7632
FMO2-HF: Total energy	-40903.429793
FMO2-MP2: Total energy	-41020.026439

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:59:ACE )

Summations of interaction energy for fragment #1(y:59:ACE )

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.
1.872	3.131	0.596	-0.765	-1.091	-0.003

Interaction energy analysis for fragmet #1(y:59:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.006

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	61	ALA	0	-0.013	0.015	3.837	0.936	1.724	-0.005	-0.347	-0.436	-0.001
4	y	62	GLU	-1	-0.924	-0.960	6.584	-0.578	-0.578	0.000	0.000	0.000	0.000
5	y	63	PHE	0	-0.009	-0.010	8.071	0.116	0.116	0.000	0.000	0.000	0.000
6	y	64	ARG	1	0.895	0.958	12.829	0.147	0.147	0.000	0.000	0.000	0.000
7	y	65	ILE	0	-0.004	-0.006	15.436	0.028	0.028	0.000	0.000	0.000	0.000
8	y	66	LYS	1	0.958	0.989	18.054	0.086	0.086	0.000	0.000	0.000	0.000
9	y	67	TYR	0	0.011	0.008	21.027	0.001	0.001	0.000	0.000	0.000	0.000
10	y	68	VAL	0	-0.019	-0.004	22.422	0.009	0.009	0.000	0.000	0.000	0.000
11	y	69	GLY	0	0.024	0.002	24.278	0.007	0.007	0.000	0.000	0.000	0.000
12	y	70	ALA	0	-0.021	-0.017	24.091	-0.007	-0.007	0.000	0.000	0.000	0.000
13	y	71	ILE	0	-0.046	-0.006	25.770	0.006	0.006	0.000	0.000	0.000	0.000
14	y	72	NME	0	0.060	0.038	26.688	-0.002	-0.002	0.000	0.000	0.000	0.000
15	y	85	ACE	0	-0.006	-0.088	22.907	0.001	0.001	0.000	0.000	0.000	0.000
16	y	86	LEU	0	0.009	0.002	22.702	0.001	0.001	0.000	0.000	0.000	0.000
17	y	87	ASP	-1	-0.866	-0.939	25.086	0.001	0.001	0.000	0.000	0.000	0.000
18	y	88	LEU	0	-0.037	-0.023	21.095	-0.003	-0.003	0.000	0.000	0.000	0.000
19	y	89	ILE	0	-0.005	0.002	23.836	-0.005	-0.005	0.000	0.000	0.000	0.000
20	y	90	ASN	0	-0.041	-0.025	26.191	-0.005	-0.005	0.000	0.000	0.000	0.000
21	y	91	TYR	0	0.010	0.020	27.998	0.000	0.000	0.000	0.000	0.000	0.000
22	y	92	ILE	0	-0.046	-0.009	24.248	-0.004	-0.004	0.000	0.000	0.000	0.000
23	y	93	NME	0	-0.012	0.001	27.669	0.000	0.000	0.000	0.000	0.000	0.000
24	y	99	ACE	0	0.024	0.001	36.143	0.001	0.001	0.000	0.000	0.000	0.000
25	y	100	LYS	1	0.923	0.943	32.655	0.037	0.037	0.000	0.000	0.000	0.000
26	y	101	LEU	0	0.042	0.036	26.721	-0.004	-0.004	0.000	0.000	0.000	0.000
27	y	102	PRO	0	0.000	0.011	29.074	0.005	0.005	0.000	0.000	0.000	0.000
28	y	103	PHE	0	0.008	0.001	29.423	-0.002	-0.002	0.000	0.000	0.000	0.000
29	y	104	VAL	0	-0.026	-0.016	29.064	-0.001	-0.001	0.000	0.000	0.000	0.000
30	y	105	PRO	0	-0.027	-0.005	25.158	0.000	0.000	0.000	0.000	0.000	0.000
31	y	106	PRO	0	0.026	0.006	26.876	0.004	0.004	0.000	0.000	0.000	0.000
32	y	107	GLU	-1	-0.887	-0.959	26.510	-0.078	-0.078	0.000	0.000	0.000	0.000
33	y	108	GLU	-1	-0.990	-0.974	25.171	-0.122	-0.122	0.000	0.000	0.000	0.000
34	y	109	GLU	-1	-0.913	-0.959	20.952	-0.132	-0.132	0.000	0.000	0.000	0.000
35	y	110	PHE	0	-0.015	-0.006	18.638	-0.008	-0.008	0.000	0.000	0.000	0.000
36	y	111	ILE	0	0.017	0.018	13.776	0.001	0.001	0.000	0.000	0.000	0.000
37	y	112	MET	0	-0.027	-0.018	12.014	-0.015	-0.015	0.000	0.000	0.000	0.000
38	y	113	GLY	0	0.037	0.009	9.815	-0.042	-0.042	0.000	0.000	0.000	0.000
39	y	114	VAL	0	-0.021	0.001	5.766	0.075	0.075	0.000	0.000	0.000	0.000
40	y	115	SER	0	0.017	-0.011	4.888	-0.641	-0.664	0.000	-0.020	0.044	0.000
41	y	116	LYS	1	0.990	0.983	4.240	0.779	0.924	0.000	-0.019	-0.127	0.000
42	y	117	TYR	0	0.017	0.012	6.104	0.264	0.264	0.000	0.000	0.000	0.000
43	y	118	GLY	0	0.048	0.027	8.727	0.167	0.167	0.000	0.000	0.000	0.000
44	y	119	ILE	0	-0.021	-0.002	9.214	-0.213	-0.213	0.000	0.000	0.000	0.000
45	y	120	LYS	1	0.964	0.990	11.489	0.563	0.563	0.000	0.000	0.000	0.000
46	y	121	VAL	0	0.024	0.025	13.432	-0.030	-0.030	0.000	0.000	0.000	0.000
47	y	122	SER	0	-0.052	-0.020	16.176	0.024	0.024	0.000	0.000	0.000	0.000
48	y	123	THR	0	0.036	0.006	18.361	0.006	0.006	0.000	0.000	0.000	0.000
49	y	124	SER	0	0.009	-0.020	20.008	-0.026	-0.026	0.000	0.000	0.000	0.000
50	y	125	NME	0	-0.034	0.004	21.306	0.009	0.009	0.000	0.000	0.000	0.000
51	y	133	ACE	0	0.027	0.005	16.132	0.005	0.005	0.000	0.000	0.000	0.000
52	y	134	ALA	0	-0.017	-0.023	13.382	-0.026	-0.026	0.000	0.000	0.000	0.000
53	y	135	LEU	0	0.013	-0.020	8.102	0.012	0.012	0.000	0.000	0.000	0.000
54	y	136	TYR	0	-0.027	-0.008	11.829	0.049	0.049	0.000	0.000	0.000	0.000
55	y	137	LEU	0	-0.016	0.014	14.793	0.020	0.020	0.000	0.000	0.000	0.000
56	y	138	ILE	0	-0.032	-0.006	12.292	0.010	0.010	0.000	0.000	0.000	0.000
57	y	139	ILE	0	0.009	0.022	15.688	0.024	0.024	0.000	0.000	0.000	0.000
58	y	140	ARG	1	0.927	1.010	16.813	0.003	0.003	0.000	0.000	0.000	0.000
59	y	141	MET	0	-0.027	0.001	11.505	-0.034	-0.034	0.000	0.000	0.000	0.000
60	y	142	VAL	0	-0.023	-0.017	16.246	0.025	0.025	0.000	0.000	0.000	0.000
61	y	143	CYS	0	-0.025	-0.001	16.664	-0.015	-0.015	0.000	0.000	0.000	0.000
62	y	144	TYR	0	0.002	0.000	18.847	0.013	0.013	0.000	0.000	0.000	0.000
63	y	145	ASP	-1	-0.839	-0.933	22.176	-0.017	-0.017	0.000	0.000	0.000	0.000
64	y	146	NME	0	-0.031	-0.001	24.796	-0.001	-0.001	0.000	0.000	0.000	0.000
65	y	152	ACE	0	0.029	0.009	23.339	-0.001	-0.001	0.000	0.000	0.000	0.000
66	y	153	SER	0	-0.033	-0.023	20.085	0.013	0.013	0.000	0.000	0.000	0.000
67	y	154	LEU	0	0.005	0.024	21.279	-0.015	-0.015	0.000	0.000	0.000	0.000
68	y	155	LEU	0	-0.006	-0.028	14.259	0.008	0.008	0.000	0.000	0.000	0.000
69	y	156	ALA	0	0.007	0.015	18.804	-0.011	-0.011	0.000	0.000	0.000	0.000
70	y	157	LEU	0	0.001	-0.021	13.975	0.007	0.007	0.000	0.000	0.000	0.000
71	y	158	LYS	1	0.951	0.995	18.106	0.030	0.030	0.000	0.000	0.000	0.000
72	y	159	THR	0	-0.026	0.000	17.634	-0.005	-0.005	0.000	0.000	0.000	0.000
73	y	160	THR	0	0.016	0.027	20.122	0.011	0.011	0.000	0.000	0.000	0.000
74	y	161	ASP	-1	-0.761	-0.879	21.633	-0.103	-0.103	0.000	0.000	0.000	0.000
75	y	162	ALA	0	-0.057	-0.020	23.979	0.003	0.003	0.000	0.000	0.000	0.000
76	y	163	SER	0	-0.072	-0.064	26.475	0.003	0.003	0.000	0.000	0.000	0.000
77	y	164	ASN	0	-0.010	0.023	25.245	0.000	0.000	0.000	0.000	0.000	0.000
78	y	165	GLU	-1	-0.932	-0.988	26.242	-0.017	-0.017	0.000	0.000	0.000	0.000
79	y	166	GLU	-1	-0.892	-0.948	27.940	-0.036	-0.036	0.000	0.000	0.000	0.000
80	y	167	TYR	0	-0.102	-0.036	24.032	-0.004	-0.004	0.000	0.000	0.000	0.000
81	y	168	SER	0	0.005	-0.011	23.110	0.002	0.002	0.000	0.000	0.000	0.000
82	y	169	LEU	0	-0.062	-0.037	22.473	0.000	0.000	0.000	0.000	0.000	0.000
83	y	170	TRP	0	-0.028	-0.043	19.321	-0.007	-0.007	0.000	0.000	0.000	0.000
84	y	171	VAL	0	0.017	0.013	20.352	0.002	0.002	0.000	0.000	0.000	0.000
85	y	172	TYR	0	0.017	-0.009	17.733	-0.015	-0.015	0.000	0.000	0.000	0.000
86	y	173	GLN	0	0.028	0.005	20.247	0.012	0.012	0.000	0.000	0.000	0.000
87	y	174	CYS	0	-0.028	0.003	16.920	-0.024	-0.024	0.000	0.000	0.000	0.000
88	y	175	ASN	0	-0.012	-0.015	19.360	0.025	0.025	0.000	0.000	0.000	0.000
89	y	176	SER	0	0.039	0.005	19.249	0.011	0.011	0.000	0.000	0.000	0.000
90	y	177	LEU	0	0.077	0.039	19.296	-0.008	-0.008	0.000	0.000	0.000	0.000
91	y	178	GLU	-1	-0.941	-0.979	17.415	0.032	0.032	0.000	0.000	0.000	0.000
92	y	179	GLN	0	-0.032	-0.009	14.662	0.003	0.003	0.000	0.000	0.000	0.000
93	y	180	ALA	0	0.046	0.008	13.734	-0.025	-0.025	0.000	0.000	0.000	0.000
94	y	181	GLN	0	0.021	0.005	14.120	0.009	0.009	0.000	0.000	0.000	0.000
95	y	182	ALA	0	-0.020	-0.004	10.953	0.045	0.045	0.000	0.000	0.000	0.000
96	y	183	ILE	0	0.014	0.003	9.204	0.016	0.016	0.000	0.000	0.000	0.000
97	y	184	CYS	0	-0.026	-0.016	9.165	-0.021	-0.021	0.000	0.000	0.000	0.000
98	y	185	LYS	1	0.965	0.997	8.477	-0.195	-0.195	0.000	0.000	0.000	0.000
99	y	186	VAL	0	0.007	0.002	3.626	0.089	0.223	0.005	-0.033	-0.106	0.000
100	y	187	LEU	0	0.034	0.000	4.748	0.022	0.071	0.000	-0.004	-0.045	0.000
101	y	188	SER	0	-0.030	-0.016	7.504	0.050	0.050	0.000	0.000	0.000	0.000
102	y	189	THR	0	-0.034	0.003	2.667	0.273	0.393	0.596	-0.331	-0.386	-0.002
103	y	190	ALA	0	-0.024	-0.017	4.746	0.118	0.164	0.000	-0.011	-0.035	0.000
104	y	191	PHE	0	-0.021	-0.028	5.462	-0.120	-0.120	0.000	0.000	0.000	0.000
105	y	192	ASP	-1	-0.896	-0.936	8.116	0.461	0.461	0.000	0.000	0.000	0.000
106	y	193	SER	0	-0.125	-0.055	4.800	-0.004	-0.004	0.000	0.000	0.000	0.000
107	y	194	VAL	0	-0.069	-0.041	6.933	-0.123	-0.123	0.000	0.000	0.000	0.000
108	y	195	LEU	0	-0.021	0.013	9.846	-0.041	-0.041	0.000	0.000	0.000	0.000
109	y	196	NME	0	0.011	0.012	11.706	-0.022	-0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(y:59:ACE )