FMO DATABASE

FMODB ID: Q1R7Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-289708.380651
FMO2-HF: Nuclear repulsion	265841.578199
FMO2-HF: Total energy	-23866.802453
FMO2-MP2: Total energy	-23932.048775

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.
-1.535	1.15	5.046	-2.937	-4.794	-0.005

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 : 0.006 / q_NPA : 0.002

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	-0.847	-0.913	3.684	-1.210	1.393	-0.024	-1.156	-1.422	0.005
4	q	63	PHE	0	-0.083	-0.070	5.845	0.226	0.226	0.000	0.000	0.000	0.000
5	q	64	ARG	1	0.806	0.894	9.672	0.487	0.487	0.000	0.000	0.000	0.000
6	q	65	ILE	0	-0.049	-0.025	12.838	-0.009	-0.009	0.000	0.000	0.000	0.000
7	q	66	LYS	1	0.872	0.946	15.394	0.174	0.174	0.000	0.000	0.000	0.000
8	q	67	TYR	0	-0.039	-0.018	15.600	0.038	0.038	0.000	0.000	0.000	0.000
9	q	68	VAL	0	-0.025	-0.011	20.035	-0.014	-0.014	0.000	0.000	0.000	0.000
10	q	69	GLY	0	0.041	0.013	21.656	0.002	0.002	0.000	0.000	0.000	0.000
11	q	70	ALA	0	-0.029	-0.001	21.064	-0.004	-0.004	0.000	0.000	0.000	0.000
12	q	71	ILE	0	-0.009	-0.007	22.944	0.001	0.001	0.000	0.000	0.000	0.000
13	q	99	GLY	0	0.023	0.000	32.976	0.001	0.001	0.000	0.000	0.000	0.000
14	q	100	LYS	1	0.916	0.948	30.525	-0.044	-0.044	0.000	0.000	0.000	0.000
15	q	101	LEU	0	0.032	0.027	24.954	0.007	0.007	0.000	0.000	0.000	0.000
16	q	102	PRO	0	0.020	0.014	26.588	-0.007	-0.007	0.000	0.000	0.000	0.000
17	q	103	PHE	0	0.033	0.006	27.259	-0.004	-0.004	0.000	0.000	0.000	0.000
18	q	104	VAL	0	-0.021	-0.011	27.873	-0.015	-0.015	0.000	0.000	0.000	0.000
19	q	105	PRO	0	-0.021	0.009	24.033	0.008	0.008	0.000	0.000	0.000	0.000
20	q	106	PRO	0	0.068	0.005	25.229	-0.021	-0.021	0.000	0.000	0.000	0.000
21	q	107	GLU	-1	-0.966	-0.958	22.552	-0.019	-0.019	0.000	0.000	0.000	0.000
22	q	108	GLU	-1	-0.869	-0.935	18.502	-0.094	-0.094	0.000	0.000	0.000	0.000
23	q	109	GLU	-1	-0.808	-0.874	17.249	-0.304	-0.304	0.000	0.000	0.000	0.000
24	q	110	PHE	0	-0.003	0.006	12.672	0.000	0.000	0.000	0.000	0.000	0.000
25	q	111	ILE	0	0.016	0.002	8.165	-0.096	-0.096	0.000	0.000	0.000	0.000
26	q	112	MET	0	-0.031	-0.017	9.093	0.228	0.228	0.000	0.000	0.000	0.000
27	q	113	GLY	0	0.027	0.022	7.209	-0.164	-0.164	0.000	0.000	0.000	0.000
28	q	114	VAL	0	-0.046	-0.030	4.657	0.233	0.333	-0.001	-0.013	-0.087	0.000
29	q	115	SER	0	0.016	0.005	2.316	-1.802	-2.218	5.021	-1.668	-2.936	-0.009
30	q	140	ARG	1	0.988	0.987	18.834	-0.108	-0.108	0.000	0.000	0.000	0.000
31	q	141	MET	0	-0.009	-0.005	12.469	0.007	0.007	0.000	0.000	0.000	0.000
32	q	142	VAL	0	0.000	-0.013	17.085	-0.016	-0.016	0.000	0.000	0.000	0.000
33	q	143	CYS	0	0.003	0.014	16.224	-0.009	-0.009	0.000	0.000	0.000	0.000
34	q	144	TYR	0	0.022	0.019	18.968	-0.004	-0.004	0.000	0.000	0.000	0.000
35	q	145	ASP	-1	-0.867	-0.930	21.983	-0.182	-0.182	0.000	0.000	0.000	0.000
36	q	146	ASP	-1	-0.772	-0.881	24.313	-0.129	-0.129	0.000	0.000	0.000	0.000
37	q	147	GLY	0	-0.021	-0.011	26.033	0.017	0.017	0.000	0.000	0.000	0.000
38	q	148	LEU	0	-0.079	-0.036	29.382	0.011	0.011	0.000	0.000	0.000	0.000
39	q	149	GLY	0	-0.010	-0.020	29.771	0.004	0.004	0.000	0.000	0.000	0.000
40	q	150	ALA	0	-0.053	-0.026	27.816	-0.011	-0.011	0.000	0.000	0.000	0.000
41	q	151	GLY	0	-0.007	-0.005	25.157	-0.018	-0.018	0.000	0.000	0.000	0.000
42	q	152	LYS	1	0.891	0.945	21.761	0.205	0.205	0.000	0.000	0.000	0.000
43	q	153	SER	0	-0.023	-0.008	18.613	0.021	0.021	0.000	0.000	0.000	0.000
44	q	154	LEU	0	-0.022	-0.011	19.329	-0.010	-0.010	0.000	0.000	0.000	0.000
45	q	155	LEU	0	-0.031	-0.010	13.673	0.058	0.058	0.000	0.000	0.000	0.000
46	q	168	SER	0	0.039	0.018	21.297	-0.001	-0.001	0.000	0.000	0.000	0.000
47	q	169	LEU	0	-0.072	-0.041	20.451	0.028	0.028	0.000	0.000	0.000	0.000
48	q	170	TRP	0	0.002	-0.003	16.722	-0.007	-0.007	0.000	0.000	0.000	0.000
49	q	171	VAL	0	0.024	0.011	18.494	-0.016	-0.016	0.000	0.000	0.000	0.000
50	q	172	TYR	0	0.035	0.016	14.448	-0.001	-0.001	0.000	0.000	0.000	0.000
51	q	173	GLN	0	0.021	0.010	17.373	-0.031	-0.031	0.000	0.000	0.000	0.000
52	q	174	CYS	0	0.002	0.006	15.180	-0.041	-0.041	0.000	0.000	0.000	0.000
53	q	175	ASN	0	0.019	0.005	15.733	0.046	0.046	0.000	0.000	0.000	0.000
54	q	184	CYS	0	0.024	-0.007	10.120	-0.062	-0.062	0.000	0.000	0.000	0.000
55	q	185	LYS	1	0.951	0.965	8.423	0.796	0.796	0.000	0.000	0.000	0.000
56	q	186	VAL	0	0.041	0.023	2.949	-0.410	-0.012	0.050	-0.100	-0.349	-0.001
57	q	187	LEU	0	0.013	0.012	5.629	0.657	0.657	0.000	0.000	0.000	0.000
58	q	188	SER	0	-0.062	-0.010	8.489	0.073	0.073	0.000	0.000	0.000	0.000

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