FMO DATABASE

FMODB ID: 22VZR

Calculation Name: 4DX9-2-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: 2

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	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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-685977.230011
FMO2-HF: Nuclear repulsion	647555.132938
FMO2-HF: Total energy	-38422.097073
FMO2-MP2: Total energy	-38531.287019

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(2:60:CYS)

Summations of interaction energy for fragment #1(2:60: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.
-7.241	-2.096	3.266	-3.882	-4.529	-0.021

Interaction energy analysis for fragmet #1(2:60:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.004

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	2	62	GLU	-1	-0.930	-0.964	3.611	-0.438	1.769	-0.015	-0.988	-1.203	0.004
4	2	63	PHE	0	0.008	0.014	5.570	0.262	0.262	0.000	0.000	0.000	0.000
5	2	64	ARG	1	0.949	0.969	9.232	0.810	0.810	0.000	0.000	0.000	0.000
6	2	65	ILE	0	-0.061	-0.035	12.522	-0.004	-0.004	0.000	0.000	0.000	0.000
7	2	66	LYS	1	0.956	0.978	15.129	0.256	0.256	0.000	0.000	0.000	0.000
8	2	67	TYR	0	-0.004	-0.019	18.096	-0.009	-0.009	0.000	0.000	0.000	0.000
9	2	68	VAL	0	-0.005	-0.005	19.664	-0.018	-0.018	0.000	0.000	0.000	0.000
10	2	69	GLY	0	0.037	0.017	22.565	0.009	0.009	0.000	0.000	0.000	0.000
11	2	70	ALA	0	-0.024	-0.008	21.510	-0.004	-0.004	0.000	0.000	0.000	0.000
12	2	71	ILE	0	0.032	0.033	23.515	0.003	0.003	0.000	0.000	0.000	0.000
13	2	84	GLY	0	0.072	0.034	25.955	0.008	0.008	0.000	0.000	0.000	0.000
14	2	85	PRO	0	-0.012	-0.019	22.251	0.010	0.010	0.000	0.000	0.000	0.000
15	2	86	LEU	0	0.052	0.017	23.962	-0.009	-0.009	0.000	0.000	0.000	0.000
16	2	87	ASP	-1	-0.831	-0.922	27.111	0.011	0.011	0.000	0.000	0.000	0.000
17	2	88	LEU	0	-0.060	-0.029	20.480	0.009	0.009	0.000	0.000	0.000	0.000
18	2	89	ILE	0	0.006	0.009	23.825	-0.002	-0.002	0.000	0.000	0.000	0.000
19	2	90	ASN	0	0.006	0.007	25.783	-0.006	-0.006	0.000	0.000	0.000	0.000
20	2	91	TYR	0	-0.037	-0.016	26.555	0.001	0.001	0.000	0.000	0.000	0.000
21	2	92	ILE	0	0.008	-0.006	22.587	0.005	0.005	0.000	0.000	0.000	0.000
22	2	93	ASP	-1	-0.937	-0.964	27.001	-0.066	-0.066	0.000	0.000	0.000	0.000
23	2	94	VAL	0	0.020	0.000	29.569	0.000	0.000	0.000	0.000	0.000	0.000
24	2	95	ALA	0	-0.053	-0.019	28.795	0.004	0.004	0.000	0.000	0.000	0.000
25	2	96	GLN	0	-0.096	-0.049	27.037	-0.007	-0.007	0.000	0.000	0.000	0.000
26	2	97	GLN	0	-0.027	0.001	30.856	0.002	0.002	0.000	0.000	0.000	0.000
27	2	111	ILE	0	0.014	0.001	9.681	-0.029	-0.029	0.000	0.000	0.000	0.000
28	2	112	MET	0	-0.029	-0.016	9.093	0.190	0.190	0.000	0.000	0.000	0.000
29	2	113	GLY	0	0.063	0.047	5.347	-0.576	-0.576	0.000	0.000	0.000	0.000
30	2	114	VAL	0	-0.043	-0.023	4.620	0.530	0.796	-0.001	-0.076	-0.190	0.000
31	2	115	SER	0	0.046	-0.001	2.417	-2.190	-0.134	3.257	-2.793	-2.520	-0.027
32	2	116	LYS	1	0.911	0.929	3.565	-5.917	-5.444	0.025	0.002	-0.500	0.002
33	2	117	TYR	0	0.055	0.035	5.878	-1.008	-1.008	0.000	0.000	0.000	0.000
34	2	118	GLY	0	0.008	0.027	7.048	-0.529	-0.529	0.000	0.000	0.000	0.000
35	2	119	ILE	0	-0.024	0.013	6.793	0.837	0.837	0.000	0.000	0.000	0.000
36	2	128	ASP	-1	-0.916	-0.966	14.804	0.176	0.176	0.000	0.000	0.000	0.000
37	2	129	VAL	0	-0.037	-0.022	12.140	-0.001	-0.001	0.000	0.000	0.000	0.000
38	2	130	LEU	0	0.007	0.023	14.486	0.027	0.027	0.000	0.000	0.000	0.000
39	2	131	HIS	0	-0.016	-0.012	14.837	-0.037	-0.037	0.000	0.000	0.000	0.000
40	2	132	ARG	1	0.975	0.978	10.330	-1.069	-1.069	0.000	0.000	0.000	0.000
41	2	133	HIS	0	0.018	0.019	12.714	0.077	0.077	0.000	0.000	0.000	0.000
42	2	134	ALA	0	0.054	0.028	11.462	0.166	0.166	0.000	0.000	0.000	0.000
43	2	135	LEU	0	0.026	-0.008	9.086	-0.163	-0.163	0.000	0.000	0.000	0.000
44	2	136	TYR	0	-0.028	-0.021	11.905	-0.133	-0.133	0.000	0.000	0.000	0.000
45	2	137	LEU	0	-0.025	-0.002	15.205	-0.090	-0.090	0.000	0.000	0.000	0.000
46	2	138	ILE	0	-0.009	-0.003	11.359	-0.092	-0.092	0.000	0.000	0.000	0.000
47	2	139	ILE	0	0.030	0.025	15.411	-0.001	-0.001	0.000	0.000	0.000	0.000
48	2	140	ARG	1	0.807	0.887	17.415	-0.134	-0.134	0.000	0.000	0.000	0.000
49	2	141	MET	0	0.021	0.022	12.647	0.035	0.035	0.000	0.000	0.000	0.000
50	2	142	VAL	0	-0.039	-0.008	16.385	-0.013	-0.013	0.000	0.000	0.000	0.000
51	2	143	CYS	0	-0.026	-0.008	17.008	-0.017	-0.017	0.000	0.000	0.000	0.000
52	2	144	TYR	0	0.020	0.011	19.063	0.006	0.006	0.000	0.000	0.000	0.000
53	2	145	ASP	-1	-0.787	-0.905	22.284	-0.238	-0.238	0.000	0.000	0.000	0.000
54	2	146	ASP	-1	-0.836	-0.907	24.881	-0.134	-0.134	0.000	0.000	0.000	0.000
55	2	147	GLY	0	-0.015	-0.019	24.686	-0.018	-0.018	0.000	0.000	0.000	0.000
56	2	148	LEU	0	0.057	0.013	26.996	0.006	0.006	0.000	0.000	0.000	0.000
57	2	149	GLY	0	-0.023	-0.011	25.671	0.009	0.009	0.000	0.000	0.000	0.000
58	2	150	ALA	0	-0.073	-0.011	26.680	-0.011	-0.011	0.000	0.000	0.000	0.000
59	2	151	GLY	0	0.013	-0.027	26.895	-0.003	-0.003	0.000	0.000	0.000	0.000
60	2	152	LYS	1	0.822	0.929	22.844	0.270	0.270	0.000	0.000	0.000	0.000
61	2	153	SER	0	-0.010	0.010	19.962	-0.052	-0.052	0.000	0.000	0.000	0.000
62	2	154	LEU	0	-0.012	0.015	20.549	-0.005	-0.005	0.000	0.000	0.000	0.000
63	2	155	LEU	0	-0.026	-0.024	13.875	-0.028	-0.028	0.000	0.000	0.000	0.000
64	2	156	ALA	0	0.028	0.023	17.858	0.031	0.031	0.000	0.000	0.000	0.000
65	2	157	LEU	0	0.009	-0.010	13.207	0.003	0.003	0.000	0.000	0.000	0.000
66	2	158	LYS	1	0.938	0.975	17.238	-0.112	-0.112	0.000	0.000	0.000	0.000
67	2	159	THR	0	-0.040	-0.012	16.658	0.028	0.028	0.000	0.000	0.000	0.000
68	2	160	THR	0	0.029	0.019	19.300	-0.026	-0.026	0.000	0.000	0.000	0.000
69	2	168	SER	0	0.018	0.012	21.645	-0.010	-0.010	0.000	0.000	0.000	0.000
70	2	169	LEU	0	-0.049	-0.038	21.279	0.011	0.011	0.000	0.000	0.000	0.000
71	2	170	TRP	0	0.004	-0.022	17.989	-0.005	-0.005	0.000	0.000	0.000	0.000
72	2	171	VAL	0	0.017	0.013	19.405	-0.012	-0.012	0.000	0.000	0.000	0.000
73	2	172	TYR	0	0.007	0.001	15.061	0.024	0.024	0.000	0.000	0.000	0.000
74	2	173	GLN	0	0.012	-0.002	18.534	-0.015	-0.015	0.000	0.000	0.000	0.000
75	2	174	CYS	0	-0.035	0.001	15.332	-0.072	-0.072	0.000	0.000	0.000	0.000
76	2	175	ASN	0	-0.011	-0.018	17.534	0.003	0.003	0.000	0.000	0.000	0.000
77	2	176	SER	0	0.060	0.013	18.745	0.022	0.022	0.000	0.000	0.000	0.000
78	2	177	LEU	0	0.086	0.049	18.103	-0.051	-0.051	0.000	0.000	0.000	0.000
79	2	178	GLU	-1	-0.917	-0.953	17.540	-0.524	-0.524	0.000	0.000	0.000	0.000
80	2	179	GLN	0	0.003	-0.009	14.168	-0.075	-0.075	0.000	0.000	0.000	0.000
81	2	180	ALA	0	0.025	0.019	13.278	-0.100	-0.100	0.000	0.000	0.000	0.000
82	2	181	GLN	0	0.032	0.005	13.908	0.047	0.047	0.000	0.000	0.000	0.000
83	2	182	ALA	0	-0.028	-0.008	10.939	-0.013	-0.013	0.000	0.000	0.000	0.000
84	2	183	ILE	0	0.021	0.007	9.148	-0.188	-0.188	0.000	0.000	0.000	0.000
85	2	184	CYS	0	-0.013	-0.009	9.329	0.113	0.113	0.000	0.000	0.000	0.000
86	2	185	LYS	1	0.952	0.990	9.698	0.718	0.718	0.000	0.000	0.000	0.000
87	2	186	VAL	0	0.000	0.014	3.783	-0.137	0.006	0.000	-0.027	-0.116	0.000
88	2	187	LEU	0	0.005	-0.001	5.897	0.544	0.544	0.000	0.000	0.000	0.000
89	2	188	SER	0	-0.037	-0.036	8.374	0.300	0.300	0.000	0.000	0.000	0.000
90	2	189	THR	0	-0.028	-0.020	4.925	0.103	0.103	0.000	0.000	0.000	0.000
91	2	190	ALA	0	-0.037	-0.020	6.117	0.759	0.759	0.000	0.000	0.000	0.000
92	2	191	PHE	0	-0.006	-0.014	7.015	0.127	0.127	0.000	0.000	0.000	0.000
93	2	192	ASP	-1	-0.849	-0.923	10.170	0.340	0.340	0.000	0.000	0.000	0.000
94	2	193	SER	0	-0.116	-0.050	7.577	0.274	0.274	0.000	0.000	0.000	0.000
95	2	194	VAL	0	-0.035	-0.008	9.691	0.132	0.132	0.000	0.000	0.000	0.000
96	2	195	LEU	0	-0.039	-0.009	12.711	-0.098	-0.098	0.000	0.000	0.000	0.000
97	2	196	THR	0	0.004	0.011	15.153	-0.050	-0.050	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(2:60:CYS)