FMO DATABASE

FMODB ID: ZY4MN

Calculation Name: 4DX9-0-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: 0

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	OptHSide
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	117
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-926402.399147
FMO2-HF: Nuclear repulsion	880233.068716
FMO2-HF: Total energy	-46169.330431
FMO2-MP2: Total energy	-46301.785223

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(0:60:CYS)

Summations of interaction energy for fragment #1(0:60: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.
-12.074	-7.744	7.371	-5.539	-6.162	-0.022

Interaction energy analysis for fragmet #1(0:60:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.009

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.	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	62	GLU	-1	-0.911	-0.953	3.252	-2.183	0.478	-0.006	-1.171	-1.484	0.003
4	63	PHE	0	-0.019	-0.022	5.346	-0.046	-0.026	-0.001	-0.003	-0.016	0.000
5	64	ARG	1	0.963	0.987	9.096	0.846	0.846	0.000	0.000	0.000	0.000
6	65	ILE	0	-0.050	-0.025	12.029	-0.005	-0.005	0.000	0.000	0.000	0.000
7	66	LYS	1	0.855	0.913	14.416	0.229	0.229	0.000	0.000	0.000	0.000
8	67	TYR	0	0.017	0.013	17.459	0.025	0.025	0.000	0.000	0.000	0.000
9	68	VAL	0	0.034	0.007	18.741	-0.018	-0.018	0.000	0.000	0.000	0.000
10	69	GLY	0	0.032	0.024	22.186	0.012	0.012	0.000	0.000	0.000	0.000
11	70	ALA	0	-0.051	-0.037	22.500	0.016	0.016	0.000	0.000	0.000	0.000
12	71	ILE	0	-0.031	-0.013	24.230	-0.006	-0.006	0.000	0.000	0.000	0.000
13	84	GLY	0	0.037	-0.005	25.716	0.006	0.006	0.000	0.000	0.000	0.000
14	85	PRO	0	-0.065	-0.035	22.848	0.011	0.011	0.000	0.000	0.000	0.000
15	86	LEU	0	0.093	0.021	23.770	-0.007	-0.007	0.000	0.000	0.000	0.000
16	87	ASP	-1	-0.956	-0.966	26.562	0.037	0.037	0.000	0.000	0.000	0.000
17	88	LEU	0	-0.010	-0.008	21.434	0.013	0.013	0.000	0.000	0.000	0.000
18	89	ILE	0	-0.024	0.004	23.565	0.008	0.008	0.000	0.000	0.000	0.000
19	90	ASN	0	0.036	0.016	25.866	-0.002	-0.002	0.000	0.000	0.000	0.000
20	91	TYR	0	-0.043	-0.012	26.998	0.006	0.006	0.000	0.000	0.000	0.000
21	92	ILE	0	-0.016	-0.025	22.989	0.011	0.011	0.000	0.000	0.000	0.000
22	93	ASP	-1	-0.798	-0.903	27.546	-0.035	-0.035	0.000	0.000	0.000	0.000
23	94	VAL	0	-0.013	-0.004	30.096	-0.004	-0.004	0.000	0.000	0.000	0.000
24	95	ALA	0	-0.015	-0.009	29.003	0.003	0.003	0.000	0.000	0.000	0.000
25	96	GLN	0	-0.021	-0.024	27.246	0.000	0.000	0.000	0.000	0.000	0.000
26	97	GLN	0	-0.037	-0.011	31.272	0.000	0.000	0.000	0.000	0.000	0.000
27	98	ASP	-1	-0.857	-0.889	34.603	0.033	0.033	0.000	0.000	0.000	0.000
28	99	GLY	0	0.000	0.000	34.118	0.000	0.000	0.000	0.000	0.000	0.000
29	100	LYS	1	0.765	0.863	31.623	-0.043	-0.043	0.000	0.000	0.000	0.000
30	101	LEU	0	-0.007	0.006	25.332	0.008	0.008	0.000	0.000	0.000	0.000
31	102	PRO	0	-0.009	0.006	26.192	-0.008	-0.008	0.000	0.000	0.000	0.000
32	103	PHE	0	0.030	0.006	27.221	-0.003	-0.003	0.000	0.000	0.000	0.000
33	104	VAL	0	-0.012	-0.010	26.856	-0.015	-0.015	0.000	0.000	0.000	0.000
34	105	PRO	0	-0.041	-0.011	22.285	0.015	0.015	0.000	0.000	0.000	0.000
35	106	PRO	0	0.039	0.012	22.734	-0.014	-0.014	0.000	0.000	0.000	0.000
36	107	GLU	-1	-0.845	-0.899	21.808	-0.191	-0.191	0.000	0.000	0.000	0.000
37	108	GLU	-1	-0.956	-0.971	19.692	0.054	0.054	0.000	0.000	0.000	0.000
38	109	GLU	-1	-0.933	-0.982	16.110	-0.329	-0.329	0.000	0.000	0.000	0.000
39	110	PHE	0	-0.034	-0.021	12.980	0.057	0.057	0.000	0.000	0.000	0.000
40	111	ILE	0	-0.015	-0.012	7.784	-0.157	-0.157	0.000	0.000	0.000	0.000
41	112	MET	0	-0.037	0.001	8.296	0.229	0.229	0.000	0.000	0.000	0.000
42	113	GLY	0	0.062	0.020	4.145	-1.082	-0.963	0.015	-0.051	-0.083	0.000
43	114	VAL	0	-0.041	-0.016	4.272	1.082	1.509	0.005	-0.111	-0.320	0.000
44	115	SER	0	0.041	-0.002	2.006	-5.832	-3.787	7.326	-5.703	-3.668	-0.024
45	116	LYS	1	0.951	0.968	3.001	-2.773	-3.938	0.028	1.553	-0.416	-0.001
46	117	TYR	0	0.002	0.006	6.347	-0.818	-0.818	0.000	0.000	0.000	0.000
47	118	GLY	0	-0.006	-0.011	7.371	-0.661	-0.661	0.000	0.000	0.000	0.000
48	119	ILE	0	-0.020	0.003	6.942	0.648	0.648	0.000	0.000	0.000	0.000
49	120	LYS	1	0.855	0.925	7.628	-1.293	-1.293	0.000	0.000	0.000	0.000
50	121	VAL	0	0.015	0.012	8.705	-0.096	-0.096	0.000	0.000	0.000	0.000
51	122	SER	0	0.032	0.032	10.486	0.116	0.116	0.000	0.000	0.000	0.000
52	123	THR	0	0.046	0.032	11.828	-0.068	-0.068	0.000	0.000	0.000	0.000
53	124	SER	0	-0.031	-0.045	12.664	-0.013	-0.013	0.000	0.000	0.000	0.000
54	125	ASP	-1	-0.868	-0.908	14.838	0.036	0.036	0.000	0.000	0.000	0.000
55	126	GLN	0	-0.013	0.011	16.753	-0.011	-0.011	0.000	0.000	0.000	0.000
56	127	TYR	0	-0.049	-0.044	17.471	0.061	0.061	0.000	0.000	0.000	0.000
57	128	ASP	-1	-0.865	-0.924	16.732	0.259	0.259	0.000	0.000	0.000	0.000
58	129	VAL	0	-0.050	-0.037	13.699	0.053	0.053	0.000	0.000	0.000	0.000
59	130	LEU	0	-0.039	-0.009	12.517	0.159	0.159	0.000	0.000	0.000	0.000
60	131	HIS	0	0.012	0.005	14.062	0.055	0.055	0.000	0.000	0.000	0.000
61	132	ARG	1	0.937	0.952	12.640	-0.908	-0.908	0.000	0.000	0.000	0.000
62	133	HIS	0	0.014	0.019	12.393	-0.066	-0.066	0.000	0.000	0.000	0.000
63	134	ALA	0	0.025	0.008	11.604	0.218	0.218	0.000	0.000	0.000	0.000
64	135	LEU	0	0.064	0.013	8.751	-0.138	-0.138	0.000	0.000	0.000	0.000
65	136	TYR	0	-0.021	-0.011	11.863	-0.097	-0.097	0.000	0.000	0.000	0.000
66	137	LEU	0	-0.034	-0.013	15.140	-0.100	-0.100	0.000	0.000	0.000	0.000
67	138	ILE	0	-0.031	0.002	11.326	-0.089	-0.089	0.000	0.000	0.000	0.000
68	139	ILE	0	-0.010	0.000	15.051	-0.015	-0.015	0.000	0.000	0.000	0.000
69	140	ARG	1	0.943	0.966	17.033	-0.092	-0.092	0.000	0.000	0.000	0.000
70	141	MET	0	-0.033	0.015	10.659	0.062	0.062	0.000	0.000	0.000	0.000
71	142	VAL	0	-0.013	-0.008	16.025	-0.042	-0.042	0.000	0.000	0.000	0.000
72	143	CYS	0	-0.027	-0.002	16.543	-0.008	-0.008	0.000	0.000	0.000	0.000
73	144	TYR	0	-0.018	-0.003	18.626	-0.019	-0.019	0.000	0.000	0.000	0.000
74	145	ASP	-1	-0.869	-0.957	22.038	-0.230	-0.230	0.000	0.000	0.000	0.000
75	146	ASP	-1	-0.928	-0.969	24.278	-0.097	-0.097	0.000	0.000	0.000	0.000
76	147	GLY	0	0.023	0.017	26.058	0.015	0.015	0.000	0.000	0.000	0.000
77	148	LEU	0	-0.058	-0.007	28.609	0.010	0.010	0.000	0.000	0.000	0.000
78	149	GLY	0	0.008	-0.011	29.859	0.009	0.009	0.000	0.000	0.000	0.000
79	150	ALA	0	-0.055	-0.046	28.449	-0.005	-0.005	0.000	0.000	0.000	0.000
80	151	GLY	0	0.002	0.007	25.311	-0.005	-0.005	0.000	0.000	0.000	0.000
81	152	LYS	1	0.925	0.967	22.384	0.226	0.226	0.000	0.000	0.000	0.000
82	153	SER	0	0.021	0.025	18.708	0.013	0.013	0.000	0.000	0.000	0.000
83	154	LEU	0	0.013	0.003	20.662	0.015	0.015	0.000	0.000	0.000	0.000
84	155	LEU	0	-0.040	-0.023	13.102	0.011	0.011	0.000	0.000	0.000	0.000
85	156	ALA	0	0.042	0.012	17.579	0.036	0.036	0.000	0.000	0.000	0.000
86	157	LEU	0	-0.030	-0.021	13.179	-0.007	-0.007	0.000	0.000	0.000	0.000
87	158	LYS	1	0.979	0.996	16.574	-0.163	-0.163	0.000	0.000	0.000	0.000
88	159	THR	0	0.005	0.012	16.355	0.038	0.038	0.000	0.000	0.000	0.000
89	168	SER	0	0.024	0.011	22.393	-0.002	-0.002	0.000	0.000	0.000	0.000
90	169	LEU	0	-0.028	-0.015	20.799	0.026	0.026	0.000	0.000	0.000	0.000
91	170	TRP	0	-0.016	-0.010	17.718	-0.005	-0.005	0.000	0.000	0.000	0.000
92	171	VAL	0	0.042	0.021	19.152	-0.019	-0.019	0.000	0.000	0.000	0.000
93	172	TYR	0	0.004	-0.006	15.325	0.032	0.032	0.000	0.000	0.000	0.000
94	173	GLN	0	0.060	0.059	17.770	-0.057	-0.057	0.000	0.000	0.000	0.000
95	174	CYS	0	-0.046	-0.022	15.638	-0.044	-0.044	0.000	0.000	0.000	0.000
96	175	ASN	0	0.016	-0.013	15.360	0.034	0.034	0.000	0.000	0.000	0.000
97	176	SER	0	-0.017	-0.026	18.017	0.005	0.005	0.000	0.000	0.000	0.000
98	177	LEU	0	0.048	0.027	19.126	0.035	0.035	0.000	0.000	0.000	0.000
99	178	GLU	-1	-0.792	-0.908	17.179	-0.537	-0.537	0.000	0.000	0.000	0.000
100	179	GLN	0	-0.001	0.005	13.953	-0.136	-0.136	0.000	0.000	0.000	0.000
101	180	ALA	0	0.039	0.027	12.753	-0.103	-0.103	0.000	0.000	0.000	0.000
102	181	GLN	0	-0.005	-0.014	13.419	0.018	0.018	0.000	0.000	0.000	0.000
103	182	ALA	0	-0.030	-0.003	10.323	-0.046	-0.046	0.000	0.000	0.000	0.000
104	183	ILE	0	0.016	0.012	8.628	-0.248	-0.248	0.000	0.000	0.000	0.000
105	184	CYS	0	-0.013	-0.015	9.051	0.151	0.151	0.000	0.000	0.000	0.000
106	185	LYS	1	0.961	0.981	9.709	0.769	0.769	0.000	0.000	0.000	0.000
107	186	VAL	0	-0.009	-0.010	3.586	-0.208	0.015	0.004	-0.053	-0.175	0.000
108	187	LEU	0	0.002	-0.001	5.879	0.398	0.398	0.000	0.000	0.000	0.000
109	188	SER	0	-0.044	-0.027	8.268	0.249	0.249	0.000	0.000	0.000	0.000
110	189	THR	0	0.049	0.032	5.635	0.132	0.132	0.000	0.000	0.000	0.000
111	190	ALA	0	-0.027	0.001	5.858	0.344	0.344	0.000	0.000	0.000	0.000
112	191	PHE	0	0.007	-0.022	7.302	0.249	0.249	0.000	0.000	0.000	0.000
113	192	ASP	-1	-0.920	-0.961	10.778	-0.030	-0.030	0.000	0.000	0.000	0.000
114	193	SER	0	-0.107	-0.045	8.534	0.067	0.067	0.000	0.000	0.000	0.000
115	194	VAL	0	-0.063	-0.044	9.711	0.011	0.011	0.000	0.000	0.000	0.000
116	195	LEU	0	-0.032	0.005	12.233	-0.028	-0.028	0.000	0.000	0.000	0.000
117	196	THR	0	-0.018	0.005	14.739	-0.078	-0.078	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(0:60:CYS)