FMO DATABASE

FMODB ID: NN56Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-800644.545625
FMO2-HF: Nuclear repulsion	758365.842481
FMO2-HF: Total energy	-42278.703144
FMO2-MP2: Total energy	-42399.321105

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.
-6.612	-2.022	4.517	-4.184	-4.922	-0.03

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 : -0.080 / q_NPA : -0.057

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	-0.931	-0.969	3.816	1.024	2.801	-0.028	-0.755	-0.993	0.000
4	u	63	PHE	0	-0.003	-0.004	6.734	-0.320	-0.320	0.000	0.000	0.000	0.000
5	u	64	ARG	1	0.892	0.956	10.177	0.193	0.193	0.000	0.000	0.000	0.000
6	u	65	ILE	0	-0.006	-0.005	12.863	-0.020	-0.020	0.000	0.000	0.000	0.000
7	u	66	LYS	1	0.961	0.991	15.386	-0.084	-0.084	0.000	0.000	0.000	0.000
8	u	67	TYR	0	0.005	-0.001	18.518	0.029	0.029	0.000	0.000	0.000	0.000
9	u	68	VAL	0	-0.001	0.005	19.640	-0.027	-0.027	0.000	0.000	0.000	0.000
10	u	69	GLY	0	0.042	0.013	21.950	-0.022	-0.022	0.000	0.000	0.000	0.000
11	u	70	ALA	0	-0.040	-0.029	21.768	0.031	0.031	0.000	0.000	0.000	0.000
12	u	71	ILE	0	0.025	0.039	23.616	-0.011	-0.011	0.000	0.000	0.000	0.000
13	u	89	ILE	0	0.006	-0.026	24.239	0.003	0.003	0.000	0.000	0.000	0.000
14	u	90	ASN	0	0.023	0.015	25.948	-0.013	-0.013	0.000	0.000	0.000	0.000
15	u	91	TYR	0	0.031	-0.007	28.225	-0.007	-0.007	0.000	0.000	0.000	0.000
16	u	92	ILE	0	-0.062	-0.019	23.019	0.008	0.008	0.000	0.000	0.000	0.000
17	u	93	ASP	-1	-0.834	-0.909	26.892	0.143	0.143	0.000	0.000	0.000	0.000
18	u	94	VAL	0	-0.051	-0.021	29.984	-0.008	-0.008	0.000	0.000	0.000	0.000
19	u	95	ALA	0	0.036	0.012	28.980	-0.006	-0.006	0.000	0.000	0.000	0.000
20	u	96	GLN	0	-0.029	-0.015	26.682	-0.007	-0.007	0.000	0.000	0.000	0.000
21	u	97	GLN	0	-0.038	-0.015	31.204	-0.013	-0.013	0.000	0.000	0.000	0.000
22	u	98	ASP	-1	-0.946	-0.959	34.097	0.118	0.118	0.000	0.000	0.000	0.000
23	u	99	GLY	0	-0.018	-0.002	33.811	-0.006	-0.006	0.000	0.000	0.000	0.000
24	u	100	LYS	1	0.879	0.940	30.770	-0.145	-0.145	0.000	0.000	0.000	0.000
25	u	101	LEU	0	-0.028	-0.011	24.771	0.011	0.011	0.000	0.000	0.000	0.000
26	u	102	PRO	0	0.031	0.017	26.848	-0.011	-0.011	0.000	0.000	0.000	0.000
27	u	103	PHE	0	0.027	0.008	27.485	0.010	0.010	0.000	0.000	0.000	0.000
28	u	104	VAL	0	-0.032	-0.018	27.233	0.002	0.002	0.000	0.000	0.000	0.000
29	u	105	PRO	0	-0.044	-0.013	22.923	0.004	0.004	0.000	0.000	0.000	0.000
30	u	106	PRO	0	0.033	0.009	24.023	-0.017	-0.017	0.000	0.000	0.000	0.000
31	u	107	GLU	-1	-0.887	-0.958	23.556	0.082	0.082	0.000	0.000	0.000	0.000
32	u	108	GLU	-1	-0.986	-0.974	21.489	0.168	0.168	0.000	0.000	0.000	0.000
33	u	109	GLU	-1	-0.935	-0.971	17.701	0.044	0.044	0.000	0.000	0.000	0.000
34	u	110	PHE	0	-0.004	-0.015	14.976	0.021	0.021	0.000	0.000	0.000	0.000
35	u	111	ILE	0	0.007	0.001	9.273	-0.041	-0.041	0.000	0.000	0.000	0.000
36	u	112	MET	0	-0.044	-0.014	9.200	0.161	0.161	0.000	0.000	0.000	0.000
37	u	113	GLY	0	0.038	0.010	5.945	-0.199	-0.199	0.000	0.000	0.000	0.000
38	u	114	VAL	0	-0.019	0.002	4.169	0.019	0.348	-0.001	-0.104	-0.223	0.000
39	u	115	SER	0	0.016	-0.016	2.289	-3.202	-0.977	4.523	-3.399	-3.350	-0.030
40	u	116	LYS	1	0.991	0.984	3.754	-1.634	-1.620	0.018	0.149	-0.181	0.000
41	u	117	TYR	0	0.024	0.014	6.659	-0.492	-0.492	0.000	0.000	0.000	0.000
42	u	118	GLY	0	0.025	0.019	7.505	-0.459	-0.459	0.000	0.000	0.000	0.000
43	u	119	ILE	0	-0.015	-0.001	6.960	0.610	0.610	0.000	0.000	0.000	0.000
44	u	120	LYS	1	0.906	0.957	7.778	-1.387	-1.387	0.000	0.000	0.000	0.000
45	u	121	VAL	0	0.044	0.045	9.588	0.005	0.005	0.000	0.000	0.000	0.000
46	u	130	LEU	0	0.003	0.009	17.282	0.011	0.011	0.000	0.000	0.000	0.000
47	u	131	HIS	0	0.075	0.043	15.242	0.015	0.015	0.000	0.000	0.000	0.000
48	u	132	ARG	1	0.951	0.972	10.109	-0.977	-0.977	0.000	0.000	0.000	0.000
49	u	133	HIS	1	0.922	0.983	12.638	-0.894	-0.894	0.000	0.000	0.000	0.000
50	u	134	ALA	0	0.041	0.020	11.914	0.193	0.193	0.000	0.000	0.000	0.000
51	u	135	LEU	0	0.037	-0.017	8.305	-0.064	-0.064	0.000	0.000	0.000	0.000
52	u	136	TYR	0	-0.018	-0.007	11.819	-0.088	-0.088	0.000	0.000	0.000	0.000
53	u	137	LEU	0	-0.013	0.014	15.393	-0.045	-0.045	0.000	0.000	0.000	0.000
54	u	138	ILE	0	-0.049	-0.017	11.668	-0.046	-0.046	0.000	0.000	0.000	0.000
55	u	139	ILE	0	0.012	0.029	15.607	-0.010	-0.010	0.000	0.000	0.000	0.000
56	u	140	ARG	1	0.945	0.958	17.535	-0.311	-0.311	0.000	0.000	0.000	0.000
57	u	141	MET	0	-0.041	-0.007	11.374	0.040	0.040	0.000	0.000	0.000	0.000
58	u	142	VAL	0	-0.026	-0.017	16.391	-0.030	-0.030	0.000	0.000	0.000	0.000
59	u	143	CYS	0	-0.029	-0.005	16.725	0.008	0.008	0.000	0.000	0.000	0.000
60	u	144	TYR	0	0.016	0.006	18.843	-0.003	-0.003	0.000	0.000	0.000	0.000
61	u	145	ASP	-1	-0.853	-0.943	22.196	0.085	0.085	0.000	0.000	0.000	0.000
62	u	146	ASP	-1	-0.864	-0.952	24.536	0.096	0.096	0.000	0.000	0.000	0.000
63	u	147	GLY	0	0.006	0.020	25.762	0.003	0.003	0.000	0.000	0.000	0.000
64	u	148	LEU	0	-0.069	-0.030	28.323	-0.007	-0.007	0.000	0.000	0.000	0.000
65	u	149	GLY	0	0.009	0.004	30.322	-0.003	-0.003	0.000	0.000	0.000	0.000
66	u	150	ALA	0	-0.058	-0.047	26.741	-0.007	-0.007	0.000	0.000	0.000	0.000
67	u	151	GLY	0	0.056	0.045	24.868	-0.011	-0.011	0.000	0.000	0.000	0.000
68	u	152	LYS	1	0.876	0.958	22.357	-0.051	-0.051	0.000	0.000	0.000	0.000
69	u	153	SER	0	0.052	0.025	19.242	0.001	0.001	0.000	0.000	0.000	0.000
70	u	154	LEU	0	0.012	0.019	20.020	0.014	0.014	0.000	0.000	0.000	0.000
71	u	155	LEU	0	-0.020	-0.035	13.101	0.012	0.012	0.000	0.000	0.000	0.000
72	u	156	ALA	0	0.019	0.020	17.769	0.010	0.010	0.000	0.000	0.000	0.000
73	u	157	LEU	0	-0.022	-0.033	12.768	0.046	0.046	0.000	0.000	0.000	0.000
74	u	158	LYS	1	0.970	1.003	17.126	-0.349	-0.349	0.000	0.000	0.000	0.000
75	u	159	THR	0	-0.014	-0.003	16.491	0.059	0.059	0.000	0.000	0.000	0.000
76	u	160	THR	0	-0.003	0.005	19.182	-0.042	-0.042	0.000	0.000	0.000	0.000
77	u	161	ASP	-1	-0.831	-0.928	20.913	0.333	0.333	0.000	0.000	0.000	0.000
78	u	162	ALA	0	-0.026	-0.031	23.324	0.001	0.001	0.000	0.000	0.000	0.000
79	u	163	SER	0	-0.046	-0.022	24.250	-0.006	-0.006	0.000	0.000	0.000	0.000
80	u	164	ASN	0	-0.070	-0.003	24.232	0.013	0.013	0.000	0.000	0.000	0.000
81	u	165	GLU	-1	-0.883	-0.944	26.801	0.196	0.196	0.000	0.000	0.000	0.000
82	u	166	GLU	-1	-0.952	-0.959	27.692	0.204	0.204	0.000	0.000	0.000	0.000
83	u	167	TYR	0	-0.030	-0.033	23.594	0.035	0.035	0.000	0.000	0.000	0.000
84	u	168	SER	0	-0.054	-0.024	21.577	-0.014	-0.014	0.000	0.000	0.000	0.000
85	u	169	LEU	0	-0.015	-0.014	21.255	0.030	0.030	0.000	0.000	0.000	0.000
86	u	170	TRP	0	-0.033	-0.046	17.516	-0.015	-0.015	0.000	0.000	0.000	0.000
87	u	171	VAL	0	0.029	0.024	18.818	0.021	0.021	0.000	0.000	0.000	0.000
88	u	172	TYR	0	-0.029	-0.058	15.682	0.033	0.033	0.000	0.000	0.000	0.000
89	u	173	GLN	0	0.057	0.019	18.221	-0.023	-0.023	0.000	0.000	0.000	0.000
90	u	174	CYS	0	-0.033	0.001	15.489	0.020	0.020	0.000	0.000	0.000	0.000
91	u	175	ASN	0	-0.035	-0.034	17.732	-0.020	-0.020	0.000	0.000	0.000	0.000
92	u	176	SER	0	0.056	0.019	18.293	-0.022	-0.022	0.000	0.000	0.000	0.000
93	u	177	LEU	0	0.094	0.051	18.571	0.022	0.022	0.000	0.000	0.000	0.000
94	u	178	GLU	-1	-0.939	-0.978	17.776	-0.008	-0.008	0.000	0.000	0.000	0.000
95	u	179	GLN	0	-0.035	-0.011	13.419	0.037	0.037	0.000	0.000	0.000	0.000
96	u	180	ALA	0	0.040	0.005	13.178	0.054	0.054	0.000	0.000	0.000	0.000
97	u	181	GLN	0	0.028	0.007	14.103	0.066	0.066	0.000	0.000	0.000	0.000
98	u	182	ALA	0	-0.019	-0.003	10.920	0.051	0.051	0.000	0.000	0.000	0.000
99	u	183	ILE	0	0.007	-0.001	8.640	0.146	0.146	0.000	0.000	0.000	0.000
100	u	184	CYS	0	-0.027	-0.017	9.438	0.266	0.266	0.000	0.000	0.000	0.000
101	u	185	LYS	1	0.966	0.997	9.718	-0.074	-0.074	0.000	0.000	0.000	0.000
102	u	186	VAL	0	0.011	0.002	4.096	-0.140	0.105	0.005	-0.075	-0.175	0.000
103	u	187	LEU	0	0.000	-0.018	6.328	0.756	0.756	0.000	0.000	0.000	0.000
104	u	188	SER	0	-0.059	-0.023	8.739	-0.112	-0.112	0.000	0.000	0.000	0.000
105	u	189	THR	0	-0.074	-0.016	5.165	-0.274	-0.274	0.000	0.000	0.000	0.000
106	u	190	ALA	0	-0.033	-0.004	6.045	-0.398	-0.398	0.000	0.000	0.000	0.000

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