FMO DATABASE

FMODB ID: 2N6GR

Calculation Name: 4DX9-A-Xray372

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: 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	OptHSide
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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-906570.670684
FMO2-HF: Nuclear repulsion	860794.020219
FMO2-HF: Total energy	-45776.650465
FMO2-MP2: Total energy	-45907.645773

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:60:CYS)

Summations of interaction energy for fragment #1(A: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.
-11.19	-7.029	7.422	-5.328	-6.249	-0.02

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.013

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	62	GLU	-1	-0.868	-0.923	3.812	-0.557	1.571	-0.023	-0.890	-1.214	0.003
4	A	63	PHE	0	0.004	0.005	6.136	0.031	0.031	0.000	0.000	0.000	0.000
5	A	64	ARG	1	0.828	0.878	9.797	0.691	0.691	0.000	0.000	0.000	0.000
6	A	65	ILE	0	-0.043	-0.024	12.968	-0.003	-0.003	0.000	0.000	0.000	0.000
7	A	66	LYS	1	0.890	0.950	15.430	0.278	0.278	0.000	0.000	0.000	0.000
8	A	67	TYR	0	0.024	0.001	17.235	0.016	0.016	0.000	0.000	0.000	0.000
9	A	68	VAL	0	0.007	0.008	19.463	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	69	GLY	0	0.030	-0.004	21.612	0.004	0.004	0.000	0.000	0.000	0.000
11	A	70	ALA	0	-0.053	-0.028	21.292	0.011	0.011	0.000	0.000	0.000	0.000
12	A	71	ILE	0	-0.009	-0.001	23.085	-0.016	-0.016	0.000	0.000	0.000	0.000
13	A	72	GLU	-1	-0.952	-0.961	24.923	0.198	0.198	0.000	0.000	0.000	0.000
14	A	83	GLU	-1	-0.920	-0.958	28.142	0.080	0.080	0.000	0.000	0.000	0.000
15	A	84	GLY	0	-0.010	0.002	25.288	0.009	0.009	0.000	0.000	0.000	0.000
16	A	85	PRO	0	-0.001	-0.034	21.683	0.010	0.010	0.000	0.000	0.000	0.000
17	A	86	LEU	0	0.021	0.002	23.682	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	87	ASP	-1	-0.801	-0.898	26.946	0.022	0.022	0.000	0.000	0.000	0.000
19	A	88	LEU	0	-0.052	-0.040	21.310	0.006	0.006	0.000	0.000	0.000	0.000
20	A	89	ILE	0	-0.009	0.009	24.053	0.001	0.001	0.000	0.000	0.000	0.000
21	A	90	ASN	0	0.038	0.025	25.980	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	91	TYR	0	-0.019	-0.011	26.299	0.000	0.000	0.000	0.000	0.000	0.000
23	A	92	ILE	0	-0.008	-0.002	22.518	0.009	0.009	0.000	0.000	0.000	0.000
24	A	93	ASP	-1	-0.821	-0.927	27.034	-0.048	-0.048	0.000	0.000	0.000	0.000
25	A	94	VAL	0	-0.049	-0.024	30.089	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	95	ALA	0	-0.022	-0.013	28.538	0.001	0.001	0.000	0.000	0.000	0.000
27	A	96	GLN	0	0.000	0.003	26.361	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	97	GLN	0	-0.049	-0.026	30.579	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	98	ASP	-1	-0.901	-0.904	33.639	0.027	0.027	0.000	0.000	0.000	0.000
30	A	99	GLY	0	-0.007	-0.021	32.781	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	100	LYS	1	0.772	0.887	29.864	-0.043	-0.043	0.000	0.000	0.000	0.000
32	A	101	LEU	0	-0.006	0.005	24.548	0.010	0.010	0.000	0.000	0.000	0.000
33	A	102	PRO	0	0.005	0.013	26.260	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	103	PHE	0	0.034	0.002	26.671	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	104	VAL	0	-0.027	-0.015	26.173	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	105	PRO	0	-0.023	0.014	22.541	0.015	0.015	0.000	0.000	0.000	0.000
37	A	106	PRO	0	0.039	0.005	24.048	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	107	GLU	-1	-0.899	-0.957	23.137	-0.209	-0.209	0.000	0.000	0.000	0.000
39	A	108	GLU	-1	-0.952	-0.973	20.626	-0.067	-0.067	0.000	0.000	0.000	0.000
40	A	109	GLU	-1	-0.813	-0.875	16.828	-0.399	-0.399	0.000	0.000	0.000	0.000
41	A	110	PHE	0	-0.023	-0.006	14.332	0.017	0.017	0.000	0.000	0.000	0.000
42	A	111	ILE	0	-0.005	-0.008	8.034	-0.094	-0.094	0.000	0.000	0.000	0.000
43	A	112	MET	0	-0.028	0.005	8.925	0.224	0.224	0.000	0.000	0.000	0.000
44	A	113	GLY	0	0.016	-0.007	5.414	-0.641	-0.641	0.000	0.000	0.000	0.000
45	A	114	VAL	0	-0.004	-0.010	4.210	0.946	1.318	0.000	-0.093	-0.278	0.000
46	A	115	SER	0	-0.052	-0.041	1.997	-5.685	-3.250	7.332	-6.026	-3.741	-0.022
47	A	116	LYS	1	0.956	0.956	2.901	-3.085	-4.394	0.107	1.788	-0.585	-0.001
48	A	117	TYR	0	-0.030	-0.010	4.687	-1.154	-0.960	0.001	-0.036	-0.158	0.000
49	A	118	GLY	0	0.071	0.039	6.666	-0.698	-0.698	0.000	0.000	0.000	0.000
50	A	119	ILE	0	-0.033	-0.003	6.431	0.854	0.854	0.000	0.000	0.000	0.000
51	A	120	LYS	1	0.891	0.944	4.226	-2.266	-2.022	0.006	-0.054	-0.195	0.000
52	A	131	HIS	0	0.006	0.001	13.877	0.069	0.069	0.000	0.000	0.000	0.000
53	A	132	ARG	1	0.902	0.943	10.420	-1.000	-1.000	0.000	0.000	0.000	0.000
54	A	133	HIS	0	0.017	0.027	11.306	-0.115	-0.115	0.000	0.000	0.000	0.000
55	A	134	ALA	0	0.010	-0.001	11.242	0.232	0.232	0.000	0.000	0.000	0.000
56	A	135	LEU	0	0.024	0.000	9.022	-0.055	-0.055	0.000	0.000	0.000	0.000
57	A	136	TYR	0	-0.012	-0.003	12.276	-0.095	-0.095	0.000	0.000	0.000	0.000
58	A	137	LEU	0	0.006	-0.003	15.915	-0.059	-0.059	0.000	0.000	0.000	0.000
59	A	138	ILE	0	-0.066	0.001	12.532	-0.068	-0.068	0.000	0.000	0.000	0.000
60	A	139	ILE	0	0.005	0.008	15.907	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	140	ARG	1	0.813	0.895	17.324	-0.098	-0.098	0.000	0.000	0.000	0.000
62	A	141	MET	0	0.014	0.015	12.621	0.024	0.024	0.000	0.000	0.000	0.000
63	A	142	VAL	0	-0.035	-0.020	16.227	-0.019	-0.019	0.000	0.000	0.000	0.000
64	A	143	CYS	0	-0.077	-0.035	16.082	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	144	TYR	0	-0.007	-0.007	19.058	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	145	ASP	-1	-0.923	-0.979	22.182	-0.244	-0.244	0.000	0.000	0.000	0.000
67	A	146	ASP	-1	-0.748	-0.863	24.612	-0.137	-0.137	0.000	0.000	0.000	0.000
68	A	147	GLY	0	-0.002	-0.003	26.555	0.010	0.010	0.000	0.000	0.000	0.000
69	A	148	LEU	0	-0.137	-0.064	29.638	0.008	0.008	0.000	0.000	0.000	0.000
70	A	149	GLY	0	0.008	-0.001	27.831	0.002	0.002	0.000	0.000	0.000	0.000
71	A	150	ALA	0	0.014	0.007	27.315	-0.020	-0.020	0.000	0.000	0.000	0.000
72	A	151	GLY	0	-0.069	-0.024	26.762	0.009	0.009	0.000	0.000	0.000	0.000
73	A	152	LYS	1	0.911	0.960	23.057	0.173	0.173	0.000	0.000	0.000	0.000
74	A	153	SER	0	0.038	0.007	19.894	-0.017	-0.017	0.000	0.000	0.000	0.000
75	A	154	LEU	0	0.000	0.014	20.707	0.012	0.012	0.000	0.000	0.000	0.000
76	A	155	LEU	0	-0.043	-0.038	13.615	-0.043	-0.043	0.000	0.000	0.000	0.000
77	A	156	ALA	0	0.037	0.030	17.772	0.031	0.031	0.000	0.000	0.000	0.000
78	A	157	LEU	0	-0.030	-0.013	13.301	0.001	0.001	0.000	0.000	0.000	0.000
79	A	158	LYS	1	0.959	0.974	16.962	-0.182	-0.182	0.000	0.000	0.000	0.000
80	A	159	THR	0	0.038	0.024	15.564	0.033	0.033	0.000	0.000	0.000	0.000
81	A	160	THR	0	0.027	-0.003	18.311	-0.038	-0.038	0.000	0.000	0.000	0.000
82	A	161	ASP	-1	-0.854	-0.914	20.501	0.435	0.435	0.000	0.000	0.000	0.000
83	A	162	ALA	0	-0.029	-0.005	22.441	-0.022	-0.022	0.000	0.000	0.000	0.000
84	A	163	SER	0	-0.055	-0.049	25.549	-0.033	-0.033	0.000	0.000	0.000	0.000
85	A	164	ASN	0	-0.105	-0.066	27.487	-0.022	-0.022	0.000	0.000	0.000	0.000
86	A	165	GLU	-1	-0.944	-0.969	28.081	0.155	0.155	0.000	0.000	0.000	0.000
87	A	166	GLU	-1	-0.893	-0.921	27.002	0.193	0.193	0.000	0.000	0.000	0.000
88	A	167	TYR	0	-0.001	-0.007	22.660	0.033	0.033	0.000	0.000	0.000	0.000
89	A	168	SER	0	-0.009	-0.005	20.325	0.001	0.001	0.000	0.000	0.000	0.000
90	A	169	LEU	0	-0.049	-0.030	20.812	0.002	0.002	0.000	0.000	0.000	0.000
91	A	170	TRP	0	0.027	0.007	16.900	-0.023	-0.023	0.000	0.000	0.000	0.000
92	A	171	VAL	0	0.059	0.029	18.405	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	172	TYR	0	-0.033	-0.029	14.078	0.015	0.015	0.000	0.000	0.000	0.000
94	A	173	GLN	0	0.053	0.020	17.822	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	174	CYS	0	-0.055	0.004	15.584	-0.059	-0.059	0.000	0.000	0.000	0.000
96	A	175	ASN	0	-0.016	-0.021	16.389	0.084	0.084	0.000	0.000	0.000	0.000
97	A	176	SER	0	0.034	0.009	18.446	0.015	0.015	0.000	0.000	0.000	0.000
98	A	177	LEU	0	0.128	0.062	18.486	-0.028	-0.028	0.000	0.000	0.000	0.000
99	A	178	GLU	-1	-0.920	-0.960	17.574	-0.524	-0.524	0.000	0.000	0.000	0.000
100	A	179	GLN	0	0.009	0.004	13.731	-0.042	-0.042	0.000	0.000	0.000	0.000
101	A	180	ALA	0	0.034	0.013	13.144	-0.097	-0.097	0.000	0.000	0.000	0.000
102	A	181	GLN	0	0.014	-0.010	14.332	0.000	0.000	0.000	0.000	0.000	0.000
103	A	182	ALA	0	-0.057	-0.028	11.375	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	183	ILE	0	0.006	0.005	9.021	-0.195	-0.195	0.000	0.000	0.000	0.000
105	A	184	CYS	0	0.021	0.012	9.131	0.036	0.036	0.000	0.000	0.000	0.000
106	A	185	LYS	1	0.941	0.965	10.255	0.702	0.702	0.000	0.000	0.000	0.000
107	A	186	VAL	0	-0.026	-0.002	4.002	-0.185	-0.088	-0.001	-0.017	-0.078	0.000
108	A	187	LEU	0	0.010	-0.010	6.612	0.355	0.355	0.000	0.000	0.000	0.000
109	A	188	SER	0	-0.017	0.006	8.729	0.175	0.175	0.000	0.000	0.000	0.000
110	A	189	THR	0	0.000	0.002	7.671	-0.010	-0.010	0.000	0.000	0.000	0.000
111	A	190	ALA	0	-0.033	-0.022	5.459	0.313	0.313	0.000	0.000	0.000	0.000
112	A	191	PHE	0	0.015	-0.002	7.274	0.273	0.273	0.000	0.000	0.000	0.000
113	A	192	ASP	-1	-0.884	-0.925	11.005	0.245	0.245	0.000	0.000	0.000	0.000
114	A	193	SER	0	-0.101	-0.043	7.966	0.224	0.224	0.000	0.000	0.000	0.000
115	A	194	VAL	0	-0.042	-0.003	10.041	0.028	0.028	0.000	0.000	0.000	0.000

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