FMO DATABASE

FMODB ID: MNGZZ

Calculation Name: 4DX9-o-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: o

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	OptAll
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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-468160.706148
FMO2-HF: Nuclear repulsion	435887.010152
FMO2-HF: Total energy	-32273.695997
FMO2-MP2: Total energy	-32363.658398

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(o:60:CYS)

Summations of interaction energy for fragment #1(o: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.
-7.89	-2.6	5.481	-4.298	-6.47	-0.034

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.062 / q_NPA : -0.037

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	o	62	GLU	-1	-0.814	-0.884	3.855	1.057	2.955	-0.024	-0.846	-1.028	0.001
4	o	63	PHE	0	-0.047	-0.054	5.771	-0.195	-0.195	0.000	0.000	0.000	0.000
5	o	84	GLY	0	0.056	0.033	23.651	0.002	0.002	0.000	0.000	0.000	0.000
6	o	85	PRO	0	0.028	0.016	20.446	0.010	0.010	0.000	0.000	0.000	0.000
7	o	86	LEU	0	0.042	0.007	22.144	0.007	0.007	0.000	0.000	0.000	0.000
8	o	87	ASP	-1	-0.810	-0.896	24.649	0.161	0.161	0.000	0.000	0.000	0.000
9	o	88	LEU	0	-0.015	0.006	18.708	-0.002	-0.002	0.000	0.000	0.000	0.000
10	o	89	ILE	0	-0.012	-0.001	22.732	0.005	0.005	0.000	0.000	0.000	0.000
11	o	90	ASN	0	-0.048	-0.026	24.615	-0.006	-0.006	0.000	0.000	0.000	0.000
12	o	91	TYR	0	-0.012	-0.006	25.922	-0.009	-0.009	0.000	0.000	0.000	0.000
13	o	92	ILE	0	-0.053	-0.021	21.920	0.004	0.004	0.000	0.000	0.000	0.000
14	o	93	ASP	-1	-0.923	-0.953	25.875	0.100	0.100	0.000	0.000	0.000	0.000
15	o	101	LEU	0	-0.014	-0.023	23.485	0.000	0.000	0.000	0.000	0.000	0.000
16	o	102	PRO	0	0.004	0.014	25.339	-0.009	-0.009	0.000	0.000	0.000	0.000
17	o	103	PHE	0	0.011	-0.002	26.083	0.007	0.007	0.000	0.000	0.000	0.000
18	o	104	VAL	0	-0.056	-0.033	26.715	-0.001	-0.001	0.000	0.000	0.000	0.000
19	o	105	PRO	0	0.027	0.007	23.657	0.001	0.001	0.000	0.000	0.000	0.000
20	o	106	PRO	0	-0.102	-0.051	25.766	-0.002	-0.002	0.000	0.000	0.000	0.000
21	o	107	GLU	-1	-0.937	-0.947	24.260	0.098	0.098	0.000	0.000	0.000	0.000
22	o	108	GLU	-1	-0.924	-0.959	20.479	0.090	0.090	0.000	0.000	0.000	0.000
23	o	109	GLU	-1	-0.881	-0.932	16.477	0.167	0.167	0.000	0.000	0.000	0.000
24	o	110	PHE	0	-0.071	-0.046	14.141	0.011	0.011	0.000	0.000	0.000	0.000
25	o	111	ILE	0	0.041	0.046	13.140	-0.013	-0.013	0.000	0.000	0.000	0.000
26	o	112	MET	0	-0.025	-0.001	8.659	0.072	0.072	0.000	0.000	0.000	0.000
27	o	113	GLY	0	0.040	0.027	6.152	-0.260	-0.260	0.000	0.000	0.000	0.000
28	o	114	VAL	0	-0.034	-0.014	4.797	0.477	0.719	-0.001	-0.050	-0.190	0.000
29	o	115	SER	0	0.067	0.011	2.134	-1.881	0.234	5.026	-4.019	-3.122	-0.020
30	o	116	LYS	1	0.890	0.943	2.780	-8.255	-7.249	0.481	0.620	-2.106	-0.015
31	o	117	TYR	0	-0.037	-0.035	5.067	-0.178	-0.149	-0.001	-0.003	-0.024	0.000
32	o	118	GLY	0	-0.003	0.000	7.306	-0.165	-0.165	0.000	0.000	0.000	0.000
33	o	119	ILE	0	-0.026	-0.018	7.424	0.357	0.357	0.000	0.000	0.000	0.000
34	o	120	LYS	1	0.818	0.912	7.203	-1.036	-1.036	0.000	0.000	0.000	0.000
35	o	121	VAL	0	0.060	0.025	9.538	0.016	0.016	0.000	0.000	0.000	0.000
36	o	140	ARG	1	0.893	0.925	14.960	-0.223	-0.223	0.000	0.000	0.000	0.000
37	o	141	MET	0	-0.015	-0.010	11.164	0.051	0.051	0.000	0.000	0.000	0.000
38	o	142	VAL	0	-0.034	-0.020	15.024	-0.030	-0.030	0.000	0.000	0.000	0.000
39	o	143	CYS	0	-0.008	0.001	15.636	0.021	0.021	0.000	0.000	0.000	0.000
40	o	144	TYR	0	-0.016	-0.004	17.683	-0.017	-0.017	0.000	0.000	0.000	0.000
41	o	145	ASP	-1	-0.860	-0.913	21.050	0.086	0.086	0.000	0.000	0.000	0.000
42	o	153	SER	0	-0.039	-0.043	19.374	-0.008	-0.008	0.000	0.000	0.000	0.000
43	o	154	LEU	0	-0.009	0.021	19.070	0.018	0.018	0.000	0.000	0.000	0.000
44	o	155	LEU	0	0.001	-0.008	12.806	0.022	0.022	0.000	0.000	0.000	0.000
45	o	156	ALA	0	0.028	0.016	16.706	-0.013	-0.013	0.000	0.000	0.000	0.000
46	o	157	LEU	0	-0.013	-0.031	12.107	0.040	0.040	0.000	0.000	0.000	0.000
47	o	158	LYS	1	0.832	0.917	16.416	-0.214	-0.214	0.000	0.000	0.000	0.000
48	o	159	THR	0	-0.091	-0.054	16.272	0.037	0.037	0.000	0.000	0.000	0.000
49	o	160	THR	0	0.025	-0.019	18.850	-0.033	-0.033	0.000	0.000	0.000	0.000
50	o	161	ASP	-1	-0.765	-0.852	20.412	0.220	0.220	0.000	0.000	0.000	0.000
51	o	162	ALA	0	-0.044	-0.031	22.878	-0.001	-0.001	0.000	0.000	0.000	0.000
52	o	163	SER	0	-0.078	-0.041	23.723	-0.012	-0.012	0.000	0.000	0.000	0.000
53	o	164	ASN	0	-0.100	-0.043	23.677	0.003	0.003	0.000	0.000	0.000	0.000
54	o	165	GLU	-1	-0.896	-0.956	26.220	0.125	0.125	0.000	0.000	0.000	0.000
55	o	166	GLU	-1	-0.859	-0.914	25.143	0.189	0.189	0.000	0.000	0.000	0.000
56	o	167	TYR	0	-0.100	-0.047	22.827	0.002	0.002	0.000	0.000	0.000	0.000
57	o	168	SER	0	0.024	-0.005	22.013	0.000	0.000	0.000	0.000	0.000	0.000
58	o	169	LEU	0	-0.066	-0.024	20.571	0.024	0.024	0.000	0.000	0.000	0.000
59	o	170	TRP	0	-0.034	-0.008	17.032	-0.004	-0.004	0.000	0.000	0.000	0.000
60	o	171	VAL	0	0.008	-0.004	18.265	0.014	0.014	0.000	0.000	0.000	0.000
61	o	172	TYR	0	-0.015	-0.014	14.368	-0.002	-0.002	0.000	0.000	0.000	0.000
62	o	173	GLN	0	0.031	0.006	17.193	0.004	0.004	0.000	0.000	0.000	0.000
63	o	174	CYS	0	-0.054	-0.018	14.190	0.013	0.013	0.000	0.000	0.000	0.000
64	o	175	ASN	0	-0.015	-0.014	16.115	0.014	0.014	0.000	0.000	0.000	0.000
65	o	176	SER	0	0.095	0.024	17.484	-0.002	-0.002	0.000	0.000	0.000	0.000
66	o	177	LEU	0	0.013	-0.003	16.921	0.016	0.016	0.000	0.000	0.000	0.000
67	o	178	GLU	-1	-0.986	-0.978	16.377	-0.010	-0.010	0.000	0.000	0.000	0.000
68	o	179	GLN	0	0.096	0.037	13.699	0.040	0.040	0.000	0.000	0.000	0.000
69	o	180	ALA	0	0.024	0.020	12.158	0.078	0.078	0.000	0.000	0.000	0.000
70	o	181	GLN	0	-0.023	-0.014	11.976	0.114	0.114	0.000	0.000	0.000	0.000
71	o	182	ALA	0	-0.008	0.007	9.067	0.087	0.087	0.000	0.000	0.000	0.000
72	o	183	ILE	0	-0.015	0.018	7.418	0.433	0.433	0.000	0.000	0.000	0.000
73	o	184	CYS	0	-0.116	-0.066	7.496	0.624	0.624	0.000	0.000	0.000	0.000
74	o	192	ASP	-1	-0.903	-0.955	8.887	-0.116	-0.116	0.000	0.000	0.000	0.000
75	o	193	SER	0	-0.035	-0.032	6.688	-0.204	-0.204	0.000	0.000	0.000	0.000
76	o	194	VAL	0	0.046	0.032	8.635	0.096	0.096	0.000	0.000	0.000	0.000
77	o	195	LEU	0	-0.056	-0.006	10.787	0.042	0.042	0.000	0.000	0.000	0.000
78	o	196	THR	0	-0.025	-0.006	12.214	-0.044	-0.044	0.000	0.000	0.000	0.000

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