FMO DATABASE

FMODB ID: 43N3N

Calculation Name: 4DX9-a-Xray321

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: a

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	122
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-938222.31285
FMO2-HF: Nuclear repulsion	891737.85085
FMO2-HF: Total energy	-46484.462001
FMO2-MP2: Total energy	-46617.664262

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(a:59:ACE )

Summations of interaction energy for fragment #1(a: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.
1.121	2.305	-0.005	-0.42	-0.754	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.003

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	a	61	ALA	0	0.010	0.019	3.839	0.924	1.707	-0.005	-0.348	-0.429	-0.001
4	a	62	GLU	-1	-0.942	-0.967	6.698	-0.572	-0.572	0.000	0.000	0.000	0.000
5	a	63	PHE	0	-0.011	-0.007	8.654	0.120	0.120	0.000	0.000	0.000	0.000
6	a	64	ARG	1	0.888	0.964	13.125	0.169	0.169	0.000	0.000	0.000	0.000
7	a	65	ILE	0	-0.033	-0.023	16.311	0.025	0.025	0.000	0.000	0.000	0.000
8	a	66	LYS	1	0.927	0.975	18.817	0.099	0.099	0.000	0.000	0.000	0.000
9	a	67	TYR	0	0.013	-0.005	21.145	-0.011	-0.011	0.000	0.000	0.000	0.000
10	a	68	VAL	0	0.008	0.010	23.065	0.009	0.009	0.000	0.000	0.000	0.000
11	a	69	GLY	0	0.034	0.004	24.726	0.008	0.008	0.000	0.000	0.000	0.000
12	a	70	ALA	0	-0.011	-0.005	24.508	-0.010	-0.010	0.000	0.000	0.000	0.000
13	a	71	ILE	0	-0.030	-0.002	26.123	0.009	0.009	0.000	0.000	0.000	0.000
14	a	72	GLU	-1	-0.937	-0.987	26.163	-0.106	-0.106	0.000	0.000	0.000	0.000
15	a	73	LYS	1	0.869	0.945	27.920	0.084	0.084	0.000	0.000	0.000	0.000
16	a	74	NME	0	0.037	0.024	28.805	0.003	0.003	0.000	0.000	0.000	0.000
17	a	80	ACE	0	0.016	-0.003	31.455	0.001	0.001	0.000	0.000	0.000	0.000
18	a	81	GLY	0	0.008	-0.005	28.653	-0.005	-0.005	0.000	0.000	0.000	0.000
19	a	82	LEU	0	0.028	0.023	27.427	0.003	0.003	0.000	0.000	0.000	0.000
20	a	83	GLU	-1	-0.957	-0.956	25.336	-0.005	-0.005	0.000	0.000	0.000	0.000
21	a	84	GLY	0	0.059	0.021	24.966	0.000	0.000	0.000	0.000	0.000	0.000
22	a	85	PRO	0	-0.058	-0.040	22.130	-0.006	-0.006	0.000	0.000	0.000	0.000
23	a	86	LEU	0	0.063	0.011	23.641	-0.006	-0.006	0.000	0.000	0.000	0.000
24	a	87	ASP	-1	-0.884	-0.927	26.961	-0.017	-0.017	0.000	0.000	0.000	0.000
25	a	88	LEU	0	-0.052	-0.041	21.766	-0.005	-0.005	0.000	0.000	0.000	0.000
26	a	89	ILE	0	0.003	0.010	24.035	-0.006	-0.006	0.000	0.000	0.000	0.000
27	a	90	ASN	0	0.048	0.015	26.681	-0.003	-0.003	0.000	0.000	0.000	0.000
28	a	91	TYR	0	-0.049	-0.021	28.154	0.001	0.001	0.000	0.000	0.000	0.000
29	a	92	ILE	0	-0.042	-0.017	24.193	-0.004	-0.004	0.000	0.000	0.000	0.000
30	a	93	ASP	-1	-0.857	-0.941	28.640	-0.039	-0.039	0.000	0.000	0.000	0.000
31	a	94	VAL	0	-0.090	-0.027	31.535	0.001	0.001	0.000	0.000	0.000	0.000
32	a	95	ALA	0	-0.027	-0.018	31.018	0.000	0.000	0.000	0.000	0.000	0.000
33	a	96	GLN	0	-0.041	-0.001	28.715	-0.007	-0.007	0.000	0.000	0.000	0.000
34	a	97	GLN	0	-0.002	-0.021	32.522	0.007	0.007	0.000	0.000	0.000	0.000
35	a	98	ASP	-1	-0.912	-0.960	35.085	-0.055	-0.055	0.000	0.000	0.000	0.000
36	a	99	GLY	0	-0.024	-0.009	35.674	0.003	0.003	0.000	0.000	0.000	0.000
37	a	100	LYS	1	0.856	0.932	32.652	0.052	0.052	0.000	0.000	0.000	0.000
38	a	101	LEU	0	-0.010	0.009	27.398	-0.005	-0.005	0.000	0.000	0.000	0.000
39	a	102	PRO	0	0.051	0.034	29.934	0.005	0.005	0.000	0.000	0.000	0.000
40	a	103	PHE	0	0.025	0.010	30.192	-0.004	-0.004	0.000	0.000	0.000	0.000
41	a	104	VAL	0	-0.056	-0.023	30.216	-0.001	-0.001	0.000	0.000	0.000	0.000
42	a	105	PRO	0	-0.018	0.008	26.163	0.000	0.000	0.000	0.000	0.000	0.000
43	a	106	PRO	0	0.022	0.010	27.228	0.005	0.005	0.000	0.000	0.000	0.000
44	a	107	GLU	-1	-0.921	-0.968	26.739	-0.103	-0.103	0.000	0.000	0.000	0.000
45	a	108	GLU	-1	-0.924	-0.956	24.622	-0.120	-0.120	0.000	0.000	0.000	0.000
46	a	109	GLU	-1	-0.905	-0.956	21.736	-0.204	-0.204	0.000	0.000	0.000	0.000
47	a	110	PHE	0	0.023	-0.007	20.301	-0.003	-0.003	0.000	0.000	0.000	0.000
48	a	111	ILE	0	-0.037	-0.017	14.338	-0.008	-0.008	0.000	0.000	0.000	0.000
49	a	112	MET	0	-0.039	-0.008	12.018	-0.009	-0.009	0.000	0.000	0.000	0.000
50	a	113	GLY	0	0.014	0.000	10.281	-0.033	-0.033	0.000	0.000	0.000	0.000
51	a	114	VAL	0	-0.006	0.004	6.003	0.047	0.047	0.000	0.000	0.000	0.000
52	a	115	SER	0	0.000	-0.019	5.260	-0.612	-0.619	0.000	-0.015	0.023	0.000
53	a	116	LYS	1	1.010	0.997	4.202	-0.423	-0.247	0.000	-0.026	-0.150	0.000
54	a	117	TYR	0	-0.045	-0.018	5.398	0.263	0.329	0.000	-0.004	-0.061	0.000
55	a	118	GLY	0	0.032	0.012	9.156	0.166	0.166	0.000	0.000	0.000	0.000
56	a	119	ILE	0	-0.027	0.002	9.520	-0.162	-0.162	0.000	0.000	0.000	0.000
57	a	120	LYS	1	0.930	0.957	11.659	0.657	0.657	0.000	0.000	0.000	0.000
58	a	121	NME	0	0.078	0.048	13.834	-0.001	-0.001	0.000	0.000	0.000	0.000
59	a	131	ACE	0	0.056	0.019	19.939	0.007	0.007	0.000	0.000	0.000	0.000
60	a	132	ARG	1	0.880	0.923	15.982	0.278	0.278	0.000	0.000	0.000	0.000
61	a	133	HIS	0	0.040	0.034	14.730	0.036	0.036	0.000	0.000	0.000	0.000
62	a	134	ALA	0	0.025	0.011	13.498	-0.074	-0.074	0.000	0.000	0.000	0.000
63	a	135	LEU	0	0.046	0.023	8.610	0.013	0.013	0.000	0.000	0.000	0.000
64	a	136	TYR	0	-0.035	-0.017	12.599	0.053	0.053	0.000	0.000	0.000	0.000
65	a	137	LEU	0	-0.050	-0.019	15.828	0.021	0.021	0.000	0.000	0.000	0.000
66	a	138	ILE	0	-0.017	0.001	12.380	0.007	0.007	0.000	0.000	0.000	0.000
67	a	139	ILE	0	-0.012	-0.001	16.142	0.024	0.024	0.000	0.000	0.000	0.000
68	a	140	ARG	1	0.931	0.958	16.941	0.029	0.029	0.000	0.000	0.000	0.000
69	a	141	MET	0	0.014	0.015	12.418	-0.015	-0.015	0.000	0.000	0.000	0.000
70	a	142	VAL	0	-0.028	-0.015	16.389	0.025	0.025	0.000	0.000	0.000	0.000
71	a	143	CYS	0	-0.038	-0.017	17.003	-0.014	-0.014	0.000	0.000	0.000	0.000
72	a	144	TYR	0	0.034	0.011	19.335	0.015	0.015	0.000	0.000	0.000	0.000
73	a	145	ASP	-1	-0.926	-0.973	22.676	-0.042	-0.042	0.000	0.000	0.000	0.000
74	a	146	ASP	-1	-0.889	-0.921	25.180	-0.048	-0.048	0.000	0.000	0.000	0.000
75	a	147	GLY	0	0.049	0.009	27.608	0.004	0.004	0.000	0.000	0.000	0.000
76	a	148	LEU	0	-0.054	-0.030	30.542	0.000	0.000	0.000	0.000	0.000	0.000
77	a	149	GLY	0	-0.012	0.003	32.499	-0.001	-0.001	0.000	0.000	0.000	0.000
78	a	150	ALA	0	0.008	0.017	29.027	-0.003	-0.003	0.000	0.000	0.000	0.000
79	a	151	GLY	0	0.004	-0.013	26.827	0.001	0.001	0.000	0.000	0.000	0.000
80	a	152	LYS	1	0.835	0.927	23.883	0.048	0.048	0.000	0.000	0.000	0.000
81	a	153	SER	0	0.043	0.008	20.722	0.009	0.009	0.000	0.000	0.000	0.000
82	a	154	LEU	0	0.013	0.022	21.884	-0.014	-0.014	0.000	0.000	0.000	0.000
83	a	155	LEU	0	-0.016	-0.028	15.118	0.003	0.003	0.000	0.000	0.000	0.000
84	a	156	ALA	0	0.035	0.022	18.927	0.001	0.001	0.000	0.000	0.000	0.000
85	a	157	LEU	0	-0.046	-0.022	14.025	0.003	0.003	0.000	0.000	0.000	0.000
86	a	158	LYS	1	0.897	0.940	18.257	0.044	0.044	0.000	0.000	0.000	0.000
87	a	159	THR	0	-0.005	-0.011	17.492	0.004	0.004	0.000	0.000	0.000	0.000
88	a	160	THR	0	0.122	0.059	19.621	0.000	0.000	0.000	0.000	0.000	0.000
89	a	161	ASH	0	-0.051	-0.022	17.957	-0.017	-0.017	0.000	0.000	0.000	0.000
90	a	162	ALA	0	-0.015	-0.017	20.436	-0.001	-0.001	0.000	0.000	0.000	0.000
91	a	163	SER	0	-0.018	-0.022	22.634	0.008	0.008	0.000	0.000	0.000	0.000
92	a	164	ASN	0	-0.003	0.016	24.216	0.000	0.000	0.000	0.000	0.000	0.000
93	a	165	GLU	-1	-0.870	-0.925	25.336	-0.060	-0.060	0.000	0.000	0.000	0.000
94	a	166	GLU	-1	-0.970	-0.979	27.464	-0.046	-0.046	0.000	0.000	0.000	0.000
95	a	167	TYR	0	-0.085	-0.048	24.188	-0.008	-0.008	0.000	0.000	0.000	0.000
96	a	168	SER	0	0.039	0.037	23.771	0.004	0.004	0.000	0.000	0.000	0.000
97	a	169	LEU	0	-0.020	-0.007	22.112	-0.007	-0.007	0.000	0.000	0.000	0.000
98	a	170	TRP	0	-0.039	-0.023	19.824	-0.003	-0.003	0.000	0.000	0.000	0.000
99	a	171	VAL	0	0.036	0.016	20.604	-0.006	-0.006	0.000	0.000	0.000	0.000
100	a	172	TYR	0	0.012	0.002	18.119	-0.014	-0.014	0.000	0.000	0.000	0.000
101	a	173	GLN	0	0.060	0.022	20.759	0.013	0.013	0.000	0.000	0.000	0.000
102	a	174	CYS	0	-0.052	-0.013	17.263	-0.022	-0.022	0.000	0.000	0.000	0.000
103	a	175	ASN	0	0.054	0.021	20.082	0.006	0.006	0.000	0.000	0.000	0.000
104	a	176	SER	0	-0.023	-0.016	20.104	0.013	0.013	0.000	0.000	0.000	0.000
105	a	177	LEU	0	0.085	0.045	20.052	-0.012	-0.012	0.000	0.000	0.000	0.000
106	a	178	GLU	-1	-0.894	-0.966	17.883	0.004	0.004	0.000	0.000	0.000	0.000
107	a	179	GLN	0	-0.024	-0.017	15.065	0.013	0.013	0.000	0.000	0.000	0.000
108	a	180	ALA	0	0.052	0.018	14.314	-0.031	-0.031	0.000	0.000	0.000	0.000
109	a	181	GLN	0	0.011	0.002	14.630	-0.006	-0.006	0.000	0.000	0.000	0.000
110	a	182	ALA	0	-0.039	-0.016	11.398	0.023	0.023	0.000	0.000	0.000	0.000
111	a	183	ILE	0	0.009	0.004	9.766	-0.014	-0.014	0.000	0.000	0.000	0.000
112	a	184	CYS	0	-0.008	-0.008	9.544	-0.047	-0.047	0.000	0.000	0.000	0.000
113	a	185	LYS	1	0.934	0.970	9.095	-0.143	-0.143	0.000	0.000	0.000	0.000
114	a	186	VAL	0	-0.016	-0.005	4.088	0.056	0.135	0.000	-0.014	-0.065	0.000
115	a	187	LEU	0	0.029	-0.002	5.184	-0.023	0.018	0.000	-0.001	-0.040	0.000
116	a	188	SER	0	-0.073	-0.020	7.858	0.064	0.064	0.000	0.000	0.000	0.000
117	a	189	THR	0	0.007	0.012	4.725	0.180	0.226	0.000	-0.012	-0.032	0.000
118	a	190	ALA	0	-0.029	-0.005	4.853	0.248	0.248	0.000	0.000	0.000	0.000
119	a	191	PHE	0	-0.017	-0.028	5.804	-0.111	-0.111	0.000	0.000	0.000	0.000
120	a	192	ASP	-1	-0.937	-0.951	9.373	0.470	0.470	0.000	0.000	0.000	0.000
121	a	193	SER	0	-0.073	-0.033	5.791	0.161	0.161	0.000	0.000	0.000	0.000
122	a	194	NME	0	-0.013	-0.004	8.118	-0.101	-0.101	0.000	0.000	0.000	0.000

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