FMO DATABASE

FMODB ID: 9G152

Calculation Name: 4DX9-3-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: 3

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	OptAll
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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-970089.968007
FMO2-HF: Nuclear repulsion	922739.530519
FMO2-HF: Total energy	-47350.437489
FMO2-MP2: Total energy	-47486.183871

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(3:60:CYS)

Summations of interaction energy for fragment #1(3:60: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.
-14.896	-13.547	13.934	-7.767	-7.514	-0.059

Interaction energy analysis for fragmet #1(3:60:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.061 / q_NPA : -0.028

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	3	62	GLU	-1	-0.777	-0.878	3.879	-0.662	1.553	-0.012	-1.027	-1.176	0.004
4	3	63	PHE	0	-0.028	-0.025	5.898	-0.242	-0.242	0.000	0.000	0.000	0.000
5	3	64	ARG	1	0.816	0.888	10.076	0.461	0.461	0.000	0.000	0.000	0.000
6	3	65	ILE	0	-0.021	-0.016	12.346	-0.054	-0.054	0.000	0.000	0.000	0.000
7	3	66	LYS	1	0.820	0.906	15.071	0.236	0.236	0.000	0.000	0.000	0.000
8	3	67	TYR	0	0.012	-0.005	16.841	-0.021	-0.021	0.000	0.000	0.000	0.000
9	3	68	VAL	0	-0.024	-0.011	18.914	0.011	0.011	0.000	0.000	0.000	0.000
10	3	69	GLY	0	0.013	-0.008	20.950	0.018	0.018	0.000	0.000	0.000	0.000
11	3	70	ALA	0	-0.015	-0.006	20.819	-0.014	-0.014	0.000	0.000	0.000	0.000
12	3	71	ILE	0	-0.014	-0.001	22.677	0.008	0.008	0.000	0.000	0.000	0.000
13	3	72	GLU	-1	-0.836	-0.900	25.008	-0.014	-0.014	0.000	0.000	0.000	0.000
14	3	85	PRO	0	0.004	0.000	21.322	0.001	0.001	0.000	0.000	0.000	0.000
15	3	86	LEU	0	0.021	-0.012	22.959	-0.010	-0.010	0.000	0.000	0.000	0.000
16	3	87	ASP	-1	-0.858	-0.931	25.688	-0.073	-0.073	0.000	0.000	0.000	0.000
17	3	88	LEU	0	-0.036	-0.024	19.606	0.006	0.006	0.000	0.000	0.000	0.000
18	3	89	ILE	0	-0.015	0.011	22.732	-0.006	-0.006	0.000	0.000	0.000	0.000
19	3	90	ASN	0	-0.006	-0.002	24.866	0.003	0.003	0.000	0.000	0.000	0.000
20	3	91	TYR	0	0.008	-0.007	27.249	0.006	0.006	0.000	0.000	0.000	0.000
21	3	92	ILE	0	-0.004	0.009	22.304	0.005	0.005	0.000	0.000	0.000	0.000
22	3	93	ASP	-1	-0.796	-0.879	26.492	-0.131	-0.131	0.000	0.000	0.000	0.000
23	3	94	VAL	0	-0.036	-0.026	28.665	0.005	0.005	0.000	0.000	0.000	0.000
24	3	95	ALA	0	0.030	0.014	28.700	0.005	0.005	0.000	0.000	0.000	0.000
25	3	96	GLN	0	-0.034	-0.015	25.803	0.002	0.002	0.000	0.000	0.000	0.000
26	3	97	GLN	0	-0.009	-0.002	30.523	0.006	0.006	0.000	0.000	0.000	0.000
27	3	98	ASP	-1	-0.912	-0.931	33.644	-0.040	-0.040	0.000	0.000	0.000	0.000
28	3	99	GLY	0	-0.013	-0.003	34.023	0.006	0.006	0.000	0.000	0.000	0.000
29	3	100	LYS	1	0.743	0.868	30.141	0.046	0.046	0.000	0.000	0.000	0.000
30	3	101	LEU	0	-0.007	-0.003	24.557	0.002	0.002	0.000	0.000	0.000	0.000
31	3	102	PRO	0	-0.005	0.006	26.897	-0.001	-0.001	0.000	0.000	0.000	0.000
32	3	103	PHE	0	0.023	-0.002	27.049	-0.007	-0.007	0.000	0.000	0.000	0.000
33	3	104	VAL	0	-0.035	-0.016	25.909	-0.015	-0.015	0.000	0.000	0.000	0.000
34	3	105	PRO	0	-0.005	0.009	21.708	0.014	0.014	0.000	0.000	0.000	0.000
35	3	106	PRO	0	0.040	0.013	22.991	0.000	0.000	0.000	0.000	0.000	0.000
36	3	107	GLU	-1	-0.917	-0.956	23.431	-0.129	-0.129	0.000	0.000	0.000	0.000
37	3	108	GLU	-1	-0.894	-0.938	21.360	-0.090	-0.090	0.000	0.000	0.000	0.000
38	3	109	GLU	-1	-0.815	-0.869	17.288	-0.294	-0.294	0.000	0.000	0.000	0.000
39	3	110	PHE	0	0.033	0.027	14.652	0.031	0.031	0.000	0.000	0.000	0.000
40	3	111	ILE	0	-0.016	0.007	9.429	-0.083	-0.083	0.000	0.000	0.000	0.000
41	3	112	MET	0	0.008	0.019	8.768	0.064	0.064	0.000	0.000	0.000	0.000
42	3	113	GLY	0	0.035	0.019	5.391	-0.091	-0.091	0.000	0.000	0.000	0.000
43	3	114	VAL	0	-0.035	-0.014	2.911	-0.745	0.262	0.104	-0.445	-0.665	0.000
44	3	115	SER	0	-0.008	-0.021	1.898	-8.500	-11.571	13.462	-5.969	-4.422	-0.062
45	3	116	LYS	1	0.942	0.941	3.610	-4.904	-4.387	0.009	-0.073	-0.453	0.001
46	3	117	TYR	0	0.014	0.017	6.072	-0.113	-0.113	0.000	0.000	0.000	0.000
47	3	118	GLY	0	0.048	0.034	7.243	-0.082	-0.082	0.000	0.000	0.000	0.000
48	3	119	ILE	0	0.033	0.038	6.647	-0.221	-0.221	0.000	0.000	0.000	0.000
49	3	120	LYS	1	0.774	0.890	6.106	-0.111	-0.111	0.000	0.000	0.000	0.000
50	3	121	VAL	0	0.027	0.006	8.351	-0.144	-0.144	0.000	0.000	0.000	0.000
51	3	122	SER	0	0.013	-0.004	10.753	0.092	0.092	0.000	0.000	0.000	0.000
52	3	123	THR	0	0.010	-0.030	12.788	-0.067	-0.067	0.000	0.000	0.000	0.000
53	3	124	SER	0	-0.006	-0.028	15.240	0.009	0.009	0.000	0.000	0.000	0.000
54	3	125	ASP	-1	-0.914	-0.950	16.836	0.009	0.009	0.000	0.000	0.000	0.000
55	3	126	GLN	0	-0.044	-0.005	10.810	0.032	0.032	0.000	0.000	0.000	0.000
56	3	127	TYR	0	-0.135	-0.086	13.678	0.082	0.082	0.000	0.000	0.000	0.000
57	3	128	ASP	-1	-0.800	-0.875	16.088	0.063	0.063	0.000	0.000	0.000	0.000
58	3	129	VAL	0	-0.085	-0.047	12.980	0.003	0.003	0.000	0.000	0.000	0.000
59	3	130	LEU	0	0.024	0.043	15.565	-0.001	-0.001	0.000	0.000	0.000	0.000
60	3	131	HIS	0	0.053	0.023	14.945	-0.006	-0.006	0.000	0.000	0.000	0.000
61	3	132	ARG	1	0.825	0.894	7.450	-0.327	-0.327	0.000	0.000	0.000	0.000
62	3	133	HIS	0	0.046	0.034	12.272	0.052	0.052	0.000	0.000	0.000	0.000
63	3	134	ALA	0	-0.030	-0.032	11.285	-0.020	-0.020	0.000	0.000	0.000	0.000
64	3	135	LEU	0	0.018	0.022	11.571	-0.028	-0.028	0.000	0.000	0.000	0.000
65	3	136	TYR	0	-0.108	-0.047	14.139	0.045	0.045	0.000	0.000	0.000	0.000
66	3	137	LEU	0	-0.008	-0.006	17.229	-0.031	-0.031	0.000	0.000	0.000	0.000
67	3	138	ILE	0	-0.015	-0.002	16.952	0.018	0.018	0.000	0.000	0.000	0.000
68	3	139	ILE	0	0.038	0.020	12.798	-0.010	-0.010	0.000	0.000	0.000	0.000
69	3	140	ARG	1	0.882	0.932	14.999	0.095	0.095	0.000	0.000	0.000	0.000
70	3	141	MET	0	0.033	0.027	10.508	-0.029	-0.029	0.000	0.000	0.000	0.000
71	3	142	VAL	0	-0.059	-0.025	15.670	0.014	0.014	0.000	0.000	0.000	0.000
72	3	143	CYS	0	-0.046	-0.013	14.989	-0.013	-0.013	0.000	0.000	0.000	0.000
73	3	144	TYR	0	-0.044	-0.054	18.167	0.000	0.000	0.000	0.000	0.000	0.000
74	3	145	ASP	-1	-0.864	-0.945	21.134	-0.252	-0.252	0.000	0.000	0.000	0.000
75	3	146	ASP	-1	-0.787	-0.907	23.193	-0.197	-0.197	0.000	0.000	0.000	0.000
76	3	147	GLY	0	0.030	0.025	25.400	0.017	0.017	0.000	0.000	0.000	0.000
77	3	148	LEU	0	-0.048	-0.010	25.941	0.015	0.015	0.000	0.000	0.000	0.000
78	3	149	GLY	0	-0.036	-0.019	28.739	-0.002	-0.002	0.000	0.000	0.000	0.000
79	3	150	ALA	0	-0.097	-0.064	26.393	-0.004	-0.004	0.000	0.000	0.000	0.000
80	3	151	GLY	0	0.026	0.027	24.753	-0.018	-0.018	0.000	0.000	0.000	0.000
81	3	152	LYS	1	0.848	0.918	22.018	0.224	0.224	0.000	0.000	0.000	0.000
82	3	153	SER	0	0.046	0.011	18.114	0.000	0.000	0.000	0.000	0.000	0.000
83	3	154	LEU	0	0.036	0.036	19.166	-0.022	-0.022	0.000	0.000	0.000	0.000
84	3	155	LEU	0	-0.047	-0.051	12.844	-0.027	-0.027	0.000	0.000	0.000	0.000
85	3	156	ALA	0	0.035	0.034	17.128	0.023	0.023	0.000	0.000	0.000	0.000
86	3	157	LEU	0	-0.030	-0.036	12.410	-0.030	-0.030	0.000	0.000	0.000	0.000
87	3	158	LYS	1	0.862	0.938	17.105	0.043	0.043	0.000	0.000	0.000	0.000
88	3	159	THR	0	0.019	0.012	16.463	-0.003	-0.003	0.000	0.000	0.000	0.000
89	3	160	THR	0	-0.013	-0.030	19.068	-0.004	-0.004	0.000	0.000	0.000	0.000
90	3	161	ASP	-1	-0.811	-0.901	20.602	0.072	0.072	0.000	0.000	0.000	0.000
91	3	162	ALA	0	-0.010	-0.008	23.212	0.012	0.012	0.000	0.000	0.000	0.000
92	3	163	SER	0	-0.003	-0.001	24.453	-0.007	-0.007	0.000	0.000	0.000	0.000
93	3	164	ASN	0	-0.089	-0.044	26.507	0.002	0.002	0.000	0.000	0.000	0.000
94	3	165	GLU	-1	-0.925	-0.951	27.356	-0.001	-0.001	0.000	0.000	0.000	0.000
95	3	166	GLU	-1	-0.894	-0.954	21.481	0.038	0.038	0.000	0.000	0.000	0.000
96	3	167	TYR	0	-0.018	0.011	23.675	-0.015	-0.015	0.000	0.000	0.000	0.000
97	3	168	SER	0	-0.008	-0.027	21.633	-0.008	-0.008	0.000	0.000	0.000	0.000
98	3	169	LEU	0	-0.051	-0.016	21.482	-0.006	-0.006	0.000	0.000	0.000	0.000
99	3	170	TRP	0	-0.013	-0.021	17.452	-0.005	-0.005	0.000	0.000	0.000	0.000
100	3	171	VAL	0	0.023	0.001	19.223	-0.022	-0.022	0.000	0.000	0.000	0.000
101	3	172	TYR	0	0.006	-0.002	15.387	0.000	0.000	0.000	0.000	0.000	0.000
102	3	173	GLN	0	-0.013	-0.007	18.092	0.006	0.006	0.000	0.000	0.000	0.000
103	3	174	CYS	0	-0.045	-0.012	14.677	-0.068	-0.068	0.000	0.000	0.000	0.000
104	3	175	ASN	0	0.044	0.015	17.225	0.072	0.072	0.000	0.000	0.000	0.000
105	3	176	SER	0	0.010	0.004	18.299	0.031	0.031	0.000	0.000	0.000	0.000
106	3	177	LEU	0	0.052	0.039	17.641	-0.059	-0.059	0.000	0.000	0.000	0.000
107	3	178	GLU	-1	-0.812	-0.908	16.264	-0.491	-0.491	0.000	0.000	0.000	0.000
108	3	179	GLN	0	-0.028	-0.013	12.862	-0.043	-0.043	0.000	0.000	0.000	0.000
109	3	180	ALA	0	0.064	0.029	12.228	-0.152	-0.152	0.000	0.000	0.000	0.000
110	3	181	GLN	0	-0.023	-0.023	12.732	-0.055	-0.055	0.000	0.000	0.000	0.000
111	3	182	ALA	0	-0.023	-0.006	9.484	-0.041	-0.041	0.000	0.000	0.000	0.000
112	3	183	ILE	0	0.002	0.006	8.109	-0.281	-0.281	0.000	0.000	0.000	0.000
113	3	184	CYS	0	0.005	-0.001	8.152	-0.038	-0.038	0.000	0.000	0.000	0.000
114	3	185	LYS	1	0.865	0.937	8.585	0.740	0.740	0.000	0.000	0.000	0.000
115	3	186	VAL	0	-0.015	-0.009	2.560	-0.787	-0.193	0.372	-0.252	-0.713	-0.002
116	3	187	LEU	0	0.020	-0.001	5.046	0.668	0.755	-0.001	-0.001	-0.085	0.000
117	3	188	SER	0	-0.031	-0.020	7.092	0.397	0.397	0.000	0.000	0.000	0.000
118	3	189	THR	0	-0.042	-0.002	5.468	0.041	0.041	0.000	0.000	0.000	0.000
119	3	190	ALA	0	-0.051	-0.016	5.459	1.220	1.220	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(3:60:CYS)