FMO DATABASE

FMODB ID: LJLJ9

Calculation Name: 4DX9-w-Xray321

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	63
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-258751.848592
FMO2-HF: Nuclear repulsion	236670.098911
FMO2-HF: Total energy	-22081.749681
FMO2-MP2: Total energy	-22143.007823

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:64:ACE )

Summations of interaction energy for fragment #1(w:64:ACE )

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.
-0.0040000000000009	1.288	4.176	-3.048	-2.418	-0.017

Interaction energy analysis for fragmet #1(w:64:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.010

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	66	LYS	1	0.944	0.997	3.878	1.642	2.286	-0.005	-0.299	-0.339	0.000
4	w	67	TYR	0	0.047	-0.001	6.796	0.056	0.056	0.000	0.000	0.000	0.000
5	w	68	VAL	0	-0.028	0.001	9.983	0.096	0.096	0.000	0.000	0.000	0.000
6	w	69	GLY	0	0.036	-0.007	12.558	0.090	0.090	0.000	0.000	0.000	0.000
7	w	70	ALA	0	-0.051	-0.009	14.487	-0.005	-0.005	0.000	0.000	0.000	0.000
8	w	71	ILE	0	0.001	0.010	15.824	0.041	0.041	0.000	0.000	0.000	0.000
9	w	72	NME	0	-0.014	0.017	19.198	0.008	0.008	0.000	0.000	0.000	0.000
10	w	98	ACE	0	0.006	-0.012	22.484	-0.004	-0.004	0.000	0.000	0.000	0.000
11	w	99	GLY	0	-0.003	-0.007	23.024	0.018	0.018	0.000	0.000	0.000	0.000
12	w	100	LYS	1	0.957	0.982	22.891	0.166	0.166	0.000	0.000	0.000	0.000
13	w	101	LEU	0	-0.028	-0.005	17.139	0.007	0.007	0.000	0.000	0.000	0.000
14	w	102	PRO	0	0.050	0.037	16.572	0.014	0.014	0.000	0.000	0.000	0.000
15	w	103	PHE	0	0.002	-0.017	17.089	-0.031	-0.031	0.000	0.000	0.000	0.000
16	w	104	VAL	0	-0.033	-0.015	14.490	-0.043	-0.043	0.000	0.000	0.000	0.000
17	w	105	PRO	0	-0.025	0.003	10.548	0.040	0.040	0.000	0.000	0.000	0.000
18	w	106	PRO	0	0.024	0.005	11.344	0.018	0.018	0.000	0.000	0.000	0.000
19	w	107	GLU	-1	-0.902	-0.958	9.815	-0.370	-0.370	0.000	0.000	0.000	0.000
20	w	108	GLU	-1	-0.978	-0.967	9.032	-0.099	-0.099	0.000	0.000	0.000	0.000
21	w	109	GLU	-1	-0.923	-0.967	4.481	0.937	1.036	0.000	-0.014	-0.085	0.000
22	w	110	PHE	0	-0.001	-0.016	3.468	-0.091	0.047	0.008	-0.066	-0.079	0.000
23	w	111	ILE	0	0.017	-0.001	2.374	-1.577	-1.129	3.844	-2.896	-1.397	-0.017
24	w	112	MET	0	-0.039	-0.007	2.479	-1.211	-1.372	0.329	0.235	-0.402	0.000
25	w	113	GLY	0	0.026	0.005	4.532	0.429	0.553	0.000	-0.008	-0.116	0.000
26	w	114	VAL	0	-0.043	-0.017	7.905	-0.115	-0.115	0.000	0.000	0.000	0.000
27	w	115	SER	0	-0.016	-0.014	10.360	0.063	0.063	0.000	0.000	0.000	0.000
28	w	116	NME	0	0.027	0.029	13.608	-0.032	-0.032	0.000	0.000	0.000	0.000
29	w	139	ACE	0	0.043	0.017	18.359	0.001	0.001	0.000	0.000	0.000	0.000
30	w	140	ARG	1	0.884	0.923	17.693	0.179	0.179	0.000	0.000	0.000	0.000
31	w	141	MET	0	0.030	0.054	11.692	-0.039	-0.039	0.000	0.000	0.000	0.000
32	w	142	VAL	0	-0.023	-0.022	15.498	0.043	0.043	0.000	0.000	0.000	0.000
33	w	143	CYS	0	0.002	-0.005	11.803	-0.059	-0.059	0.000	0.000	0.000	0.000
34	w	144	NME	0	0.026	0.034	15.213	0.044	0.044	0.000	0.000	0.000	0.000
35	w	152	ACE	0	0.022	0.001	14.463	0.012	0.012	0.000	0.000	0.000	0.000
36	w	153	SER	0	-0.019	-0.018	9.058	-0.089	-0.089	0.000	0.000	0.000	0.000
37	w	154	LEU	0	0.011	-0.003	10.812	-0.091	-0.091	0.000	0.000	0.000	0.000
38	w	155	LEU	0	0.015	0.005	6.992	0.116	0.116	0.000	0.000	0.000	0.000
39	w	156	ALA	0	-0.026	-0.006	11.018	-0.004	-0.004	0.000	0.000	0.000	0.000
40	w	157	LEU	0	0.046	0.016	10.440	0.038	0.038	0.000	0.000	0.000	0.000
41	w	158	LYS	1	0.959	0.995	14.944	0.182	0.182	0.000	0.000	0.000	0.000
42	w	159	NME	0	-0.006	-0.010	18.393	0.008	0.008	0.000	0.000	0.000	0.000
43	w	167	ACE	0	0.025	0.005	24.623	0.002	0.002	0.000	0.000	0.000	0.000
44	w	168	SER	0	0.001	-0.038	19.700	0.005	0.005	0.000	0.000	0.000	0.000
45	w	169	LEU	0	-0.078	-0.029	18.471	0.002	0.002	0.000	0.000	0.000	0.000
46	w	170	TRP	0	0.047	0.022	13.336	-0.009	-0.009	0.000	0.000	0.000	0.000
47	w	171	VAL	0	0.000	-0.004	12.787	0.008	0.008	0.000	0.000	0.000	0.000
48	w	172	TYR	0	0.040	0.025	7.341	0.043	0.043	0.000	0.000	0.000	0.000
49	w	173	GLN	0	0.011	0.011	8.312	0.119	0.119	0.000	0.000	0.000	0.000
50	w	174	CYS	0	0.010	0.010	4.997	-0.902	-0.902	0.000	0.000	0.000	0.000
51	w	175	ASN	0	0.030	0.029	5.462	0.207	0.207	0.000	0.000	0.000	0.000
52	w	176	NME	0	-0.002	-0.003	6.951	0.029	0.029	0.000	0.000	0.000	0.000
53	w	183	ACE	0	0.051	0.022	7.759	-0.001	-0.001	0.000	0.000	0.000	0.000
54	w	184	CYS	0	-0.024	-0.036	8.438	-0.022	-0.022	0.000	0.000	0.000	0.000
55	w	185	LYS	1	1.006	0.999	12.123	0.119	0.119	0.000	0.000	0.000	0.000
56	w	186	VAL	0	0.061	0.046	9.797	0.011	0.011	0.000	0.000	0.000	0.000
57	w	187	LEU	0	0.004	-0.003	11.343	0.008	0.008	0.000	0.000	0.000	0.000
58	w	188	SER	0	-0.030	-0.034	13.346	0.008	0.008	0.000	0.000	0.000	0.000
59	w	189	THR	0	-0.016	-0.011	15.866	0.014	0.014	0.000	0.000	0.000	0.000
60	w	190	ALA	0	-0.026	0.001	15.935	0.011	0.011	0.000	0.000	0.000	0.000
61	w	191	PHE	0	-0.084	-0.035	16.696	-0.003	-0.003	0.000	0.000	0.000	0.000
62	w	192	ASP	-1	-0.911	-0.939	20.345	-0.048	-0.048	0.000	0.000	0.000	0.000
63	w	193	NME	0	-0.025	-0.010	22.052	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(w:64:ACE )