FMO DATABASE

FMODB ID: R5738

Calculation Name: 4DX9-0-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: 0

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	117
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-930942.335543
FMO2-HF: Nuclear repulsion	884772.432511
FMO2-HF: Total energy	-46169.903032
FMO2-MP2: Total energy	-46302.35976

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(0:60:CYS)

Summations of interaction energy for fragment #1(0:60: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.
-7.827	-5.574	7.555	-3.352	-6.456	-0.026

Interaction energy analysis for fragmet #1(0:60:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / 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.	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	62	GLU	-1	-0.917	-0.964	3.296	-1.902	0.648	0.024	-1.101	-1.473	0.002
4	63	PHE	0	-0.012	-0.017	5.337	0.057	0.077	-0.001	-0.002	-0.016	0.000
5	64	ARG	1	0.898	0.946	9.105	0.822	0.822	0.000	0.000	0.000	0.000
6	65	ILE	0	-0.035	-0.022	12.200	0.012	0.012	0.000	0.000	0.000	0.000
7	66	LYS	1	0.851	0.917	14.544	0.241	0.241	0.000	0.000	0.000	0.000
8	67	TYR	0	0.002	-0.003	17.591	0.023	0.023	0.000	0.000	0.000	0.000
9	68	VAL	0	-0.001	0.001	18.744	-0.021	-0.021	0.000	0.000	0.000	0.000
10	69	GLY	0	0.050	0.018	21.662	-0.001	-0.001	0.000	0.000	0.000	0.000
11	70	ALA	0	-0.043	-0.026	21.840	0.020	0.020	0.000	0.000	0.000	0.000
12	71	ILE	0	-0.024	-0.006	23.678	-0.010	-0.010	0.000	0.000	0.000	0.000
13	84	GLY	0	0.036	0.004	26.288	0.006	0.006	0.000	0.000	0.000	0.000
14	85	PRO	0	-0.050	-0.038	23.180	0.013	0.013	0.000	0.000	0.000	0.000
15	86	LEU	0	0.078	0.020	23.869	-0.009	-0.009	0.000	0.000	0.000	0.000
16	87	ASP	-1	-0.932	-0.956	26.667	0.069	0.069	0.000	0.000	0.000	0.000
17	88	LEU	0	-0.021	-0.022	21.423	0.009	0.009	0.000	0.000	0.000	0.000
18	89	ILE	0	-0.024	0.013	23.578	0.007	0.007	0.000	0.000	0.000	0.000
19	90	ASN	0	0.053	0.028	25.960	-0.004	-0.004	0.000	0.000	0.000	0.000
20	91	TYR	0	-0.055	-0.026	26.949	0.003	0.003	0.000	0.000	0.000	0.000
21	92	ILE	0	-0.012	-0.013	23.033	0.010	0.010	0.000	0.000	0.000	0.000
22	93	ASP	-1	-0.785	-0.887	27.487	-0.019	-0.019	0.000	0.000	0.000	0.000
23	94	VAL	0	-0.011	-0.011	30.000	-0.004	-0.004	0.000	0.000	0.000	0.000
24	95	ALA	0	0.009	0.003	29.282	0.000	0.000	0.000	0.000	0.000	0.000
25	96	GLN	0	-0.037	-0.018	27.225	-0.001	-0.001	0.000	0.000	0.000	0.000
26	97	GLN	0	-0.042	-0.016	31.415	-0.002	-0.002	0.000	0.000	0.000	0.000
27	98	ASP	-1	-0.864	-0.916	34.552	0.042	0.042	0.000	0.000	0.000	0.000
28	99	GLY	0	-0.015	-0.003	34.300	0.005	0.005	0.000	0.000	0.000	0.000
29	100	LYS	1	0.756	0.868	31.831	-0.043	-0.043	0.000	0.000	0.000	0.000
30	101	LEU	0	-0.021	0.001	25.041	0.009	0.009	0.000	0.000	0.000	0.000
31	102	PRO	0	0.005	0.009	26.064	-0.008	-0.008	0.000	0.000	0.000	0.000
32	103	PHE	0	0.042	0.007	27.284	-0.001	-0.001	0.000	0.000	0.000	0.000
33	104	VAL	0	-0.037	-0.019	26.433	-0.017	-0.017	0.000	0.000	0.000	0.000
34	105	PRO	0	-0.023	0.001	21.974	0.016	0.016	0.000	0.000	0.000	0.000
35	106	PRO	0	0.058	0.023	22.841	-0.012	-0.012	0.000	0.000	0.000	0.000
36	107	GLU	-1	-0.845	-0.890	22.399	-0.211	-0.211	0.000	0.000	0.000	0.000
37	108	GLU	-1	-0.949	-0.978	19.631	0.010	0.010	0.000	0.000	0.000	0.000
38	109	GLU	-1	-0.876	-0.942	15.894	-0.409	-0.409	0.000	0.000	0.000	0.000
39	110	PHE	0	-0.031	-0.012	12.937	0.054	0.054	0.000	0.000	0.000	0.000
40	111	ILE	0	0.005	0.009	7.712	-0.112	-0.112	0.000	0.000	0.000	0.000
41	112	MET	0	-0.043	-0.010	8.562	0.238	0.238	0.000	0.000	0.000	0.000
42	113	GLY	0	0.066	0.028	4.549	-0.987	-0.924	0.000	-0.020	-0.044	0.000
43	114	VAL	0	-0.039	-0.019	4.319	0.997	1.447	0.010	-0.147	-0.313	0.000
44	115	SER	0	0.050	-0.007	2.214	-2.735	-2.027	7.501	-4.260	-3.949	-0.027
45	116	LYS	1	0.883	0.922	3.259	-2.788	-4.501	0.019	2.212	-0.518	-0.001
46	117	TYR	0	0.054	0.026	6.214	-0.751	-0.751	0.000	0.000	0.000	0.000
47	118	GLY	0	-0.011	0.005	7.401	-0.701	-0.701	0.000	0.000	0.000	0.000
48	119	ILE	0	-0.017	0.004	6.714	1.090	1.090	0.000	0.000	0.000	0.000
49	120	LYS	1	0.836	0.921	7.458	-1.023	-1.023	0.000	0.000	0.000	0.000
50	121	VAL	0	0.004	0.001	8.507	-0.155	-0.155	0.000	0.000	0.000	0.000
51	122	SER	0	0.016	0.019	10.558	0.132	0.132	0.000	0.000	0.000	0.000
52	123	THR	0	0.039	0.020	12.111	-0.092	-0.092	0.000	0.000	0.000	0.000
53	124	SER	0	-0.035	-0.049	13.076	-0.037	-0.037	0.000	0.000	0.000	0.000
54	125	ASP	-1	-0.863	-0.903	15.307	-0.035	-0.035	0.000	0.000	0.000	0.000
55	126	GLN	0	-0.013	0.007	17.174	0.001	0.001	0.000	0.000	0.000	0.000
56	127	TYR	0	-0.052	-0.045	17.682	0.059	0.059	0.000	0.000	0.000	0.000
57	128	ASP	-1	-0.877	-0.930	16.724	0.202	0.202	0.000	0.000	0.000	0.000
58	129	VAL	0	-0.044	-0.027	13.437	0.038	0.038	0.000	0.000	0.000	0.000
59	130	LEU	0	-0.019	0.004	12.292	0.132	0.132	0.000	0.000	0.000	0.000
60	131	HIS	0	0.031	0.015	13.950	0.082	0.082	0.000	0.000	0.000	0.000
61	132	ARG	1	0.928	0.946	12.095	-0.868	-0.868	0.000	0.000	0.000	0.000
62	133	HIS	0	0.009	0.013	11.695	-0.073	-0.073	0.000	0.000	0.000	0.000
63	134	ALA	0	0.028	0.013	11.392	0.237	0.237	0.000	0.000	0.000	0.000
64	135	LEU	0	0.057	0.007	8.694	-0.156	-0.156	0.000	0.000	0.000	0.000
65	136	TYR	0	-0.031	-0.020	11.598	-0.112	-0.112	0.000	0.000	0.000	0.000
66	137	LEU	0	-0.032	-0.010	14.888	-0.111	-0.111	0.000	0.000	0.000	0.000
67	138	ILE	0	-0.028	0.005	11.252	-0.093	-0.093	0.000	0.000	0.000	0.000
68	139	ILE	0	-0.006	-0.003	15.169	-0.003	-0.003	0.000	0.000	0.000	0.000
69	140	ARG	1	0.904	0.953	17.150	-0.166	-0.166	0.000	0.000	0.000	0.000
70	141	MET	0	-0.016	0.011	10.862	0.075	0.075	0.000	0.000	0.000	0.000
71	142	VAL	0	-0.017	-0.004	16.134	-0.031	-0.031	0.000	0.000	0.000	0.000
72	143	CYS	0	-0.017	-0.005	16.920	-0.007	-0.007	0.000	0.000	0.000	0.000
73	144	TYR	0	-0.005	-0.006	18.941	-0.012	-0.012	0.000	0.000	0.000	0.000
74	145	ASP	-1	-0.836	-0.920	22.236	-0.210	-0.210	0.000	0.000	0.000	0.000
75	146	ASP	-1	-0.858	-0.924	24.443	-0.094	-0.094	0.000	0.000	0.000	0.000
76	147	GLY	0	0.004	0.011	26.040	0.017	0.017	0.000	0.000	0.000	0.000
77	148	LEU	0	-0.079	-0.038	28.430	0.003	0.003	0.000	0.000	0.000	0.000
78	149	GLY	0	0.017	0.003	30.138	0.007	0.007	0.000	0.000	0.000	0.000
79	150	ALA	0	-0.067	-0.037	28.553	-0.004	-0.004	0.000	0.000	0.000	0.000
80	151	GLY	0	0.029	0.023	25.769	-0.018	-0.018	0.000	0.000	0.000	0.000
81	152	LYS	1	0.874	0.937	22.154	0.218	0.218	0.000	0.000	0.000	0.000
82	153	SER	0	-0.030	-0.028	19.110	-0.024	-0.024	0.000	0.000	0.000	0.000
83	154	LEU	0	0.046	0.038	20.239	-0.005	-0.005	0.000	0.000	0.000	0.000
84	155	LEU	0	-0.017	-0.014	13.591	0.006	0.006	0.000	0.000	0.000	0.000
85	156	ALA	0	0.031	0.014	18.141	0.029	0.029	0.000	0.000	0.000	0.000
86	157	LEU	0	-0.022	-0.018	13.426	-0.002	-0.002	0.000	0.000	0.000	0.000
87	158	LYS	1	0.960	0.986	16.854	-0.204	-0.204	0.000	0.000	0.000	0.000
88	159	THR	0	0.011	0.007	16.600	0.032	0.032	0.000	0.000	0.000	0.000
89	168	SER	0	0.011	0.010	22.100	0.003	0.003	0.000	0.000	0.000	0.000
90	169	LEU	0	0.002	-0.004	20.793	0.020	0.020	0.000	0.000	0.000	0.000
91	170	TRP	0	-0.019	-0.010	17.849	-0.012	-0.012	0.000	0.000	0.000	0.000
92	171	VAL	0	0.026	0.012	19.273	-0.008	-0.008	0.000	0.000	0.000	0.000
93	172	TYR	0	0.024	-0.008	14.836	0.017	0.017	0.000	0.000	0.000	0.000
94	173	GLN	0	0.029	0.021	18.049	-0.040	-0.040	0.000	0.000	0.000	0.000
95	174	CYS	0	-0.045	-0.013	15.711	-0.043	-0.043	0.000	0.000	0.000	0.000
96	175	ASN	0	-0.020	-0.025	15.065	0.036	0.036	0.000	0.000	0.000	0.000
97	176	SER	0	-0.010	-0.019	17.775	0.010	0.010	0.000	0.000	0.000	0.000
98	177	LEU	0	0.076	0.034	18.409	-0.011	-0.011	0.000	0.000	0.000	0.000
99	178	GLU	-1	-0.819	-0.905	17.351	-0.485	-0.485	0.000	0.000	0.000	0.000
100	179	GLN	0	0.012	0.012	13.631	-0.147	-0.147	0.000	0.000	0.000	0.000
101	180	ALA	0	0.060	0.036	12.822	-0.085	-0.085	0.000	0.000	0.000	0.000
102	181	GLN	0	-0.035	-0.032	13.561	0.049	0.049	0.000	0.000	0.000	0.000
103	182	ALA	0	-0.038	-0.012	10.686	-0.017	-0.017	0.000	0.000	0.000	0.000
104	183	ILE	0	0.028	0.012	8.802	-0.160	-0.160	0.000	0.000	0.000	0.000
105	184	CYS	0	-0.022	-0.020	9.113	0.200	0.200	0.000	0.000	0.000	0.000
106	185	LYS	1	0.948	0.983	9.906	0.617	0.617	0.000	0.000	0.000	0.000
107	186	VAL	0	0.002	-0.002	3.936	-0.137	0.038	0.002	-0.034	-0.143	0.000
108	187	LEU	0	0.004	-0.003	6.420	0.602	0.602	0.000	0.000	0.000	0.000
109	188	SER	0	-0.058	-0.035	8.333	0.228	0.228	0.000	0.000	0.000	0.000
110	189	THR	0	0.043	0.032	5.440	0.163	0.163	0.000	0.000	0.000	0.000
111	190	ALA	0	-0.031	-0.003	5.942	0.424	0.424	0.000	0.000	0.000	0.000
112	191	PHE	0	0.011	-0.017	7.488	0.144	0.144	0.000	0.000	0.000	0.000
113	192	ASP	-1	-0.909	-0.962	10.600	0.161	0.161	0.000	0.000	0.000	0.000
114	193	SER	0	-0.065	-0.023	8.216	0.104	0.104	0.000	0.000	0.000	0.000
115	194	VAL	0	-0.029	-0.018	10.202	-0.019	-0.019	0.000	0.000	0.000	0.000
116	195	LEU	0	-0.050	-0.004	12.617	-0.072	-0.072	0.000	0.000	0.000	0.000
117	196	THR	0	-0.040	-0.013	14.164	-0.109	-0.109	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(0:60:CYS)