FMO DATABASE

FMODB ID: 3Q12L

Calculation Name: 4DX9-3-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: 3

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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-962818.011101
FMO2-HF: Nuclear repulsion	915468.764398
FMO2-HF: Total energy	-47349.246703
FMO2-MP2: Total energy	-47484.909785

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(3:60:CYS)

Summations of interaction energy for fragment #1(3:60: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.
-12.259	-5.627	2.025	-3.688	-4.967	-0.022

Interaction energy analysis for fragmet #1(3:60:CYS)

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 : -0.013

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	3	62	GLU	-1	-0.915	-0.956	3.819	-1.871	0.486	-0.035	-1.055	-1.266	0.005
4	3	63	PHE	0	-0.034	-0.027	6.069	-0.066	-0.066	0.000	0.000	0.000	0.000
5	3	64	ARG	1	0.957	1.000	9.971	0.453	0.453	0.000	0.000	0.000	0.000
6	3	65	ILE	0	0.003	-0.012	12.401	-0.021	-0.021	0.000	0.000	0.000	0.000
7	3	66	LYS	1	0.928	0.978	15.135	0.264	0.264	0.000	0.000	0.000	0.000
8	3	67	TYR	0	0.020	0.008	17.228	-0.011	-0.011	0.000	0.000	0.000	0.000
9	3	68	VAL	0	-0.001	0.006	19.496	0.018	0.018	0.000	0.000	0.000	0.000
10	3	69	GLY	0	0.022	0.005	21.482	0.021	0.021	0.000	0.000	0.000	0.000
11	3	70	ALA	0	-0.017	-0.015	21.537	-0.015	-0.015	0.000	0.000	0.000	0.000
12	3	71	ILE	0	-0.025	-0.008	23.402	0.013	0.013	0.000	0.000	0.000	0.000
13	3	72	GLU	-1	-0.904	-0.950	25.653	-0.042	-0.042	0.000	0.000	0.000	0.000
14	3	85	PRO	0	0.022	-0.016	21.126	0.004	0.004	0.000	0.000	0.000	0.000
15	3	86	LEU	0	0.049	0.005	22.697	-0.010	-0.010	0.000	0.000	0.000	0.000
16	3	87	ASP	-1	-0.884	-0.926	25.580	-0.076	-0.076	0.000	0.000	0.000	0.000
17	3	88	LEU	0	-0.068	-0.038	20.163	0.007	0.007	0.000	0.000	0.000	0.000
18	3	89	ILE	0	-0.042	-0.011	22.950	-0.012	-0.012	0.000	0.000	0.000	0.000
19	3	90	ASN	0	0.029	0.003	25.168	-0.001	-0.001	0.000	0.000	0.000	0.000
20	3	91	TYR	0	0.005	-0.001	27.584	0.005	0.005	0.000	0.000	0.000	0.000
21	3	92	ILE	0	-0.031	0.001	22.674	0.004	0.004	0.000	0.000	0.000	0.000
22	3	93	ASP	-1	-0.801	-0.899	26.766	-0.148	-0.148	0.000	0.000	0.000	0.000
23	3	94	VAL	0	-0.025	-0.012	28.957	0.004	0.004	0.000	0.000	0.000	0.000
24	3	95	ALA	0	0.039	0.027	29.288	0.005	0.005	0.000	0.000	0.000	0.000
25	3	96	GLN	0	-0.049	-0.038	25.777	0.005	0.005	0.000	0.000	0.000	0.000
26	3	97	GLN	0	-0.028	-0.016	30.892	0.003	0.003	0.000	0.000	0.000	0.000
27	3	98	ASP	-1	-0.945	-0.958	34.099	-0.063	-0.063	0.000	0.000	0.000	0.000
28	3	99	GLY	0	-0.061	-0.023	34.041	0.005	0.005	0.000	0.000	0.000	0.000
29	3	100	LYS	1	0.873	0.943	30.105	0.066	0.066	0.000	0.000	0.000	0.000
30	3	101	LEU	0	-0.022	-0.001	24.563	0.001	0.001	0.000	0.000	0.000	0.000
31	3	102	PRO	0	0.007	0.009	27.448	0.001	0.001	0.000	0.000	0.000	0.000
32	3	103	PHE	0	0.046	0.012	27.157	-0.010	-0.010	0.000	0.000	0.000	0.000
33	3	104	VAL	0	-0.067	-0.029	26.302	-0.017	-0.017	0.000	0.000	0.000	0.000
34	3	105	PRO	0	-0.014	0.005	22.124	0.012	0.012	0.000	0.000	0.000	0.000
35	3	106	PRO	0	0.042	0.007	23.411	0.000	0.000	0.000	0.000	0.000	0.000
36	3	107	GLU	-1	-1.001	-1.011	23.109	-0.161	-0.161	0.000	0.000	0.000	0.000
37	3	108	GLU	-1	-0.935	-0.958	21.324	-0.143	-0.143	0.000	0.000	0.000	0.000
38	3	109	GLU	-1	-0.936	-0.967	17.261	-0.317	-0.317	0.000	0.000	0.000	0.000
39	3	110	PHE	0	0.038	0.026	14.763	0.019	0.019	0.000	0.000	0.000	0.000
40	3	111	ILE	0	-0.026	-0.005	9.126	-0.070	-0.070	0.000	0.000	0.000	0.000
41	3	112	MET	0	-0.021	-0.006	9.550	0.024	0.024	0.000	0.000	0.000	0.000
42	3	113	GLY	0	-0.015	0.001	5.439	-0.181	-0.181	0.000	0.000	0.000	0.000
43	3	114	VAL	0	-0.014	-0.008	2.792	-0.282	0.392	0.186	-0.245	-0.615	0.000
44	3	115	SER	0	-0.066	-0.059	2.570	-5.351	-2.602	1.608	-2.117	-2.240	-0.026
45	3	116	LYS	1	1.005	0.979	3.491	-4.580	-4.276	0.003	-0.055	-0.252	0.000
46	3	117	TYR	0	-0.014	0.004	6.775	-0.173	-0.173	0.000	0.000	0.000	0.000
47	3	118	GLY	0	0.083	0.026	8.667	-0.045	-0.045	0.000	0.000	0.000	0.000
48	3	119	ILE	0	0.005	0.026	7.778	-0.108	-0.108	0.000	0.000	0.000	0.000
49	3	120	LYS	1	0.898	0.957	6.122	0.374	0.374	0.000	0.000	0.000	0.000
50	3	121	VAL	0	0.042	0.031	8.591	-0.147	-0.147	0.000	0.000	0.000	0.000
51	3	122	SER	0	-0.031	-0.020	11.027	0.077	0.077	0.000	0.000	0.000	0.000
52	3	123	THR	0	0.048	-0.010	12.768	-0.056	-0.056	0.000	0.000	0.000	0.000
53	3	124	SER	0	-0.007	-0.012	15.048	0.009	0.009	0.000	0.000	0.000	0.000
54	3	125	ASP	-1	-0.897	-0.949	16.401	-0.066	-0.066	0.000	0.000	0.000	0.000
55	3	126	GLN	0	-0.053	-0.020	11.189	0.068	0.068	0.000	0.000	0.000	0.000
56	3	127	TYR	0	-0.115	-0.074	13.653	0.045	0.045	0.000	0.000	0.000	0.000
57	3	128	ASP	-1	-0.832	-0.881	16.314	-0.021	-0.021	0.000	0.000	0.000	0.000
58	3	129	VAL	0	-0.091	-0.054	13.173	-0.020	-0.020	0.000	0.000	0.000	0.000
59	3	130	LEU	0	0.024	0.026	15.640	0.008	0.008	0.000	0.000	0.000	0.000
60	3	131	HIS	0	0.055	0.017	15.613	0.010	0.010	0.000	0.000	0.000	0.000
61	3	132	ARG	1	0.921	0.963	8.209	-0.124	-0.124	0.000	0.000	0.000	0.000
62	3	133	HIS	0	0.038	0.019	13.491	0.054	0.054	0.000	0.000	0.000	0.000
63	3	134	ALA	0	-0.037	-0.038	12.207	-0.026	-0.026	0.000	0.000	0.000	0.000
64	3	135	LEU	0	0.080	0.080	12.204	-0.015	-0.015	0.000	0.000	0.000	0.000
65	3	136	TYR	0	-0.167	-0.100	15.261	0.035	0.035	0.000	0.000	0.000	0.000
66	3	137	LEU	0	0.000	0.005	18.066	-0.031	-0.031	0.000	0.000	0.000	0.000
67	3	138	ILE	0	-0.007	0.001	17.414	0.008	0.008	0.000	0.000	0.000	0.000
68	3	139	ILE	0	0.020	0.018	13.110	-0.017	-0.017	0.000	0.000	0.000	0.000
69	3	140	ARG	1	0.927	0.963	15.432	0.093	0.093	0.000	0.000	0.000	0.000
70	3	141	MET	0	0.005	0.009	10.807	-0.025	-0.025	0.000	0.000	0.000	0.000
71	3	142	VAL	0	-0.061	-0.036	15.866	0.008	0.008	0.000	0.000	0.000	0.000
72	3	143	CYS	0	-0.049	-0.021	14.431	-0.009	-0.009	0.000	0.000	0.000	0.000
73	3	144	TYR	0	-0.042	-0.032	17.762	-0.005	-0.005	0.000	0.000	0.000	0.000
74	3	145	ASP	-1	-0.896	-0.967	20.920	-0.267	-0.267	0.000	0.000	0.000	0.000
75	3	146	ASP	-1	-0.862	-0.942	23.178	-0.210	-0.210	0.000	0.000	0.000	0.000
76	3	147	GLY	0	0.023	0.032	25.675	0.018	0.018	0.000	0.000	0.000	0.000
77	3	148	LEU	0	-0.029	-0.021	26.320	0.016	0.016	0.000	0.000	0.000	0.000
78	3	149	GLY	0	-0.023	-0.013	28.965	-0.001	-0.001	0.000	0.000	0.000	0.000
79	3	150	ALA	0	-0.074	-0.048	25.545	-0.003	-0.003	0.000	0.000	0.000	0.000
80	3	151	GLY	0	0.022	0.033	24.761	-0.013	-0.013	0.000	0.000	0.000	0.000
81	3	152	LYS	1	0.856	0.936	21.660	0.247	0.247	0.000	0.000	0.000	0.000
82	3	153	SER	0	0.045	0.029	17.737	0.000	0.000	0.000	0.000	0.000	0.000
83	3	154	LEU	0	0.003	0.001	19.647	-0.015	-0.015	0.000	0.000	0.000	0.000
84	3	155	LEU	0	-0.055	-0.039	13.004	-0.008	-0.008	0.000	0.000	0.000	0.000
85	3	156	ALA	0	0.050	0.039	16.952	0.025	0.025	0.000	0.000	0.000	0.000
86	3	157	LEU	0	-0.048	-0.040	12.467	-0.018	-0.018	0.000	0.000	0.000	0.000
87	3	158	LYS	1	0.910	0.988	17.160	0.057	0.057	0.000	0.000	0.000	0.000
88	3	159	THR	0	0.030	0.005	17.048	0.001	0.001	0.000	0.000	0.000	0.000
89	3	160	THR	0	-0.025	-0.030	19.645	-0.001	-0.001	0.000	0.000	0.000	0.000
90	3	161	ASP	-1	-0.830	-0.910	21.422	0.028	0.028	0.000	0.000	0.000	0.000
91	3	162	ALA	0	0.002	-0.003	24.089	0.014	0.014	0.000	0.000	0.000	0.000
92	3	163	SER	0	-0.004	-0.001	25.221	-0.006	-0.006	0.000	0.000	0.000	0.000
93	3	164	ASN	0	-0.075	-0.036	27.309	0.004	0.004	0.000	0.000	0.000	0.000
94	3	165	GLU	-1	-0.922	-0.956	27.848	-0.018	-0.018	0.000	0.000	0.000	0.000
95	3	166	GLU	-1	-0.888	-0.970	22.470	0.013	0.013	0.000	0.000	0.000	0.000
96	3	167	TYR	0	-0.069	-0.022	23.914	-0.013	-0.013	0.000	0.000	0.000	0.000
97	3	168	SER	0	0.033	0.022	21.840	-0.005	-0.005	0.000	0.000	0.000	0.000
98	3	169	LEU	0	-0.025	-0.015	21.854	-0.008	-0.008	0.000	0.000	0.000	0.000
99	3	170	TRP	0	-0.062	-0.032	17.924	-0.013	-0.013	0.000	0.000	0.000	0.000
100	3	171	VAL	0	0.047	0.016	19.672	-0.015	-0.015	0.000	0.000	0.000	0.000
101	3	172	TYR	0	-0.009	-0.021	15.960	-0.007	-0.007	0.000	0.000	0.000	0.000
102	3	173	GLN	0	0.047	0.029	18.015	-0.006	-0.006	0.000	0.000	0.000	0.000
103	3	174	CYS	0	-0.014	-0.005	14.880	-0.069	-0.069	0.000	0.000	0.000	0.000
104	3	175	ASN	0	-0.006	-0.019	17.504	0.074	0.074	0.000	0.000	0.000	0.000
105	3	176	SER	0	0.080	0.032	18.032	0.028	0.028	0.000	0.000	0.000	0.000
106	3	177	LEU	0	0.083	0.041	17.231	-0.065	-0.065	0.000	0.000	0.000	0.000
107	3	178	GLU	-1	-0.894	-0.945	16.229	-0.481	-0.481	0.000	0.000	0.000	0.000
108	3	179	GLN	0	-0.051	-0.029	12.376	-0.021	-0.021	0.000	0.000	0.000	0.000
109	3	180	ALA	0	0.025	0.010	12.072	-0.152	-0.152	0.000	0.000	0.000	0.000
110	3	181	GLN	0	-0.005	-0.012	12.876	-0.048	-0.048	0.000	0.000	0.000	0.000
111	3	182	ALA	0	-0.036	-0.018	9.522	-0.029	-0.029	0.000	0.000	0.000	0.000
112	3	183	ILE	0	-0.003	0.003	8.084	-0.325	-0.325	0.000	0.000	0.000	0.000
113	3	184	CYS	0	0.040	0.011	8.237	-0.005	-0.005	0.000	0.000	0.000	0.000
114	3	185	LYS	1	0.897	0.959	8.583	0.739	0.739	0.000	0.000	0.000	0.000
115	3	186	VAL	0	-0.003	-0.002	2.723	-0.690	-0.142	0.263	-0.216	-0.594	-0.001
116	3	187	LEU	0	0.021	0.001	5.272	0.700	0.700	0.000	0.000	0.000	0.000
117	3	188	SER	0	-0.015	-0.001	7.106	0.316	0.316	0.000	0.000	0.000	0.000
118	3	189	THR	0	-0.047	-0.010	6.112	0.020	0.020	0.000	0.000	0.000	0.000
119	3	190	ALA	0	-0.073	-0.015	5.118	0.566	0.566	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(3:60:CYS)