FMO DATABASE

FMODB ID: 6636Z

Calculation Name: 4DX9-o-Xray321

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: o

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	90
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-496678.303259
FMO2-HF: Nuclear repulsion	463379.749137
FMO2-HF: Total energy	-33298.554122
FMO2-MP2: Total energy	-33391.830336

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(o:59:ACE )

Summations of interaction energy for fragment #1(o: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.
-0.033999999999999	1.297	0.197	-0.866	-0.661	-0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / 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

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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	o	61	ALA	0	0.013	0.024	3.854	0.861	1.712	-0.005	-0.370	-0.476	-0.001
4	o	62	GLU	-1	-0.973	-0.993	6.031	-0.415	-0.415	0.000	0.000	0.000	0.000
5	o	63	PHE	0	-0.005	-0.015	6.196	0.115	0.115	0.000	0.000	0.000	0.000
6	o	64	NME	0	-0.017	0.020	10.978	0.040	0.040	0.000	0.000	0.000	0.000
7	o	83	ACE	0	-0.004	-0.019	21.412	0.000	0.000	0.000	0.000	0.000	0.000
8	o	84	GLY	0	0.045	0.001	21.489	-0.002	-0.002	0.000	0.000	0.000	0.000
9	o	85	PRO	0	-0.029	-0.018	18.608	-0.006	-0.006	0.000	0.000	0.000	0.000
10	o	86	LEU	0	0.042	0.004	20.432	0.000	0.000	0.000	0.000	0.000	0.000
11	o	87	ASP	-1	-0.945	-0.956	23.576	0.069	0.069	0.000	0.000	0.000	0.000
12	o	88	LEU	0	-0.046	-0.032	17.141	-0.006	-0.006	0.000	0.000	0.000	0.000
13	o	89	ILE	0	-0.033	-0.018	20.807	-0.002	-0.002	0.000	0.000	0.000	0.000
14	o	90	ASN	0	-0.031	-0.012	22.753	-0.011	-0.011	0.000	0.000	0.000	0.000
15	o	91	TYR	0	0.034	0.031	24.886	-0.008	-0.008	0.000	0.000	0.000	0.000
16	o	92	ILE	0	-0.078	-0.037	21.065	-0.008	-0.008	0.000	0.000	0.000	0.000
17	o	93	ASP	-1	-0.847	-0.923	25.068	0.079	0.079	0.000	0.000	0.000	0.000
18	o	94	NME	0	-0.077	-0.016	27.533	-0.007	-0.007	0.000	0.000	0.000	0.000
19	o	100	ACE	0	-0.015	-0.019	29.290	0.000	0.000	0.000	0.000	0.000	0.000
20	o	101	LEU	0	-0.003	-0.017	23.292	-0.002	-0.002	0.000	0.000	0.000	0.000
21	o	102	PRO	0	0.004	0.026	25.349	0.002	0.002	0.000	0.000	0.000	0.000
22	o	103	PHE	0	0.007	-0.007	25.838	0.004	0.004	0.000	0.000	0.000	0.000
23	o	104	VAL	0	-0.025	-0.024	25.645	0.004	0.004	0.000	0.000	0.000	0.000
24	o	105	PRO	0	0.039	0.076	24.203	-0.003	-0.003	0.000	0.000	0.000	0.000
25	o	106	PRO	0	-0.099	-0.088	26.299	-0.004	-0.004	0.000	0.000	0.000	0.000
26	o	107	GLU	-1	-0.906	-0.957	26.413	0.003	0.003	0.000	0.000	0.000	0.000
27	o	108	GLU	-1	-1.005	-1.004	21.394	-0.019	-0.019	0.000	0.000	0.000	0.000
28	o	109	GLU	-1	-0.842	-0.932	19.556	0.023	0.023	0.000	0.000	0.000	0.000
29	o	110	PHE	0	-0.048	-0.022	17.269	-0.006	-0.006	0.000	0.000	0.000	0.000
30	o	111	ILE	0	0.090	0.018	12.087	0.017	0.017	0.000	0.000	0.000	0.000
31	o	112	MET	0	-0.004	-0.001	8.555	0.009	0.009	0.000	0.000	0.000	0.000
32	o	113	GLY	0	0.033	0.047	8.214	-0.023	-0.023	0.000	0.000	0.000	0.000
33	o	114	VAL	0	-0.031	-0.013	5.214	0.023	0.023	0.000	0.000	0.000	0.000
34	o	115	SER	0	0.022	-0.005	4.270	-0.629	-0.561	0.001	-0.040	-0.028	0.000
35	o	116	LYS	1	0.893	0.950	3.228	-2.897	-2.529	0.201	-0.452	-0.117	-0.003
36	o	117	TYR	0	-0.010	-0.019	4.976	0.093	0.137	0.000	-0.004	-0.040	0.000
37	o	118	GLY	0	0.005	0.015	8.590	0.128	0.128	0.000	0.000	0.000	0.000
38	o	119	ILE	0	0.009	-0.009	8.966	-0.078	-0.078	0.000	0.000	0.000	0.000
39	o	120	LYS	1	0.951	0.976	10.407	0.438	0.438	0.000	0.000	0.000	0.000
40	o	121	VAL	0	0.014	0.015	11.423	-0.024	-0.024	0.000	0.000	0.000	0.000
41	o	122	NME	0	-0.021	-0.009	13.755	0.004	0.004	0.000	0.000	0.000	0.000
42	o	139	ACE	0	0.046	0.013	13.457	-0.008	-0.008	0.000	0.000	0.000	0.000
43	o	140	ARG	1	0.870	0.940	13.903	-0.132	-0.132	0.000	0.000	0.000	0.000
44	o	141	MET	0	0.049	0.045	9.265	-0.006	-0.006	0.000	0.000	0.000	0.000
45	o	142	VAL	0	-0.049	-0.030	13.382	0.035	0.035	0.000	0.000	0.000	0.000
46	o	143	CYS	0	-0.012	0.011	12.684	-0.025	-0.025	0.000	0.000	0.000	0.000
47	o	144	TYR	0	0.010	-0.004	15.634	0.009	0.009	0.000	0.000	0.000	0.000
48	o	145	ASP	-1	-0.916	-0.965	19.025	0.129	0.129	0.000	0.000	0.000	0.000
49	o	146	NME	0	-0.024	0.003	21.097	-0.011	-0.011	0.000	0.000	0.000	0.000
50	o	152	ACE	0	0.036	0.011	21.196	-0.003	-0.003	0.000	0.000	0.000	0.000
51	o	153	SER	0	-0.020	-0.030	17.885	0.019	0.019	0.000	0.000	0.000	0.000
52	o	154	LEU	0	0.021	0.042	18.138	-0.005	-0.005	0.000	0.000	0.000	0.000
53	o	155	LEU	0	0.003	-0.004	12.163	0.033	0.033	0.000	0.000	0.000	0.000
54	o	156	ALA	0	0.035	0.018	15.565	-0.030	-0.030	0.000	0.000	0.000	0.000
55	o	157	LEU	0	-0.034	-0.036	11.476	0.032	0.032	0.000	0.000	0.000	0.000
56	o	158	LYS	1	0.912	0.982	15.633	-0.101	-0.101	0.000	0.000	0.000	0.000
57	o	159	THR	0	-0.082	-0.049	16.199	-0.001	-0.001	0.000	0.000	0.000	0.000
58	o	160	THR	0	-0.006	-0.040	18.370	0.009	0.009	0.000	0.000	0.000	0.000
59	o	161	ASP	-1	-0.787	-0.881	20.396	-0.020	-0.020	0.000	0.000	0.000	0.000
60	o	162	ALA	0	-0.032	-0.030	23.061	0.003	0.003	0.000	0.000	0.000	0.000
61	o	163	SER	0	-0.101	-0.055	24.004	0.001	0.001	0.000	0.000	0.000	0.000
62	o	164	ASN	0	-0.084	-0.027	23.098	0.010	0.010	0.000	0.000	0.000	0.000
63	o	165	GLU	-1	-0.858	-0.911	25.885	0.003	0.003	0.000	0.000	0.000	0.000
64	o	166	GLU	-1	-0.842	-0.913	25.093	0.020	0.020	0.000	0.000	0.000	0.000
65	o	167	TYR	0	-0.117	-0.059	21.476	0.010	0.010	0.000	0.000	0.000	0.000
66	o	168	SER	0	0.020	0.005	22.078	0.003	0.003	0.000	0.000	0.000	0.000
67	o	169	LEU	0	-0.061	-0.042	19.972	0.011	0.011	0.000	0.000	0.000	0.000
68	o	170	TRP	0	-0.034	-0.007	17.065	-0.015	-0.015	0.000	0.000	0.000	0.000
69	o	171	VAL	0	0.030	0.012	17.342	0.018	0.018	0.000	0.000	0.000	0.000
70	o	172	TYR	0	-0.021	-0.006	15.148	-0.025	-0.025	0.000	0.000	0.000	0.000
71	o	173	GLN	0	0.040	0.007	17.029	0.038	0.038	0.000	0.000	0.000	0.000
72	o	174	CYS	0	-0.038	-0.013	16.352	-0.023	-0.023	0.000	0.000	0.000	0.000
73	o	175	ASN	0	-0.044	-0.017	13.762	0.028	0.028	0.000	0.000	0.000	0.000
74	o	176	SER	0	0.069	0.028	16.841	0.003	0.003	0.000	0.000	0.000	0.000
75	o	177	LEU	0	0.051	0.017	15.942	0.028	0.028	0.000	0.000	0.000	0.000
76	o	178	GLU	-1	-0.982	-0.994	15.327	0.300	0.300	0.000	0.000	0.000	0.000
77	o	179	GLN	0	0.030	0.007	13.245	0.036	0.036	0.000	0.000	0.000	0.000
78	o	180	ALA	0	-0.014	0.002	11.487	0.058	0.058	0.000	0.000	0.000	0.000
79	o	181	GLN	0	-0.022	-0.017	10.811	0.091	0.091	0.000	0.000	0.000	0.000
80	o	182	ALA	0	-0.023	-0.004	8.218	0.180	0.180	0.000	0.000	0.000	0.000
81	o	183	ILE	0	-0.037	-0.018	6.050	0.427	0.427	0.000	0.000	0.000	0.000
82	o	184	CYS	0	-0.074	-0.035	5.358	0.206	0.206	0.000	0.000	0.000	0.000
83	o	185	NME	0	-0.039	0.002	4.848	0.212	0.212	0.000	0.000	0.000	0.000
84	o	191	ACE	0	0.005	-0.060	9.672	-0.006	-0.006	0.000	0.000	0.000	0.000
85	o	192	ASP	-1	-0.875	-0.931	6.888	0.694	0.694	0.000	0.000	0.000	0.000
86	o	193	SER	0	0.003	0.002	5.262	0.011	0.011	0.000	0.000	0.000	0.000
87	o	194	VAL	0	0.022	0.012	7.351	-0.079	-0.079	0.000	0.000	0.000	0.000
88	o	195	LEU	0	-0.066	0.029	10.152	-0.003	-0.003	0.000	0.000	0.000	0.000
89	o	196	THR	0	-0.030	-0.008	12.761	0.023	0.023	0.000	0.000	0.000	0.000
90	o	197	NME	0	0.021	0.009	13.990	0.017	0.017	0.000	0.000	0.000	0.000

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