FMO DATABASE

FMODB ID: M356Z

Calculation Name: 4DX9-w-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: w

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	51
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-235571.014437
FMO2-HF: Nuclear repulsion	214514.854817
FMO2-HF: Total energy	-21056.159619
FMO2-MP2: Total energy	-21114.117877

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(w:65:ILE)

Summations of interaction energy for fragment #1(w:65:ILE)

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.
-22.234	-12.1	15.008	-8.468	-16.674	-0.026

Interaction energy analysis for fragmet #1(w:65:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.015

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	w	67	TYR	0	0.029	-0.011	3.807	-0.311	2.385	-0.022	-1.265	-1.410	0.006
4	w	68	VAL	0	-0.024	0.002	5.549	0.216	0.216	0.000	0.000	0.000	0.000
5	w	69	GLY	0	0.036	-0.006	7.942	0.031	0.031	0.000	0.000	0.000	0.000
6	w	70	ALA	0	-0.059	-0.008	8.464	0.154	0.154	0.000	0.000	0.000	0.000
7	w	71	ILE	0	0.000	0.016	9.944	-0.006	-0.006	0.000	0.000	0.000	0.000
8	w	99	GLY	0	0.002	-0.010	18.171	0.007	0.007	0.000	0.000	0.000	0.000
9	w	100	LYS	1	0.959	0.972	17.471	-0.018	-0.018	0.000	0.000	0.000	0.000
10	w	101	LEU	0	-0.012	0.005	12.156	-0.028	-0.028	0.000	0.000	0.000	0.000
11	w	102	PRO	0	0.033	0.029	12.226	0.046	0.046	0.000	0.000	0.000	0.000
12	w	103	PHE	0	0.002	-0.020	12.688	0.029	0.029	0.000	0.000	0.000	0.000
13	w	104	VAL	0	-0.033	-0.016	11.120	0.065	0.065	0.000	0.000	0.000	0.000
14	w	105	PRO	0	-0.029	0.005	6.904	0.038	0.038	0.000	0.000	0.000	0.000
15	w	106	PRO	0	0.031	0.006	9.033	0.067	0.067	0.000	0.000	0.000	0.000
16	w	107	GLU	-1	-0.851	-0.917	8.142	-1.561	-1.561	0.000	0.000	0.000	0.000
17	w	108	GLU	-1	-0.984	-0.971	7.643	-1.764	-1.764	0.000	0.000	0.000	0.000
18	w	109	GLU	-1	-0.947	-0.976	4.727	-3.293	-3.162	-0.001	-0.011	-0.118	0.000
19	w	110	PHE	0	-0.004	-0.019	2.580	0.832	1.754	0.455	-0.262	-1.114	0.001
20	w	111	ILE	0	-0.009	0.008	3.050	-4.460	-2.818	0.200	-0.958	-0.884	-0.009
21	w	112	MET	0	0.010	-0.008	2.238	-3.857	-2.358	4.203	-1.501	-4.201	-0.004
22	w	113	GLY	0	0.005	0.003	3.689	-0.146	0.032	0.016	-0.017	-0.177	0.000
23	w	114	VAL	0	-0.037	-0.016	7.199	-0.070	-0.070	0.000	0.000	0.000	0.000
24	w	115	SER	0	0.014	0.016	9.603	-0.035	-0.035	0.000	0.000	0.000	0.000
25	w	140	ARG	1	0.987	0.990	12.995	-0.452	-0.452	0.000	0.000	0.000	0.000
26	w	141	MET	0	0.023	0.027	6.747	0.087	0.087	0.000	0.000	0.000	0.000
27	w	142	VAL	0	-0.014	-0.020	10.517	-0.126	-0.126	0.000	0.000	0.000	0.000
28	w	143	CYS	0	0.027	0.029	8.343	0.030	0.030	0.000	0.000	0.000	0.000
29	w	153	SER	0	0.034	0.022	6.538	0.164	0.164	0.000	0.000	0.000	0.000
30	w	154	LEU	0	-0.015	-0.037	6.349	-0.094	-0.094	0.000	0.000	0.000	0.000
31	w	155	LEU	0	0.005	-0.001	2.518	-0.835	-0.294	0.592	-0.242	-0.892	0.002
32	w	156	ALA	0	-0.031	-0.006	6.042	-0.056	-0.056	0.000	0.000	0.000	0.000
33	w	157	LEU	0	0.040	0.013	5.724	0.033	0.033	0.000	0.000	0.000	0.000
34	w	158	LYS	1	0.989	1.009	9.493	-0.413	-0.413	0.000	0.000	0.000	0.000
35	w	168	SER	0	-0.032	-0.026	14.093	-0.006	-0.006	0.000	0.000	0.000	0.000
36	w	169	LEU	0	-0.053	-0.035	13.047	0.061	0.061	0.000	0.000	0.000	0.000
37	w	170	TRP	0	0.029	0.003	7.885	-0.147	-0.147	0.000	0.000	0.000	0.000
38	w	171	VAL	0	-0.002	-0.002	7.507	0.189	0.189	0.000	0.000	0.000	0.000
39	w	172	TYR	0	0.036	0.025	2.099	-2.581	-0.989	4.063	-1.691	-3.964	-0.004
40	w	173	GLN	0	0.018	0.015	3.923	-0.154	0.389	0.005	-0.114	-0.434	0.000
41	w	174	CYS	0	-0.003	0.003	2.386	-2.147	-1.844	5.492	-2.394	-3.401	-0.018
42	w	175	ASN	0	0.053	0.034	3.770	-0.532	-0.445	0.005	-0.013	-0.079	0.000
43	w	184	CYS	0	0.011	-0.016	7.884	0.014	0.014	0.000	0.000	0.000	0.000
44	w	185	LYS	1	0.987	0.992	9.447	-1.042	-1.042	0.000	0.000	0.000	0.000
45	w	186	VAL	0	0.059	0.035	9.761	-0.118	-0.118	0.000	0.000	0.000	0.000
46	w	187	LEU	0	-0.006	-0.006	8.301	-0.097	-0.097	0.000	0.000	0.000	0.000
47	w	188	SER	0	-0.029	-0.038	11.127	-0.134	-0.134	0.000	0.000	0.000	0.000
48	w	189	THR	0	-0.011	-0.004	14.160	-0.093	-0.093	0.000	0.000	0.000	0.000
49	w	190	ALA	0	-0.042	-0.007	14.357	-0.063	-0.063	0.000	0.000	0.000	0.000
50	w	191	PHE	0	-0.071	-0.032	12.983	-0.032	-0.032	0.000	0.000	0.000	0.000
51	w	192	ASP	-1	-0.935	-0.946	18.034	0.374	0.374	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(w:65:ILE)