FMO DATABASE

FMODB ID: VR341

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	OptH
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	-938851.503391
FMO2-HF: Nuclear repulsion	892177.580461
FMO2-HF: Total energy	-46673.92293
FMO2-MP2: Total energy	-46807.853216

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.
39.926	44.475	2.259	-3.37	-3.438	-0.01

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 : -0.961 / q_NPA : -0.976

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	i	62	GLU	-1	-0.923	-0.959	3.323	49.837	52.759	0.025	-1.579	-1.368	0.000
4	i	63	PHE	0	-0.017	-0.010	6.237	-2.910	-2.910	0.000	0.000	0.000	0.000
5	i	64	ARG	1	0.820	0.901	9.961	-16.232	-16.232	0.000	0.000	0.000	0.000
6	i	65	ILE	0	-0.038	-0.020	12.450	-0.635	-0.635	0.000	0.000	0.000	0.000
7	i	66	LYS	1	0.831	0.923	15.066	-15.507	-15.507	0.000	0.000	0.000	0.000
8	i	67	TYR	0	0.000	-0.021	17.298	0.375	0.375	0.000	0.000	0.000	0.000
9	i	68	VAL	0	-0.018	-0.003	20.172	-0.524	-0.524	0.000	0.000	0.000	0.000
10	i	69	GLY	0	0.023	0.006	22.611	-0.634	-0.634	0.000	0.000	0.000	0.000
11	i	70	ALA	0	-0.030	-0.018	22.265	0.673	0.673	0.000	0.000	0.000	0.000
12	i	71	ILE	0	0.035	0.041	23.848	-0.335	-0.335	0.000	0.000	0.000	0.000
13	i	82	LEU	0	0.048	0.019	27.571	-0.045	-0.045	0.000	0.000	0.000	0.000
14	i	83	GLU	-1	-0.993	-1.009	27.433	10.324	10.324	0.000	0.000	0.000	0.000
15	i	84	GLY	0	0.044	0.015	25.953	-0.069	-0.069	0.000	0.000	0.000	0.000
16	i	85	PRO	0	-0.086	-0.051	23.161	0.232	0.232	0.000	0.000	0.000	0.000
17	i	86	LEU	0	0.062	0.008	24.557	0.120	0.120	0.000	0.000	0.000	0.000
18	i	87	ASP	-1	-0.889	-0.930	27.697	9.930	9.930	0.000	0.000	0.000	0.000
19	i	88	LEU	0	-0.065	-0.033	23.235	-0.116	-0.116	0.000	0.000	0.000	0.000
20	i	89	ILE	0	-0.014	-0.009	24.676	0.088	0.088	0.000	0.000	0.000	0.000
21	i	90	ASN	0	0.013	0.025	27.346	-0.248	-0.248	0.000	0.000	0.000	0.000
22	i	91	TYR	0	0.007	-0.003	27.598	-0.351	-0.351	0.000	0.000	0.000	0.000
23	i	92	ILE	0	0.004	0.012	23.707	0.186	0.186	0.000	0.000	0.000	0.000
24	i	93	ASP	-1	-0.822	-0.921	27.911	10.086	10.086	0.000	0.000	0.000	0.000
25	i	94	VAL	0	-0.052	-0.033	31.024	-0.310	-0.310	0.000	0.000	0.000	0.000
26	i	95	ALA	0	-0.049	-0.031	29.160	-0.215	-0.215	0.000	0.000	0.000	0.000
27	i	96	GLN	0	-0.018	0.003	27.479	-0.334	-0.334	0.000	0.000	0.000	0.000
28	i	97	GLN	0	-0.026	-0.020	31.890	-0.342	-0.342	0.000	0.000	0.000	0.000
29	i	98	ASP	-1	-0.860	-0.936	35.200	7.668	7.668	0.000	0.000	0.000	0.000
30	i	99	GLY	0	-0.047	-0.017	37.221	0.112	0.112	0.000	0.000	0.000	0.000
31	i	100	LYS	1	0.789	0.907	33.887	-8.855	-8.855	0.000	0.000	0.000	0.000
32	i	101	LEU	0	0.079	0.020	31.459	0.051	0.051	0.000	0.000	0.000	0.000
33	i	102	PRO	0	-0.056	0.000	27.577	0.182	0.182	0.000	0.000	0.000	0.000
34	i	103	PHE	0	0.020	0.006	27.620	0.315	0.315	0.000	0.000	0.000	0.000
35	i	104	VAL	0	-0.010	-0.009	27.068	0.272	0.272	0.000	0.000	0.000	0.000
36	i	105	PRO	0	-0.025	0.003	22.362	-0.022	-0.022	0.000	0.000	0.000	0.000
37	i	106	PRO	0	-0.015	-0.003	23.082	-0.227	-0.227	0.000	0.000	0.000	0.000
38	i	107	GLU	-1	-0.826	-0.916	20.207	15.495	15.495	0.000	0.000	0.000	0.000
39	i	108	GLU	-1	-0.861	-0.956	20.261	14.013	14.013	0.000	0.000	0.000	0.000
40	i	109	GLU	-1	-0.941	-0.958	15.203	18.313	18.313	0.000	0.000	0.000	0.000
41	i	110	PHE	0	0.003	0.020	14.878	0.868	0.868	0.000	0.000	0.000	0.000
42	i	111	ILE	0	0.025	0.005	8.581	0.078	0.078	0.000	0.000	0.000	0.000
43	i	112	MET	0	-0.044	-0.030	8.993	-0.297	-0.297	0.000	0.000	0.000	0.000
44	i	113	GLY	0	0.041	0.039	4.931	0.535	0.535	0.000	0.000	0.000	0.000
45	i	114	VAL	0	-0.023	-0.008	4.020	-3.485	-3.156	0.000	-0.080	-0.249	0.000
46	i	115	SER	0	0.015	0.050	2.370	12.266	13.503	2.235	-1.685	-1.787	-0.010
47	i	116	LYS	1	0.918	0.905	4.651	-43.972	-43.911	-0.001	-0.026	-0.034	0.000
48	i	117	TYR	0	0.024	-0.023	7.163	-3.073	-3.073	0.000	0.000	0.000	0.000
49	i	118	GLY	0	0.053	0.029	8.394	-3.640	-3.640	0.000	0.000	0.000	0.000
50	i	119	ILE	0	0.022	0.029	7.141	3.882	3.882	0.000	0.000	0.000	0.000
51	i	120	LYS	1	0.927	0.973	7.720	-38.340	-38.340	0.000	0.000	0.000	0.000
52	i	121	VAL	0	-0.006	0.010	9.329	0.854	0.854	0.000	0.000	0.000	0.000
53	i	122	SER	0	0.009	0.012	11.398	-0.052	-0.052	0.000	0.000	0.000	0.000
54	i	131	HIS	0	-0.010	-0.010	13.992	-0.045	-0.045	0.000	0.000	0.000	0.000
55	i	132	ARG	1	0.936	0.955	13.031	-18.310	-18.310	0.000	0.000	0.000	0.000
56	i	133	HIS	0	0.075	0.048	12.640	-1.369	-1.369	0.000	0.000	0.000	0.000
57	i	134	ALA	0	0.035	0.011	11.762	2.409	2.409	0.000	0.000	0.000	0.000
58	i	135	LEU	0	0.011	-0.004	9.578	-1.586	-1.586	0.000	0.000	0.000	0.000
59	i	136	TYR	0	-0.029	-0.004	13.700	-0.490	-0.490	0.000	0.000	0.000	0.000
60	i	137	LEU	0	-0.009	0.003	16.515	-0.913	-0.913	0.000	0.000	0.000	0.000
61	i	138	ILE	0	-0.043	-0.021	12.085	-0.730	-0.730	0.000	0.000	0.000	0.000
62	i	139	ILE	0	-0.004	0.018	16.184	0.012	0.012	0.000	0.000	0.000	0.000
63	i	140	ARG	1	0.922	0.946	17.770	-13.677	-13.677	0.000	0.000	0.000	0.000
64	i	141	MET	0	0.002	0.018	13.292	0.632	0.632	0.000	0.000	0.000	0.000
65	i	142	VAL	0	-0.046	-0.033	16.660	-0.503	-0.503	0.000	0.000	0.000	0.000
66	i	143	CYS	0	-0.051	-0.009	17.144	0.056	0.056	0.000	0.000	0.000	0.000
67	i	144	TYR	0	0.012	-0.007	19.238	-0.139	-0.139	0.000	0.000	0.000	0.000
68	i	145	ASP	-1	-0.869	-0.945	22.631	11.875	11.875	0.000	0.000	0.000	0.000
69	i	146	ASP	-1	-0.881	-0.949	24.784	11.562	11.562	0.000	0.000	0.000	0.000
70	i	147	GLY	0	-0.003	0.019	26.568	-0.407	-0.407	0.000	0.000	0.000	0.000
71	i	148	LEU	0	-0.046	-0.030	29.630	-0.299	-0.299	0.000	0.000	0.000	0.000
72	i	149	GLY	0	-0.033	-0.004	28.753	0.318	0.318	0.000	0.000	0.000	0.000
73	i	150	ALA	0	0.052	-0.005	28.179	-0.235	-0.235	0.000	0.000	0.000	0.000
74	i	151	GLY	0	-0.053	0.005	24.630	0.237	0.237	0.000	0.000	0.000	0.000
75	i	152	LYS	1	0.882	0.941	22.666	-11.690	-11.690	0.000	0.000	0.000	0.000
76	i	153	SER	0	0.061	0.046	19.526	0.084	0.084	0.000	0.000	0.000	0.000
77	i	154	LEU	0	-0.001	-0.007	20.680	0.341	0.341	0.000	0.000	0.000	0.000
78	i	155	LEU	0	-0.018	-0.001	14.473	0.435	0.435	0.000	0.000	0.000	0.000
79	i	156	ALA	0	0.031	0.014	18.094	-0.671	-0.671	0.000	0.000	0.000	0.000
80	i	157	LEU	0	-0.030	-0.021	13.526	0.901	0.901	0.000	0.000	0.000	0.000
81	i	158	LYS	1	0.946	0.981	17.693	-12.799	-12.799	0.000	0.000	0.000	0.000
82	i	159	THR	0	-0.022	-0.020	16.979	0.877	0.877	0.000	0.000	0.000	0.000
83	i	160	THR	0	0.052	0.006	19.928	-0.826	-0.826	0.000	0.000	0.000	0.000
84	i	161	ASP	-1	-0.747	-0.865	22.214	12.642	12.642	0.000	0.000	0.000	0.000
85	i	162	ALA	0	-0.039	-0.023	22.494	0.312	0.312	0.000	0.000	0.000	0.000
86	i	163	SER	0	-0.069	-0.043	24.430	-0.313	-0.313	0.000	0.000	0.000	0.000
87	i	164	ASN	0	-0.157	-0.089	26.399	-0.032	-0.032	0.000	0.000	0.000	0.000
88	i	165	GLU	-1	-0.875	-0.913	27.820	10.034	10.034	0.000	0.000	0.000	0.000
89	i	166	GLU	-1	-0.935	-0.963	26.429	11.347	11.347	0.000	0.000	0.000	0.000
90	i	167	TYR	0	-0.092	-0.053	24.687	0.777	0.777	0.000	0.000	0.000	0.000
91	i	168	SER	0	-0.036	-0.014	22.226	-0.448	-0.448	0.000	0.000	0.000	0.000
92	i	169	LEU	0	-0.046	-0.009	20.967	0.568	0.568	0.000	0.000	0.000	0.000
93	i	170	TRP	0	-0.007	-0.010	17.561	-0.451	-0.451	0.000	0.000	0.000	0.000
94	i	171	VAL	0	0.018	0.010	19.257	0.306	0.306	0.000	0.000	0.000	0.000
95	i	172	TYR	0	-0.001	-0.019	14.499	0.439	0.439	0.000	0.000	0.000	0.000
96	i	173	GLN	0	0.049	0.015	17.864	-0.002	-0.002	0.000	0.000	0.000	0.000
97	i	174	CYS	0	-0.057	-0.021	14.606	1.115	1.115	0.000	0.000	0.000	0.000
98	i	175	ASN	0	0.009	-0.013	18.015	-0.874	-0.874	0.000	0.000	0.000	0.000
99	i	176	SER	0	0.006	0.007	18.790	-0.399	-0.399	0.000	0.000	0.000	0.000
100	i	177	LEU	0	0.103	0.053	18.810	0.747	0.747	0.000	0.000	0.000	0.000
101	i	178	GLU	-1	-0.891	-0.972	17.952	14.269	14.269	0.000	0.000	0.000	0.000
102	i	179	GLN	0	-0.031	-0.009	13.431	1.779	1.779	0.000	0.000	0.000	0.000
103	i	180	ALA	0	0.087	0.032	13.663	1.426	1.426	0.000	0.000	0.000	0.000
104	i	181	GLN	0	-0.007	-0.012	14.679	0.892	0.892	0.000	0.000	0.000	0.000
105	i	182	ALA	0	-0.029	-0.012	11.780	0.566	0.566	0.000	0.000	0.000	0.000
106	i	183	ILE	0	0.002	0.010	9.508	1.778	1.778	0.000	0.000	0.000	0.000
107	i	184	CYS	0	-0.009	0.002	10.249	1.218	1.218	0.000	0.000	0.000	0.000
108	i	185	LYS	1	0.954	0.971	11.804	-17.127	-17.127	0.000	0.000	0.000	0.000
109	i	186	VAL	0	0.028	0.020	5.446	0.431	0.431	0.000	0.000	0.000	0.000
110	i	187	LEU	0	0.004	0.016	7.829	2.659	2.659	0.000	0.000	0.000	0.000
111	i	188	SER	0	-0.037	-0.028	9.351	-0.745	-0.745	0.000	0.000	0.000	0.000
112	i	189	THR	0	-0.043	-0.028	6.988	0.481	0.481	0.000	0.000	0.000	0.000
113	i	190	ALA	0	0.003	0.010	7.552	-0.379	-0.379	0.000	0.000	0.000	0.000
114	i	191	PHE	0	0.006	-0.019	9.255	-1.327	-1.327	0.000	0.000	0.000	0.000
115	i	192	ASP	-1	-0.925	-0.949	12.335	18.624	18.624	0.000	0.000	0.000	0.000
116	i	193	SER	0	-0.080	-0.022	10.117	0.475	0.475	0.000	0.000	0.000	0.000
117	i	194	VAL	0	-0.066	-0.045	10.807	-0.509	-0.509	0.000	0.000	0.000	0.000
118	i	195	LEU	0	-0.013	0.015	13.332	-1.388	-1.388	0.000	0.000	0.000	0.000

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