FMO DATABASE

FMODB ID: 3JYGL

Calculation Name: 4DX9-u-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: u

ChEMBL ID: CHEMBL1905

UniProt ID: P05556

Base Structure: X-ray

Registration Date: 2023-09-24

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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-805507.617281
FMO2-HF: Nuclear repulsion	763228.025472
FMO2-HF: Total energy	-42279.591809
FMO2-MP2: Total energy	-42400.346145

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(u:60:CYS)

Summations of interaction energy for fragment #1(u: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.
-15.089	-15.864	16.468	-8.197	-7.497	-0.062

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.070 / q_NPA : -0.039

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	u	62	GLU	-1	-0.793	-0.890	3.878	-0.123	2.270	-0.007	-1.130	-1.257	0.004
4	u	63	PHE	0	-0.007	-0.008	6.313	-0.149	-0.149	0.000	0.000	0.000	0.000
5	u	64	ARG	1	0.851	0.914	9.727	0.468	0.468	0.000	0.000	0.000	0.000
6	u	65	ILE	0	-0.021	-0.007	12.412	-0.050	-0.050	0.000	0.000	0.000	0.000
7	u	66	LYS	1	0.880	0.937	14.974	0.235	0.235	0.000	0.000	0.000	0.000
8	u	67	TYR	0	-0.007	-0.019	17.474	-0.015	-0.015	0.000	0.000	0.000	0.000
9	u	68	VAL	0	-0.002	-0.006	18.785	0.007	0.007	0.000	0.000	0.000	0.000
10	u	69	GLY	0	0.057	0.023	20.977	0.017	0.017	0.000	0.000	0.000	0.000
11	u	70	ALA	0	-0.052	-0.032	20.497	-0.012	-0.012	0.000	0.000	0.000	0.000
12	u	71	ILE	0	0.039	0.041	22.395	0.004	0.004	0.000	0.000	0.000	0.000
13	u	89	ILE	0	0.030	-0.005	23.948	0.005	0.005	0.000	0.000	0.000	0.000
14	u	90	ASN	0	0.007	0.009	25.694	0.004	0.004	0.000	0.000	0.000	0.000
15	u	91	TYR	0	0.038	-0.008	27.772	0.003	0.003	0.000	0.000	0.000	0.000
16	u	92	ILE	0	-0.038	0.003	22.591	0.008	0.008	0.000	0.000	0.000	0.000
17	u	93	ASP	-1	-0.792	-0.883	26.518	-0.122	-0.122	0.000	0.000	0.000	0.000
18	u	94	VAL	0	-0.026	-0.012	29.523	0.006	0.006	0.000	0.000	0.000	0.000
19	u	95	ALA	0	0.020	0.011	28.139	0.006	0.006	0.000	0.000	0.000	0.000
20	u	96	GLN	0	-0.039	-0.025	26.266	0.001	0.001	0.000	0.000	0.000	0.000
21	u	97	GLN	0	-0.037	-0.020	30.555	0.007	0.007	0.000	0.000	0.000	0.000
22	u	98	ASP	-1	-0.865	-0.924	32.924	-0.027	-0.027	0.000	0.000	0.000	0.000
23	u	99	GLY	0	-0.026	-0.001	32.992	0.006	0.006	0.000	0.000	0.000	0.000
24	u	100	LYS	1	0.767	0.877	30.203	0.025	0.025	0.000	0.000	0.000	0.000
25	u	101	LEU	0	-0.031	-0.008	24.605	0.003	0.003	0.000	0.000	0.000	0.000
26	u	102	PRO	0	0.023	0.013	26.032	-0.003	-0.003	0.000	0.000	0.000	0.000
27	u	103	PHE	0	0.036	0.018	26.883	-0.009	-0.009	0.000	0.000	0.000	0.000
28	u	104	VAL	0	-0.038	-0.016	26.281	-0.017	-0.017	0.000	0.000	0.000	0.000
29	u	105	PRO	0	-0.027	-0.004	22.042	0.013	0.013	0.000	0.000	0.000	0.000
30	u	106	PRO	0	0.027	0.006	23.104	0.000	0.000	0.000	0.000	0.000	0.000
31	u	107	GLU	-1	-0.853	-0.914	22.843	-0.153	-0.153	0.000	0.000	0.000	0.000
32	u	108	GLU	-1	-0.943	-0.966	20.623	-0.025	-0.025	0.000	0.000	0.000	0.000
33	u	109	GLU	-1	-0.864	-0.925	16.658	-0.262	-0.262	0.000	0.000	0.000	0.000
34	u	110	PHE	0	-0.024	-0.011	13.757	0.051	0.051	0.000	0.000	0.000	0.000
35	u	111	ILE	0	-0.013	-0.012	8.356	-0.095	-0.095	0.000	0.000	0.000	0.000
36	u	112	MET	0	-0.020	0.000	8.433	0.115	0.115	0.000	0.000	0.000	0.000
37	u	113	GLY	0	0.052	0.027	4.718	-0.289	-0.274	-0.001	-0.008	-0.006	0.000
38	u	114	VAL	0	-0.036	-0.009	4.052	-0.073	0.690	-0.001	-0.369	-0.393	0.000
39	u	115	SER	0	0.016	-0.008	1.889	-9.486	-13.377	16.401	-7.253	-5.257	-0.066
40	u	116	LYS	1	1.007	0.986	3.267	-2.647	-3.011	0.063	0.640	-0.339	0.000
41	u	117	TYR	0	0.027	0.016	6.105	-0.463	-0.463	0.000	0.000	0.000	0.000
42	u	118	GLY	0	0.019	0.026	6.800	-0.279	-0.279	0.000	0.000	0.000	0.000
43	u	119	ILE	0	-0.023	-0.005	5.888	-0.034	-0.034	0.000	0.000	0.000	0.000
44	u	120	LYS	1	0.801	0.899	6.337	-0.885	-0.885	0.000	0.000	0.000	0.000
45	u	121	VAL	0	0.067	0.040	8.337	-0.146	-0.146	0.000	0.000	0.000	0.000
46	u	130	LEU	0	0.011	0.007	15.812	0.017	0.017	0.000	0.000	0.000	0.000
47	u	131	HIS	0	0.053	0.038	13.815	-0.037	-0.037	0.000	0.000	0.000	0.000
48	u	132	ARG	1	0.943	0.974	9.298	-0.961	-0.961	0.000	0.000	0.000	0.000
49	u	133	HIS	1	0.872	0.936	11.150	-0.098	-0.098	0.000	0.000	0.000	0.000
50	u	134	ALA	0	0.059	0.037	10.585	0.041	0.041	0.000	0.000	0.000	0.000
51	u	135	LEU	0	0.069	0.003	8.673	-0.106	-0.106	0.000	0.000	0.000	0.000
52	u	136	TYR	0	-0.016	-0.012	11.523	-0.098	-0.098	0.000	0.000	0.000	0.000
53	u	137	LEU	0	-0.003	0.021	14.731	-0.033	-0.033	0.000	0.000	0.000	0.000
54	u	138	ILE	0	-0.062	-0.030	11.071	-0.056	-0.056	0.000	0.000	0.000	0.000
55	u	139	ILE	0	0.013	0.020	15.269	-0.008	-0.008	0.000	0.000	0.000	0.000
56	u	140	ARG	1	0.925	0.952	16.998	0.091	0.091	0.000	0.000	0.000	0.000
57	u	141	MET	0	-0.017	0.010	11.511	0.014	0.014	0.000	0.000	0.000	0.000
58	u	142	VAL	0	-0.022	-0.014	15.982	-0.001	-0.001	0.000	0.000	0.000	0.000
59	u	143	CYS	0	-0.018	-0.016	16.866	-0.027	-0.027	0.000	0.000	0.000	0.000
60	u	144	TYR	0	-0.042	-0.031	18.918	-0.004	-0.004	0.000	0.000	0.000	0.000
61	u	145	ASP	-1	-0.824	-0.924	22.264	-0.284	-0.284	0.000	0.000	0.000	0.000
62	u	146	ASP	-1	-0.896	-0.975	24.238	-0.185	-0.185	0.000	0.000	0.000	0.000
63	u	147	GLY	0	0.018	0.029	25.675	0.018	0.018	0.000	0.000	0.000	0.000
64	u	148	LEU	0	-0.043	-0.014	28.384	0.016	0.016	0.000	0.000	0.000	0.000
65	u	149	GLY	0	-0.002	0.000	29.350	-0.013	-0.013	0.000	0.000	0.000	0.000
66	u	150	ALA	0	-0.046	-0.041	27.196	0.003	0.003	0.000	0.000	0.000	0.000
67	u	151	GLY	0	0.036	0.033	25.192	-0.015	-0.015	0.000	0.000	0.000	0.000
68	u	152	LYS	1	0.893	0.952	22.449	0.177	0.177	0.000	0.000	0.000	0.000
69	u	153	SER	0	0.015	-0.001	19.662	-0.002	-0.002	0.000	0.000	0.000	0.000
70	u	154	LEU	0	0.007	0.029	19.955	-0.020	-0.020	0.000	0.000	0.000	0.000
71	u	155	LEU	0	-0.018	-0.031	13.198	-0.034	-0.034	0.000	0.000	0.000	0.000
72	u	156	ALA	0	0.015	0.012	17.776	0.036	0.036	0.000	0.000	0.000	0.000
73	u	157	LEU	0	-0.023	-0.022	12.227	-0.028	-0.028	0.000	0.000	0.000	0.000
74	u	158	LYS	1	0.931	0.983	16.694	0.024	0.024	0.000	0.000	0.000	0.000
75	u	159	THR	0	-0.005	-0.007	15.970	0.001	0.001	0.000	0.000	0.000	0.000
76	u	160	THR	0	-0.004	-0.016	18.731	-0.018	-0.018	0.000	0.000	0.000	0.000
77	u	161	ASP	-1	-0.801	-0.880	20.233	0.154	0.154	0.000	0.000	0.000	0.000
78	u	162	ALA	0	-0.039	-0.029	22.622	0.007	0.007	0.000	0.000	0.000	0.000
79	u	163	SER	0	-0.064	-0.029	23.518	0.004	0.004	0.000	0.000	0.000	0.000
80	u	164	ASN	0	-0.059	-0.036	23.817	-0.001	-0.001	0.000	0.000	0.000	0.000
81	u	165	GLU	-1	-0.896	-0.951	26.042	0.080	0.080	0.000	0.000	0.000	0.000
82	u	166	GLU	-1	-0.885	-0.932	26.697	0.035	0.035	0.000	0.000	0.000	0.000
83	u	167	TYR	0	-0.079	-0.054	23.042	0.001	0.001	0.000	0.000	0.000	0.000
84	u	168	SER	0	-0.052	-0.021	20.739	0.006	0.006	0.000	0.000	0.000	0.000
85	u	169	LEU	0	-0.018	-0.005	20.559	-0.010	-0.010	0.000	0.000	0.000	0.000
86	u	170	TRP	0	-0.008	-0.018	16.784	0.017	0.017	0.000	0.000	0.000	0.000
87	u	171	VAL	0	0.027	0.008	18.147	-0.036	-0.036	0.000	0.000	0.000	0.000
88	u	172	TYR	0	-0.007	-0.025	14.651	0.020	0.020	0.000	0.000	0.000	0.000
89	u	173	GLN	0	0.048	0.028	18.024	0.000	0.000	0.000	0.000	0.000	0.000
90	u	174	CYS	0	-0.043	0.008	15.576	-0.047	-0.047	0.000	0.000	0.000	0.000
91	u	175	ASN	0	-0.003	-0.021	17.450	0.020	0.020	0.000	0.000	0.000	0.000
92	u	176	SER	0	0.048	0.016	18.605	0.007	0.007	0.000	0.000	0.000	0.000
93	u	177	LEU	0	0.043	0.029	18.329	-0.062	-0.062	0.000	0.000	0.000	0.000
94	u	178	GLU	-1	-0.925	-0.970	17.215	-0.545	-0.545	0.000	0.000	0.000	0.000
95	u	179	GLN	0	0.007	0.004	13.764	-0.058	-0.058	0.000	0.000	0.000	0.000
96	u	180	ALA	0	0.050	0.008	13.225	-0.143	-0.143	0.000	0.000	0.000	0.000
97	u	181	GLN	0	0.025	0.003	13.637	-0.085	-0.085	0.000	0.000	0.000	0.000
98	u	182	ALA	0	-0.019	-0.005	10.726	-0.077	-0.077	0.000	0.000	0.000	0.000
99	u	183	ILE	0	-0.001	0.002	8.837	-0.312	-0.312	0.000	0.000	0.000	0.000
100	u	184	CYS	0	-0.029	-0.022	9.056	-0.058	-0.058	0.000	0.000	0.000	0.000
101	u	185	LYS	1	0.952	0.995	8.814	0.912	0.912	0.000	0.000	0.000	0.000
102	u	186	VAL	0	0.018	0.019	3.365	-0.357	-0.048	0.013	-0.077	-0.245	0.000
103	u	187	LEU	0	0.007	-0.005	5.983	0.479	0.479	0.000	0.000	0.000	0.000
104	u	188	SER	0	-0.058	-0.034	8.494	0.326	0.326	0.000	0.000	0.000	0.000
105	u	189	THR	0	-0.071	-0.026	4.873	-0.040	-0.040	0.000	0.000	0.000	0.000
106	u	190	ALA	0	-0.081	-0.038	5.829	0.644	0.644	0.000	0.000	0.000	0.000

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