FMO DATABASE

FMODB ID: LN8R9

Calculation Name: 4DX9-o-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: o

ChEMBL ID: CHEMBL1905

UniProt ID: P05556

Base Structure: X-ray

Registration Date: 2023-09-24

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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-465162.596426
FMO2-HF: Nuclear repulsion	432889.738279
FMO2-HF: Total energy	-32272.858147
FMO2-MP2: Total energy	-32362.813681

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(o:60:CYS)

Summations of interaction energy for fragment #1(o: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.
-9.053	-3.686	1.681	-3.33	-3.717	-0.02

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.062 / q_NPA : -0.041

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	o	62	GLU	-1	-0.964	-0.987	3.814	-1.848	0.011	-0.028	-0.830	-1.001	0.000
4	o	63	PHE	0	-0.032	-0.029	5.268	0.289	0.289	0.000	0.000	0.000	0.000
5	o	84	GLY	0	0.021	-0.001	24.086	-0.001	-0.001	0.000	0.000	0.000	0.000
6	o	85	PRO	0	-0.004	-0.024	20.416	-0.002	-0.002	0.000	0.000	0.000	0.000
7	o	86	LEU	0	0.040	0.000	22.163	-0.009	-0.009	0.000	0.000	0.000	0.000
8	o	87	ASP	-1	-0.941	-0.954	25.195	-0.078	-0.078	0.000	0.000	0.000	0.000
9	o	88	LEU	0	-0.046	-0.032	18.416	0.003	0.003	0.000	0.000	0.000	0.000
10	o	89	ILE	0	-0.041	-0.021	22.091	-0.007	-0.007	0.000	0.000	0.000	0.000
11	o	90	ASN	0	-0.026	-0.010	23.986	0.003	0.003	0.000	0.000	0.000	0.000
12	o	91	TYR	0	0.037	0.032	25.949	0.005	0.005	0.000	0.000	0.000	0.000
13	o	92	ILE	0	-0.063	-0.030	21.816	0.001	0.001	0.000	0.000	0.000	0.000
14	o	93	ASP	-1	-0.931	-0.950	25.879	-0.118	-0.118	0.000	0.000	0.000	0.000
15	o	101	LEU	0	-0.020	-0.029	23.463	0.001	0.001	0.000	0.000	0.000	0.000
16	o	102	PRO	0	0.008	0.020	25.284	0.007	0.007	0.000	0.000	0.000	0.000
17	o	103	PHE	0	-0.014	-0.011	25.909	-0.007	-0.007	0.000	0.000	0.000	0.000
18	o	104	VAL	0	-0.031	-0.025	25.560	-0.013	-0.013	0.000	0.000	0.000	0.000
19	o	105	PRO	0	0.057	0.034	23.645	0.010	0.010	0.000	0.000	0.000	0.000
20	o	106	PRO	0	-0.126	-0.080	25.767	0.010	0.010	0.000	0.000	0.000	0.000
21	o	107	GLU	-1	-0.942	-0.939	24.297	-0.140	-0.140	0.000	0.000	0.000	0.000
22	o	108	GLU	-1	-0.915	-0.960	20.250	-0.226	-0.226	0.000	0.000	0.000	0.000
23	o	109	GLU	-1	-0.888	-0.939	16.842	-0.321	-0.321	0.000	0.000	0.000	0.000
24	o	110	PHE	0	-0.077	-0.051	14.399	-0.045	-0.045	0.000	0.000	0.000	0.000
25	o	111	ILE	0	0.000	0.011	12.990	-0.066	-0.066	0.000	0.000	0.000	0.000
26	o	112	MET	0	0.000	0.008	8.660	-0.027	-0.027	0.000	0.000	0.000	0.000
27	o	113	GLY	0	0.044	0.038	5.637	-0.423	-0.423	0.000	0.000	0.000	0.000
28	o	114	VAL	0	-0.042	-0.016	4.731	0.702	0.865	-0.001	-0.027	-0.136	0.000
29	o	115	SER	0	0.029	0.001	2.373	-3.397	-1.361	1.598	-1.974	-1.659	-0.013
30	o	116	LYS	1	0.883	0.933	2.983	-2.481	-1.172	0.112	-0.499	-0.921	-0.007
31	o	117	TYR	0	-0.030	-0.023	5.662	0.270	0.270	0.000	0.000	0.000	0.000
32	o	118	GLY	0	-0.005	0.009	8.674	-0.132	-0.132	0.000	0.000	0.000	0.000
33	o	119	ILE	0	0.008	-0.007	8.203	-0.050	-0.050	0.000	0.000	0.000	0.000
34	o	120	LYS	1	0.959	0.982	8.374	-0.099	-0.099	0.000	0.000	0.000	0.000
35	o	121	VAL	0	0.047	0.032	9.553	-0.141	-0.141	0.000	0.000	0.000	0.000
36	o	140	ARG	1	0.931	0.958	15.607	0.116	0.116	0.000	0.000	0.000	0.000
37	o	141	MET	0	0.019	0.019	10.533	-0.015	-0.015	0.000	0.000	0.000	0.000
38	o	142	VAL	0	-0.039	-0.021	14.711	0.006	0.006	0.000	0.000	0.000	0.000
39	o	143	CYS	0	-0.021	0.006	13.661	0.009	0.009	0.000	0.000	0.000	0.000
40	o	144	TYR	0	0.037	0.013	16.632	0.019	0.019	0.000	0.000	0.000	0.000
41	o	145	ASP	-1	-0.942	-0.966	19.783	-0.211	-0.211	0.000	0.000	0.000	0.000
42	o	153	SER	0	-0.025	-0.025	18.037	0.006	0.006	0.000	0.000	0.000	0.000
43	o	154	LEU	0	0.020	0.026	18.209	-0.028	-0.028	0.000	0.000	0.000	0.000
44	o	155	LEU	0	-0.007	-0.006	12.334	-0.016	-0.016	0.000	0.000	0.000	0.000
45	o	156	ALA	0	0.037	0.017	16.288	0.027	0.027	0.000	0.000	0.000	0.000
46	o	157	LEU	0	-0.029	-0.033	12.235	-0.028	-0.028	0.000	0.000	0.000	0.000
47	o	158	LYS	1	0.911	0.980	16.460	0.126	0.126	0.000	0.000	0.000	0.000
48	o	159	THR	0	-0.070	-0.042	16.746	-0.005	-0.005	0.000	0.000	0.000	0.000
49	o	160	THR	0	0.002	-0.037	19.258	-0.002	-0.002	0.000	0.000	0.000	0.000
50	o	161	ASP	-1	-0.786	-0.848	20.704	0.007	0.007	0.000	0.000	0.000	0.000
51	o	162	ALA	0	-0.027	-0.026	22.877	0.003	0.003	0.000	0.000	0.000	0.000
52	o	163	SER	0	-0.070	-0.050	23.984	0.007	0.007	0.000	0.000	0.000	0.000
53	o	164	ASN	0	-0.096	-0.034	24.069	-0.005	-0.005	0.000	0.000	0.000	0.000
54	o	165	GLU	-1	-0.885	-0.946	26.654	-0.001	-0.001	0.000	0.000	0.000	0.000
55	o	166	GLU	-1	-0.846	-0.914	25.735	-0.056	-0.056	0.000	0.000	0.000	0.000
56	o	167	TYR	0	-0.112	-0.057	22.759	-0.003	-0.003	0.000	0.000	0.000	0.000
57	o	168	SER	0	0.021	0.007	22.492	-0.008	-0.008	0.000	0.000	0.000	0.000
58	o	169	LEU	0	-0.065	-0.044	20.765	-0.012	-0.012	0.000	0.000	0.000	0.000
59	o	170	TRP	0	-0.026	-0.003	17.476	0.003	0.003	0.000	0.000	0.000	0.000
60	o	171	VAL	0	0.029	0.014	17.800	-0.028	-0.028	0.000	0.000	0.000	0.000
61	o	172	TYR	0	-0.012	-0.012	15.180	0.007	0.007	0.000	0.000	0.000	0.000
62	o	173	GLN	0	0.040	0.018	17.051	-0.001	-0.001	0.000	0.000	0.000	0.000
63	o	174	CYS	0	-0.067	-0.027	13.780	-0.023	-0.023	0.000	0.000	0.000	0.000
64	o	175	ASN	0	0.005	-0.006	15.584	0.055	0.055	0.000	0.000	0.000	0.000
65	o	176	SER	0	0.081	0.024	16.291	0.035	0.035	0.000	0.000	0.000	0.000
66	o	177	LEU	0	0.045	0.014	15.938	-0.047	-0.047	0.000	0.000	0.000	0.000
67	o	178	GLU	-1	-0.965	-0.987	15.807	-0.314	-0.314	0.000	0.000	0.000	0.000
68	o	179	GLN	0	0.068	0.031	13.078	0.005	0.005	0.000	0.000	0.000	0.000
69	o	180	ALA	0	-0.025	-0.005	11.390	-0.116	-0.116	0.000	0.000	0.000	0.000
70	o	181	GLN	0	-0.015	-0.015	11.396	-0.054	-0.054	0.000	0.000	0.000	0.000
71	o	182	ALA	0	-0.030	-0.003	8.263	0.014	0.014	0.000	0.000	0.000	0.000
72	o	183	ILE	0	-0.004	0.021	6.214	-0.158	-0.158	0.000	0.000	0.000	0.000
73	o	184	CYS	0	-0.040	-0.009	6.396	-0.205	-0.205	0.000	0.000	0.000	0.000
74	o	192	ASP	-1	-0.913	-0.956	9.204	-0.040	-0.040	0.000	0.000	0.000	0.000
75	o	193	SER	0	-0.027	-0.021	6.717	0.074	0.074	0.000	0.000	0.000	0.000
76	o	194	VAL	0	0.019	0.005	8.740	0.134	0.134	0.000	0.000	0.000	0.000
77	o	195	LEU	0	-0.045	-0.004	11.194	0.022	0.022	0.000	0.000	0.000	0.000
78	o	196	THR	0	-0.014	-0.006	13.189	-0.022	-0.022	0.000	0.000	0.000	0.000

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