FMO DATABASE

FMODB ID: M3QKZ

Calculation Name: 4DX9-2-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: 2

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	OptH
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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-682533.776204
FMO2-HF: Nuclear repulsion	644112.291083
FMO2-HF: Total energy	-38421.48512
FMO2-MP2: Total energy	-38530.671923

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(2:60:CYS)

Summations of interaction energy for fragment #1(2:60: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.
-9.277	-3.843	2.335	-3.717	-4.051	-0.017

Interaction energy analysis for fragmet #1(2:60:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.013

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	2	62	GLU	-1	-0.933	-0.958	3.814	0.403	2.552	-0.027	-0.979	-1.143	0.003
4	2	63	PHE	0	0.004	0.000	6.422	-0.179	-0.151	-0.001	-0.001	-0.025	0.000
5	2	64	ARG	1	0.971	0.970	9.725	0.407	0.407	0.000	0.000	0.000	0.000
6	2	65	ILE	0	-0.066	-0.027	13.032	-0.051	-0.051	0.000	0.000	0.000	0.000
7	2	66	LYS	1	0.936	0.961	15.316	0.121	0.121	0.000	0.000	0.000	0.000
8	2	67	TYR	0	-0.012	-0.035	18.158	-0.004	-0.004	0.000	0.000	0.000	0.000
9	2	68	VAL	0	0.004	0.010	20.175	-0.011	-0.011	0.000	0.000	0.000	0.000
10	2	69	GLY	0	0.040	0.007	22.726	0.004	0.004	0.000	0.000	0.000	0.000
11	2	70	ALA	0	-0.047	-0.009	21.315	-0.008	-0.008	0.000	0.000	0.000	0.000
12	2	71	ILE	0	0.039	0.030	23.465	0.007	0.007	0.000	0.000	0.000	0.000
13	2	84	GLY	0	0.080	0.036	25.993	0.004	0.004	0.000	0.000	0.000	0.000
14	2	85	PRO	0	-0.032	-0.038	22.061	0.007	0.007	0.000	0.000	0.000	0.000
15	2	86	LEU	0	0.056	0.019	23.835	-0.006	-0.006	0.000	0.000	0.000	0.000
16	2	87	ASP	-1	-0.873	-0.931	26.902	0.006	0.006	0.000	0.000	0.000	0.000
17	2	88	LEU	0	-0.098	-0.053	20.590	0.009	0.009	0.000	0.000	0.000	0.000
18	2	89	ILE	0	0.020	0.010	23.766	0.003	0.003	0.000	0.000	0.000	0.000
19	2	90	ASN	0	0.038	0.024	25.851	-0.003	-0.003	0.000	0.000	0.000	0.000
20	2	91	TYR	0	-0.016	-0.002	27.271	0.002	0.002	0.000	0.000	0.000	0.000
21	2	92	ILE	0	-0.012	-0.018	22.690	0.005	0.005	0.000	0.000	0.000	0.000
22	2	93	ASP	-1	-0.930	-0.973	27.023	-0.030	-0.030	0.000	0.000	0.000	0.000
23	2	94	VAL	0	-0.009	0.002	29.476	-0.001	-0.001	0.000	0.000	0.000	0.000
24	2	95	ALA	0	-0.066	-0.027	28.836	0.002	0.002	0.000	0.000	0.000	0.000
25	2	96	GLN	0	-0.031	-0.014	26.303	-0.003	-0.003	0.000	0.000	0.000	0.000
26	2	97	GLN	0	-0.009	0.016	30.826	0.001	0.001	0.000	0.000	0.000	0.000
27	2	111	ILE	0	0.027	0.004	9.751	-0.047	-0.047	0.000	0.000	0.000	0.000
28	2	112	MET	0	-0.048	-0.015	8.780	0.049	0.049	0.000	0.000	0.000	0.000
29	2	113	GLY	0	0.060	0.036	5.927	-0.374	-0.374	0.000	0.000	0.000	0.000
30	2	114	VAL	0	-0.031	0.003	4.804	0.356	0.591	-0.001	-0.054	-0.180	0.000
31	2	115	SER	0	0.033	-0.015	2.412	-3.775	-1.733	2.318	-2.315	-2.044	-0.024
32	2	116	LYS	1	0.961	0.958	3.408	-5.977	-5.123	0.046	-0.342	-0.558	0.004
33	2	117	TYR	0	0.049	0.020	6.251	-0.718	-0.718	0.000	0.000	0.000	0.000
34	2	118	GLY	0	0.027	0.028	7.330	-0.366	-0.366	0.000	0.000	0.000	0.000
35	2	119	ILE	0	-0.018	0.020	6.842	0.577	0.577	0.000	0.000	0.000	0.000
36	2	128	ASP	-1	-0.926	-0.968	15.074	0.273	0.273	0.000	0.000	0.000	0.000
37	2	129	VAL	0	-0.051	-0.031	12.723	0.020	0.020	0.000	0.000	0.000	0.000
38	2	130	LEU	0	0.003	0.009	14.973	-0.019	-0.019	0.000	0.000	0.000	0.000
39	2	131	HIS	0	0.009	0.017	15.107	-0.048	-0.048	0.000	0.000	0.000	0.000
40	2	132	ARG	1	0.970	0.980	11.030	-0.768	-0.768	0.000	0.000	0.000	0.000
41	2	133	HIS	0	0.014	0.021	12.818	0.019	0.019	0.000	0.000	0.000	0.000
42	2	134	ALA	0	0.043	0.012	11.659	0.125	0.125	0.000	0.000	0.000	0.000
43	2	135	LEU	0	0.026	-0.012	8.898	-0.088	-0.088	0.000	0.000	0.000	0.000
44	2	136	TYR	0	-0.027	-0.006	12.537	-0.091	-0.091	0.000	0.000	0.000	0.000
45	2	137	LEU	0	-0.044	-0.007	15.688	-0.057	-0.057	0.000	0.000	0.000	0.000
46	2	138	ILE	0	0.011	-0.005	11.827	-0.058	-0.058	0.000	0.000	0.000	0.000
47	2	139	ILE	0	0.049	0.035	15.573	0.003	0.003	0.000	0.000	0.000	0.000
48	2	140	ARG	1	0.844	0.918	17.172	-0.070	-0.070	0.000	0.000	0.000	0.000
49	2	141	MET	0	0.007	0.011	12.586	0.018	0.018	0.000	0.000	0.000	0.000
50	2	142	VAL	0	-0.031	-0.017	16.183	-0.017	-0.017	0.000	0.000	0.000	0.000
51	2	143	CYS	0	-0.052	-0.004	16.514	0.009	0.009	0.000	0.000	0.000	0.000
52	2	144	TYR	0	0.031	0.006	18.788	0.004	0.004	0.000	0.000	0.000	0.000
53	2	145	ASP	-1	-0.837	-0.944	22.008	-0.131	-0.131	0.000	0.000	0.000	0.000
54	2	146	ASP	-1	-0.791	-0.884	24.610	-0.058	-0.058	0.000	0.000	0.000	0.000
55	2	147	GLY	0	-0.071	-0.044	24.670	-0.003	-0.003	0.000	0.000	0.000	0.000
56	2	148	LEU	0	0.054	0.022	27.217	0.001	0.001	0.000	0.000	0.000	0.000
57	2	149	GLY	0	-0.062	-0.029	25.381	0.008	0.008	0.000	0.000	0.000	0.000
58	2	150	ALA	0	-0.074	-0.017	26.379	-0.003	-0.003	0.000	0.000	0.000	0.000
59	2	151	GLY	0	0.008	-0.027	26.983	0.000	0.000	0.000	0.000	0.000	0.000
60	2	152	LYS	1	0.812	0.934	22.655	0.125	0.125	0.000	0.000	0.000	0.000
61	2	153	SER	0	0.008	0.006	19.458	-0.023	-0.023	0.000	0.000	0.000	0.000
62	2	154	LEU	0	-0.003	0.012	20.329	0.004	0.004	0.000	0.000	0.000	0.000
63	2	155	LEU	0	-0.022	-0.030	13.615	-0.021	-0.021	0.000	0.000	0.000	0.000
64	2	156	ALA	0	0.040	0.026	17.608	0.028	0.028	0.000	0.000	0.000	0.000
65	2	157	LEU	0	-0.016	-0.016	13.127	-0.005	-0.005	0.000	0.000	0.000	0.000
66	2	158	LYS	1	0.961	0.991	17.252	-0.068	-0.068	0.000	0.000	0.000	0.000
67	2	159	THR	0	-0.038	0.002	16.735	0.018	0.018	0.000	0.000	0.000	0.000
68	2	160	THR	0	0.013	0.015	19.331	-0.026	-0.026	0.000	0.000	0.000	0.000
69	2	168	SER	0	0.013	0.013	22.099	-0.007	-0.007	0.000	0.000	0.000	0.000
70	2	169	LEU	0	-0.045	-0.039	21.411	0.004	0.004	0.000	0.000	0.000	0.000
71	2	170	TRP	0	0.014	-0.026	17.713	0.005	0.005	0.000	0.000	0.000	0.000
72	2	171	VAL	0	0.038	0.027	19.111	-0.014	-0.014	0.000	0.000	0.000	0.000
73	2	172	TYR	0	-0.018	-0.010	15.562	0.023	0.023	0.000	0.000	0.000	0.000
74	2	173	GLN	0	0.055	0.038	18.235	-0.014	-0.014	0.000	0.000	0.000	0.000
75	2	174	CYS	0	-0.037	0.009	15.491	-0.025	-0.025	0.000	0.000	0.000	0.000
76	2	175	ASN	0	-0.040	-0.033	17.651	0.018	0.018	0.000	0.000	0.000	0.000
77	2	176	SER	0	0.067	0.014	18.061	0.015	0.015	0.000	0.000	0.000	0.000
78	2	177	LEU	0	0.135	0.064	17.920	-0.025	-0.025	0.000	0.000	0.000	0.000
79	2	178	GLU	-1	-0.887	-0.938	17.439	-0.361	-0.361	0.000	0.000	0.000	0.000
80	2	179	GLN	0	0.000	-0.014	14.113	-0.062	-0.062	0.000	0.000	0.000	0.000
81	2	180	ALA	0	0.020	0.011	13.130	-0.083	-0.083	0.000	0.000	0.000	0.000
82	2	181	GLN	0	-0.025	-0.028	14.162	0.038	0.038	0.000	0.000	0.000	0.000
83	2	182	ALA	0	-0.024	-0.008	10.892	-0.032	-0.032	0.000	0.000	0.000	0.000
84	2	183	ILE	0	0.016	0.006	8.893	-0.236	-0.236	0.000	0.000	0.000	0.000
85	2	184	CYS	0	-0.002	0.001	9.120	0.018	0.018	0.000	0.000	0.000	0.000
86	2	185	LYS	1	0.948	0.991	9.792	0.597	0.597	0.000	0.000	0.000	0.000
87	2	186	VAL	0	0.010	0.014	3.713	-0.169	-0.043	0.000	-0.026	-0.101	0.000
88	2	187	LEU	0	-0.009	-0.013	5.725	0.247	0.247	0.000	0.000	0.000	0.000
89	2	188	SER	0	-0.037	-0.039	8.058	0.257	0.257	0.000	0.000	0.000	0.000
90	2	189	THR	0	-0.028	-0.003	5.157	0.004	0.004	0.000	0.000	0.000	0.000
91	2	190	ALA	0	-0.056	-0.026	6.193	0.485	0.485	0.000	0.000	0.000	0.000
92	2	191	PHE	0	0.004	-0.013	7.271	0.134	0.134	0.000	0.000	0.000	0.000
93	2	192	ASP	-1	-0.873	-0.932	10.674	0.180	0.180	0.000	0.000	0.000	0.000
94	2	193	SER	0	-0.108	-0.051	8.160	0.212	0.212	0.000	0.000	0.000	0.000
95	2	194	VAL	0	-0.055	-0.009	10.213	0.060	0.060	0.000	0.000	0.000	0.000
96	2	195	LEU	0	-0.020	-0.011	12.879	-0.053	-0.053	0.000	0.000	0.000	0.000
97	2	196	THR	0	0.010	0.019	15.074	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(2:60:CYS)