FMO DATABASE

FMODB ID: LJ1M9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-727836.563382
FMO2-HF: Nuclear repulsion	687787.177224
FMO2-HF: Total energy	-40049.386158
FMO2-MP2: Total energy	-40163.369776

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.
-14.178	-13.673	15.547	-8.311	-7.74	-0.066

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 : -0.065 / 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	-0.799	-0.894	3.873	-0.882	1.466	-0.016	-1.126	-1.206	0.004
4	y	63	PHE	0	-0.019	-0.013	6.106	-0.057	-0.057	0.000	0.000	0.000	0.000
5	y	64	ARG	1	0.851	0.916	9.796	0.475	0.475	0.000	0.000	0.000	0.000
6	y	65	ILE	0	-0.017	-0.008	12.557	-0.040	-0.040	0.000	0.000	0.000	0.000
7	y	66	LYS	1	0.885	0.943	15.108	0.259	0.259	0.000	0.000	0.000	0.000
8	y	67	TYR	0	0.018	0.006	17.687	-0.021	-0.021	0.000	0.000	0.000	0.000
9	y	68	VAL	0	-0.025	-0.017	18.835	0.008	0.008	0.000	0.000	0.000	0.000
10	y	69	GLY	0	0.034	0.004	21.149	0.019	0.019	0.000	0.000	0.000	0.000
11	y	70	ALA	0	-0.021	-0.012	20.894	-0.015	-0.015	0.000	0.000	0.000	0.000
12	y	71	ILE	0	-0.007	0.017	22.689	0.006	0.006	0.000	0.000	0.000	0.000
13	y	86	LEU	0	0.000	-0.006	23.852	-0.002	-0.002	0.000	0.000	0.000	0.000
14	y	87	ASP	-1	-0.803	-0.901	25.444	-0.085	-0.085	0.000	0.000	0.000	0.000
15	y	88	LEU	0	0.006	-0.008	20.342	0.005	0.005	0.000	0.000	0.000	0.000
16	y	89	ILE	0	0.024	0.018	23.501	-0.003	-0.003	0.000	0.000	0.000	0.000
17	y	90	ASN	0	-0.071	-0.015	25.503	0.009	0.009	0.000	0.000	0.000	0.000
18	y	91	TYR	0	-0.003	0.006	26.852	0.007	0.007	0.000	0.000	0.000	0.000
19	y	92	ILE	0	-0.058	-0.033	23.000	0.004	0.004	0.000	0.000	0.000	0.000
20	y	100	LYS	1	0.965	0.956	29.777	0.030	0.030	0.000	0.000	0.000	0.000
21	y	101	LEU	0	0.019	0.022	24.618	0.003	0.003	0.000	0.000	0.000	0.000
22	y	102	PRO	0	-0.001	0.009	26.154	0.001	0.001	0.000	0.000	0.000	0.000
23	y	103	PHE	0	-0.001	-0.004	26.827	-0.008	-0.008	0.000	0.000	0.000	0.000
24	y	104	VAL	0	-0.030	-0.012	26.404	-0.015	-0.015	0.000	0.000	0.000	0.000
25	y	105	PRO	0	-0.010	0.007	22.199	0.014	0.014	0.000	0.000	0.000	0.000
26	y	106	PRO	0	0.017	0.000	23.006	0.004	0.004	0.000	0.000	0.000	0.000
27	y	107	GLU	-1	-0.866	-0.926	23.046	-0.168	-0.168	0.000	0.000	0.000	0.000
28	y	108	GLU	-1	-0.952	-0.967	20.896	-0.063	-0.063	0.000	0.000	0.000	0.000
29	y	109	GLU	-1	-0.828	-0.905	16.833	-0.289	-0.289	0.000	0.000	0.000	0.000
30	y	110	PHE	0	-0.037	-0.007	13.966	0.046	0.046	0.000	0.000	0.000	0.000
31	y	111	ILE	0	-0.033	-0.012	8.714	-0.094	-0.094	0.000	0.000	0.000	0.000
32	y	112	MET	0	-0.003	-0.002	8.530	0.098	0.098	0.000	0.000	0.000	0.000
33	y	113	GLY	0	0.064	0.034	4.783	-0.313	-0.299	-0.001	-0.007	-0.006	0.000
34	y	114	VAL	0	-0.040	-0.009	4.007	-0.193	0.551	0.000	-0.346	-0.398	0.000
35	y	115	SER	0	0.026	-0.002	1.914	-10.362	-13.261	15.381	-7.255	-5.227	-0.069
36	y	116	LYS	1	1.012	0.986	3.280	-2.289	-2.613	0.059	0.594	-0.329	0.000
37	y	117	TYR	0	0.025	0.021	6.120	-0.416	-0.416	0.000	0.000	0.000	0.000
38	y	118	GLY	0	0.034	0.027	6.781	-0.241	-0.241	0.000	0.000	0.000	0.000
39	y	119	ILE	0	-0.034	-0.009	6.003	-0.143	-0.143	0.000	0.000	0.000	0.000
40	y	120	LYS	1	0.840	0.932	6.269	-0.206	-0.206	0.000	0.000	0.000	0.000
41	y	121	VAL	0	0.037	0.006	8.093	-0.230	-0.230	0.000	0.000	0.000	0.000
42	y	122	SER	0	0.000	0.006	10.868	0.113	0.113	0.000	0.000	0.000	0.000
43	y	123	THR	0	0.044	0.024	12.756	-0.077	-0.077	0.000	0.000	0.000	0.000
44	y	124	SER	0	-0.062	-0.043	14.913	0.022	0.022	0.000	0.000	0.000	0.000
45	y	134	ALA	0	0.003	-0.009	11.388	0.003	0.003	0.000	0.000	0.000	0.000
46	y	135	LEU	0	0.035	-0.010	8.688	-0.100	-0.100	0.000	0.000	0.000	0.000
47	y	136	TYR	0	-0.011	-0.014	11.490	-0.092	-0.092	0.000	0.000	0.000	0.000
48	y	137	LEU	0	-0.016	0.012	14.701	-0.031	-0.031	0.000	0.000	0.000	0.000
49	y	138	ILE	0	-0.051	-0.017	11.085	-0.055	-0.055	0.000	0.000	0.000	0.000
50	y	139	ILE	0	0.007	0.013	15.212	0.002	0.002	0.000	0.000	0.000	0.000
51	y	140	ARG	1	0.831	0.894	17.109	0.085	0.085	0.000	0.000	0.000	0.000
52	y	141	MET	0	-0.008	0.009	11.401	0.000	0.000	0.000	0.000	0.000	0.000
53	y	142	VAL	0	-0.021	-0.012	15.953	0.001	0.001	0.000	0.000	0.000	0.000
54	y	143	CYS	0	-0.017	-0.011	16.644	-0.025	-0.025	0.000	0.000	0.000	0.000
55	y	144	TYR	0	0.003	0.009	18.720	0.008	0.008	0.000	0.000	0.000	0.000
56	y	145	ASP	-1	-0.879	-0.938	22.055	-0.269	-0.269	0.000	0.000	0.000	0.000
57	y	153	SER	0	0.025	0.012	19.416	-0.009	-0.009	0.000	0.000	0.000	0.000
58	y	154	LEU	0	-0.038	-0.012	19.677	-0.024	-0.024	0.000	0.000	0.000	0.000
59	y	155	LEU	0	-0.006	-0.025	13.115	-0.031	-0.031	0.000	0.000	0.000	0.000
60	y	156	ALA	0	0.008	0.013	17.673	0.029	0.029	0.000	0.000	0.000	0.000
61	y	157	LEU	0	-0.001	-0.014	12.505	-0.029	-0.029	0.000	0.000	0.000	0.000
62	y	158	LYS	1	0.903	0.974	16.853	0.036	0.036	0.000	0.000	0.000	0.000
63	y	159	THR	0	-0.036	-0.032	16.043	-0.008	-0.008	0.000	0.000	0.000	0.000
64	y	160	THR	0	-0.026	-0.029	18.704	-0.014	-0.014	0.000	0.000	0.000	0.000
65	y	161	ASP	-1	-0.768	-0.844	20.381	0.097	0.097	0.000	0.000	0.000	0.000
66	y	162	ALA	0	0.067	0.027	22.469	-0.008	-0.008	0.000	0.000	0.000	0.000
67	y	163	SER	0	-0.069	-0.038	24.310	0.004	0.004	0.000	0.000	0.000	0.000
68	y	164	ASN	0	-0.102	-0.062	26.133	-0.002	-0.002	0.000	0.000	0.000	0.000
69	y	165	GLU	-1	-0.920	-0.945	26.690	0.103	0.103	0.000	0.000	0.000	0.000
70	y	166	GLU	-1	-0.869	-0.926	26.312	0.012	0.012	0.000	0.000	0.000	0.000
71	y	167	TYR	0	-0.051	-0.045	23.055	0.007	0.007	0.000	0.000	0.000	0.000
72	y	168	SER	0	-0.020	-0.009	20.872	-0.007	-0.007	0.000	0.000	0.000	0.000
73	y	169	LEU	0	-0.053	-0.031	20.710	-0.011	-0.011	0.000	0.000	0.000	0.000
74	y	170	TRP	0	-0.016	-0.020	16.987	0.002	0.002	0.000	0.000	0.000	0.000
75	y	171	VAL	0	0.008	0.000	18.213	-0.035	-0.035	0.000	0.000	0.000	0.000
76	y	172	TYR	0	0.030	0.006	14.945	0.017	0.017	0.000	0.000	0.000	0.000
77	y	173	GLN	0	0.007	-0.005	18.002	0.006	0.006	0.000	0.000	0.000	0.000
78	y	174	CYS	0	-0.030	0.013	15.310	-0.055	-0.055	0.000	0.000	0.000	0.000
79	y	175	ASN	0	0.010	0.000	17.568	0.019	0.019	0.000	0.000	0.000	0.000
80	y	176	SER	0	0.035	0.001	18.320	0.006	0.006	0.000	0.000	0.000	0.000
81	y	177	LEU	0	0.055	0.029	18.097	-0.059	-0.059	0.000	0.000	0.000	0.000
82	y	178	GLU	-1	-0.927	-0.964	16.639	-0.522	-0.522	0.000	0.000	0.000	0.000
83	y	179	GLN	0	0.019	0.011	13.530	-0.052	-0.052	0.000	0.000	0.000	0.000
84	y	180	ALA	0	0.057	0.011	12.841	-0.147	-0.147	0.000	0.000	0.000	0.000
85	y	181	GLN	0	0.004	-0.006	13.207	-0.060	-0.060	0.000	0.000	0.000	0.000
86	y	182	ALA	0	-0.021	-0.008	10.164	-0.061	-0.061	0.000	0.000	0.000	0.000
87	y	183	ILE	0	0.012	0.009	8.535	-0.313	-0.313	0.000	0.000	0.000	0.000
88	y	184	CYS	0	-0.025	-0.017	8.560	-0.051	-0.051	0.000	0.000	0.000	0.000
89	y	185	LYS	1	0.949	0.993	8.168	0.911	0.911	0.000	0.000	0.000	0.000
90	y	186	VAL	0	0.014	0.021	2.756	-0.564	-0.002	0.125	-0.169	-0.518	-0.001
91	y	187	LEU	0	0.027	0.004	5.409	0.661	0.661	0.000	0.000	0.000	0.000
92	y	188	SER	0	-0.036	-0.021	7.987	0.351	0.351	0.000	0.000	0.000	0.000
93	y	189	THR	0	-0.020	-0.019	4.587	-0.006	0.054	-0.001	-0.002	-0.056	0.000
94	y	190	ALA	0	-0.043	-0.019	5.510	0.661	0.661	0.000	0.000	0.000	0.000
95	y	191	PHE	0	-0.002	-0.019	6.760	0.119	0.119	0.000	0.000	0.000	0.000
96	y	192	ASP	-1	-0.859	-0.923	9.947	0.095	0.095	0.000	0.000	0.000	0.000
97	y	193	SER	0	-0.141	-0.078	7.290	0.293	0.293	0.000	0.000	0.000	0.000
98	y	194	VAL	0	-0.086	-0.032	9.379	0.131	0.131	0.000	0.000	0.000	0.000
99	y	195	LEU	0	-0.022	0.011	12.296	-0.108	-0.108	0.000	0.000	0.000	0.000

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