FMO DATABASE

FMODB ID: 7GJGK

Calculation Name: 4DX9-s-Xray321

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: s

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	-922515.320735
FMO2-HF: Nuclear repulsion	876443.564387
FMO2-HF: Total energy	-46071.756348
FMO2-MP2: Total energy	-46203.903811

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(s:59:ACE )

Summations of interaction energy for fragment #1(s: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.
0.857	2.356	0.153	-0.585	-1.064	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.005

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	s	61	ALA	0	0.005	0.017	3.839	0.872	1.681	-0.005	-0.362	-0.441	-0.001
4	s	62	GLU	-1	-0.937	-0.964	6.703	-0.567	-0.567	0.000	0.000	0.000	0.000
5	s	63	PHE	0	-0.009	-0.007	8.664	0.117	0.117	0.000	0.000	0.000	0.000
6	s	64	ARG	1	0.916	0.970	13.128	0.171	0.171	0.000	0.000	0.000	0.000
7	s	65	ILE	0	0.013	0.003	16.322	0.021	0.021	0.000	0.000	0.000	0.000
8	s	66	LYS	1	1.009	1.022	18.823	0.106	0.106	0.000	0.000	0.000	0.000
9	s	67	TYR	0	-0.027	-0.025	21.158	-0.013	-0.013	0.000	0.000	0.000	0.000
10	s	68	VAL	0	0.011	0.013	23.080	0.010	0.010	0.000	0.000	0.000	0.000
11	s	69	GLY	0	0.030	0.000	24.740	0.009	0.009	0.000	0.000	0.000	0.000
12	s	70	ALA	0	-0.026	-0.013	24.522	-0.010	-0.010	0.000	0.000	0.000	0.000
13	s	71	ILE	0	-0.030	-0.002	26.137	0.009	0.009	0.000	0.000	0.000	0.000
14	s	72	NME	0	0.042	0.026	27.149	-0.001	-0.001	0.000	0.000	0.000	0.000
15	s	83	ACE	0	0.003	-0.013	25.260	-0.001	-0.001	0.000	0.000	0.000	0.000
16	s	84	GLY	0	0.025	0.006	25.194	0.007	0.007	0.000	0.000	0.000	0.000
17	s	85	PRO	0	-0.044	-0.023	22.135	-0.007	-0.007	0.000	0.000	0.000	0.000
18	s	86	LEU	0	0.074	0.020	23.651	-0.006	-0.006	0.000	0.000	0.000	0.000
19	s	87	ASP	-1	-0.896	-0.940	26.972	-0.019	-0.019	0.000	0.000	0.000	0.000
20	s	88	LEU	0	-0.051	-0.039	21.764	-0.004	-0.004	0.000	0.000	0.000	0.000
21	s	89	ILE	0	0.007	0.013	24.050	-0.006	-0.006	0.000	0.000	0.000	0.000
22	s	90	ASN	0	0.048	0.015	26.693	-0.003	-0.003	0.000	0.000	0.000	0.000
23	s	91	TYR	0	-0.055	-0.021	28.171	0.001	0.001	0.000	0.000	0.000	0.000
24	s	92	ILE	0	-0.043	-0.018	24.182	-0.004	-0.004	0.000	0.000	0.000	0.000
25	s	93	ASP	-1	-0.841	-0.924	28.653	-0.041	-0.041	0.000	0.000	0.000	0.000
26	s	94	VAL	0	-0.063	-0.025	31.545	0.001	0.001	0.000	0.000	0.000	0.000
27	s	95	ALA	0	0.016	0.006	31.021	0.000	0.000	0.000	0.000	0.000	0.000
28	s	96	GLN	0	-0.014	-0.019	28.846	0.001	0.001	0.000	0.000	0.000	0.000
29	s	97	GLN	0	-0.052	-0.012	33.230	0.002	0.002	0.000	0.000	0.000	0.000
30	s	98	ASP	-1	-0.941	-0.968	36.151	-0.039	-0.039	0.000	0.000	0.000	0.000
31	s	99	GLY	0	-0.031	-0.006	36.298	0.001	0.001	0.000	0.000	0.000	0.000
32	s	100	LYS	1	0.859	0.939	32.674	0.050	0.050	0.000	0.000	0.000	0.000
33	s	101	LEU	0	-0.017	-0.007	27.411	-0.006	-0.006	0.000	0.000	0.000	0.000
34	s	102	PRO	0	0.018	0.020	29.940	0.005	0.005	0.000	0.000	0.000	0.000
35	s	103	PHE	0	0.022	-0.003	30.215	-0.004	-0.004	0.000	0.000	0.000	0.000
36	s	104	VAL	0	-0.048	-0.018	30.342	-0.001	-0.001	0.000	0.000	0.000	0.000
37	s	105	PRO	0	-0.021	0.000	26.181	0.001	0.001	0.000	0.000	0.000	0.000
38	s	106	PRO	0	0.031	0.009	27.929	0.005	0.005	0.000	0.000	0.000	0.000
39	s	107	GLU	-1	-0.947	-0.957	27.715	-0.094	-0.094	0.000	0.000	0.000	0.000
40	s	108	GLU	-1	-0.961	-0.991	25.334	-0.126	-0.126	0.000	0.000	0.000	0.000
41	s	109	GLU	-1	-0.933	-0.985	21.391	-0.165	-0.165	0.000	0.000	0.000	0.000
42	s	110	PHE	0	-0.049	-0.027	19.839	-0.010	-0.010	0.000	0.000	0.000	0.000
43	s	111	ILE	0	0.006	-0.004	14.335	0.000	0.000	0.000	0.000	0.000	0.000
44	s	112	MET	0	-0.048	-0.008	12.040	-0.006	-0.006	0.000	0.000	0.000	0.000
45	s	113	GLY	0	0.038	0.012	10.289	-0.030	-0.030	0.000	0.000	0.000	0.000
46	s	114	VAL	0	-0.003	0.010	6.043	0.045	0.045	0.000	0.000	0.000	0.000
47	s	115	SER	0	-0.006	-0.017	5.259	-0.630	-0.638	0.000	-0.015	0.024	0.000
48	s	116	LYS	1	0.978	0.970	2.827	-0.387	-0.003	0.158	-0.168	-0.374	0.000
49	s	117	TYR	0	-0.005	0.014	5.053	0.356	0.450	0.000	-0.005	-0.089	0.000
50	s	118	GLY	0	0.033	0.026	8.501	0.065	0.065	0.000	0.000	0.000	0.000
51	s	119	ILE	0	-0.011	-0.006	8.943	-0.244	-0.244	0.000	0.000	0.000	0.000
52	s	120	LYS	1	0.915	0.957	11.129	0.635	0.635	0.000	0.000	0.000	0.000
53	s	121	NME	0	0.034	0.024	12.917	-0.023	-0.023	0.000	0.000	0.000	0.000
54	s	129	ACE	0	-0.032	-0.026	19.705	-0.006	-0.006	0.000	0.000	0.000	0.000
55	s	130	LEU	0	0.028	0.009	20.069	0.017	0.017	0.000	0.000	0.000	0.000
56	s	131	HIS	1	0.943	0.973	18.782	0.204	0.204	0.000	0.000	0.000	0.000
57	s	132	ARG	1	0.952	0.973	15.969	0.262	0.262	0.000	0.000	0.000	0.000
58	s	133	HIS	0	0.041	0.045	14.747	0.010	0.010	0.000	0.000	0.000	0.000
59	s	134	ALA	0	0.055	0.023	13.465	-0.070	-0.070	0.000	0.000	0.000	0.000
60	s	135	LEU	0	0.054	-0.006	8.798	0.007	0.007	0.000	0.000	0.000	0.000
61	s	136	TYR	0	-0.053	-0.015	12.355	0.040	0.040	0.000	0.000	0.000	0.000
62	s	137	LEU	0	0.008	0.011	15.500	0.016	0.016	0.000	0.000	0.000	0.000
63	s	138	ILE	0	-0.038	-0.002	12.326	0.002	0.002	0.000	0.000	0.000	0.000
64	s	139	ILE	0	-0.007	0.019	16.131	0.024	0.024	0.000	0.000	0.000	0.000
65	s	140	ARG	1	0.901	0.942	16.951	0.034	0.034	0.000	0.000	0.000	0.000
66	s	141	MET	0	0.014	0.020	13.052	-0.021	-0.021	0.000	0.000	0.000	0.000
67	s	142	VAL	0	-0.033	-0.017	16.404	0.025	0.025	0.000	0.000	0.000	0.000
68	s	143	CYS	0	-0.024	-0.009	17.048	-0.014	-0.014	0.000	0.000	0.000	0.000
69	s	144	TYR	0	0.041	0.012	19.342	0.012	0.012	0.000	0.000	0.000	0.000
70	s	145	ASP	-1	-0.829	-0.923	22.683	-0.047	-0.047	0.000	0.000	0.000	0.000
71	s	146	ASP	-1	-0.823	-0.899	25.187	-0.051	-0.051	0.000	0.000	0.000	0.000
72	s	147	GLY	0	0.049	0.006	27.611	0.003	0.003	0.000	0.000	0.000	0.000
73	s	148	LEU	0	-0.080	-0.033	28.819	0.005	0.005	0.000	0.000	0.000	0.000
74	s	149	GLY	0	-0.057	-0.029	30.315	0.002	0.002	0.000	0.000	0.000	0.000
75	s	150	ALA	0	-0.053	-0.034	29.692	-0.001	-0.001	0.000	0.000	0.000	0.000
76	s	151	GLY	0	0.058	0.038	26.007	-0.001	-0.001	0.000	0.000	0.000	0.000
77	s	152	LYS	1	0.769	0.884	24.286	0.060	0.060	0.000	0.000	0.000	0.000
78	s	153	SER	0	0.010	0.001	20.826	0.008	0.008	0.000	0.000	0.000	0.000
79	s	154	LEU	0	0.002	-0.002	21.822	-0.012	-0.012	0.000	0.000	0.000	0.000
80	s	155	LEU	0	-0.034	-0.018	15.292	0.004	0.004	0.000	0.000	0.000	0.000
81	s	156	ALA	0	0.032	0.028	19.075	-0.003	-0.003	0.000	0.000	0.000	0.000
82	s	157	LEU	0	-0.029	-0.030	14.362	-0.002	-0.002	0.000	0.000	0.000	0.000
83	s	158	LYS	1	0.950	0.991	18.569	0.045	0.045	0.000	0.000	0.000	0.000
84	s	159	THR	0	0.080	0.016	18.623	0.003	0.003	0.000	0.000	0.000	0.000
85	s	160	THR	0	-0.096	-0.047	21.110	0.014	0.014	0.000	0.000	0.000	0.000
86	s	161	ASP	-1	-0.887	-0.962	20.968	-0.168	-0.168	0.000	0.000	0.000	0.000
87	s	162	ALA	0	-0.075	-0.032	22.671	-0.006	-0.006	0.000	0.000	0.000	0.000
88	s	163	SER	0	-0.017	-0.011	25.212	0.006	0.006	0.000	0.000	0.000	0.000
89	s	164	ASN	0	-0.004	-0.024	26.773	-0.002	-0.002	0.000	0.000	0.000	0.000
90	s	165	GLU	-1	-0.891	-0.931	27.986	-0.033	-0.033	0.000	0.000	0.000	0.000
91	s	166	GLU	-1	-0.818	-0.896	26.193	-0.085	-0.085	0.000	0.000	0.000	0.000
92	s	167	TYR	0	-0.068	-0.030	24.208	-0.005	-0.005	0.000	0.000	0.000	0.000
93	s	168	SER	0	-0.018	-0.011	23.797	0.007	0.007	0.000	0.000	0.000	0.000
94	s	169	LEU	0	0.000	0.008	22.146	-0.006	-0.006	0.000	0.000	0.000	0.000
95	s	170	TRP	0	-0.074	-0.043	19.839	-0.002	-0.002	0.000	0.000	0.000	0.000
96	s	171	VAL	0	0.037	0.013	20.612	-0.006	-0.006	0.000	0.000	0.000	0.000
97	s	172	TYR	0	-0.010	-0.011	18.122	-0.014	-0.014	0.000	0.000	0.000	0.000
98	s	173	GLN	0	0.056	0.018	20.770	0.013	0.013	0.000	0.000	0.000	0.000
99	s	174	CYS	0	-0.045	-0.002	17.265	-0.022	-0.022	0.000	0.000	0.000	0.000
100	s	175	ASN	0	0.052	0.023	20.087	0.007	0.007	0.000	0.000	0.000	0.000
101	s	176	SER	0	-0.009	-0.002	20.094	0.012	0.012	0.000	0.000	0.000	0.000
102	s	177	LEU	0	0.095	0.052	20.052	-0.012	-0.012	0.000	0.000	0.000	0.000
103	s	178	GLU	-1	-0.896	-0.968	17.878	-0.007	-0.007	0.000	0.000	0.000	0.000
104	s	179	GLN	0	-0.022	-0.016	15.067	0.012	0.012	0.000	0.000	0.000	0.000
105	s	180	ALA	0	0.050	0.016	14.319	-0.034	-0.034	0.000	0.000	0.000	0.000
106	s	181	GLN	0	0.019	0.003	14.648	-0.007	-0.007	0.000	0.000	0.000	0.000
107	s	182	ALA	0	-0.035	-0.014	11.399	0.020	0.020	0.000	0.000	0.000	0.000
108	s	183	ILE	0	0.006	0.002	9.766	-0.022	-0.022	0.000	0.000	0.000	0.000
109	s	184	CYS	0	-0.013	-0.012	9.553	-0.050	-0.050	0.000	0.000	0.000	0.000
110	s	185	LYS	1	0.944	0.974	9.094	-0.122	-0.122	0.000	0.000	0.000	0.000
111	s	186	VAL	0	-0.015	-0.004	4.090	0.049	0.128	0.000	-0.015	-0.065	0.000
112	s	187	LEU	0	0.034	-0.005	5.189	-0.024	0.017	0.000	-0.001	-0.039	0.000
113	s	188	SER	0	-0.070	-0.020	7.868	0.072	0.072	0.000	0.000	0.000	0.000
114	s	189	THR	0	0.006	0.006	4.722	0.172	0.215	0.000	-0.012	-0.030	0.000
115	s	190	ALA	0	-0.031	-0.010	4.714	0.209	0.266	0.000	-0.007	-0.050	0.000
116	s	191	PHE	0	0.013	0.015	5.633	-0.070	-0.070	0.000	0.000	0.000	0.000
117	s	192	ASP	-1	-0.898	-0.936	8.831	0.336	0.336	0.000	0.000	0.000	0.000
118	s	193	SER	0	-0.127	-0.080	5.959	0.124	0.124	0.000	0.000	0.000	0.000
119	s	194	VAL	0	-0.039	-0.024	7.958	-0.061	-0.061	0.000	0.000	0.000	0.000
120	s	195	LEU	0	-0.018	0.009	10.347	-0.038	-0.038	0.000	0.000	0.000	0.000
121	s	196	NME	0	0.002	0.012	13.122	0.002	0.002	0.000	0.000	0.000	0.000

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