FMO DATABASE

FMODB ID: 98JQ2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-465628.312344
FMO2-HF: Nuclear repulsion	433355.026377
FMO2-HF: Total energy	-32273.285967
FMO2-MP2: Total energy	-32363.230726

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.
-6.289	-0.758	1.726	-3.328	-3.931	-0.022

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 : -0.060 / q_NPA : -0.042

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	-0.888	-0.954	3.814	0.080	1.873	-0.029	-0.776	-0.988	0.000
4	o	63	PHE	0	-0.027	-0.020	5.962	-0.095	-0.095	0.000	0.000	0.000	0.000
5	o	84	GLY	0	0.043	0.019	24.199	0.002	0.002	0.000	0.000	0.000	0.000
6	o	85	PRO	0	-0.001	-0.018	20.723	0.007	0.007	0.000	0.000	0.000	0.000
7	o	86	LEU	0	0.046	0.010	22.562	0.005	0.005	0.000	0.000	0.000	0.000
8	o	87	ASP	-1	-0.891	-0.931	25.739	0.127	0.127	0.000	0.000	0.000	0.000
9	o	88	LEU	0	-0.025	-0.020	19.131	0.001	0.001	0.000	0.000	0.000	0.000
10	o	89	ILE	0	-0.032	-0.015	22.894	0.004	0.004	0.000	0.000	0.000	0.000
11	o	90	ASN	0	-0.034	-0.016	24.772	-0.004	-0.004	0.000	0.000	0.000	0.000
12	o	91	TYR	0	0.013	0.014	26.573	-0.006	-0.006	0.000	0.000	0.000	0.000
13	o	92	ILE	0	-0.054	-0.022	22.386	0.002	0.002	0.000	0.000	0.000	0.000
14	o	93	ASP	-1	-0.945	-0.955	26.618	0.075	0.075	0.000	0.000	0.000	0.000
15	o	101	LEU	0	-0.021	-0.026	23.827	0.000	0.000	0.000	0.000	0.000	0.000
16	o	102	PRO	0	0.007	0.018	25.566	-0.007	-0.007	0.000	0.000	0.000	0.000
17	o	103	PHE	0	0.000	-0.006	26.414	0.006	0.006	0.000	0.000	0.000	0.000
18	o	104	VAL	0	-0.034	-0.029	26.237	0.001	0.001	0.000	0.000	0.000	0.000
19	o	105	PRO	0	0.052	0.021	23.965	0.004	0.004	0.000	0.000	0.000	0.000
20	o	106	PRO	0	-0.120	-0.067	26.104	-0.001	-0.001	0.000	0.000	0.000	0.000
21	o	107	GLU	-1	-0.939	-0.941	24.474	0.055	0.055	0.000	0.000	0.000	0.000
22	o	108	GLU	-1	-0.918	-0.960	20.644	0.037	0.037	0.000	0.000	0.000	0.000
23	o	109	GLU	-1	-0.889	-0.934	16.715	0.070	0.070	0.000	0.000	0.000	0.000
24	o	110	PHE	0	-0.084	-0.060	14.360	0.011	0.011	0.000	0.000	0.000	0.000
25	o	111	ILE	0	0.015	0.018	12.964	-0.024	-0.024	0.000	0.000	0.000	0.000
26	o	112	MET	0	-0.014	-0.010	8.444	0.036	0.036	0.000	0.000	0.000	0.000
27	o	113	GLY	0	0.025	0.035	5.622	-0.224	-0.224	0.000	0.000	0.000	0.000
28	o	114	VAL	0	-0.029	-0.011	4.691	0.116	0.278	-0.001	-0.030	-0.131	0.000
29	o	115	SER	0	0.039	0.001	2.376	-0.788	1.402	1.647	-1.992	-1.846	-0.014
30	o	116	LYS	1	0.893	0.948	2.969	-6.158	-4.772	0.109	-0.530	-0.966	-0.008
31	o	117	TYR	0	-0.046	-0.034	5.654	-0.120	-0.120	0.000	0.000	0.000	0.000
32	o	118	GLY	0	0.007	0.011	8.633	-0.142	-0.142	0.000	0.000	0.000	0.000
33	o	119	ILE	0	-0.010	-0.019	8.190	0.225	0.225	0.000	0.000	0.000	0.000
34	o	120	LYS	1	0.886	0.950	7.715	-0.688	-0.688	0.000	0.000	0.000	0.000
35	o	121	VAL	0	0.044	0.037	9.535	0.024	0.024	0.000	0.000	0.000	0.000
36	o	140	ARG	1	0.935	0.963	15.061	-0.208	-0.208	0.000	0.000	0.000	0.000
37	o	141	MET	0	0.001	-0.006	11.402	0.042	0.042	0.000	0.000	0.000	0.000
38	o	142	VAL	0	-0.041	-0.025	15.323	-0.017	-0.017	0.000	0.000	0.000	0.000
39	o	143	CYS	0	-0.014	0.004	15.500	0.004	0.004	0.000	0.000	0.000	0.000
40	o	144	TYR	0	0.027	0.012	17.606	-0.019	-0.019	0.000	0.000	0.000	0.000
41	o	145	ASP	-1	-0.914	-0.955	20.785	0.040	0.040	0.000	0.000	0.000	0.000
42	o	153	SER	0	-0.024	-0.025	18.933	-0.010	-0.010	0.000	0.000	0.000	0.000
43	o	154	LEU	0	0.017	0.029	19.210	0.011	0.011	0.000	0.000	0.000	0.000
44	o	155	LEU	0	-0.014	-0.010	13.173	0.022	0.022	0.000	0.000	0.000	0.000
45	o	156	ALA	0	0.033	0.014	17.200	-0.014	-0.014	0.000	0.000	0.000	0.000
46	o	157	LEU	0	-0.022	-0.034	12.443	0.041	0.041	0.000	0.000	0.000	0.000
47	o	158	LYS	1	0.857	0.956	16.824	-0.193	-0.193	0.000	0.000	0.000	0.000
48	o	159	THR	0	-0.070	-0.040	16.698	0.036	0.036	0.000	0.000	0.000	0.000
49	o	160	THR	0	0.008	-0.030	19.224	-0.031	-0.031	0.000	0.000	0.000	0.000
50	o	161	ASP	-1	-0.784	-0.853	20.684	0.210	0.210	0.000	0.000	0.000	0.000
51	o	162	ALA	0	-0.023	-0.019	22.860	-0.001	-0.001	0.000	0.000	0.000	0.000
52	o	163	SER	0	-0.068	-0.043	23.976	-0.011	-0.011	0.000	0.000	0.000	0.000
53	o	164	ASN	0	-0.105	-0.042	24.091	0.005	0.005	0.000	0.000	0.000	0.000
54	o	165	GLU	-1	-0.887	-0.954	26.654	0.119	0.119	0.000	0.000	0.000	0.000
55	o	166	GLU	-1	-0.869	-0.925	25.588	0.166	0.166	0.000	0.000	0.000	0.000
56	o	167	TYR	0	-0.098	-0.049	23.030	0.003	0.003	0.000	0.000	0.000	0.000
57	o	168	SER	0	0.021	0.010	22.450	-0.007	-0.007	0.000	0.000	0.000	0.000
58	o	169	LEU	0	-0.058	-0.041	20.928	0.024	0.024	0.000	0.000	0.000	0.000
59	o	170	TRP	0	-0.040	-0.016	17.406	-0.009	-0.009	0.000	0.000	0.000	0.000
60	o	171	VAL	0	0.028	0.015	18.057	0.024	0.024	0.000	0.000	0.000	0.000
61	o	172	TYR	0	-0.007	-0.010	15.202	0.000	0.000	0.000	0.000	0.000	0.000
62	o	173	GLN	0	0.048	0.021	17.530	0.003	0.003	0.000	0.000	0.000	0.000
63	o	174	CYS	0	-0.055	-0.012	14.492	0.015	0.015	0.000	0.000	0.000	0.000
64	o	175	ASN	0	0.002	-0.018	16.407	0.015	0.015	0.000	0.000	0.000	0.000
65	o	176	SER	0	0.076	0.025	17.303	0.003	0.003	0.000	0.000	0.000	0.000
66	o	177	LEU	0	0.051	0.020	16.908	0.011	0.011	0.000	0.000	0.000	0.000
67	o	178	GLU	-1	-0.987	-0.993	16.489	-0.080	-0.080	0.000	0.000	0.000	0.000
68	o	179	GLN	0	0.079	0.037	13.795	0.023	0.023	0.000	0.000	0.000	0.000
69	o	180	ALA	0	-0.022	-0.002	12.311	0.055	0.055	0.000	0.000	0.000	0.000
70	o	181	GLN	0	-0.025	-0.022	12.376	0.092	0.092	0.000	0.000	0.000	0.000
71	o	182	ALA	0	-0.017	0.002	8.844	0.032	0.032	0.000	0.000	0.000	0.000
72	o	183	ILE	0	-0.001	0.016	7.229	0.338	0.338	0.000	0.000	0.000	0.000
73	o	184	CYS	0	-0.080	-0.031	7.337	0.413	0.413	0.000	0.000	0.000	0.000
74	o	192	ASP	-1	-0.913	-0.956	9.145	-0.053	-0.053	0.000	0.000	0.000	0.000
75	o	193	SER	0	-0.017	-0.023	6.704	-0.083	-0.083	0.000	0.000	0.000	0.000
76	o	194	VAL	0	0.021	0.018	8.745	0.108	0.108	0.000	0.000	0.000	0.000
77	o	195	LEU	0	-0.051	-0.005	11.191	0.023	0.023	0.000	0.000	0.000	0.000
78	o	196	THR	0	-0.013	-0.004	13.029	-0.062	-0.062	0.000	0.000	0.000	0.000

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