FMO DATABASE

FMODB ID: ZY2YN

Calculation Name: 4DX9-k-Xray321

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: k

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	127
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1025851.168543
FMO2-HF: Nuclear repulsion	976724.88885
FMO2-HF: Total energy	-49126.279694
FMO2-MP2: Total energy	-49267.254587

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(k:59:ACE )

Summations of interaction energy for fragment #1(k: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.
15.809	1.276	7.515	9.028	-2.011	-0.008

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / 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

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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	k	61	ALA	0	-0.045	-0.011	3.776	1.706	2.192	-0.006	-0.178	-0.302	0.000
4	k	62	GLU	-1	-0.934	-0.960	6.686	-0.531	-0.531	0.000	0.000	0.000	0.000
5	k	63	PHE	0	-0.028	-0.018	9.126	0.152	0.152	0.000	0.000	0.000	0.000
6	k	64	ARG	1	0.953	0.983	13.364	0.104	0.104	0.000	0.000	0.000	0.000
7	k	65	ILE	0	-0.010	-0.005	16.832	0.030	0.030	0.000	0.000	0.000	0.000
8	k	66	LYS	1	1.031	1.025	19.279	0.069	0.069	0.000	0.000	0.000	0.000
9	k	67	TYR	0	0.006	-0.005	21.861	-0.007	-0.007	0.000	0.000	0.000	0.000
10	k	68	VAL	0	-0.011	-0.001	23.815	0.009	0.009	0.000	0.000	0.000	0.000
11	k	69	GLY	0	0.037	0.005	25.682	0.007	0.007	0.000	0.000	0.000	0.000
12	k	70	ALA	0	-0.023	-0.014	25.545	-0.010	-0.010	0.000	0.000	0.000	0.000
13	k	71	ILE	0	-0.053	-0.017	27.229	0.009	0.009	0.000	0.000	0.000	0.000
14	k	72	GLU	-1	-0.876	-0.924	28.383	-0.102	-0.102	0.000	0.000	0.000	0.000
15	k	73	NME	0	0.011	0.013	29.987	0.002	0.002	0.000	0.000	0.000	0.000
16	k	83	ACE	0	0.012	-0.008	26.672	-0.002	-0.002	0.000	0.000	0.000	0.000
17	k	84	GLY	0	0.016	0.001	26.600	0.006	0.006	0.000	0.000	0.000	0.000
18	k	85	PRO	0	-0.042	-0.021	23.434	-0.006	-0.006	0.000	0.000	0.000	0.000
19	k	86	LEU	0	0.068	0.017	24.969	-0.003	-0.003	0.000	0.000	0.000	0.000
20	k	87	ASP	-1	-0.901	-0.943	28.246	-0.023	-0.023	0.000	0.000	0.000	0.000
21	k	88	LEU	0	-0.041	-0.033	23.136	-0.004	-0.004	0.000	0.000	0.000	0.000
22	k	89	ILE	0	0.007	0.015	25.206	-0.004	-0.004	0.000	0.000	0.000	0.000
23	k	90	ASN	0	0.043	0.011	27.918	-0.001	-0.001	0.000	0.000	0.000	0.000
24	k	91	TYR	0	-0.051	-0.018	29.468	0.001	0.001	0.000	0.000	0.000	0.000
25	k	92	ILE	0	-0.033	-0.015	25.488	-0.004	-0.004	0.000	0.000	0.000	0.000
26	k	93	ASP	-1	-0.847	-0.927	29.834	-0.030	-0.030	0.000	0.000	0.000	0.000
27	k	94	VAL	0	-0.065	-0.026	32.679	0.001	0.001	0.000	0.000	0.000	0.000
28	k	95	ALA	0	-0.001	-0.008	32.187	0.000	0.000	0.000	0.000	0.000	0.000
29	k	96	GLN	0	-0.008	-0.018	29.951	0.001	0.001	0.000	0.000	0.000	0.000
30	k	97	GLN	0	-0.064	-0.016	34.217	0.002	0.002	0.000	0.000	0.000	0.000
31	k	98	ASP	-1	-0.943	-0.952	37.874	-0.034	-0.034	0.000	0.000	0.000	0.000
32	k	99	GLY	0	-0.034	-0.018	37.435	0.001	0.001	0.000	0.000	0.000	0.000
33	k	100	LYS	1	0.860	0.944	33.771	0.051	0.051	0.000	0.000	0.000	0.000
34	k	101	LEU	0	-0.009	-0.004	28.427	-0.005	-0.005	0.000	0.000	0.000	0.000
35	k	102	PRO	0	0.012	0.016	30.781	0.005	0.005	0.000	0.000	0.000	0.000
36	k	103	PHE	0	0.034	0.006	31.090	-0.003	-0.003	0.000	0.000	0.000	0.000
37	k	104	VAL	0	-0.043	-0.021	30.781	0.000	0.000	0.000	0.000	0.000	0.000
38	k	105	PRO	0	-0.028	-0.002	26.863	-0.001	-0.001	0.000	0.000	0.000	0.000
39	k	106	PRO	0	0.023	-0.003	28.539	0.005	0.005	0.000	0.000	0.000	0.000
40	k	107	GLU	-1	-0.962	-0.981	28.159	-0.067	-0.067	0.000	0.000	0.000	0.000
41	k	108	GLU	-1	-0.970	-0.976	26.814	-0.108	-0.108	0.000	0.000	0.000	0.000
42	k	109	GLU	-1	-0.990	-0.992	22.139	-0.106	-0.106	0.000	0.000	0.000	0.000
43	k	110	PHE	0	-0.068	-0.057	19.890	-0.011	-0.011	0.000	0.000	0.000	0.000
44	k	111	ILE	0	-0.009	-0.001	14.460	0.013	0.013	0.000	0.000	0.000	0.000
45	k	112	MET	0	-0.034	-0.019	12.856	-0.008	-0.008	0.000	0.000	0.000	0.000
46	k	113	GLY	0	0.025	0.008	10.641	0.000	0.000	0.000	0.000	0.000	0.000
47	k	114	VAL	0	-0.033	-0.013	7.184	0.040	0.040	0.000	0.000	0.000	0.000
48	k	115	SER	0	0.092	0.040	5.949	-0.401	-0.401	0.000	0.000	0.000	0.000
49	k	116	LYN	0	-0.044	-0.025	2.428	14.214	-0.805	7.521	9.206	-1.709	-0.008
50	k	117	TYR	0	-0.038	-0.017	7.000	0.315	0.315	0.000	0.000	0.000	0.000
51	k	118	GLY	0	0.011	0.002	10.287	0.175	0.175	0.000	0.000	0.000	0.000
52	k	119	ILE	0	-0.028	0.001	11.187	-0.131	-0.131	0.000	0.000	0.000	0.000
53	k	120	LYS	1	0.849	0.927	12.624	0.558	0.558	0.000	0.000	0.000	0.000
54	k	121	VAL	0	0.003	0.010	14.670	-0.002	-0.002	0.000	0.000	0.000	0.000
55	k	122	SER	0	0.033	0.012	17.528	0.011	0.011	0.000	0.000	0.000	0.000
56	k	123	THR	0	0.052	0.018	19.221	-0.005	-0.005	0.000	0.000	0.000	0.000
57	k	124	SER	0	-0.013	-0.045	20.223	-0.017	-0.017	0.000	0.000	0.000	0.000
58	k	125	ASP	-1	-0.849	-0.876	20.800	-0.165	-0.165	0.000	0.000	0.000	0.000
59	k	126	GLN	0	-0.075	-0.034	20.430	-0.014	-0.014	0.000	0.000	0.000	0.000
60	k	127	TYR	0	-0.013	-0.014	17.265	-0.035	-0.035	0.000	0.000	0.000	0.000
61	k	128	ASP	-1	-0.762	-0.860	17.208	-0.320	-0.320	0.000	0.000	0.000	0.000
62	k	129	VAL	0	-0.069	-0.052	18.046	-0.014	-0.014	0.000	0.000	0.000	0.000
63	k	130	LEU	0	-0.001	0.009	20.466	0.024	0.024	0.000	0.000	0.000	0.000
64	k	131	HIS	1	0.877	0.941	19.279	0.204	0.204	0.000	0.000	0.000	0.000
65	k	132	ARG	1	0.896	0.936	16.710	0.303	0.303	0.000	0.000	0.000	0.000
66	k	133	HIS	0	0.002	0.015	15.893	0.019	0.019	0.000	0.000	0.000	0.000
67	k	134	ALA	0	0.061	0.030	14.854	-0.068	-0.068	0.000	0.000	0.000	0.000
68	k	135	LEU	0	0.071	0.022	9.745	0.050	0.050	0.000	0.000	0.000	0.000
69	k	136	TYR	0	-0.008	-0.006	14.133	0.032	0.032	0.000	0.000	0.000	0.000
70	k	137	LEU	0	-0.019	-0.001	17.415	0.021	0.021	0.000	0.000	0.000	0.000
71	k	138	ILE	0	-0.019	0.003	13.777	0.021	0.021	0.000	0.000	0.000	0.000
72	k	139	ILE	0	-0.034	-0.007	17.561	0.019	0.019	0.000	0.000	0.000	0.000
73	k	140	ARG	1	0.921	0.948	18.374	0.048	0.048	0.000	0.000	0.000	0.000
74	k	141	MET	0	0.029	0.033	13.757	-0.008	-0.008	0.000	0.000	0.000	0.000
75	k	142	VAL	0	-0.043	-0.026	17.753	0.023	0.023	0.000	0.000	0.000	0.000
76	k	143	CYS	0	-0.027	-0.002	18.029	-0.008	-0.008	0.000	0.000	0.000	0.000
77	k	144	TYR	0	0.010	-0.002	20.391	0.010	0.010	0.000	0.000	0.000	0.000
78	k	145	ASP	-1	-0.871	-0.954	23.644	-0.014	-0.014	0.000	0.000	0.000	0.000
79	k	146	ASP	-1	-0.850	-0.937	26.012	-0.028	-0.028	0.000	0.000	0.000	0.000
80	k	147	GLY	0	0.019	0.020	28.474	0.001	0.001	0.000	0.000	0.000	0.000
81	k	148	LEU	0	-0.079	-0.033	31.330	0.002	0.002	0.000	0.000	0.000	0.000
82	k	149	GLY	0	-0.001	-0.017	32.218	-0.001	-0.001	0.000	0.000	0.000	0.000
83	k	150	ALA	0	-0.071	-0.037	30.893	0.004	0.004	0.000	0.000	0.000	0.000
84	k	151	GLY	0	-0.013	0.018	28.780	-0.003	-0.003	0.000	0.000	0.000	0.000
85	k	152	LYS	1	0.888	0.960	25.019	0.047	0.047	0.000	0.000	0.000	0.000
86	k	153	SER	0	0.014	-0.015	21.358	0.000	0.000	0.000	0.000	0.000	0.000
87	k	154	LEU	0	0.008	0.014	22.622	-0.012	-0.012	0.000	0.000	0.000	0.000
88	k	155	LEU	0	-0.013	-0.033	16.346	0.008	0.008	0.000	0.000	0.000	0.000
89	k	156	ALA	0	0.001	0.023	20.263	-0.015	-0.015	0.000	0.000	0.000	0.000
90	k	157	LEU	0	0.000	-0.015	15.701	-0.001	-0.001	0.000	0.000	0.000	0.000
91	k	158	LYS	1	0.932	0.974	19.664	0.068	0.068	0.000	0.000	0.000	0.000
92	k	159	THR	0	-0.013	-0.017	18.886	-0.018	-0.018	0.000	0.000	0.000	0.000
93	k	160	THR	0	-0.030	-0.015	21.290	0.019	0.019	0.000	0.000	0.000	0.000
94	k	161	ASP	-1	-0.883	-0.941	23.108	-0.149	-0.149	0.000	0.000	0.000	0.000
95	k	162	ALA	0	-0.037	-0.018	25.770	0.003	0.003	0.000	0.000	0.000	0.000
96	k	163	SER	0	-0.048	-0.040	28.481	0.005	0.005	0.000	0.000	0.000	0.000
97	k	164	ASN	0	-0.087	-0.054	29.378	-0.002	-0.002	0.000	0.000	0.000	0.000
98	k	165	GLU	-1	-0.902	-0.936	30.343	-0.055	-0.055	0.000	0.000	0.000	0.000
99	k	166	GLU	-1	-0.882	-0.930	29.166	-0.082	-0.082	0.000	0.000	0.000	0.000
100	k	167	TYR	0	-0.071	-0.041	25.626	-0.006	-0.006	0.000	0.000	0.000	0.000
101	k	168	SER	0	0.051	0.029	25.055	0.006	0.006	0.000	0.000	0.000	0.000
102	k	169	LEU	0	-0.064	-0.033	23.399	-0.008	-0.008	0.000	0.000	0.000	0.000
103	k	170	TRP	0	-0.025	-0.026	20.968	0.001	0.001	0.000	0.000	0.000	0.000
104	k	171	VAL	0	0.014	0.004	21.750	-0.002	-0.002	0.000	0.000	0.000	0.000
105	k	172	TYR	0	0.025	0.011	19.131	-0.012	-0.012	0.000	0.000	0.000	0.000
106	k	173	GLN	0	0.049	0.002	21.604	0.013	0.013	0.000	0.000	0.000	0.000
107	k	174	CYS	0	-0.033	-0.005	17.862	-0.017	-0.017	0.000	0.000	0.000	0.000
108	k	175	ASN	0	0.017	-0.007	20.679	0.004	0.004	0.000	0.000	0.000	0.000
109	k	176	SER	0	0.033	0.009	20.426	0.011	0.011	0.000	0.000	0.000	0.000
110	k	177	LEU	0	0.068	0.063	20.602	-0.010	-0.010	0.000	0.000	0.000	0.000
111	k	178	GLU	-1	-0.891	-0.962	18.186	0.067	0.067	0.000	0.000	0.000	0.000
112	k	179	GLN	0	-0.019	-0.014	15.449	0.018	0.018	0.000	0.000	0.000	0.000
113	k	180	ALA	0	0.057	0.025	14.878	-0.019	-0.019	0.000	0.000	0.000	0.000
114	k	181	GLN	0	0.003	-0.006	15.509	-0.014	-0.014	0.000	0.000	0.000	0.000
115	k	182	ALA	0	-0.042	-0.018	11.742	0.022	0.022	0.000	0.000	0.000	0.000
116	k	183	ILE	0	0.021	0.011	10.453	0.017	0.017	0.000	0.000	0.000	0.000
117	k	184	CYS	0	-0.014	-0.012	10.600	-0.046	-0.046	0.000	0.000	0.000	0.000
118	k	185	LYS	1	0.922	0.962	9.780	-0.216	-0.216	0.000	0.000	0.000	0.000
119	k	186	VAL	0	0.003	0.006	4.891	0.121	0.121	0.000	0.000	0.000	0.000
120	k	187	LEU	0	0.045	0.009	6.533	-0.084	-0.084	0.000	0.000	0.000	0.000
121	k	188	SER	0	-0.068	-0.016	9.251	0.015	0.015	0.000	0.000	0.000	0.000
122	k	189	THR	0	-0.023	-0.011	5.776	0.114	0.114	0.000	0.000	0.000	0.000
123	k	190	ALA	0	0.009	0.012	6.157	0.009	0.009	0.000	0.000	0.000	0.000
124	k	191	PHE	0	-0.038	-0.024	7.445	-0.064	-0.064	0.000	0.000	0.000	0.000
125	k	192	ASP	-1	-0.942	-0.956	10.631	0.098	0.098	0.000	0.000	0.000	0.000
126	k	193	SER	0	-0.092	-0.043	8.110	0.029	0.029	0.000	0.000	0.000	0.000
127	k	194	NME	0	-0.018	0.001	10.280	-0.018	-0.018	0.000	0.000	0.000	0.000

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