FMO DATABASE

FMODB ID: 9GYG2

Calculation Name: 4DX9-U-Xray321

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: U

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	-951876.395509
FMO2-HF: Nuclear repulsion	905276.881102
FMO2-HF: Total energy	-46599.514407
FMO2-MP2: Total energy	-46733.275466

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(U:59:ACE )

Summations of interaction energy for fragment #1(U: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.
0.816	2.162	0.444	-0.74	-1.049	0.001

Interaction energy analysis for fragmet #1(U: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 : -0.002

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	U	61	ALA	0	-0.011	0.019	3.847	0.936	1.679	-0.005	-0.327	-0.412	-0.001
4	U	62	GLU	-1	-0.922	-0.954	6.713	-0.617	-0.617	0.000	0.000	0.000	0.000
5	U	63	PHE	0	-0.007	0.001	8.373	0.111	0.111	0.000	0.000	0.000	0.000
6	U	64	ARG	1	0.925	0.980	13.021	0.185	0.185	0.000	0.000	0.000	0.000
7	U	65	ILE	0	-0.004	-0.004	16.098	0.021	0.021	0.000	0.000	0.000	0.000
8	U	66	LYS	1	0.993	1.005	18.622	0.114	0.114	0.000	0.000	0.000	0.000
9	U	67	TYR	0	0.011	-0.009	21.397	-0.005	-0.005	0.000	0.000	0.000	0.000
10	U	68	VAL	0	0.003	0.002	23.087	0.008	0.008	0.000	0.000	0.000	0.000
11	U	69	GLY	0	0.045	0.018	24.872	0.009	0.009	0.000	0.000	0.000	0.000
12	U	70	ALA	0	-0.027	-0.020	24.745	-0.010	-0.010	0.000	0.000	0.000	0.000
13	U	71	ILE	0	-0.004	0.014	26.397	0.008	0.008	0.000	0.000	0.000	0.000
14	U	72	GLU	-1	-0.925	-0.973	27.432	-0.101	-0.101	0.000	0.000	0.000	0.000
15	U	73	LYS	1	0.836	0.906	28.377	0.061	0.061	0.000	0.000	0.000	0.000
16	U	74	LEU	0	0.014	-0.001	27.520	0.006	0.006	0.000	0.000	0.000	0.000
17	U	75	NME	0	-0.023	0.017	30.308	0.000	0.000	0.000	0.000	0.000	0.000
18	U	83	ACE	0	-0.019	-0.023	24.853	0.001	0.001	0.000	0.000	0.000	0.000
19	U	84	GLY	0	0.071	0.016	24.773	0.002	0.002	0.000	0.000	0.000	0.000
20	U	85	PRO	0	-0.049	-0.032	22.144	-0.007	-0.007	0.000	0.000	0.000	0.000
21	U	86	LEU	0	0.075	0.021	23.965	-0.007	-0.007	0.000	0.000	0.000	0.000
22	U	87	ASP	-1	-0.885	-0.930	27.036	-0.017	-0.017	0.000	0.000	0.000	0.000
23	U	88	LEU	0	-0.071	-0.040	21.971	-0.004	-0.004	0.000	0.000	0.000	0.000
24	U	89	ILE	0	0.000	0.006	24.359	-0.004	-0.004	0.000	0.000	0.000	0.000
25	U	90	ASN	0	0.041	0.021	26.857	-0.002	-0.002	0.000	0.000	0.000	0.000
26	U	91	TYR	0	-0.006	-0.001	28.810	-0.001	-0.001	0.000	0.000	0.000	0.000
27	U	92	ILE	0	-0.013	-0.014	24.501	-0.003	-0.003	0.000	0.000	0.000	0.000
28	U	93	ASP	-1	-0.866	-0.926	28.975	-0.038	-0.038	0.000	0.000	0.000	0.000
29	U	94	VAL	0	-0.066	-0.034	31.665	0.001	0.001	0.000	0.000	0.000	0.000
30	U	95	ALA	0	-0.035	-0.037	30.792	0.000	0.000	0.000	0.000	0.000	0.000
31	U	96	GLN	0	-0.009	-0.008	28.647	0.002	0.002	0.000	0.000	0.000	0.000
32	U	97	GLN	0	-0.042	-0.012	33.079	0.001	0.001	0.000	0.000	0.000	0.000
33	U	98	ASP	-1	-0.854	-0.904	36.030	-0.034	-0.034	0.000	0.000	0.000	0.000
34	U	99	GLY	0	-0.048	-0.015	36.040	0.001	0.001	0.000	0.000	0.000	0.000
35	U	100	LYS	1	0.783	0.893	33.109	0.039	0.039	0.000	0.000	0.000	0.000
36	U	101	LEU	0	-0.002	0.001	27.761	-0.006	-0.006	0.000	0.000	0.000	0.000
37	U	102	PRO	0	0.003	0.020	29.577	0.005	0.005	0.000	0.000	0.000	0.000
38	U	103	PHE	0	0.041	0.007	30.152	-0.003	-0.003	0.000	0.000	0.000	0.000
39	U	104	VAL	0	-0.050	-0.033	29.500	-0.002	-0.002	0.000	0.000	0.000	0.000
40	U	105	PRO	0	-0.018	-0.002	25.407	0.000	0.000	0.000	0.000	0.000	0.000
41	U	106	PRO	0	0.018	0.022	27.095	0.005	0.005	0.000	0.000	0.000	0.000
42	U	107	GLU	-1	-0.952	-0.992	26.973	-0.088	-0.088	0.000	0.000	0.000	0.000
43	U	108	GLU	-1	-0.984	-0.985	25.440	-0.131	-0.131	0.000	0.000	0.000	0.000
44	U	109	GLU	-1	-0.961	-0.978	21.533	-0.150	-0.150	0.000	0.000	0.000	0.000
45	U	110	PHE	0	-0.011	-0.015	19.299	-0.011	-0.011	0.000	0.000	0.000	0.000
46	U	111	ILE	0	0.000	0.000	13.946	0.002	0.002	0.000	0.000	0.000	0.000
47	U	112	MET	0	-0.040	-0.018	12.168	-0.007	-0.007	0.000	0.000	0.000	0.000
48	U	113	GLY	0	0.011	0.003	10.113	-0.048	-0.048	0.000	0.000	0.000	0.000
49	U	114	VAL	0	-0.008	-0.001	6.219	0.118	0.118	0.000	0.000	0.000	0.000
50	U	115	SER	0	-0.007	-0.016	5.001	-0.712	-0.743	0.000	-0.017	0.049	0.000
51	U	116	LYS	1	1.015	0.987	2.472	-0.516	-0.095	0.440	-0.332	-0.529	0.002
52	U	117	TYR	0	-0.010	-0.001	6.023	0.226	0.226	0.000	0.000	0.000	0.000
53	U	118	GLY	0	0.014	0.017	8.692	0.164	0.164	0.000	0.000	0.000	0.000
54	U	119	ILE	0	-0.004	0.003	9.379	-0.220	-0.220	0.000	0.000	0.000	0.000
55	U	120	LYS	1	0.897	0.939	11.748	0.616	0.616	0.000	0.000	0.000	0.000
56	U	121	NME	0	0.051	0.041	13.605	-0.036	-0.036	0.000	0.000	0.000	0.000
57	U	130	ACE	0	0.041	0.016	20.601	-0.002	-0.002	0.000	0.000	0.000	0.000
58	U	131	HIS	1	0.907	0.951	18.735	0.200	0.200	0.000	0.000	0.000	0.000
59	U	132	ARG	1	0.976	0.976	15.756	0.265	0.265	0.000	0.000	0.000	0.000
60	U	133	HIS	0	0.037	0.045	15.138	0.027	0.027	0.000	0.000	0.000	0.000
61	U	134	ALA	0	0.053	0.020	13.954	-0.059	-0.059	0.000	0.000	0.000	0.000
62	U	135	LEU	0	0.052	0.002	8.998	0.007	0.007	0.000	0.000	0.000	0.000
63	U	136	TYR	0	-0.025	-0.008	12.774	0.036	0.036	0.000	0.000	0.000	0.000
64	U	137	LEU	0	-0.007	0.011	15.729	0.017	0.017	0.000	0.000	0.000	0.000
65	U	138	ILE	0	-0.038	-0.010	13.313	0.002	0.002	0.000	0.000	0.000	0.000
66	U	139	ILE	0	-0.010	0.013	16.583	0.020	0.020	0.000	0.000	0.000	0.000
67	U	140	ARG	1	0.920	0.964	17.642	0.031	0.031	0.000	0.000	0.000	0.000
68	U	141	MET	0	0.003	0.018	12.779	-0.014	-0.014	0.000	0.000	0.000	0.000
69	U	142	VAL	0	-0.024	-0.021	16.815	0.024	0.024	0.000	0.000	0.000	0.000
70	U	143	CYS	0	-0.067	-0.021	16.245	-0.010	-0.010	0.000	0.000	0.000	0.000
71	U	144	TYR	0	0.036	0.017	19.341	0.013	0.013	0.000	0.000	0.000	0.000
72	U	145	ASP	-1	-0.768	-0.891	22.626	-0.047	-0.047	0.000	0.000	0.000	0.000
73	U	146	ASP	-1	-0.926	-0.965	24.901	-0.053	-0.053	0.000	0.000	0.000	0.000
74	U	147	GLY	0	0.020	0.019	27.607	0.004	0.004	0.000	0.000	0.000	0.000
75	U	148	LEU	0	-0.066	-0.039	28.666	0.002	0.002	0.000	0.000	0.000	0.000
76	U	149	GLY	0	-0.007	0.005	26.400	0.003	0.003	0.000	0.000	0.000	0.000
77	U	150	ALA	0	-0.093	-0.048	25.959	-0.004	-0.004	0.000	0.000	0.000	0.000
78	U	151	GLY	0	0.003	-0.015	26.576	0.000	0.000	0.000	0.000	0.000	0.000
79	U	152	LYS	1	0.851	0.942	24.218	0.075	0.075	0.000	0.000	0.000	0.000
80	U	153	SER	0	0.066	0.040	20.841	0.004	0.004	0.000	0.000	0.000	0.000
81	U	154	LEU	0	0.021	0.015	22.004	-0.016	-0.016	0.000	0.000	0.000	0.000
82	U	155	LEU	0	-0.035	-0.037	14.940	0.005	0.005	0.000	0.000	0.000	0.000
83	U	156	ALA	0	0.029	0.016	19.438	-0.010	-0.010	0.000	0.000	0.000	0.000
84	U	157	LEU	0	-0.019	-0.025	14.826	-0.001	-0.001	0.000	0.000	0.000	0.000
85	U	158	LYS	1	0.966	0.995	18.926	0.051	0.051	0.000	0.000	0.000	0.000
86	U	159	THR	0	-0.001	-0.004	18.149	-0.007	-0.007	0.000	0.000	0.000	0.000
87	U	160	THR	0	-0.018	-0.018	20.745	0.012	0.012	0.000	0.000	0.000	0.000
88	U	161	ASP	-1	-0.833	-0.897	22.227	-0.112	-0.112	0.000	0.000	0.000	0.000
89	U	162	ALA	0	-0.024	-0.023	25.063	0.009	0.009	0.000	0.000	0.000	0.000
90	U	163	SER	0	-0.025	-0.040	27.338	-0.002	-0.002	0.000	0.000	0.000	0.000
91	U	164	ASN	0	-0.099	-0.055	23.433	-0.001	-0.001	0.000	0.000	0.000	0.000
92	U	165	GLU	-1	-0.886	-0.895	26.018	-0.027	-0.027	0.000	0.000	0.000	0.000
93	U	166	GLU	-1	-0.838	-0.899	27.968	-0.050	-0.050	0.000	0.000	0.000	0.000
94	U	167	TYR	0	-0.033	-0.030	24.576	-0.003	-0.003	0.000	0.000	0.000	0.000
95	U	168	SER	0	0.008	-0.010	23.905	0.004	0.004	0.000	0.000	0.000	0.000
96	U	169	LEU	0	-0.043	-0.013	23.119	-0.005	-0.005	0.000	0.000	0.000	0.000
97	U	170	TRP	0	-0.012	-0.026	20.100	-0.009	-0.009	0.000	0.000	0.000	0.000
98	U	171	VAL	0	0.044	0.021	20.915	-0.004	-0.004	0.000	0.000	0.000	0.000
99	U	172	TYR	0	-0.045	-0.036	18.530	-0.014	-0.014	0.000	0.000	0.000	0.000
100	U	173	GLN	0	0.041	0.016	20.947	0.013	0.013	0.000	0.000	0.000	0.000
101	U	174	CYS	0	-0.029	0.004	17.428	-0.027	-0.027	0.000	0.000	0.000	0.000
102	U	175	ASN	0	-0.040	-0.033	19.837	0.007	0.007	0.000	0.000	0.000	0.000
103	U	176	SER	0	0.063	0.025	19.494	0.013	0.013	0.000	0.000	0.000	0.000
104	U	177	LEU	0	0.083	0.040	19.354	-0.013	-0.013	0.000	0.000	0.000	0.000
105	U	178	GLU	-1	-0.867	-0.935	17.826	-0.010	-0.010	0.000	0.000	0.000	0.000
106	U	179	GLN	0	-0.053	-0.029	14.663	0.014	0.014	0.000	0.000	0.000	0.000
107	U	180	ALA	0	0.051	0.016	14.157	-0.034	-0.034	0.000	0.000	0.000	0.000
108	U	181	GLN	0	0.009	-0.010	14.603	-0.010	-0.010	0.000	0.000	0.000	0.000
109	U	182	ALA	0	-0.025	-0.002	11.240	0.024	0.024	0.000	0.000	0.000	0.000
110	U	183	ILE	0	0.005	-0.002	9.687	-0.018	-0.018	0.000	0.000	0.000	0.000
111	U	184	CYS	0	0.022	0.010	9.674	-0.036	-0.036	0.000	0.000	0.000	0.000
112	U	185	LYS	1	0.933	0.975	9.263	-0.128	-0.128	0.000	0.000	0.000	0.000
113	U	186	VAL	0	-0.008	-0.008	3.957	0.037	0.119	0.001	-0.017	-0.066	0.000
114	U	187	LEU	0	0.009	0.000	5.632	-0.002	-0.002	0.000	0.000	0.000	0.000
115	U	188	SER	0	0.013	0.000	8.319	0.051	0.051	0.000	0.000	0.000	0.000
116	U	189	THR	0	-0.011	0.009	3.666	0.092	0.223	0.008	-0.047	-0.091	0.000
117	U	190	ALA	0	-0.044	-0.024	5.561	0.152	0.152	0.000	0.000	0.000	0.000
118	U	191	PHE	0	-0.014	-0.025	6.341	-0.040	-0.040	0.000	0.000	0.000	0.000
119	U	192	ASP	-1	-0.876	-0.927	9.021	0.373	0.373	0.000	0.000	0.000	0.000
120	U	193	SER	0	-0.160	-0.078	5.887	0.234	0.234	0.000	0.000	0.000	0.000
121	U	194	VAL	0	-0.076	-0.032	7.938	-0.060	-0.060	0.000	0.000	0.000	0.000
122	U	195	NME	0	0.005	0.022	10.489	-0.039	-0.039	0.000	0.000	0.000	0.000

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