FMO DATABASE

FMODB ID: K3R33

Calculation Name: 4DX9-A-Xray321

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: A

ChEMBL ID: CHEMBL1905

UniProt ID: P05556

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	121
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-923225.949853
FMO2-HF: Nuclear repulsion	876937.227345
FMO2-HF: Total energy	-46288.722508
FMO2-MP2: Total energy	-46421.341845

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(A:59:ACE )

Summations of interaction energy for fragment #1(A:59:ACE )

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.
0.166	2.164	1.397	-1.403	-1.993	-0.002

Interaction energy analysis for fragmet #1(A:59:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.009

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	A	61	ALA	0	0.004	0.038	3.842	0.844	1.819	-0.006	-0.433	-0.536	-0.001
4	A	62	GLU	-1	-0.939	-0.962	5.983	-0.731	-0.731	0.000	0.000	0.000	0.000
5	A	63	PHE	0	-0.019	-0.009	7.137	0.152	0.152	0.000	0.000	0.000	0.000
6	A	64	ARG	1	0.834	0.898	11.996	0.132	0.132	0.000	0.000	0.000	0.000
7	A	65	ILE	0	-0.033	-0.012	14.925	0.025	0.025	0.000	0.000	0.000	0.000
8	A	66	LYS	1	0.970	0.991	17.564	0.093	0.093	0.000	0.000	0.000	0.000
9	A	67	TYR	0	0.030	0.006	19.650	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	68	VAL	0	-0.003	0.006	21.748	0.011	0.011	0.000	0.000	0.000	0.000
11	A	69	GLY	0	0.028	-0.007	23.422	0.007	0.007	0.000	0.000	0.000	0.000
12	A	70	ALA	0	-0.041	-0.021	23.183	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	71	ILE	0	-0.021	-0.010	24.777	0.008	0.008	0.000	0.000	0.000	0.000
14	A	72	GLU	-1	-0.955	-0.974	26.337	-0.083	-0.083	0.000	0.000	0.000	0.000
15	A	73	NME	0	0.006	0.017	28.430	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	82	ACE	0	-0.028	-0.027	28.479	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	83	GLU	-1	-0.937	-0.960	27.123	0.022	0.022	0.000	0.000	0.000	0.000
18	A	84	GLY	0	-0.017	-0.018	24.226	0.008	0.008	0.000	0.000	0.000	0.000
19	A	85	PRO	0	-0.038	-0.035	20.911	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	86	LEU	0	0.039	0.000	22.898	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	87	ASP	-1	-0.788	-0.876	26.269	0.003	0.003	0.000	0.000	0.000	0.000
22	A	88	LEU	0	-0.063	-0.042	20.692	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	89	ILE	0	-0.017	0.004	23.732	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	90	ASN	0	0.063	0.042	25.737	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	91	TYR	0	-0.024	-0.016	26.861	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	92	ILE	0	-0.024	-0.011	22.901	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	93	ASP	-1	-0.841	-0.930	27.410	-0.024	-0.024	0.000	0.000	0.000	0.000
28	A	94	VAL	0	-0.062	-0.028	30.351	0.001	0.001	0.000	0.000	0.000	0.000
29	A	95	ALA	0	-0.020	-0.012	29.348	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	96	GLN	0	-0.007	-0.006	27.091	0.000	0.000	0.000	0.000	0.000	0.000
31	A	97	GLN	0	-0.051	-0.032	31.505	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	98	ASP	-1	-0.954	-0.944	34.611	-0.027	-0.027	0.000	0.000	0.000	0.000
33	A	99	GLY	0	-0.017	-0.020	34.100	0.000	0.000	0.000	0.000	0.000	0.000
34	A	100	LYS	1	0.860	0.940	31.188	0.035	0.035	0.000	0.000	0.000	0.000
35	A	101	LEU	0	-0.014	-0.010	25.574	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	102	PRO	0	0.011	0.022	27.973	0.006	0.006	0.000	0.000	0.000	0.000
37	A	103	PHE	0	0.033	0.006	28.156	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	104	VAL	0	-0.024	-0.016	27.613	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	105	PRO	0	-0.009	0.013	24.481	0.000	0.000	0.000	0.000	0.000	0.000
40	A	106	PRO	0	0.032	-0.002	26.961	0.004	0.004	0.000	0.000	0.000	0.000
41	A	107	GLU	-1	-1.007	-1.022	25.876	-0.081	-0.081	0.000	0.000	0.000	0.000
42	A	108	GLU	-1	-0.929	-0.952	24.426	-0.127	-0.127	0.000	0.000	0.000	0.000
43	A	109	GLU	-1	-0.854	-0.911	20.286	-0.139	-0.139	0.000	0.000	0.000	0.000
44	A	110	PHE	0	-0.023	-0.006	18.172	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	111	ILE	0	0.012	-0.002	12.545	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	112	MET	0	-0.006	0.010	10.739	0.000	0.000	0.000	0.000	0.000	0.000
47	A	113	GLY	0	0.028	-0.003	8.762	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	114	VAL	0	-0.009	-0.013	4.974	0.090	0.090	0.000	0.000	0.000	0.000
49	A	115	SER	0	-0.074	-0.057	3.855	-1.530	-1.331	0.009	-0.157	-0.051	0.000
50	A	116	LYS	1	0.983	0.976	2.528	-0.534	-0.148	1.384	-0.702	-1.068	-0.001
51	A	117	TYR	0	-0.042	-0.014	4.367	0.258	0.385	0.001	-0.024	-0.104	0.000
52	A	118	GLY	0	0.075	0.043	7.795	0.221	0.221	0.000	0.000	0.000	0.000
53	A	119	ILE	0	-0.042	-0.006	8.476	-0.297	-0.297	0.000	0.000	0.000	0.000
54	A	120	LYS	1	0.933	0.972	9.488	0.838	0.838	0.000	0.000	0.000	0.000
55	A	121	NME	0	0.026	0.030	11.346	0.073	0.073	0.000	0.000	0.000	0.000
56	A	130	ACE	0	-0.021	-0.020	19.438	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	131	HIS	0	0.045	0.005	17.296	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	132	ARG	1	0.876	0.954	13.586	0.319	0.319	0.000	0.000	0.000	0.000
59	A	133	HIS	0	0.050	0.044	13.205	0.061	0.061	0.000	0.000	0.000	0.000
60	A	134	ALA	0	0.009	-0.001	12.141	-0.063	-0.063	0.000	0.000	0.000	0.000
61	A	135	LEU	0	0.021	-0.004	7.179	-0.023	-0.023	0.000	0.000	0.000	0.000
62	A	136	TYR	0	-0.012	0.000	11.169	0.059	0.059	0.000	0.000	0.000	0.000
63	A	137	LEU	0	-0.018	0.002	14.237	0.011	0.011	0.000	0.000	0.000	0.000
64	A	138	ILE	0	-0.040	0.003	11.810	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	139	ILE	0	0.006	0.012	15.260	0.029	0.029	0.000	0.000	0.000	0.000
66	A	140	ARG	1	0.875	0.919	16.335	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	141	MET	0	0.011	0.018	12.534	-0.027	-0.027	0.000	0.000	0.000	0.000
68	A	142	VAL	0	-0.042	-0.019	15.680	0.024	0.024	0.000	0.000	0.000	0.000
69	A	143	CYS	0	-0.064	-0.035	15.806	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	144	TYR	0	0.033	0.011	18.938	0.013	0.013	0.000	0.000	0.000	0.000
71	A	145	ASP	-1	-0.921	-0.981	22.342	-0.025	-0.025	0.000	0.000	0.000	0.000
72	A	146	ASP	-1	-0.813	-0.908	24.881	-0.032	-0.032	0.000	0.000	0.000	0.000
73	A	147	GLY	0	-0.013	-0.009	26.844	0.004	0.004	0.000	0.000	0.000	0.000
74	A	148	LEU	0	-0.080	-0.040	29.425	0.001	0.001	0.000	0.000	0.000	0.000
75	A	149	GLY	0	0.032	0.030	28.963	0.001	0.001	0.000	0.000	0.000	0.000
76	A	150	ALA	0	-0.090	-0.052	29.920	0.001	0.001	0.000	0.000	0.000	0.000
77	A	151	GLY	0	-0.023	0.001	27.384	0.000	0.000	0.000	0.000	0.000	0.000
78	A	152	LYS	1	0.923	0.969	23.857	0.057	0.057	0.000	0.000	0.000	0.000
79	A	153	SER	0	0.040	0.014	20.480	0.008	0.008	0.000	0.000	0.000	0.000
80	A	154	LEU	0	0.001	0.011	21.406	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	155	LEU	0	-0.039	-0.037	14.046	0.000	0.000	0.000	0.000	0.000	0.000
82	A	156	ALA	0	0.035	0.031	17.826	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	157	LEU	0	-0.027	-0.009	13.556	0.004	0.004	0.000	0.000	0.000	0.000
84	A	158	LYS	1	0.952	0.975	16.870	0.020	0.020	0.000	0.000	0.000	0.000
85	A	159	THR	0	0.015	0.011	16.043	0.012	0.012	0.000	0.000	0.000	0.000
86	A	160	THR	0	0.062	0.032	18.571	0.009	0.009	0.000	0.000	0.000	0.000
87	A	161	ASP	-1	-0.910	-1.002	20.638	-0.077	-0.077	0.000	0.000	0.000	0.000
88	A	162	ALA	0	0.034	0.046	22.203	0.010	0.010	0.000	0.000	0.000	0.000
89	A	163	SER	0	-0.067	-0.052	24.187	0.007	0.007	0.000	0.000	0.000	0.000
90	A	164	ASN	0	-0.106	-0.059	24.464	0.006	0.006	0.000	0.000	0.000	0.000
91	A	165	GLU	-1	-0.872	-0.921	26.972	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	166	GLU	-1	-0.946	-0.966	27.230	-0.047	-0.047	0.000	0.000	0.000	0.000
93	A	167	TYR	0	-0.037	-0.025	22.360	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	168	SER	0	0.000	0.008	21.267	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	169	LEU	0	-0.042	-0.037	21.182	0.005	0.005	0.000	0.000	0.000	0.000
96	A	170	TRP	0	0.017	0.011	18.066	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	171	VAL	0	0.063	0.031	19.234	0.003	0.003	0.000	0.000	0.000	0.000
98	A	172	TYR	0	-0.037	-0.024	16.262	-0.023	-0.023	0.000	0.000	0.000	0.000
99	A	173	GLN	0	0.026	0.006	19.442	0.023	0.023	0.000	0.000	0.000	0.000
100	A	174	CYS	0	-0.042	0.012	16.263	-0.022	-0.022	0.000	0.000	0.000	0.000
101	A	175	ASN	0	-0.002	-0.004	18.582	0.011	0.011	0.000	0.000	0.000	0.000
102	A	176	SER	0	0.030	0.005	19.223	0.008	0.008	0.000	0.000	0.000	0.000
103	A	177	LEU	0	0.140	0.067	18.999	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	178	GLU	-1	-0.913	-0.956	17.682	0.028	0.028	0.000	0.000	0.000	0.000
105	A	179	GLN	0	0.001	-0.009	14.280	0.007	0.007	0.000	0.000	0.000	0.000
106	A	180	ALA	0	0.030	0.009	13.548	-0.021	-0.021	0.000	0.000	0.000	0.000
107	A	181	GLN	0	0.005	-0.007	14.335	0.008	0.008	0.000	0.000	0.000	0.000
108	A	182	ALA	0	-0.049	-0.025	11.489	0.041	0.041	0.000	0.000	0.000	0.000
109	A	183	ILE	0	0.020	0.010	9.246	0.041	0.041	0.000	0.000	0.000	0.000
110	A	184	CYS	0	0.014	-0.002	8.755	0.009	0.009	0.000	0.000	0.000	0.000
111	A	185	LYS	1	0.949	0.977	9.593	-0.149	-0.149	0.000	0.000	0.000	0.000
112	A	186	VAL	0	-0.023	-0.003	3.611	0.014	0.177	0.007	-0.053	-0.118	0.000
113	A	187	LEU	0	0.014	-0.014	5.131	0.289	0.384	0.000	-0.004	-0.091	0.000
114	A	188	SER	0	-0.031	0.001	7.519	0.027	0.027	0.000	0.000	0.000	0.000
115	A	189	THR	0	-0.005	0.003	5.579	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	190	ALA	0	-0.033	-0.025	3.872	0.189	0.280	0.002	-0.026	-0.068	0.000
117	A	191	PHE	0	0.006	-0.003	5.125	-0.296	-0.334	0.000	-0.004	0.043	0.000
118	A	192	ASP	-1	-0.879	-0.927	8.799	0.497	0.497	0.000	0.000	0.000	0.000
119	A	193	SER	0	-0.134	-0.055	4.914	0.199	0.199	0.000	0.000	0.000	0.000
120	A	194	VAL	0	-0.074	-0.029	6.900	-0.171	-0.171	0.000	0.000	0.000	0.000
121	A	195	NME	0	0.021	0.017	9.594	0.017	0.017	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:59:ACE )