FMO DATABASE

FMODB ID: YYQQ2

Calculation Name: 4DX9-2-Xray321

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	107
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-709505.537602
FMO2-HF: Nuclear repulsion	670229.432038
FMO2-HF: Total energy	-39276.105564
FMO2-MP2: Total energy	-39388.053369

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(2:59:ACE )

Summations of interaction energy for fragment #1(2:59:ACE )

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.
7.637	-6.18	19.365	-3.148	-2.399	0.002

Interaction energy analysis for fragmet #1(2:59:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.075

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	61	ALA	0	0.006	0.017	3.779	0.943	1.604	-0.008	-0.197	-0.456	0.000
4	2	62	GLU	-1	-0.930	-0.955	6.608	-0.496	-0.496	0.000	0.000	0.000	0.000
5	2	63	PHE	0	0.004	-0.002	9.315	0.149	0.149	0.000	0.000	0.000	0.000
6	2	64	ARG	1	0.960	0.972	12.838	0.174	0.174	0.000	0.000	0.000	0.000
7	2	65	ILE	0	-0.070	-0.027	16.318	0.029	0.029	0.000	0.000	0.000	0.000
8	2	66	LYS	1	0.934	0.987	18.708	0.104	0.104	0.000	0.000	0.000	0.000
9	2	67	TYR	0	-0.012	-0.035	21.581	-0.003	-0.003	0.000	0.000	0.000	0.000
10	2	68	VAL	0	0.004	0.010	23.791	0.008	0.008	0.000	0.000	0.000	0.000
11	2	69	GLY	0	0.040	0.007	25.909	0.004	0.004	0.000	0.000	0.000	0.000
12	2	70	ALA	0	-0.054	-0.013	24.300	0.002	0.002	0.000	0.000	0.000	0.000
13	2	71	ILE	0	0.041	0.024	26.407	0.001	0.001	0.000	0.000	0.000	0.000
14	2	72	NME	0	0.009	0.009	28.058	0.001	0.001	0.000	0.000	0.000	0.000
15	2	83	ACE	0	0.047	0.009	27.718	-0.001	-0.001	0.000	0.000	0.000	0.000
16	2	84	GLY	0	0.044	0.016	26.175	0.006	0.006	0.000	0.000	0.000	0.000
17	2	85	PRO	0	-0.032	-0.030	22.411	-0.007	-0.007	0.000	0.000	0.000	0.000
18	2	86	LEU	0	0.059	0.021	24.298	-0.006	-0.006	0.000	0.000	0.000	0.000
19	2	87	ASP	-1	-0.873	-0.932	27.478	-0.008	-0.008	0.000	0.000	0.000	0.000
20	2	88	LEU	0	-0.102	-0.055	21.583	-0.003	-0.003	0.000	0.000	0.000	0.000
21	2	89	ILE	0	0.020	0.009	24.811	-0.006	-0.006	0.000	0.000	0.000	0.000
22	2	90	ASN	0	0.037	0.024	26.951	-0.003	-0.003	0.000	0.000	0.000	0.000
23	2	91	TYR	0	-0.012	0.000	28.719	0.001	0.001	0.000	0.000	0.000	0.000
24	2	92	ILE	0	-0.024	-0.022	24.497	-0.004	-0.004	0.000	0.000	0.000	0.000
25	2	93	ASP	-1	-0.874	-0.953	28.845	-0.032	-0.032	0.000	0.000	0.000	0.000
26	2	94	VAL	0	-0.020	-0.004	31.145	0.001	0.001	0.000	0.000	0.000	0.000
27	2	95	ALA	0	-0.063	-0.024	31.055	0.000	0.000	0.000	0.000	0.000	0.000
28	2	96	GLN	0	-0.048	-0.017	28.626	0.001	0.001	0.000	0.000	0.000	0.000
29	2	97	GLN	0	-0.003	0.017	33.208	0.000	0.000	0.000	0.000	0.000	0.000
30	2	98	NME	0	-0.012	-0.002	36.486	-0.001	-0.001	0.000	0.000	0.000	0.000
31	2	110	ACE	0	0.055	-0.015	20.188	0.005	0.005	0.000	0.000	0.000	0.000
32	2	111	ILE	0	-0.027	-0.018	14.447	0.006	0.006	0.000	0.000	0.000	0.000
33	2	112	MET	0	-0.037	-0.006	11.934	0.027	0.027	0.000	0.000	0.000	0.000
34	2	113	GLY	0	0.063	0.039	10.123	-0.037	-0.037	0.000	0.000	0.000	0.000
35	2	114	VAL	0	-0.033	0.000	6.566	0.060	0.060	0.000	0.000	0.000	0.000
36	2	115	SER	0	0.035	-0.012	5.673	-0.687	-0.687	0.000	0.000	0.000	0.000
37	2	116	LYS	1	0.922	1.006	2.028	6.032	-8.576	19.370	-2.907	-1.855	0.002
38	2	117	TYR	0	0.044	0.017	6.378	0.311	0.311	0.000	0.000	0.000	0.000
39	2	118	GLY	0	0.023	0.021	9.192	0.121	0.121	0.000	0.000	0.000	0.000
40	2	119	ILE	0	-0.020	0.018	9.827	-0.208	-0.208	0.000	0.000	0.000	0.000
41	2	120	NME	0	-0.011	0.002	12.185	-0.022	-0.022	0.000	0.000	0.000	0.000
42	2	127	ACE	0	-0.021	-0.023	22.612	-0.001	-0.001	0.000	0.000	0.000	0.000
43	2	128	ASP	-1	-0.916	-0.957	20.766	-0.225	-0.225	0.000	0.000	0.000	0.000
44	2	129	VAL	0	-0.040	-0.018	17.373	-0.015	-0.015	0.000	0.000	0.000	0.000
45	2	130	LEU	0	0.003	0.009	19.884	0.018	0.018	0.000	0.000	0.000	0.000
46	2	131	HIS	0	0.011	0.018	18.930	0.027	0.027	0.000	0.000	0.000	0.000
47	2	132	ARG	1	0.974	0.984	14.860	0.317	0.317	0.000	0.000	0.000	0.000
48	2	133	HIS	0	0.010	0.017	15.358	0.001	0.001	0.000	0.000	0.000	0.000
49	2	134	ALA	0	0.050	0.012	14.148	-0.055	-0.055	0.000	0.000	0.000	0.000
50	2	135	LEU	0	0.030	-0.009	9.191	0.004	0.004	0.000	0.000	0.000	0.000
51	2	136	TYR	0	-0.029	-0.006	13.214	0.044	0.044	0.000	0.000	0.000	0.000
52	2	137	LEU	0	-0.044	-0.009	16.683	0.014	0.014	0.000	0.000	0.000	0.000
53	2	138	ILE	0	0.012	-0.004	13.248	0.015	0.015	0.000	0.000	0.000	0.000
54	2	139	ILE	0	0.040	0.032	15.916	0.017	0.017	0.000	0.000	0.000	0.000
55	2	140	ARG	1	0.837	0.923	17.774	0.021	0.021	0.000	0.000	0.000	0.000
56	2	141	MET	0	0.012	0.013	13.944	-0.027	-0.027	0.000	0.000	0.000	0.000
57	2	142	VAL	0	-0.032	-0.017	17.023	0.022	0.022	0.000	0.000	0.000	0.000
58	2	143	CYS	0	-0.055	-0.005	17.578	-0.009	-0.009	0.000	0.000	0.000	0.000
59	2	144	TYR	0	0.025	0.003	19.934	0.013	0.013	0.000	0.000	0.000	0.000
60	2	145	ASP	-1	-0.793	-0.896	23.379	-0.037	-0.037	0.000	0.000	0.000	0.000
61	2	146	ASP	-1	-0.932	-0.929	25.959	-0.043	-0.043	0.000	0.000	0.000	0.000
62	2	147	GLY	0	0.020	-0.017	28.381	0.001	0.001	0.000	0.000	0.000	0.000
63	2	148	LEU	0	-0.105	-0.030	30.939	0.004	0.004	0.000	0.000	0.000	0.000
64	2	149	GLY	0	0.107	0.056	29.450	-0.002	-0.002	0.000	0.000	0.000	0.000
65	2	150	ALA	0	-0.029	-0.030	28.901	-0.006	-0.006	0.000	0.000	0.000	0.000
66	2	151	GLY	0	0.001	-0.026	28.774	-0.001	-0.001	0.000	0.000	0.000	0.000
67	2	152	LYS	1	0.796	0.910	24.681	0.063	0.063	0.000	0.000	0.000	0.000
68	2	153	SER	0	-0.018	-0.019	21.267	0.002	0.002	0.000	0.000	0.000	0.000
69	2	154	LEU	0	0.027	0.023	22.491	-0.015	-0.015	0.000	0.000	0.000	0.000
70	2	155	LEU	0	-0.031	-0.035	15.701	0.003	0.003	0.000	0.000	0.000	0.000
71	2	156	ALA	0	0.031	0.022	19.120	-0.001	-0.001	0.000	0.000	0.000	0.000
72	2	157	LEU	0	-0.012	-0.015	14.951	-0.001	-0.001	0.000	0.000	0.000	0.000
73	2	158	LYS	1	0.959	0.991	18.972	0.032	0.032	0.000	0.000	0.000	0.000
74	2	159	THR	0	-0.028	0.005	18.410	-0.001	-0.001	0.000	0.000	0.000	0.000
75	2	160	THR	0	-0.016	-0.002	20.799	0.006	0.006	0.000	0.000	0.000	0.000
76	2	161	NME	0	0.033	0.017	23.129	-0.005	-0.005	0.000	0.000	0.000	0.000
77	2	167	ACE	0	-0.002	-0.004	25.847	0.002	0.002	0.000	0.000	0.000	0.000
78	2	168	SER	0	-0.041	-0.023	24.250	0.000	0.000	0.000	0.000	0.000	0.000
79	2	169	LEU	0	0.002	0.002	23.343	0.001	0.001	0.000	0.000	0.000	0.000
80	2	170	TRP	0	0.020	-0.022	20.161	-0.009	-0.009	0.000	0.000	0.000	0.000
81	2	171	VAL	0	0.032	0.024	21.389	0.000	0.000	0.000	0.000	0.000	0.000
82	2	172	TYR	0	-0.018	-0.011	18.864	-0.013	-0.013	0.000	0.000	0.000	0.000
83	2	173	GLN	0	0.039	0.031	21.115	0.007	0.007	0.000	0.000	0.000	0.000
84	2	174	CYS	0	-0.043	0.005	18.062	-0.021	-0.021	0.000	0.000	0.000	0.000
85	2	175	ASN	0	-0.043	-0.031	20.075	0.003	0.003	0.000	0.000	0.000	0.000
86	2	176	SER	0	0.072	0.016	19.686	0.015	0.015	0.000	0.000	0.000	0.000
87	2	177	LEU	0	0.145	0.068	19.519	-0.013	-0.013	0.000	0.000	0.000	0.000
88	2	178	GLU	-1	-0.895	-0.940	18.431	0.002	0.002	0.000	0.000	0.000	0.000
89	2	179	GLN	0	0.001	-0.013	15.551	0.012	0.012	0.000	0.000	0.000	0.000
90	2	180	ALA	0	0.020	0.011	14.659	-0.026	-0.026	0.000	0.000	0.000	0.000
91	2	181	GLN	0	-0.021	-0.027	15.397	-0.005	-0.005	0.000	0.000	0.000	0.000
92	2	182	ALA	0	-0.025	-0.008	12.003	0.028	0.028	0.000	0.000	0.000	0.000
93	2	183	ILE	0	0.014	0.005	10.339	0.004	0.004	0.000	0.000	0.000	0.000
94	2	184	CYS	0	-0.003	0.001	10.231	-0.023	-0.023	0.000	0.000	0.000	0.000
95	2	185	LYS	1	0.949	0.992	9.729	-0.118	-0.118	0.000	0.000	0.000	0.000
96	2	186	VAL	0	0.012	0.015	5.126	0.145	0.145	0.000	0.000	0.000	0.000
97	2	187	LEU	0	-0.008	-0.012	5.924	0.031	0.031	0.000	0.000	0.000	0.000
98	2	188	SER	0	-0.041	-0.039	8.548	0.048	0.048	0.000	0.000	0.000	0.000
99	2	189	THR	0	-0.031	-0.005	3.862	0.075	0.205	0.003	-0.044	-0.088	0.000
100	2	190	ALA	0	-0.055	-0.026	5.753	0.331	0.331	0.000	0.000	0.000	0.000
101	2	191	PHE	0	0.003	-0.014	6.508	0.006	0.006	0.000	0.000	0.000	0.000
102	2	192	ASP	-1	-0.872	-0.932	8.844	0.425	0.425	0.000	0.000	0.000	0.000
103	2	193	SER	0	-0.106	-0.050	6.200	0.136	0.136	0.000	0.000	0.000	0.000
104	2	194	VAL	0	-0.055	-0.010	8.346	-0.099	-0.099	0.000	0.000	0.000	0.000
105	2	195	LEU	0	-0.023	-0.017	11.455	-0.041	-0.041	0.000	0.000	0.000	0.000
106	2	196	THR	0	-0.017	0.011	13.062	0.061	0.061	0.000	0.000	0.000	0.000
107	2	197	NME	0	0.027	0.011	14.969	0.031	0.031	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(2:59:ACE )