FMO DATABASE

FMODB ID: 432RN

Calculation Name: 4DX9-k-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: k

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	OptH
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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1013273.882221
FMO2-HF: Nuclear repulsion	964488.214748
FMO2-HF: Total energy	-48785.667473
FMO2-MP2: Total energy	-48925.529463

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(k:60:CYS)

Summations of interaction energy for fragment #1(k: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.
-30.063	-27.87	12.383	-6.93	-7.645	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.053 / q_NPA : -0.024

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

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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	k	62	GLU	-1	-0.923	-0.957	3.816	-0.101	2.086	-0.027	-0.998	-1.162	0.001
4	k	63	PHE	0	-0.018	-0.008	6.947	-0.317	-0.317	0.000	0.000	0.000	0.000
5	k	64	ARG	1	0.972	0.993	10.211	0.576	0.576	0.000	0.000	0.000	0.000
6	k	65	ILE	0	-0.014	-0.006	13.297	-0.024	-0.024	0.000	0.000	0.000	0.000
7	k	66	LYS	1	1.043	1.032	15.882	0.173	0.173	0.000	0.000	0.000	0.000
8	k	67	TYR	0	0.003	-0.007	18.303	0.019	0.019	0.000	0.000	0.000	0.000
9	k	68	VAL	0	-0.009	0.001	20.020	-0.011	-0.011	0.000	0.000	0.000	0.000
10	k	69	GLY	0	0.043	0.008	22.083	-0.003	-0.003	0.000	0.000	0.000	0.000
11	k	70	ALA	0	-0.026	-0.018	21.955	0.016	0.016	0.000	0.000	0.000	0.000
12	k	71	ILE	0	-0.039	-0.004	23.662	-0.017	-0.017	0.000	0.000	0.000	0.000
13	k	72	GLU	-1	-0.818	-0.878	25.208	0.242	0.242	0.000	0.000	0.000	0.000
14	k	84	GLY	0	0.029	0.000	25.909	0.008	0.008	0.000	0.000	0.000	0.000
15	k	85	PRO	0	-0.048	-0.032	22.615	0.007	0.007	0.000	0.000	0.000	0.000
16	k	86	LEU	0	0.071	0.018	24.020	-0.007	-0.007	0.000	0.000	0.000	0.000
17	k	87	ASP	-1	-0.901	-0.943	27.168	0.097	0.097	0.000	0.000	0.000	0.000
18	k	88	LEU	0	-0.040	-0.033	21.484	0.005	0.005	0.000	0.000	0.000	0.000
19	k	89	ILE	0	0.005	0.013	23.928	-0.001	-0.001	0.000	0.000	0.000	0.000
20	k	90	ASN	0	0.047	0.013	26.169	-0.012	-0.012	0.000	0.000	0.000	0.000
21	k	91	TYR	0	-0.049	-0.017	26.909	-0.006	-0.006	0.000	0.000	0.000	0.000
22	k	92	ILE	0	-0.033	-0.015	23.130	0.004	0.004	0.000	0.000	0.000	0.000
23	k	93	ASP	-1	-0.850	-0.929	27.332	0.004	0.004	0.000	0.000	0.000	0.000
24	k	94	VAL	0	-0.060	-0.023	30.332	-0.004	-0.004	0.000	0.000	0.000	0.000
25	k	95	ALA	0	0.002	-0.006	29.293	-0.002	-0.002	0.000	0.000	0.000	0.000
26	k	96	GLN	0	-0.015	-0.022	27.268	0.000	0.000	0.000	0.000	0.000	0.000
27	k	97	GLN	0	-0.060	-0.015	31.300	-0.006	-0.006	0.000	0.000	0.000	0.000
28	k	98	ASP	-1	-0.941	-0.950	34.960	0.042	0.042	0.000	0.000	0.000	0.000
29	k	99	GLY	0	-0.033	-0.018	34.263	-0.003	-0.003	0.000	0.000	0.000	0.000
30	k	100	LYS	1	0.865	0.946	30.378	-0.077	-0.077	0.000	0.000	0.000	0.000
31	k	101	LEU	0	-0.011	-0.006	25.099	0.003	0.003	0.000	0.000	0.000	0.000
32	k	102	PRO	0	0.012	0.017	27.264	-0.005	-0.005	0.000	0.000	0.000	0.000
33	k	103	PHE	0	0.035	0.007	27.875	-0.002	-0.002	0.000	0.000	0.000	0.000
34	k	104	VAL	0	-0.042	-0.021	27.818	-0.011	-0.011	0.000	0.000	0.000	0.000
35	k	105	PRO	0	-0.033	-0.005	23.624	0.009	0.009	0.000	0.000	0.000	0.000
36	k	106	PRO	0	0.025	-0.002	24.736	-0.013	-0.013	0.000	0.000	0.000	0.000
37	k	107	GLU	-1	-0.959	-0.979	24.455	-0.136	-0.136	0.000	0.000	0.000	0.000
38	k	108	GLU	-1	-0.967	-0.974	22.014	-0.013	-0.013	0.000	0.000	0.000	0.000
39	k	109	GLU	-1	-0.983	-0.989	18.061	-0.222	-0.222	0.000	0.000	0.000	0.000
40	k	110	PHE	0	-0.065	-0.052	15.301	0.029	0.029	0.000	0.000	0.000	0.000
41	k	111	ILE	0	-0.014	-0.005	9.598	-0.071	-0.071	0.000	0.000	0.000	0.000
42	k	112	MET	0	-0.026	-0.014	9.115	0.145	0.145	0.000	0.000	0.000	0.000
43	k	113	GLY	0	0.020	0.004	6.259	-0.395	-0.395	0.000	0.000	0.000	0.000
44	k	114	VAL	0	0.001	0.012	4.454	0.553	0.853	-0.001	-0.087	-0.211	0.000
45	k	115	SER	0	0.037	-0.003	2.337	-4.825	-2.635	5.001	-3.920	-3.271	-0.032
46	k	116	LYS	1	0.927	0.936	2.121	-25.391	-28.094	7.406	-1.866	-2.838	0.029
47	k	117	TYR	0	-0.002	0.000	5.231	-1.041	-1.041	0.000	0.000	0.000	0.000
48	k	118	GLY	0	0.036	0.016	7.076	-0.615	-0.615	0.000	0.000	0.000	0.000
49	k	119	ILE	0	-0.030	0.001	7.247	0.525	0.525	0.000	0.000	0.000	0.000
50	k	120	LYS	1	0.918	0.967	8.221	-0.699	-0.699	0.000	0.000	0.000	0.000
51	k	121	VAL	0	0.001	0.006	9.865	-0.116	-0.116	0.000	0.000	0.000	0.000
52	k	122	SER	0	0.007	0.000	11.989	0.064	0.064	0.000	0.000	0.000	0.000
53	k	123	THR	0	0.035	0.033	13.972	-0.046	-0.046	0.000	0.000	0.000	0.000
54	k	124	SER	0	-0.020	-0.044	14.668	-0.021	-0.021	0.000	0.000	0.000	0.000
55	k	125	ASP	-1	-0.918	-0.939	16.154	-0.205	-0.205	0.000	0.000	0.000	0.000
56	k	126	GLN	0	-0.008	-0.004	17.187	0.012	0.012	0.000	0.000	0.000	0.000
57	k	127	TYR	0	-0.050	-0.023	14.154	0.002	0.002	0.000	0.000	0.000	0.000
58	k	128	ASP	-1	-0.769	-0.891	16.128	0.189	0.189	0.000	0.000	0.000	0.000
59	k	129	VAL	0	-0.137	-0.097	12.899	0.066	0.066	0.000	0.000	0.000	0.000
60	k	130	LEU	0	0.047	0.051	15.077	0.024	0.024	0.000	0.000	0.000	0.000
61	k	131	HIS	1	0.883	0.950	15.056	-0.258	-0.258	0.000	0.000	0.000	0.000
62	k	132	ARG	1	0.967	0.979	11.570	-0.641	-0.641	0.000	0.000	0.000	0.000
63	k	133	HIS	0	0.010	0.020	12.321	-0.049	-0.049	0.000	0.000	0.000	0.000
64	k	134	ALA	0	0.048	0.023	11.503	0.237	0.237	0.000	0.000	0.000	0.000
65	k	135	LEU	0	0.039	0.005	8.025	-0.158	-0.158	0.000	0.000	0.000	0.000
66	k	136	TYR	0	0.006	0.001	12.175	-0.077	-0.077	0.000	0.000	0.000	0.000
67	k	137	LEU	0	-0.021	0.000	15.290	-0.080	-0.080	0.000	0.000	0.000	0.000
68	k	138	ILE	0	-0.023	0.001	11.414	-0.088	-0.088	0.000	0.000	0.000	0.000
69	k	139	ILE	0	-0.022	-0.001	15.508	0.001	0.001	0.000	0.000	0.000	0.000
70	k	140	ARG	1	0.925	0.952	17.271	-0.219	-0.219	0.000	0.000	0.000	0.000
71	k	141	MET	0	0.014	0.024	11.249	-0.017	-0.017	0.000	0.000	0.000	0.000
72	k	142	VAL	0	-0.035	-0.022	16.166	-0.016	-0.016	0.000	0.000	0.000	0.000
73	k	143	CYS	0	-0.031	-0.005	16.760	-0.020	-0.020	0.000	0.000	0.000	0.000
74	k	144	TYR	0	0.015	0.002	18.896	0.006	0.006	0.000	0.000	0.000	0.000
75	k	145	ASP	-1	-0.870	-0.952	22.179	-0.125	-0.125	0.000	0.000	0.000	0.000
76	k	146	ASP	-1	-0.840	-0.935	24.465	-0.074	-0.074	0.000	0.000	0.000	0.000
77	k	147	GLY	0	0.040	0.029	26.572	0.013	0.013	0.000	0.000	0.000	0.000
78	k	148	LEU	0	-0.099	-0.044	28.329	0.006	0.006	0.000	0.000	0.000	0.000
79	k	149	GLY	0	-0.017	-0.020	31.009	-0.003	-0.003	0.000	0.000	0.000	0.000
80	k	150	ALA	0	-0.025	-0.012	29.436	0.004	0.004	0.000	0.000	0.000	0.000
81	k	151	GLY	0	0.012	-0.004	27.045	-0.007	-0.007	0.000	0.000	0.000	0.000
82	k	152	LYS	1	0.813	0.953	22.718	0.126	0.126	0.000	0.000	0.000	0.000
83	k	153	SER	0	0.021	-0.009	19.594	0.011	0.011	0.000	0.000	0.000	0.000
84	k	154	LEU	0	0.017	0.019	20.101	-0.010	-0.010	0.000	0.000	0.000	0.000
85	k	155	LEU	0	-0.021	-0.037	13.668	-0.017	-0.017	0.000	0.000	0.000	0.000
86	k	156	ALA	0	0.012	0.029	17.528	0.026	0.026	0.000	0.000	0.000	0.000
87	k	157	LEU	0	-0.019	-0.024	12.618	0.011	0.011	0.000	0.000	0.000	0.000
88	k	158	LYS	1	0.954	0.986	17.053	-0.253	-0.253	0.000	0.000	0.000	0.000
89	k	159	THR	0	-0.026	-0.026	16.065	0.068	0.068	0.000	0.000	0.000	0.000
90	k	160	THR	0	-0.005	-0.005	18.717	-0.054	-0.054	0.000	0.000	0.000	0.000
91	k	161	ASP	-1	-0.760	-0.865	20.333	0.362	0.362	0.000	0.000	0.000	0.000
92	k	162	ALA	0	-0.084	-0.039	22.928	0.000	0.000	0.000	0.000	0.000	0.000
93	k	163	SER	0	-0.122	-0.072	25.061	-0.011	-0.011	0.000	0.000	0.000	0.000
94	k	164	ASN	0	-0.063	-0.055	27.000	-0.031	-0.031	0.000	0.000	0.000	0.000
95	k	165	GLU	-1	-0.949	-0.976	27.471	0.255	0.255	0.000	0.000	0.000	0.000
96	k	166	GLU	-1	-0.857	-0.919	26.726	0.187	0.187	0.000	0.000	0.000	0.000
97	k	167	TYR	0	-0.132	-0.072	23.522	0.045	0.045	0.000	0.000	0.000	0.000
98	k	168	SER	0	0.042	0.024	21.887	-0.022	-0.022	0.000	0.000	0.000	0.000
99	k	169	LEU	0	-0.066	-0.035	20.484	0.032	0.032	0.000	0.000	0.000	0.000
100	k	170	TRP	0	-0.026	-0.028	17.563	-0.036	-0.036	0.000	0.000	0.000	0.000
101	k	171	VAL	0	0.018	0.007	18.645	0.000	0.000	0.000	0.000	0.000	0.000
102	k	172	TYR	0	0.013	0.006	15.470	0.003	0.003	0.000	0.000	0.000	0.000
103	k	173	GLN	0	0.059	0.007	18.343	-0.012	-0.012	0.000	0.000	0.000	0.000
104	k	174	CYS	0	-0.040	-0.009	15.291	-0.029	-0.029	0.000	0.000	0.000	0.000
105	k	175	ASN	0	0.023	-0.004	18.201	0.021	0.021	0.000	0.000	0.000	0.000
106	k	176	SER	0	0.034	0.011	18.795	0.001	0.001	0.000	0.000	0.000	0.000
107	k	177	LEU	0	0.072	0.065	18.891	-0.009	-0.009	0.000	0.000	0.000	0.000
108	k	178	GLU	-1	-0.889	-0.960	17.129	-0.338	-0.338	0.000	0.000	0.000	0.000
109	k	179	GLN	0	-0.020	-0.015	13.595	0.003	0.003	0.000	0.000	0.000	0.000
110	k	180	ALA	0	0.058	0.025	13.195	-0.074	-0.074	0.000	0.000	0.000	0.000
111	k	181	GLN	0	0.011	-0.001	13.985	0.082	0.082	0.000	0.000	0.000	0.000
112	k	182	ALA	0	-0.042	-0.018	10.500	0.013	0.013	0.000	0.000	0.000	0.000
113	k	183	ILE	0	0.013	0.005	8.948	-0.176	-0.176	0.000	0.000	0.000	0.000
114	k	184	CYS	0	-0.004	-0.006	9.111	0.159	0.159	0.000	0.000	0.000	0.000
115	k	185	LYS	1	0.934	0.970	9.494	0.428	0.428	0.000	0.000	0.000	0.000
116	k	186	VAL	0	-0.027	-0.009	3.533	-0.224	-0.005	0.004	-0.059	-0.163	0.000
117	k	187	LEU	0	0.033	0.002	5.928	0.848	0.848	0.000	0.000	0.000	0.000
118	k	188	SER	0	-0.039	-0.001	8.393	0.178	0.178	0.000	0.000	0.000	0.000
119	k	189	THR	0	-0.017	-0.007	6.462	0.058	0.058	0.000	0.000	0.000	0.000
120	k	190	ALA	0	-0.064	-0.026	5.643	0.517	0.517	0.000	0.000	0.000	0.000
121	k	191	PHE	0	-0.008	-0.012	7.466	0.000	0.000	0.000	0.000	0.000	0.000
122	k	192	ASP	-1	-0.931	-0.945	11.156	0.754	0.754	0.000	0.000	0.000	0.000
123	k	193	SER	0	-0.094	-0.038	8.901	0.214	0.214	0.000	0.000	0.000	0.000

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