FMO DATABASE

FMODB ID: 7G18K

Calculation Name: 4DX9-2-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: 2

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-682878.913541
FMO2-HF: Nuclear repulsion	644457.115306
FMO2-HF: Total energy	-38421.798234
FMO2-MP2: Total energy	-38530.971429

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(2:60:CYS)

Summations of interaction energy for fragment #1(2:60: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.
-6.571	-1.526	2.298	-3.391	-3.953	-0.019

Interaction energy analysis for fragmet #1(2:60:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.003

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	2	62	GLU	-1	-0.938	-0.962	3.814	-0.602	1.660	-0.027	-0.994	-1.241	0.003
4	2	63	PHE	0	0.001	-0.001	5.373	0.323	0.361	-0.001	-0.003	-0.034	0.000
5	2	64	ARG	1	0.970	0.972	9.021	0.837	0.837	0.000	0.000	0.000	0.000
6	2	65	ILE	0	-0.066	-0.031	12.330	-0.005	-0.005	0.000	0.000	0.000	0.000
7	2	66	LYS	1	0.954	0.971	14.898	0.300	0.300	0.000	0.000	0.000	0.000
8	2	67	TYR	0	-0.017	-0.034	18.078	-0.008	-0.008	0.000	0.000	0.000	0.000
9	2	68	VAL	0	0.000	0.004	19.983	-0.008	-0.008	0.000	0.000	0.000	0.000
10	2	69	GLY	0	0.041	0.011	22.730	0.013	0.013	0.000	0.000	0.000	0.000
11	2	70	ALA	0	-0.050	-0.011	21.331	-0.011	-0.011	0.000	0.000	0.000	0.000
12	2	71	ILE	0	0.051	0.032	23.473	0.012	0.012	0.000	0.000	0.000	0.000
13	2	84	GLY	0	0.074	0.050	26.003	0.006	0.006	0.000	0.000	0.000	0.000
14	2	85	PRO	0	-0.020	-0.035	22.042	0.006	0.006	0.000	0.000	0.000	0.000
15	2	86	LEU	0	0.049	0.019	23.848	-0.012	-0.012	0.000	0.000	0.000	0.000
16	2	87	ASP	-1	-0.855	-0.932	26.912	-0.030	-0.030	0.000	0.000	0.000	0.000
17	2	88	LEU	0	-0.082	-0.046	20.694	0.011	0.011	0.000	0.000	0.000	0.000
18	2	89	ILE	0	0.017	0.011	23.672	0.001	0.001	0.000	0.000	0.000	0.000
19	2	90	ASN	0	0.023	0.015	25.864	-0.004	-0.004	0.000	0.000	0.000	0.000
20	2	91	TYR	0	-0.017	0.000	26.880	0.004	0.004	0.000	0.000	0.000	0.000
21	2	92	ILE	0	-0.006	-0.016	22.673	0.006	0.006	0.000	0.000	0.000	0.000
22	2	93	ASP	-1	-0.947	-0.979	27.023	-0.095	-0.095	0.000	0.000	0.000	0.000
23	2	94	VAL	0	0.005	0.005	29.476	0.001	0.001	0.000	0.000	0.000	0.000
24	2	95	ALA	0	-0.065	-0.023	28.832	0.005	0.005	0.000	0.000	0.000	0.000
25	2	96	GLN	0	-0.066	-0.037	27.230	-0.006	-0.006	0.000	0.000	0.000	0.000
26	2	97	GLN	0	-0.005	0.019	30.832	0.004	0.004	0.000	0.000	0.000	0.000
27	2	111	ILE	0	0.017	0.002	9.137	-0.029	-0.029	0.000	0.000	0.000	0.000
28	2	112	MET	0	-0.043	-0.014	8.793	0.177	0.177	0.000	0.000	0.000	0.000
29	2	113	GLY	0	0.064	0.037	5.442	-0.642	-0.642	0.000	0.000	0.000	0.000
30	2	114	VAL	0	-0.044	-0.006	4.724	0.767	1.012	-0.001	-0.054	-0.190	0.000
31	2	115	SER	0	0.041	-0.011	2.414	-2.791	-0.753	2.323	-2.270	-2.091	-0.023
32	2	116	LYS	1	0.925	0.939	3.711	-4.636	-4.308	0.004	-0.043	-0.289	0.001
33	2	117	TYR	0	0.010	-0.006	6.226	-0.764	-0.764	0.000	0.000	0.000	0.000
34	2	118	GLY	0	0.024	0.027	7.319	-0.425	-0.425	0.000	0.000	0.000	0.000
35	2	119	ILE	0	-0.004	0.026	6.841	0.694	0.694	0.000	0.000	0.000	0.000
36	2	128	ASP	-1	-0.928	-0.971	14.802	0.201	0.201	0.000	0.000	0.000	0.000
37	2	129	VAL	0	-0.040	-0.022	12.327	-0.005	-0.005	0.000	0.000	0.000	0.000
38	2	130	LEU	0	0.007	0.019	14.825	-0.001	-0.001	0.000	0.000	0.000	0.000
39	2	131	HIS	0	-0.005	-0.010	14.982	-0.038	-0.038	0.000	0.000	0.000	0.000
40	2	132	ARG	1	0.969	0.983	10.763	-0.996	-0.996	0.000	0.000	0.000	0.000
41	2	133	HIS	0	0.008	0.021	12.787	0.027	0.027	0.000	0.000	0.000	0.000
42	2	134	ALA	0	0.045	0.014	11.656	0.147	0.147	0.000	0.000	0.000	0.000
43	2	135	LEU	0	0.027	-0.011	9.052	-0.119	-0.119	0.000	0.000	0.000	0.000
44	2	136	TYR	0	-0.002	0.010	12.519	-0.066	-0.066	0.000	0.000	0.000	0.000
45	2	137	LEU	0	-0.037	-0.002	15.677	-0.069	-0.069	0.000	0.000	0.000	0.000
46	2	138	ILE	0	0.019	-0.001	11.684	-0.071	-0.071	0.000	0.000	0.000	0.000
47	2	139	ILE	0	0.044	0.030	15.608	0.008	0.008	0.000	0.000	0.000	0.000
48	2	140	ARG	1	0.814	0.890	17.212	-0.048	-0.048	0.000	0.000	0.000	0.000
49	2	141	MET	0	0.012	0.012	12.655	0.018	0.018	0.000	0.000	0.000	0.000
50	2	142	VAL	0	-0.032	-0.013	16.229	-0.013	-0.013	0.000	0.000	0.000	0.000
51	2	143	CYS	0	-0.026	-0.001	16.746	-0.011	-0.011	0.000	0.000	0.000	0.000
52	2	144	TYR	0	0.018	-0.001	18.790	0.011	0.011	0.000	0.000	0.000	0.000
53	2	145	ASP	-1	-0.834	-0.936	22.005	-0.263	-0.263	0.000	0.000	0.000	0.000
54	2	146	ASP	-1	-0.799	-0.898	24.605	-0.154	-0.154	0.000	0.000	0.000	0.000
55	2	147	GLY	0	-0.066	-0.037	24.410	-0.016	-0.016	0.000	0.000	0.000	0.000
56	2	148	LEU	0	0.064	0.022	26.950	0.007	0.007	0.000	0.000	0.000	0.000
57	2	149	GLY	0	-0.042	-0.018	25.369	0.009	0.009	0.000	0.000	0.000	0.000
58	2	150	ALA	0	-0.074	-0.014	26.383	-0.010	-0.010	0.000	0.000	0.000	0.000
59	2	151	GLY	0	0.022	-0.021	26.974	-0.001	-0.001	0.000	0.000	0.000	0.000
60	2	152	LYS	1	0.816	0.934	22.717	0.284	0.284	0.000	0.000	0.000	0.000
61	2	153	SER	0	0.012	0.011	19.552	-0.032	-0.032	0.000	0.000	0.000	0.000
62	2	154	LEU	0	0.000	0.019	20.362	-0.011	-0.011	0.000	0.000	0.000	0.000
63	2	155	LEU	0	-0.034	-0.039	13.760	-0.026	-0.026	0.000	0.000	0.000	0.000
64	2	156	ALA	0	0.037	0.025	17.587	0.038	0.038	0.000	0.000	0.000	0.000
65	2	157	LEU	0	-0.007	-0.017	12.998	-0.003	-0.003	0.000	0.000	0.000	0.000
66	2	158	LYS	1	0.960	0.992	17.247	-0.039	-0.039	0.000	0.000	0.000	0.000
67	2	159	THR	0	-0.030	0.003	16.773	0.022	0.022	0.000	0.000	0.000	0.000
68	2	160	THR	0	0.009	0.012	19.322	-0.031	-0.031	0.000	0.000	0.000	0.000
69	2	168	SER	0	0.017	0.014	22.015	-0.008	-0.008	0.000	0.000	0.000	0.000
70	2	169	LEU	0	-0.058	-0.043	21.390	0.005	0.005	0.000	0.000	0.000	0.000
71	2	170	TRP	0	0.006	-0.022	17.753	0.003	0.003	0.000	0.000	0.000	0.000
72	2	171	VAL	0	0.042	0.029	19.113	-0.020	-0.020	0.000	0.000	0.000	0.000
73	2	172	TYR	0	-0.014	-0.010	14.757	0.022	0.022	0.000	0.000	0.000	0.000
74	2	173	GLN	0	0.027	0.021	18.242	-0.021	-0.021	0.000	0.000	0.000	0.000
75	2	174	CYS	0	-0.028	0.015	15.405	-0.069	-0.069	0.000	0.000	0.000	0.000
76	2	175	ASN	0	-0.006	-0.016	17.342	0.013	0.013	0.000	0.000	0.000	0.000
77	2	176	SER	0	0.065	0.017	18.167	0.036	0.036	0.000	0.000	0.000	0.000
78	2	177	LEU	0	0.121	0.055	17.907	-0.047	-0.047	0.000	0.000	0.000	0.000
79	2	178	GLU	-1	-0.896	-0.940	17.463	-0.551	-0.551	0.000	0.000	0.000	0.000
80	2	179	GLN	0	-0.012	-0.013	14.093	-0.062	-0.062	0.000	0.000	0.000	0.000
81	2	180	ALA	0	0.004	0.004	13.116	-0.121	-0.121	0.000	0.000	0.000	0.000
82	2	181	GLN	0	0.021	0.000	14.157	0.055	0.055	0.000	0.000	0.000	0.000
83	2	182	ALA	0	-0.037	-0.013	10.888	-0.022	-0.022	0.000	0.000	0.000	0.000
84	2	183	ILE	0	0.012	0.004	8.885	-0.250	-0.250	0.000	0.000	0.000	0.000
85	2	184	CYS	0	-0.012	-0.006	9.123	0.072	0.072	0.000	0.000	0.000	0.000
86	2	185	LYS	1	0.949	0.988	9.798	0.789	0.789	0.000	0.000	0.000	0.000
87	2	186	VAL	0	0.007	0.010	3.685	-0.146	-0.012	0.000	-0.027	-0.108	0.000
88	2	187	LEU	0	-0.006	-0.010	5.733	0.362	0.362	0.000	0.000	0.000	0.000
89	2	188	SER	0	-0.031	-0.034	8.074	0.300	0.300	0.000	0.000	0.000	0.000
90	2	189	THR	0	-0.026	0.001	5.232	0.091	0.091	0.000	0.000	0.000	0.000
91	2	190	ALA	0	-0.042	-0.025	6.159	0.531	0.531	0.000	0.000	0.000	0.000
92	2	191	PHE	0	0.000	-0.013	7.298	0.154	0.154	0.000	0.000	0.000	0.000
93	2	192	ASP	-1	-0.866	-0.928	10.650	0.195	0.195	0.000	0.000	0.000	0.000
94	2	193	SER	0	-0.094	-0.032	8.123	0.249	0.249	0.000	0.000	0.000	0.000
95	2	194	VAL	0	-0.055	-0.013	10.233	0.083	0.083	0.000	0.000	0.000	0.000
96	2	195	LEU	0	-0.025	-0.009	12.909	-0.049	-0.049	0.000	0.000	0.000	0.000
97	2	196	THR	0	0.017	0.020	15.091	-0.013	-0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(2:60:CYS)