FMO DATABASE

FMODB ID: 22K2R

Calculation Name: 4DX9-q-Xray321

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: 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	68
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-309231.798038
FMO2-HF: Nuclear repulsion	284510.368848
FMO2-HF: Total energy	-24721.42919
FMO2-MP2: Total energy	-24789.410709

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:59:ACE )

Summations of interaction energy for fragment #1(q:59: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.
0.327	1.46	0.056	-0.47	-0.718	-0.001

Interaction energy analysis for fragmet #1(q:59:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.005

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

Sort

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	q	61	ALA	0	-0.027	-0.004	3.838	1.000	1.810	-0.006	-0.370	-0.435	-0.001
4	q	62	GLU	-1	-0.850	-0.915	6.901	-0.621	-0.621	0.000	0.000	0.000	0.000
5	q	63	PHE	0	-0.053	-0.031	10.519	0.103	0.103	0.000	0.000	0.000	0.000
6	q	64	ARG	1	0.809	0.883	13.813	0.118	0.118	0.000	0.000	0.000	0.000
7	q	65	ILE	0	-0.078	-0.027	15.878	0.024	0.024	0.000	0.000	0.000	0.000
8	q	66	LYS	1	0.924	0.981	18.706	0.091	0.091	0.000	0.000	0.000	0.000
9	q	67	TYR	0	-0.022	-0.005	20.224	-0.005	-0.005	0.000	0.000	0.000	0.000
10	q	68	VAL	0	-0.027	0.003	22.877	0.013	0.013	0.000	0.000	0.000	0.000
11	q	69	GLY	0	0.032	0.003	24.276	0.008	0.008	0.000	0.000	0.000	0.000
12	q	70	ALA	0	-0.025	0.002	23.507	0.002	0.002	0.000	0.000	0.000	0.000
13	q	71	ILE	0	-0.026	-0.018	25.269	0.007	0.007	0.000	0.000	0.000	0.000
14	q	72	NME	0	0.009	0.006	26.832	-0.001	-0.001	0.000	0.000	0.000	0.000
15	q	98	ACE	0	-0.001	-0.015	37.691	0.000	0.000	0.000	0.000	0.000	0.000
16	q	99	GLY	0	0.029	0.005	34.918	0.001	0.001	0.000	0.000	0.000	0.000
17	q	100	LYS	1	0.906	0.955	32.422	0.036	0.036	0.000	0.000	0.000	0.000
18	q	101	LEU	0	0.035	0.026	27.011	-0.004	-0.004	0.000	0.000	0.000	0.000
19	q	102	PRO	0	0.017	0.018	29.048	0.005	0.005	0.000	0.000	0.000	0.000
20	q	103	PHE	0	0.042	0.007	29.479	-0.003	-0.003	0.000	0.000	0.000	0.000
21	q	104	VAL	0	-0.017	-0.005	29.913	0.000	0.000	0.000	0.000	0.000	0.000
22	q	105	PRO	0	-0.027	-0.005	26.397	0.001	0.001	0.000	0.000	0.000	0.000
23	q	106	PRO	0	0.042	0.026	28.441	0.000	0.000	0.000	0.000	0.000	0.000
24	q	107	GLU	-1	-0.966	-0.997	25.395	-0.100	-0.100	0.000	0.000	0.000	0.000
25	q	108	GLU	-1	-0.889	-0.952	23.978	-0.122	-0.122	0.000	0.000	0.000	0.000
26	q	109	GLU	-1	-0.820	-0.887	21.714	-0.142	-0.142	0.000	0.000	0.000	0.000
27	q	110	PHE	0	-0.024	-0.008	17.701	-0.008	-0.008	0.000	0.000	0.000	0.000
28	q	111	ILE	0	0.024	-0.005	14.179	0.014	0.014	0.000	0.000	0.000	0.000
29	q	112	MET	0	-0.028	-0.011	11.558	0.008	0.008	0.000	0.000	0.000	0.000
30	q	113	GLY	0	0.027	0.023	10.909	-0.110	-0.110	0.000	0.000	0.000	0.000
31	q	114	VAL	0	-0.044	-0.032	6.255	0.055	0.055	0.000	0.000	0.000	0.000
32	q	115	SER	0	0.011	-0.013	5.272	-0.270	-0.246	0.000	-0.013	-0.010	0.000
33	q	116	NME	0	-0.003	0.016	5.279	0.045	0.045	0.000	0.000	0.000	0.000
34	q	139	ACE	0	0.038	0.008	19.648	-0.003	-0.003	0.000	0.000	0.000	0.000
35	q	140	ARG	1	0.905	0.936	18.611	0.007	0.007	0.000	0.000	0.000	0.000
36	q	141	MET	0	0.035	0.039	12.010	-0.028	-0.028	0.000	0.000	0.000	0.000
37	q	142	VAL	0	-0.002	-0.012	16.954	0.020	0.020	0.000	0.000	0.000	0.000
38	q	143	CYS	0	0.002	0.010	16.286	-0.016	-0.016	0.000	0.000	0.000	0.000
39	q	144	TYR	0	-0.003	0.010	19.242	0.012	0.012	0.000	0.000	0.000	0.000
40	q	145	ASP	-1	-0.867	-0.931	22.570	-0.007	-0.007	0.000	0.000	0.000	0.000
41	q	146	ASP	-1	-0.851	-0.939	25.125	-0.029	-0.029	0.000	0.000	0.000	0.000
42	q	147	GLY	0	-0.023	-0.016	27.103	-0.002	-0.002	0.000	0.000	0.000	0.000
43	q	148	LEU	0	-0.047	-0.030	30.244	0.002	0.002	0.000	0.000	0.000	0.000
44	q	149	GLY	0	-0.001	0.007	29.407	0.000	0.000	0.000	0.000	0.000	0.000
45	q	150	ALA	0	-0.015	-0.007	28.732	-0.005	-0.005	0.000	0.000	0.000	0.000
46	q	151	GLY	0	-0.022	-0.004	27.061	-0.003	-0.003	0.000	0.000	0.000	0.000
47	q	152	LYS	1	0.892	0.939	23.156	0.059	0.059	0.000	0.000	0.000	0.000
48	q	153	SER	0	-0.028	-0.007	19.461	0.003	0.003	0.000	0.000	0.000	0.000
49	q	154	LEU	0	-0.023	-0.010	20.711	-0.017	-0.017	0.000	0.000	0.000	0.000
50	q	155	LEU	0	0.019	-0.008	14.820	0.006	0.006	0.000	0.000	0.000	0.000
51	q	156	NME	0	-0.041	0.003	19.099	-0.006	-0.006	0.000	0.000	0.000	0.000
52	q	167	ACE	0	0.011	-0.006	23.548	-0.001	-0.001	0.000	0.000	0.000	0.000
53	q	168	SER	0	-0.054	-0.029	22.914	0.004	0.004	0.000	0.000	0.000	0.000
54	q	169	LEU	0	-0.001	0.006	21.707	-0.008	-0.008	0.000	0.000	0.000	0.000
55	q	170	TRP	0	0.025	0.009	18.570	-0.006	-0.006	0.000	0.000	0.000	0.000
56	q	171	VAL	0	0.001	0.000	20.046	0.008	0.008	0.000	0.000	0.000	0.000
57	q	172	TYR	0	0.023	0.013	16.808	-0.013	-0.013	0.000	0.000	0.000	0.000
58	q	173	GLN	0	0.046	0.026	19.593	0.012	0.012	0.000	0.000	0.000	0.000
59	q	174	CYS	0	-0.006	-0.012	16.495	-0.028	-0.028	0.000	0.000	0.000	0.000
60	q	175	ASN	0	-0.007	0.000	17.562	-0.002	-0.002	0.000	0.000	0.000	0.000
61	q	176	NME	0	0.055	0.022	19.041	0.009	0.009	0.000	0.000	0.000	0.000
62	q	183	ACE	0	0.037	0.014	9.816	-0.017	-0.017	0.000	0.000	0.000	0.000
63	q	184	CYS	0	-0.014	-0.034	9.963	0.028	0.028	0.000	0.000	0.000	0.000
64	q	185	LYS	1	0.950	0.974	7.889	-0.196	-0.196	0.000	0.000	0.000	0.000
65	q	186	VAL	0	0.029	0.017	3.069	0.110	0.335	0.062	-0.084	-0.202	0.000
66	q	187	LEU	0	0.030	0.016	4.892	0.105	0.179	0.000	-0.003	-0.071	0.000
67	q	188	SER	0	-0.067	-0.016	7.474	-0.030	-0.030	0.000	0.000	0.000	0.000
68	q	189	NME	0	0.028	0.026	7.584	0.214	0.214	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(q:59:ACE )