FMO DATABASE

FMODB ID: JQJK9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-801792.919571
FMO2-HF: Nuclear repulsion	759513.701133
FMO2-HF: Total energy	-42279.218437
FMO2-MP2: Total energy	-42399.885239

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.
-14.379	-11.58	10.999	-6.962	-6.836	-0.055

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 : -0.072 / q_NPA : -0.036

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	-0.868	-0.938	3.816	-0.033	2.451	-0.028	-1.186	-1.270	0.004
4	u	63	PHE	0	0.006	0.003	6.462	-0.138	-0.138	0.000	0.000	0.000	0.000
5	u	64	ARG	1	0.844	0.911	10.131	0.495	0.495	0.000	0.000	0.000	0.000
6	u	65	ILE	0	-0.006	-0.008	12.637	-0.027	-0.027	0.000	0.000	0.000	0.000
7	u	66	LYS	1	0.897	0.950	15.074	0.256	0.256	0.000	0.000	0.000	0.000
8	u	67	TYR	0	-0.004	-0.008	17.717	-0.015	-0.015	0.000	0.000	0.000	0.000
9	u	68	VAL	0	-0.001	0.004	19.021	0.011	0.011	0.000	0.000	0.000	0.000
10	u	69	GLY	0	0.049	0.019	21.466	0.019	0.019	0.000	0.000	0.000	0.000
11	u	70	ALA	0	-0.047	-0.033	21.096	-0.015	-0.015	0.000	0.000	0.000	0.000
12	u	71	ILE	0	0.037	0.046	23.060	0.008	0.008	0.000	0.000	0.000	0.000
13	u	89	ILE	0	0.008	-0.019	23.723	0.005	0.005	0.000	0.000	0.000	0.000
14	u	90	ASN	0	0.012	0.012	25.883	0.000	0.000	0.000	0.000	0.000	0.000
15	u	91	TYR	0	0.036	-0.009	28.104	0.003	0.003	0.000	0.000	0.000	0.000
16	u	92	ILE	0	-0.050	-0.013	22.951	0.007	0.007	0.000	0.000	0.000	0.000
17	u	93	ASP	-1	-0.803	-0.900	26.858	-0.130	-0.130	0.000	0.000	0.000	0.000
18	u	94	VAL	0	-0.038	-0.016	29.947	0.006	0.006	0.000	0.000	0.000	0.000
19	u	95	ALA	0	0.026	0.009	28.830	0.005	0.005	0.000	0.000	0.000	0.000
20	u	96	GLN	0	-0.027	-0.014	26.803	0.003	0.003	0.000	0.000	0.000	0.000
21	u	97	GLN	0	-0.029	-0.011	31.113	0.007	0.007	0.000	0.000	0.000	0.000
22	u	98	ASP	-1	-0.860	-0.897	33.765	-0.036	-0.036	0.000	0.000	0.000	0.000
23	u	99	GLY	0	-0.010	-0.003	33.587	0.005	0.005	0.000	0.000	0.000	0.000
24	u	100	LYS	1	0.757	0.867	30.505	0.032	0.032	0.000	0.000	0.000	0.000
25	u	101	LEU	0	-0.023	-0.007	24.774	0.002	0.002	0.000	0.000	0.000	0.000
26	u	102	PRO	0	0.035	0.016	26.451	-0.002	-0.002	0.000	0.000	0.000	0.000
27	u	103	PHE	0	0.029	0.010	27.244	-0.010	-0.010	0.000	0.000	0.000	0.000
28	u	104	VAL	0	-0.034	-0.018	27.035	-0.018	-0.018	0.000	0.000	0.000	0.000
29	u	105	PRO	0	-0.032	-0.008	22.483	0.012	0.012	0.000	0.000	0.000	0.000
30	u	106	PRO	0	0.035	0.009	23.357	-0.001	-0.001	0.000	0.000	0.000	0.000
31	u	107	GLU	-1	-0.862	-0.927	22.912	-0.162	-0.162	0.000	0.000	0.000	0.000
32	u	108	GLU	-1	-0.955	-0.968	20.636	-0.046	-0.046	0.000	0.000	0.000	0.000
33	u	109	GLU	-1	-0.880	-0.926	16.959	-0.281	-0.281	0.000	0.000	0.000	0.000
34	u	110	PHE	0	-0.015	-0.017	14.063	0.046	0.046	0.000	0.000	0.000	0.000
35	u	111	ILE	0	-0.006	-0.004	8.648	-0.097	-0.097	0.000	0.000	0.000	0.000
36	u	112	MET	0	-0.032	-0.004	8.914	0.084	0.084	0.000	0.000	0.000	0.000
37	u	113	GLY	0	0.025	0.002	4.994	-0.259	-0.259	0.000	0.000	0.000	0.000
38	u	114	VAL	0	-0.015	0.004	4.089	0.104	0.634	0.000	-0.232	-0.298	0.000
39	u	115	SER	0	0.021	-0.011	2.040	-9.286	-9.729	10.957	-5.765	-4.749	-0.058
40	u	116	LYS	1	1.011	0.996	3.388	-2.688	-2.808	0.046	0.314	-0.240	0.000
41	u	117	TYR	0	0.017	0.011	6.637	-0.429	-0.429	0.000	0.000	0.000	0.000
42	u	118	GLY	0	0.024	0.020	6.924	-0.244	-0.244	0.000	0.000	0.000	0.000
43	u	119	ILE	0	-0.026	-0.008	6.320	-0.108	-0.108	0.000	0.000	0.000	0.000
44	u	120	LYS	1	0.844	0.923	6.417	-0.854	-0.854	0.000	0.000	0.000	0.000
45	u	121	VAL	0	0.047	0.044	8.497	-0.097	-0.097	0.000	0.000	0.000	0.000
46	u	130	LEU	0	0.001	0.005	16.295	0.014	0.014	0.000	0.000	0.000	0.000
47	u	131	HIS	0	0.060	0.033	14.251	-0.033	-0.033	0.000	0.000	0.000	0.000
48	u	132	ARG	1	0.956	0.979	9.747	-0.802	-0.802	0.000	0.000	0.000	0.000
49	u	133	HIS	1	0.930	0.978	12.089	0.006	0.006	0.000	0.000	0.000	0.000
50	u	134	ALA	0	0.031	0.020	11.193	0.007	0.007	0.000	0.000	0.000	0.000
51	u	135	LEU	0	0.043	-0.012	8.753	-0.102	-0.102	0.000	0.000	0.000	0.000
52	u	136	TYR	0	-0.011	-0.004	11.752	-0.075	-0.075	0.000	0.000	0.000	0.000
53	u	137	LEU	0	-0.012	0.013	15.142	-0.035	-0.035	0.000	0.000	0.000	0.000
54	u	138	ILE	0	-0.051	-0.022	11.623	-0.054	-0.054	0.000	0.000	0.000	0.000
55	u	139	ILE	0	0.017	0.032	15.580	0.005	0.005	0.000	0.000	0.000	0.000
56	u	140	ARG	1	0.943	0.956	17.349	0.101	0.101	0.000	0.000	0.000	0.000
57	u	141	MET	0	-0.040	-0.006	11.325	0.019	0.019	0.000	0.000	0.000	0.000
58	u	142	VAL	0	-0.023	-0.019	16.380	-0.001	-0.001	0.000	0.000	0.000	0.000
59	u	143	CYS	0	-0.019	-0.012	16.464	-0.029	-0.029	0.000	0.000	0.000	0.000
60	u	144	TYR	0	-0.032	-0.007	18.574	-0.002	-0.002	0.000	0.000	0.000	0.000
61	u	145	ASP	-1	-0.841	-0.932	21.856	-0.296	-0.296	0.000	0.000	0.000	0.000
62	u	146	ASP	-1	-0.897	-0.972	24.267	-0.195	-0.195	0.000	0.000	0.000	0.000
63	u	147	GLY	0	0.005	0.026	25.722	0.017	0.017	0.000	0.000	0.000	0.000
64	u	148	LEU	0	-0.058	-0.028	28.630	0.019	0.019	0.000	0.000	0.000	0.000
65	u	149	GLY	0	-0.003	0.000	30.162	-0.005	-0.005	0.000	0.000	0.000	0.000
66	u	150	ALA	0	-0.047	-0.040	26.773	0.005	0.005	0.000	0.000	0.000	0.000
67	u	151	GLY	0	0.048	0.040	24.536	-0.015	-0.015	0.000	0.000	0.000	0.000
68	u	152	LYS	1	0.864	0.946	22.336	0.198	0.198	0.000	0.000	0.000	0.000
69	u	153	SER	0	0.057	0.019	19.386	0.002	0.002	0.000	0.000	0.000	0.000
70	u	154	LEU	0	0.005	0.021	19.986	-0.015	-0.015	0.000	0.000	0.000	0.000
71	u	155	LEU	0	-0.020	-0.038	13.225	-0.025	-0.025	0.000	0.000	0.000	0.000
72	u	156	ALA	0	0.012	0.016	17.732	0.035	0.035	0.000	0.000	0.000	0.000
73	u	157	LEU	0	-0.020	-0.031	12.668	-0.016	-0.016	0.000	0.000	0.000	0.000
74	u	158	LYS	1	0.961	1.003	17.096	0.047	0.047	0.000	0.000	0.000	0.000
75	u	159	THR	0	-0.010	-0.011	16.205	0.006	0.006	0.000	0.000	0.000	0.000
76	u	160	THR	0	-0.013	-0.005	18.976	-0.013	-0.013	0.000	0.000	0.000	0.000
77	u	161	ASP	-1	-0.799	-0.898	20.477	0.134	0.134	0.000	0.000	0.000	0.000
78	u	162	ALA	0	-0.033	-0.030	22.622	0.001	0.001	0.000	0.000	0.000	0.000
79	u	163	SER	0	-0.029	-0.019	23.691	0.006	0.006	0.000	0.000	0.000	0.000
80	u	164	ASN	0	-0.122	-0.042	23.913	-0.010	-0.010	0.000	0.000	0.000	0.000
81	u	165	GLU	-1	-0.893	-0.945	26.541	0.073	0.073	0.000	0.000	0.000	0.000
82	u	166	GLU	-1	-0.918	-0.947	27.126	0.022	0.022	0.000	0.000	0.000	0.000
83	u	167	TYR	0	-0.037	-0.038	23.393	0.003	0.003	0.000	0.000	0.000	0.000
84	u	168	SER	0	-0.046	-0.018	21.057	0.003	0.003	0.000	0.000	0.000	0.000
85	u	169	LEU	0	-0.013	-0.010	21.098	-0.011	-0.011	0.000	0.000	0.000	0.000
86	u	170	TRP	0	-0.036	-0.042	17.216	0.012	0.012	0.000	0.000	0.000	0.000
87	u	171	VAL	0	0.038	0.025	18.693	-0.034	-0.034	0.000	0.000	0.000	0.000
88	u	172	TYR	0	-0.028	-0.050	15.070	0.015	0.015	0.000	0.000	0.000	0.000
89	u	173	GLN	0	0.071	0.037	18.037	-0.008	-0.008	0.000	0.000	0.000	0.000
90	u	174	CYS	0	-0.046	-0.004	15.489	-0.053	-0.053	0.000	0.000	0.000	0.000
91	u	175	ASN	0	-0.010	-0.018	17.704	0.009	0.009	0.000	0.000	0.000	0.000
92	u	176	SER	0	0.057	0.016	18.255	-0.001	-0.001	0.000	0.000	0.000	0.000
93	u	177	LEU	0	0.063	0.038	18.349	-0.050	-0.050	0.000	0.000	0.000	0.000
94	u	178	GLU	-1	-0.924	-0.972	16.909	-0.544	-0.544	0.000	0.000	0.000	0.000
95	u	179	GLN	0	-0.009	-0.001	13.599	-0.071	-0.071	0.000	0.000	0.000	0.000
96	u	180	ALA	0	0.038	0.005	12.820	-0.146	-0.146	0.000	0.000	0.000	0.000
97	u	181	GLN	0	0.034	0.014	13.648	-0.059	-0.059	0.000	0.000	0.000	0.000
98	u	182	ALA	0	-0.018	-0.003	10.266	-0.061	-0.061	0.000	0.000	0.000	0.000
99	u	183	ILE	0	0.002	0.000	8.546	-0.349	-0.349	0.000	0.000	0.000	0.000
100	u	184	CYS	0	-0.020	-0.015	8.920	0.007	0.007	0.000	0.000	0.000	0.000
101	u	185	LYS	1	0.962	0.996	8.657	0.917	0.917	0.000	0.000	0.000	0.000
102	u	186	VAL	0	0.012	0.001	3.068	-0.354	-0.006	0.024	-0.093	-0.279	-0.001
103	u	187	LEU	0	0.012	-0.003	5.461	0.472	0.472	0.000	0.000	0.000	0.000
104	u	188	SER	0	-0.061	-0.027	8.071	0.329	0.329	0.000	0.000	0.000	0.000
105	u	189	THR	0	-0.078	-0.022	4.805	-0.039	-0.039	0.000	0.000	0.000	0.000
106	u	190	ALA	0	-0.052	-0.015	5.840	0.506	0.506	0.000	0.000	0.000	0.000

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