FMO DATABASE

FMODB ID: R5ZN8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-289644.578168
FMO2-HF: Nuclear repulsion	265777.892505
FMO2-HF: Total energy	-23866.685663
FMO2-MP2: Total energy	-23931.906046

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.
-2.223	0.815	2.994	-2.262	-3.77	-0.006

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 : -0.050 / q_NPA : -0.038

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	-0.843	-0.905	3.815	0.946	2.737	-0.027	-0.682	-1.081	0.001
4	q	63	PHE	0	-0.083	-0.069	6.767	-0.205	-0.205	0.000	0.000	0.000	0.000
5	q	64	ARG	1	0.814	0.898	10.442	-0.305	-0.305	0.000	0.000	0.000	0.000
6	q	65	ILE	0	-0.064	-0.030	13.039	0.004	0.004	0.000	0.000	0.000	0.000
7	q	66	LYS	1	0.916	0.981	15.703	-0.217	-0.217	0.000	0.000	0.000	0.000
8	q	67	TYR	0	-0.049	-0.019	16.006	0.045	0.045	0.000	0.000	0.000	0.000
9	q	68	VAL	0	-0.023	-0.005	20.146	-0.033	-0.033	0.000	0.000	0.000	0.000
10	q	69	GLY	0	0.044	0.010	21.644	-0.027	-0.027	0.000	0.000	0.000	0.000
11	q	70	ALA	0	-0.030	-0.001	21.054	0.011	0.011	0.000	0.000	0.000	0.000
12	q	71	ILE	0	-0.020	-0.010	22.934	-0.019	-0.019	0.000	0.000	0.000	0.000
13	q	99	GLY	0	0.023	0.000	32.959	0.000	0.000	0.000	0.000	0.000	0.000
14	q	100	LYS	1	0.916	0.947	30.536	-0.154	-0.154	0.000	0.000	0.000	0.000
15	q	101	LEU	0	0.029	0.024	24.872	0.006	0.006	0.000	0.000	0.000	0.000
16	q	102	PRO	0	0.020	0.019	26.492	-0.011	-0.011	0.000	0.000	0.000	0.000
17	q	103	PHE	0	0.043	0.007	27.239	0.010	0.010	0.000	0.000	0.000	0.000
18	q	104	VAL	0	-0.023	-0.008	27.851	0.005	0.005	0.000	0.000	0.000	0.000
19	q	105	PRO	0	-0.022	0.000	23.877	-0.010	-0.010	0.000	0.000	0.000	0.000
20	q	106	PRO	0	0.043	0.007	25.622	-0.002	-0.002	0.000	0.000	0.000	0.000
21	q	107	GLU	-1	-1.002	-0.994	22.929	0.205	0.205	0.000	0.000	0.000	0.000
22	q	108	GLU	-1	-0.855	-0.933	18.784	0.222	0.222	0.000	0.000	0.000	0.000
23	q	109	GLU	-1	-0.806	-0.879	18.182	0.270	0.270	0.000	0.000	0.000	0.000
24	q	110	PHE	0	0.002	0.011	13.001	-0.005	-0.005	0.000	0.000	0.000	0.000
25	q	111	ILE	0	0.020	0.002	8.755	-0.015	-0.015	0.000	0.000	0.000	0.000
26	q	112	MET	0	-0.042	-0.024	9.100	0.009	0.009	0.000	0.000	0.000	0.000
27	q	113	GLY	0	0.027	0.021	7.419	0.236	0.236	0.000	0.000	0.000	0.000
28	q	114	VAL	0	-0.036	-0.023	4.613	-0.186	-0.090	-0.001	-0.012	-0.083	0.000
29	q	115	SER	0	0.014	0.003	2.329	-1.763	-1.012	3.001	-1.421	-2.331	-0.008
30	q	140	ARG	1	0.992	0.989	18.846	-0.297	-0.297	0.000	0.000	0.000	0.000
31	q	141	MET	0	-0.012	-0.005	12.933	0.056	0.056	0.000	0.000	0.000	0.000
32	q	142	VAL	0	-0.003	-0.013	17.235	-0.030	-0.030	0.000	0.000	0.000	0.000
33	q	143	CYS	0	-0.003	0.007	16.441	0.025	0.025	0.000	0.000	0.000	0.000
34	q	144	TYR	0	0.012	0.017	19.238	-0.021	-0.021	0.000	0.000	0.000	0.000
35	q	145	ASP	-1	-0.865	-0.928	22.055	0.193	0.193	0.000	0.000	0.000	0.000
36	q	146	ASP	-1	-0.767	-0.884	24.295	0.165	0.165	0.000	0.000	0.000	0.000
37	q	147	GLY	0	-0.030	-0.018	26.013	0.002	0.002	0.000	0.000	0.000	0.000
38	q	148	LEU	0	-0.086	-0.036	29.364	-0.009	-0.009	0.000	0.000	0.000	0.000
39	q	149	GLY	0	0.010	-0.011	29.689	-0.009	-0.009	0.000	0.000	0.000	0.000
40	q	150	ALA	0	-0.063	-0.036	28.009	-0.007	-0.007	0.000	0.000	0.000	0.000
41	q	151	GLY	0	-0.006	-0.002	25.045	-0.001	-0.001	0.000	0.000	0.000	0.000
42	q	152	LYS	1	0.890	0.950	21.715	-0.164	-0.164	0.000	0.000	0.000	0.000
43	q	153	SER	0	-0.025	-0.013	18.535	0.012	0.012	0.000	0.000	0.000	0.000
44	q	154	LEU	0	-0.057	-0.022	19.308	0.025	0.025	0.000	0.000	0.000	0.000
45	q	155	LEU	0	-0.002	-0.003	13.570	0.020	0.020	0.000	0.000	0.000	0.000
46	q	168	SER	0	0.014	0.002	21.745	-0.006	-0.006	0.000	0.000	0.000	0.000
47	q	169	LEU	0	-0.044	-0.024	20.449	0.035	0.035	0.000	0.000	0.000	0.000
48	q	170	TRP	0	0.024	0.009	16.708	-0.009	-0.009	0.000	0.000	0.000	0.000
49	q	171	VAL	0	-0.004	-0.001	18.484	0.010	0.010	0.000	0.000	0.000	0.000
50	q	172	TYR	0	0.039	0.022	14.573	0.000	0.000	0.000	0.000	0.000	0.000
51	q	173	GLN	0	0.036	0.021	17.355	-0.018	-0.018	0.000	0.000	0.000	0.000
52	q	174	CYS	0	0.013	0.006	15.333	0.051	0.051	0.000	0.000	0.000	0.000
53	q	175	ASN	0	0.011	0.002	15.790	-0.009	-0.009	0.000	0.000	0.000	0.000
54	q	184	CYS	0	-0.002	-0.021	10.638	0.035	0.035	0.000	0.000	0.000	0.000
55	q	185	LYS	1	0.975	0.975	9.476	-0.541	-0.541	0.000	0.000	0.000	0.000
56	q	186	VAL	0	0.032	0.020	3.607	-0.673	-0.273	0.021	-0.147	-0.275	0.001
57	q	187	LEU	0	0.008	0.007	6.593	0.153	0.153	0.000	0.000	0.000	0.000
58	q	188	SER	0	-0.034	0.008	9.170	-0.228	-0.228	0.000	0.000	0.000	0.000

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