FMO DATABASE

FMODB ID: K3Y73

Calculation Name: 4DX9-q-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: q

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	OptAll
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	58
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-291439.84118
FMO2-HF: Nuclear repulsion	267572.768311
FMO2-HF: Total energy	-23867.07287
FMO2-MP2: Total energy	-23932.333661

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(q:60:CYS)

Summations of interaction energy for fragment #1(q: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.
-4.444	-0.492	6.76	-4.381	-6.328	-0.018

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : 0.003

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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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	q	62	GLU	-1	-0.874	-0.933	3.730	-1.079	1.439	-0.020	-1.191	-1.307	0.004
4	q	63	PHE	0	-0.079	-0.058	6.110	-0.032	-0.032	0.000	0.000	0.000	0.000
5	q	64	ARG	1	0.808	0.886	9.886	0.548	0.548	0.000	0.000	0.000	0.000
6	q	65	ILE	0	-0.048	-0.027	12.911	-0.017	-0.017	0.000	0.000	0.000	0.000
7	q	66	LYS	1	0.898	0.962	15.500	0.196	0.196	0.000	0.000	0.000	0.000
8	q	67	TYR	0	0.004	-0.001	15.699	0.024	0.024	0.000	0.000	0.000	0.000
9	q	68	VAL	0	-0.022	-0.011	19.691	-0.015	-0.015	0.000	0.000	0.000	0.000
10	q	69	GLY	0	0.034	0.007	21.395	0.005	0.005	0.000	0.000	0.000	0.000
11	q	70	ALA	0	-0.003	0.003	20.729	0.003	0.003	0.000	0.000	0.000	0.000
12	q	71	ILE	0	-0.035	-0.009	22.516	0.001	0.001	0.000	0.000	0.000	0.000
13	q	99	GLY	0	0.026	0.001	32.558	0.000	0.000	0.000	0.000	0.000	0.000
14	q	100	LYS	1	0.912	0.943	30.262	-0.028	-0.028	0.000	0.000	0.000	0.000
15	q	101	LEU	0	0.031	0.029	24.528	0.010	0.010	0.000	0.000	0.000	0.000
16	q	102	PRO	0	0.000	0.013	26.179	-0.005	-0.005	0.000	0.000	0.000	0.000
17	q	103	PHE	0	0.035	-0.003	26.895	-0.006	-0.006	0.000	0.000	0.000	0.000
18	q	104	VAL	0	-0.020	-0.006	27.565	-0.016	-0.016	0.000	0.000	0.000	0.000
19	q	105	PRO	0	-0.010	0.015	23.430	0.011	0.011	0.000	0.000	0.000	0.000
20	q	106	PRO	0	0.024	-0.004	25.156	-0.021	-0.021	0.000	0.000	0.000	0.000
21	q	107	GLU	-1	-0.944	-0.959	21.892	-0.045	-0.045	0.000	0.000	0.000	0.000
22	q	108	GLU	-1	-0.897	-0.945	18.487	-0.129	-0.129	0.000	0.000	0.000	0.000
23	q	109	GLU	-1	-0.830	-0.886	17.326	-0.342	-0.342	0.000	0.000	0.000	0.000
24	q	110	PHE	0	0.000	0.000	12.620	0.008	0.008	0.000	0.000	0.000	0.000
25	q	111	ILE	0	0.025	0.013	8.449	-0.101	-0.101	0.000	0.000	0.000	0.000
26	q	112	MET	0	-0.016	-0.013	9.072	0.247	0.247	0.000	0.000	0.000	0.000
27	q	113	GLY	0	0.039	0.026	6.563	-0.354	-0.354	0.000	0.000	0.000	0.000
28	q	114	VAL	0	-0.059	-0.034	4.270	0.576	0.785	-0.001	-0.036	-0.172	0.000
29	q	115	SER	0	0.029	0.008	2.167	-4.882	-4.253	6.517	-2.965	-4.180	-0.021
30	q	140	ARG	1	0.984	0.984	18.450	-0.080	-0.080	0.000	0.000	0.000	0.000
31	q	141	MET	0	-0.002	0.003	11.728	-0.012	-0.012	0.000	0.000	0.000	0.000
32	q	142	VAL	0	0.004	-0.010	16.342	-0.007	-0.007	0.000	0.000	0.000	0.000
33	q	143	CYS	0	-0.025	-0.001	15.861	-0.020	-0.020	0.000	0.000	0.000	0.000
34	q	144	TYR	0	0.029	0.017	18.527	0.012	0.012	0.000	0.000	0.000	0.000
35	q	145	ASP	-1	-0.851	-0.919	21.565	-0.207	-0.207	0.000	0.000	0.000	0.000
36	q	146	ASP	-1	-0.790	-0.885	24.125	-0.152	-0.152	0.000	0.000	0.000	0.000
37	q	147	GLY	0	-0.011	-0.011	25.596	0.017	0.017	0.000	0.000	0.000	0.000
38	q	148	LEU	0	-0.079	-0.035	28.871	0.012	0.012	0.000	0.000	0.000	0.000
39	q	149	GLY	0	0.002	-0.011	29.352	0.004	0.004	0.000	0.000	0.000	0.000
40	q	150	ALA	0	-0.055	-0.025	27.467	-0.011	-0.011	0.000	0.000	0.000	0.000
41	q	151	GLY	0	0.017	0.006	24.755	-0.019	-0.019	0.000	0.000	0.000	0.000
42	q	152	LYS	1	0.884	0.946	21.928	0.218	0.218	0.000	0.000	0.000	0.000
43	q	153	SER	0	-0.040	-0.032	18.722	0.015	0.015	0.000	0.000	0.000	0.000
44	q	154	LEU	0	0.019	0.016	19.408	-0.018	-0.018	0.000	0.000	0.000	0.000
45	q	155	LEU	0	-0.008	0.000	13.277	0.060	0.060	0.000	0.000	0.000	0.000
46	q	168	SER	0	0.022	0.015	20.491	0.003	0.003	0.000	0.000	0.000	0.000
47	q	169	LEU	0	-0.063	-0.039	20.212	0.022	0.022	0.000	0.000	0.000	0.000
48	q	170	TRP	0	0.018	0.000	16.977	-0.003	-0.003	0.000	0.000	0.000	0.000
49	q	171	VAL	0	-0.002	0.006	18.710	-0.016	-0.016	0.000	0.000	0.000	0.000
50	q	172	TYR	0	0.023	0.006	14.620	0.005	0.005	0.000	0.000	0.000	0.000
51	q	173	GLN	0	0.001	0.000	17.576	-0.029	-0.029	0.000	0.000	0.000	0.000
52	q	174	CYS	0	-0.008	0.004	15.235	-0.051	-0.051	0.000	0.000	0.000	0.000
53	q	175	ASN	0	0.014	0.007	15.758	0.046	0.046	0.000	0.000	0.000	0.000
54	q	184	CYS	0	0.050	0.004	9.381	-0.060	-0.060	0.000	0.000	0.000	0.000
55	q	185	LYS	1	0.971	0.982	8.356	0.918	0.918	0.000	0.000	0.000	0.000
56	q	186	VAL	0	0.011	0.009	2.546	-0.437	0.078	0.265	-0.189	-0.591	-0.001
57	q	187	LEU	0	0.009	0.015	5.322	0.722	0.803	-0.001	0.000	-0.078	0.000
58	q	188	SER	0	-0.058	-0.019	8.138	0.067	0.067	0.000	0.000	0.000	0.000

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