FMO DATABASE

FMODB ID: GN3M1

Calculation Name: 4DX9-i-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: i

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	118
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-942194.551182
FMO2-HF: Nuclear repulsion	895519.381909
FMO2-HF: Total energy	-46675.169273
FMO2-MP2: Total energy	-46809.04481

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(i:60:CYM)

Summations of interaction energy for fragment #1(i:60:CYM)

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.
-2.579	-34.444	58.029	-13.832	-12.335	0.136

Interaction energy analysis for fragmet #1(i:60:CYM)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.835 / q_NPA : -0.834

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	i	62	GLU	-1	-0.925	-0.962	3.894	40.605	42.416	-0.017	-1.004	-0.790	0.001
4	i	63	PHE	0	-0.024	-0.016	6.650	-2.461	-2.461	0.000	0.000	0.000	0.000
5	i	64	ARG	1	0.792	0.896	10.242	-15.264	-15.264	0.000	0.000	0.000	0.000
6	i	65	ILE	0	-0.050	-0.020	12.885	-0.356	-0.356	0.000	0.000	0.000	0.000
7	i	66	LYS	1	0.797	0.911	15.464	-14.591	-14.591	0.000	0.000	0.000	0.000
8	i	67	TYR	0	-0.002	-0.017	17.402	0.501	0.501	0.000	0.000	0.000	0.000
9	i	68	VAL	0	0.000	-0.010	19.711	-0.583	-0.583	0.000	0.000	0.000	0.000
10	i	69	GLY	0	0.011	0.005	22.026	-0.706	-0.706	0.000	0.000	0.000	0.000
11	i	70	ALA	0	-0.037	-0.014	21.849	0.765	0.765	0.000	0.000	0.000	0.000
12	i	71	ILE	0	0.005	0.008	23.347	-0.517	-0.517	0.000	0.000	0.000	0.000
13	i	82	LEU	0	0.063	0.016	26.471	-0.074	-0.074	0.000	0.000	0.000	0.000
14	i	83	GLU	-1	-0.947	-0.975	26.470	10.970	10.970	0.000	0.000	0.000	0.000
15	i	84	GLY	0	0.012	0.013	25.365	0.256	0.256	0.000	0.000	0.000	0.000
16	i	85	PRO	0	-0.057	-0.034	22.410	0.148	0.148	0.000	0.000	0.000	0.000
17	i	86	LEU	0	0.045	0.005	24.078	0.078	0.078	0.000	0.000	0.000	0.000
18	i	87	ASP	-1	-0.871	-0.931	27.232	10.604	10.604	0.000	0.000	0.000	0.000
19	i	88	LEU	0	-0.071	-0.029	22.608	-0.129	-0.129	0.000	0.000	0.000	0.000
20	i	89	ILE	0	0.008	0.007	23.408	0.036	0.036	0.000	0.000	0.000	0.000
21	i	90	ASN	0	-0.043	-0.001	26.810	-0.439	-0.439	0.000	0.000	0.000	0.000
22	i	91	TYR	0	-0.025	-0.022	26.691	-0.429	-0.429	0.000	0.000	0.000	0.000
23	i	92	ILE	0	0.025	0.020	22.915	0.249	0.249	0.000	0.000	0.000	0.000
24	i	93	ASP	-1	-0.803	-0.902	27.391	10.323	10.323	0.000	0.000	0.000	0.000
25	i	94	VAL	0	-0.034	-0.024	30.308	-0.306	-0.306	0.000	0.000	0.000	0.000
26	i	95	ALA	0	-0.037	-0.025	29.062	-0.261	-0.261	0.000	0.000	0.000	0.000
27	i	96	GLN	0	-0.016	0.005	27.450	-0.297	-0.297	0.000	0.000	0.000	0.000
28	i	97	GLN	0	-0.010	-0.006	31.942	-0.299	-0.299	0.000	0.000	0.000	0.000
29	i	98	ASP	-1	-0.862	-0.948	35.161	7.633	7.633	0.000	0.000	0.000	0.000
30	i	99	GLY	0	-0.041	-0.011	36.959	0.141	0.141	0.000	0.000	0.000	0.000
31	i	100	LYS	1	0.779	0.902	33.375	-8.926	-8.926	0.000	0.000	0.000	0.000
32	i	101	LEU	0	0.044	0.005	30.964	0.059	0.059	0.000	0.000	0.000	0.000
33	i	102	PRO	0	-0.009	0.002	27.423	0.104	0.104	0.000	0.000	0.000	0.000
34	i	103	PHE	0	0.012	0.018	27.622	0.299	0.299	0.000	0.000	0.000	0.000
35	i	104	VAL	0	-0.010	-0.005	27.044	0.177	0.177	0.000	0.000	0.000	0.000
36	i	105	PRO	0	-0.016	0.012	22.397	-0.054	-0.054	0.000	0.000	0.000	0.000
37	i	106	PRO	0	-0.028	-0.014	23.280	-0.260	-0.260	0.000	0.000	0.000	0.000
38	i	107	GLU	-1	-0.821	-0.913	20.243	14.987	14.987	0.000	0.000	0.000	0.000
39	i	108	GLU	-1	-0.857	-0.960	21.063	13.200	13.200	0.000	0.000	0.000	0.000
40	i	109	GLU	-1	-0.860	-0.918	16.462	16.398	16.398	0.000	0.000	0.000	0.000
41	i	110	PHE	0	0.009	0.016	15.278	1.000	1.000	0.000	0.000	0.000	0.000
42	i	111	ILE	0	0.008	0.002	9.506	0.226	0.226	0.000	0.000	0.000	0.000
43	i	112	MET	0	-0.030	-0.014	9.085	0.084	0.084	0.000	0.000	0.000	0.000
44	i	113	GLY	0	0.041	0.030	5.208	-0.718	-0.718	0.000	0.000	0.000	0.000
45	i	114	VAL	0	-0.055	-0.024	4.277	-0.410	-0.037	-0.001	-0.087	-0.286	0.000
46	i	115	SER	0	-0.051	-0.125	1.862	-7.921	-33.395	58.111	-22.926	-9.711	0.128
47	i	116	LYS	1	0.907	0.922	3.384	-62.025	-70.713	-0.062	10.252	-1.503	0.007
48	i	117	TYR	0	-0.029	-0.002	5.469	-9.859	-9.815	-0.001	-0.058	0.014	0.000
49	i	118	GLY	0	0.069	0.010	6.702	-6.660	-6.660	0.000	0.000	0.000	0.000
50	i	119	ILE	0	-0.038	-0.009	6.762	5.261	5.261	0.000	0.000	0.000	0.000
51	i	120	LYS	1	0.958	0.999	6.833	-35.576	-35.576	0.000	0.000	0.000	0.000
52	i	121	VAL	0	-0.009	-0.013	8.654	0.097	0.097	0.000	0.000	0.000	0.000
53	i	122	SER	0	-0.008	0.006	11.266	0.049	0.049	0.000	0.000	0.000	0.000
54	i	131	HIS	0	0.001	-0.005	13.499	0.154	0.154	0.000	0.000	0.000	0.000
55	i	132	ARG	1	0.923	0.948	11.989	-19.081	-19.081	0.000	0.000	0.000	0.000
56	i	133	HIS	0	0.062	0.055	11.837	-0.994	-0.994	0.000	0.000	0.000	0.000
57	i	134	ALA	0	0.053	0.017	11.050	3.112	3.112	0.000	0.000	0.000	0.000
58	i	135	LEU	0	0.044	0.013	9.264	-2.091	-2.091	0.000	0.000	0.000	0.000
59	i	136	TYR	0	-0.049	-0.013	12.954	-0.891	-0.891	0.000	0.000	0.000	0.000
60	i	137	LEU	0	-0.003	0.010	15.679	-1.147	-1.147	0.000	0.000	0.000	0.000
61	i	138	ILE	0	-0.046	-0.024	11.545	-0.929	-0.929	0.000	0.000	0.000	0.000
62	i	139	ILE	0	0.007	0.022	15.568	0.334	0.334	0.000	0.000	0.000	0.000
63	i	140	ARG	1	0.919	0.946	16.938	-14.659	-14.659	0.000	0.000	0.000	0.000
64	i	141	MET	0	-0.002	0.014	12.379	0.564	0.564	0.000	0.000	0.000	0.000
65	i	142	VAL	0	-0.034	-0.018	16.243	-0.474	-0.474	0.000	0.000	0.000	0.000
66	i	143	CYS	0	-0.050	-0.011	16.877	0.231	0.231	0.000	0.000	0.000	0.000
67	i	144	TYR	0	-0.015	-0.023	19.126	-0.050	-0.050	0.000	0.000	0.000	0.000
68	i	145	ASP	-1	-0.865	-0.943	22.589	11.715	11.715	0.000	0.000	0.000	0.000
69	i	146	ASP	-1	-0.822	-0.926	24.537	11.501	11.501	0.000	0.000	0.000	0.000
70	i	147	GLY	0	0.004	0.011	26.624	-0.377	-0.377	0.000	0.000	0.000	0.000
71	i	148	LEU	0	-0.052	-0.016	28.962	-0.443	-0.443	0.000	0.000	0.000	0.000
72	i	149	GLY	0	-0.018	-0.022	29.733	0.133	0.133	0.000	0.000	0.000	0.000
73	i	150	ALA	0	-0.011	-0.013	28.325	-0.230	-0.230	0.000	0.000	0.000	0.000
74	i	151	GLY	0	-0.003	0.015	24.486	0.205	0.205	0.000	0.000	0.000	0.000
75	i	152	LYS	1	0.789	0.909	22.599	-11.514	-11.514	0.000	0.000	0.000	0.000
76	i	153	SER	0	0.051	0.019	19.741	0.043	0.043	0.000	0.000	0.000	0.000
77	i	154	LEU	0	0.027	0.025	20.424	0.569	0.569	0.000	0.000	0.000	0.000
78	i	155	LEU	0	-0.020	-0.018	14.345	0.297	0.297	0.000	0.000	0.000	0.000
79	i	156	ALA	0	0.031	0.017	18.200	-0.186	-0.186	0.000	0.000	0.000	0.000
80	i	157	LEU	0	0.001	-0.014	13.076	0.867	0.867	0.000	0.000	0.000	0.000
81	i	158	LYS	1	0.914	0.949	17.235	-13.396	-13.396	0.000	0.000	0.000	0.000
82	i	159	THR	0	-0.050	-0.038	16.851	1.023	1.023	0.000	0.000	0.000	0.000
83	i	160	THR	0	0.047	0.013	19.604	-0.671	-0.671	0.000	0.000	0.000	0.000
84	i	161	ASP	-1	-0.736	-0.860	20.850	13.803	13.803	0.000	0.000	0.000	0.000
85	i	162	ALA	0	-0.044	-0.026	21.117	0.087	0.087	0.000	0.000	0.000	0.000
86	i	163	SER	0	-0.068	-0.033	23.119	-0.309	-0.309	0.000	0.000	0.000	0.000
87	i	164	ASN	0	-0.134	-0.079	26.015	-0.092	-0.092	0.000	0.000	0.000	0.000
88	i	165	GLU	-1	-0.895	-0.931	27.318	10.412	10.412	0.000	0.000	0.000	0.000
89	i	166	GLU	-1	-0.932	-0.967	25.664	11.912	11.912	0.000	0.000	0.000	0.000
90	i	167	TYR	0	-0.078	-0.038	24.467	0.923	0.923	0.000	0.000	0.000	0.000
91	i	168	SER	0	0.009	0.006	22.545	-0.516	-0.516	0.000	0.000	0.000	0.000
92	i	169	LEU	0	-0.047	-0.007	20.634	0.617	0.617	0.000	0.000	0.000	0.000
93	i	170	TRP	0	-0.015	-0.012	17.696	-0.699	-0.699	0.000	0.000	0.000	0.000
94	i	171	VAL	0	0.012	0.012	19.093	0.392	0.392	0.000	0.000	0.000	0.000
95	i	172	TYR	0	0.007	0.003	15.022	0.138	0.138	0.000	0.000	0.000	0.000
96	i	173	GLN	0	-0.012	-0.023	18.116	-0.385	-0.385	0.000	0.000	0.000	0.000
97	i	174	CYS	0	-0.031	0.002	14.859	0.836	0.836	0.000	0.000	0.000	0.000
98	i	175	ASN	0	0.049	0.004	18.014	-0.856	-0.856	0.000	0.000	0.000	0.000
99	i	176	SER	0	-0.034	-0.029	19.050	-0.372	-0.372	0.000	0.000	0.000	0.000
100	i	177	LEU	0	0.086	0.052	18.346	0.814	0.814	0.000	0.000	0.000	0.000
101	i	178	GLU	-1	-0.838	-0.907	18.062	14.399	14.399	0.000	0.000	0.000	0.000
102	i	179	GLN	0	-0.032	-0.018	13.621	1.234	1.234	0.000	0.000	0.000	0.000
103	i	180	ALA	0	0.092	0.041	13.466	1.487	1.487	0.000	0.000	0.000	0.000
104	i	181	GLN	0	0.011	-0.011	14.022	1.366	1.366	0.000	0.000	0.000	0.000
105	i	182	ALA	0	-0.016	-0.006	11.498	0.904	0.904	0.000	0.000	0.000	0.000
106	i	183	ILE	0	0.024	0.020	9.200	2.099	2.099	0.000	0.000	0.000	0.000
107	i	184	CYS	0	-0.044	-0.024	9.377	1.761	1.761	0.000	0.000	0.000	0.000
108	i	185	LYS	1	0.883	0.945	11.104	-17.487	-17.487	0.000	0.000	0.000	0.000
109	i	186	VAL	0	0.035	0.022	4.555	0.700	0.769	-0.001	-0.009	-0.059	0.000
110	i	187	LEU	0	0.028	0.022	6.750	3.405	3.405	0.000	0.000	0.000	0.000
111	i	188	SER	0	-0.041	-0.034	8.134	-0.335	-0.335	0.000	0.000	0.000	0.000
112	i	189	THR	0	-0.052	-0.036	6.283	1.206	1.206	0.000	0.000	0.000	0.000
113	i	190	ALA	0	-0.014	0.000	6.339	1.513	1.513	0.000	0.000	0.000	0.000
114	i	191	PHE	0	0.009	-0.018	7.891	-1.335	-1.335	0.000	0.000	0.000	0.000
115	i	192	ASP	-1	-0.942	-0.961	11.545	21.791	21.791	0.000	0.000	0.000	0.000
116	i	193	SER	0	-0.042	-0.017	8.863	0.692	0.692	0.000	0.000	0.000	0.000
117	i	194	VAL	0	-0.055	-0.012	9.917	0.496	0.496	0.000	0.000	0.000	0.000
118	i	195	LEU	0	-0.025	0.009	12.669	-1.924	-1.924	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(i:60:CYM)