FMO DATABASE

FMODB ID: R5158

Calculation Name: 4DX9-i-Xray321

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: i

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	124
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-960384.350408
FMO2-HF: Nuclear repulsion	913197.065257
FMO2-HF: Total energy	-47187.285151
FMO2-MP2: Total energy	-47322.952202

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(i:59:ACE )

Summations of interaction energy for fragment #1(i: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.
0.927	1.893	0.005	-0.439	-0.532	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.005

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].
3	i	61	ALA	0	0.039	0.031	3.874	0.949	1.696	-0.005	-0.326	-0.416
4	i	62	GLU	-1	-0.910	-0.949	6.940	-1.073	-1.073	0.000	0.000	0.000
5	i	63	PHE	0	0.006	0.003	9.675	0.107	0.107	0.000	0.000	0.000
6	i	64	ARG	1	0.853	0.923	13.712	0.159	0.159	0.000	0.000	0.000
7	i	65	ILE	0	-0.029	-0.015	16.420	0.016	0.016	0.000	0.000	0.000
8	i	66	LYS	1	0.832	0.911	19.036	0.157	0.157	0.000	0.000	0.000
9	i	67	TYR	0	-0.019	-0.029	21.125	-0.011	-0.011	0.000	0.000	0.000
10	i	68	VAL	0	0.004	0.009	24.067	0.009	0.009	0.000	0.000	0.000
11	i	69	GLY	0	0.039	0.016	26.166	0.010	0.010	0.000	0.000	0.000
12	i	70	ALA	0	-0.068	-0.042	25.870	-0.012	-0.012	0.000	0.000	0.000
13	i	71	ILE	0	-0.018	0.001	27.136	0.009	0.009	0.000	0.000	0.000
14	i	72	NME	0	0.089	0.065	27.252	-0.008	-0.008	0.000	0.000	0.000
15	i	81	ACE	0	0.014	0.000	33.119	0.001	0.001	0.000	0.000	0.000
16	i	82	LEU	0	0.032	0.005	29.244	-0.003	-0.003	0.000	0.000	0.000
17	i	83	GLU	-1	-0.980	-0.992	28.813	-0.042	-0.042	0.000	0.000	0.000
18	i	84	GLY	0	0.046	0.018	26.610	0.005	0.005	0.000	0.000	0.000
19	i	85	PRO	0	-0.087	-0.052	23.805	-0.006	-0.006	0.000	0.000	0.000
20	i	86	LEU	0	0.064	0.009	25.458	-0.004	-0.004	0.000	0.000	0.000
21	i	87	ASP	-1	-0.916	-0.941	28.731	-0.036	-0.036	0.000	0.000	0.000
22	i	88	LEU	0	-0.048	-0.025	25.094	-0.002	-0.002	0.000	0.000	0.000
23	i	89	ILE	0	-0.021	-0.014	26.310	-0.003	-0.003	0.000	0.000	0.000
24	i	90	ASN	0	0.008	0.023	29.054	0.001	0.001	0.000	0.000	0.000
25	i	91	TYR	0	0.033	0.009	29.878	0.002	0.002	0.000	0.000	0.000
26	i	92	ILE	0	-0.008	0.007	26.124	-0.003	-0.003	0.000	0.000	0.000
27	i	93	ASP	-1	-0.824	-0.925	30.552	-0.058	-0.058	0.000	0.000	0.000
28	i	94	VAL	0	-0.034	-0.021	33.598	0.003	0.003	0.000	0.000	0.000
29	i	95	ALA	0	-0.037	-0.019	32.165	0.001	0.001	0.000	0.000	0.000
30	i	96	GLN	0	-0.045	-0.011	30.457	0.004	0.004	0.000	0.000	0.000
31	i	97	GLN	0	-0.012	-0.005	34.948	0.005	0.005	0.000	0.000	0.000
32	i	98	ASP	-1	-0.857	-0.927	38.093	-0.038	-0.038	0.000	0.000	0.000
33	i	99	GLY	0	0.034	0.033	37.193	0.001	0.001	0.000	0.000	0.000
34	i	100	LYS	1	0.747	0.855	38.069	0.042	0.042	0.000	0.000	0.000
35	i	101	LEU	0	0.028	0.009	35.512	0.000	0.000	0.000	0.000	0.000
36	i	102	PRO	0	-0.055	-0.009	30.947	-0.003	-0.003	0.000	0.000	0.000
37	i	103	PHE	0	0.004	-0.008	30.941	-0.003	-0.003	0.000	0.000	0.000
38	i	104	VAL	0	-0.007	-0.008	30.533	-0.003	-0.003	0.000	0.000	0.000
39	i	105	PRO	0	-0.047	-0.012	26.173	-0.002	-0.002	0.000	0.000	0.000
40	i	106	PRO	0	0.031	0.036	27.346	0.004	0.004	0.000	0.000	0.000
41	i	107	GLU	-1	-0.866	-0.960	26.560	-0.107	-0.107	0.000	0.000	0.000
42	i	108	GLU	-1	-0.925	-0.952	23.025	-0.154	-0.154	0.000	0.000	0.000
43	i	109	GLU	-1	-0.860	-0.925	21.920	-0.159	-0.159	0.000	0.000	0.000
44	i	110	PHE	0	-0.018	-0.013	19.445	-0.023	-0.023	0.000	0.000	0.000
45	i	111	ILE	0	0.002	-0.001	13.855	-0.001	-0.001	0.000	0.000	0.000
46	i	112	MET	0	-0.030	-0.025	12.764	0.004	0.004	0.000	0.000	0.000
47	i	113	GLY	0	0.033	0.030	9.415	-0.038	-0.038	0.000	0.000	0.000
48	i	114	VAL	0	-0.012	-0.010	6.509	0.127	0.127	0.000	0.000	0.000
49	i	115	SER	0	-0.224	0.106	5.648	-0.924	-1.060	0.000	-0.014	0.150
50	i	116	LYS	1	1.149	0.986	3.517	0.437	0.751	0.010	-0.091	-0.233
51	i	117	TYR	0	0.025	-0.133	5.336	0.405	0.446	0.000	-0.008	-0.033
52	i	118	GLY	0	0.044	0.037	9.735	0.101	0.101	0.000	0.000	0.000
53	i	119	ILE	0	0.001	-0.004	9.731	-0.173	-0.173	0.000	0.000	0.000
54	i	120	LYS	1	0.886	0.962	11.541	0.631	0.631	0.000	0.000	0.000
55	i	121	VAL	0	-0.024	0.001	13.207	-0.020	-0.020	0.000	0.000	0.000
56	i	122	SER	0	-0.054	-0.014	16.302	0.020	0.020	0.000	0.000	0.000
57	i	123	NME	0	0.079	0.066	18.157	-0.015	-0.015	0.000	0.000	0.000
58	i	130	ACE	0	0.059	-0.005	19.192	0.001	0.001	0.000	0.000	0.000
59	i	131	HIS	1	0.848	0.923	17.798	0.241	0.241	0.000	0.000	0.000
60	i	132	ARG	1	0.967	0.980	16.326	0.184	0.184	0.000	0.000	0.000
61	i	133	HIS	0	0.091	0.058	15.499	0.035	0.035	0.000	0.000	0.000
62	i	134	ALA	0	0.052	0.016	13.650	-0.070	-0.070	0.000	0.000	0.000
63	i	135	LEU	0	0.042	0.004	10.319	0.011	0.011	0.000	0.000	0.000
64	i	136	TYR	0	-0.006	0.011	14.363	0.016	0.016	0.000	0.000	0.000
65	i	137	LEU	0	-0.003	0.008	17.583	0.012	0.012	0.000	0.000	0.000
66	i	138	ILE	0	-0.056	-0.030	13.994	0.004	0.004	0.000	0.000	0.000
67	i	139	ILE	0	0.012	0.027	17.487	0.013	0.013	0.000	0.000	0.000
68	i	140	ARG	1	0.926	0.950	18.477	0.064	0.064	0.000	0.000	0.000
69	i	141	MET	0	-0.009	0.011	15.099	-0.025	-0.025	0.000	0.000	0.000
70	i	142	VAL	0	-0.036	-0.027	18.012	0.021	0.021	0.000	0.000	0.000
71	i	143	CYS	0	-0.060	-0.014	18.694	-0.006	-0.006	0.000	0.000	0.000
72	i	144	TYR	0	0.020	-0.003	20.911	0.010	0.010	0.000	0.000	0.000
73	i	145	ASP	-1	-0.869	-0.947	24.368	-0.070	-0.070	0.000	0.000	0.000
74	i	146	ASP	-1	-0.886	-0.951	26.752	-0.077	-0.077	0.000	0.000	0.000
75	i	147	GLY	0	0.003	0.022	28.982	0.005	0.005	0.000	0.000	0.000
76	i	148	LEU	0	-0.044	-0.028	32.049	0.004	0.004	0.000	0.000	0.000
77	i	149	GLY	0	-0.032	-0.003	31.420	-0.004	-0.004	0.000	0.000	0.000
78	i	150	ALA	0	0.059	-0.002	30.639	0.005	0.005	0.000	0.000	0.000
79	i	151	GLY	0	-0.053	0.004	26.653	-0.004	-0.004	0.000	0.000	0.000
80	i	152	LYS	1	0.876	0.938	25.087	0.079	0.079	0.000	0.000	0.000
81	i	153	SER	0	0.067	0.049	21.904	0.000	0.000	0.000	0.000	0.000
82	i	154	LEU	0	0.009	-0.002	23.492	-0.012	-0.012	0.000	0.000	0.000
83	i	155	LEU	0	-0.037	-0.009	17.045	-0.004	-0.004	0.000	0.000	0.000
84	i	156	ALA	0	0.042	0.021	20.340	0.010	0.010	0.000	0.000	0.000
85	i	157	LEU	0	-0.046	-0.030	16.262	-0.016	-0.016	0.000	0.000	0.000
86	i	158	LYS	1	0.958	0.987	20.065	0.072	0.072	0.000	0.000	0.000
87	i	159	THR	0	-0.047	-0.034	19.311	-0.013	-0.013	0.000	0.000	0.000
88	i	160	THR	0	0.039	0.009	21.924	0.010	0.010	0.000	0.000	0.000
89	i	161	ASP	-1	-0.746	-0.856	23.903	-0.087	-0.087	0.000	0.000	0.000
90	i	162	ALA	0	-0.047	-0.007	22.889	-0.002	-0.002	0.000	0.000	0.000
91	i	163	SER	0	-0.102	-0.060	24.929	0.004	0.004	0.000	0.000	0.000
92	i	164	ASN	0	-0.133	-0.075	27.644	0.007	0.007	0.000	0.000	0.000
93	i	165	GLU	-1	-0.899	-0.954	27.766	-0.056	-0.056	0.000	0.000	0.000
94	i	166	GLU	-1	-0.885	-0.949	29.028	-0.065	-0.065	0.000	0.000	0.000
95	i	167	TYR	0	-0.042	-0.020	26.736	-0.009	-0.009	0.000	0.000	0.000
96	i	168	SER	0	-0.032	-0.032	24.886	0.001	0.001	0.000	0.000	0.000
97	i	169	LEU	0	-0.051	-0.002	23.535	-0.007	-0.007	0.000	0.000	0.000
98	i	170	TRP	0	-0.030	-0.024	20.429	0.000	0.000	0.000	0.000	0.000
99	i	171	VAL	0	0.036	0.020	22.153	-0.004	-0.004	0.000	0.000	0.000
100	i	172	TYR	0	-0.016	-0.030	18.326	-0.018	-0.018	0.000	0.000	0.000
101	i	173	GLN	0	0.062	0.024	20.981	0.005	0.005	0.000	0.000	0.000
102	i	174	CYS	0	-0.071	-0.029	17.361	-0.027	-0.027	0.000	0.000	0.000
103	i	175	ASN	0	-0.002	-0.019	21.008	0.015	0.015	0.000	0.000	0.000
104	i	176	SER	0	0.010	0.010	20.693	0.007	0.007	0.000	0.000	0.000
105	i	177	LEU	0	0.112	0.057	20.974	-0.014	-0.014	0.000	0.000	0.000
106	i	178	GLU	-1	-0.882	-0.966	18.934	-0.062	-0.062	0.000	0.000	0.000
107	i	179	GLN	0	-0.043	-0.015	16.087	-0.026	-0.026	0.000	0.000	0.000
108	i	180	ALA	0	0.085	0.030	15.616	-0.031	-0.031	0.000	0.000	0.000
109	i	181	GLN	0	0.003	-0.006	16.260	-0.002	-0.002	0.000	0.000	0.000
110	i	182	ALA	0	-0.027	-0.011	12.758	0.011	0.011	0.000	0.000	0.000
111	i	183	ILE	0	-0.010	0.002	11.505	-0.025	-0.025	0.000	0.000	0.000
112	i	184	CYS	0	-0.009	0.002	11.424	-0.034	-0.034	0.000	0.000	0.000
113	i	185	LYS	1	0.964	0.977	11.352	0.012	0.012	0.000	0.000	0.000
114	i	186	VAL	0	0.014	0.011	5.920	0.054	0.054	0.000	0.000	0.000
115	i	187	LEU	0	-0.009	0.008	7.305	-0.029	-0.029	0.000	0.000	0.000
116	i	188	SER	0	-0.030	-0.023	9.672	0.034	0.034	0.000	0.000	0.000
117	i	189	THR	0	-0.056	-0.034	5.511	0.049	0.049	0.000	0.000	0.000
118	i	190	ALA	0	0.020	0.018	7.064	0.145	0.145	0.000	0.000	0.000
119	i	191	PHE	0	-0.012	-0.027	7.829	0.058	0.058	0.000	0.000	0.000
120	i	192	ASP	-1	-0.937	-0.958	10.108	0.279	0.279	0.000	0.000	0.000
121	i	193	SER	0	-0.061	-0.017	7.452	-0.001	-0.001	0.000	0.000	0.000
122	i	194	VAL	0	-0.070	-0.045	9.239	-0.034	-0.034	0.000	0.000	0.000
123	i	195	LEU	0	-0.032	0.002	11.466	-0.032	-0.032	0.000	0.000	0.000
124	i	196	NME	0	0.002	0.007	14.704	0.029	0.029	0.000	0.000	0.000

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