FMO DATABASE

FMODB ID: 22Y7R

Calculation Name: 4DX9-s-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: s

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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-897456.132118
FMO2-HF: Nuclear repulsion	851899.065968
FMO2-HF: Total energy	-45557.066151
FMO2-MP2: Total energy	-45687.576078

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(s:60:CYS)

Summations of interaction energy for fragment #1(s: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.
-3.753	-0.043999999999998	4.991	-3.749	-4.956	-0.029

Interaction energy analysis for fragmet #1(s: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

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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	s	62	GLU	-1	-0.938	-0.967	3.814	1.196	2.918	-0.027	-0.700	-0.996	-0.001
4	s	63	PHE	0	-0.012	-0.006	6.933	-0.407	-0.407	0.000	0.000	0.000	0.000
5	s	64	ARG	1	0.913	0.967	10.215	0.161	0.161	0.000	0.000	0.000	0.000
6	s	65	ILE	0	0.015	0.004	13.294	-0.031	-0.031	0.000	0.000	0.000	0.000
7	s	66	LYS	1	1.009	1.022	15.883	-0.077	-0.077	0.000	0.000	0.000	0.000
8	s	67	TYR	0	-0.033	-0.029	18.305	0.036	0.036	0.000	0.000	0.000	0.000
9	s	68	VAL	0	0.007	0.011	20.028	-0.025	-0.025	0.000	0.000	0.000	0.000
10	s	69	GLY	0	0.038	0.005	22.084	-0.021	-0.021	0.000	0.000	0.000	0.000
11	s	70	ALA	0	-0.026	-0.016	21.960	0.033	0.033	0.000	0.000	0.000	0.000
12	s	71	ILE	0	0.010	0.028	23.666	-0.018	-0.018	0.000	0.000	0.000	0.000
13	s	84	GLY	0	0.046	0.007	25.823	0.005	0.005	0.000	0.000	0.000	0.000
14	s	85	PRO	0	-0.055	-0.033	22.928	0.012	0.012	0.000	0.000	0.000	0.000
15	s	86	LEU	0	0.060	0.011	24.159	0.003	0.003	0.000	0.000	0.000	0.000
16	s	87	ASP	-1	-0.896	-0.940	27.255	0.163	0.163	0.000	0.000	0.000	0.000
17	s	88	LEU	0	-0.023	-0.022	21.439	0.001	0.001	0.000	0.000	0.000	0.000
18	s	89	ILE	0	-0.009	0.004	24.030	0.004	0.004	0.000	0.000	0.000	0.000
19	s	90	ASN	0	0.043	0.010	26.163	-0.010	-0.010	0.000	0.000	0.000	0.000
20	s	91	TYR	0	-0.046	-0.016	26.910	-0.011	-0.011	0.000	0.000	0.000	0.000
21	s	92	ILE	0	-0.038	-0.016	23.104	0.004	0.004	0.000	0.000	0.000	0.000
22	s	93	ASP	-1	-0.852	-0.929	27.327	0.119	0.119	0.000	0.000	0.000	0.000
23	s	94	VAL	0	-0.060	-0.024	30.328	-0.009	-0.009	0.000	0.000	0.000	0.000
24	s	95	ALA	0	0.022	0.010	29.292	-0.006	-0.006	0.000	0.000	0.000	0.000
25	s	96	GLN	0	-0.021	-0.023	27.163	-0.003	-0.003	0.000	0.000	0.000	0.000
26	s	97	GLN	0	-0.056	-0.014	31.381	-0.013	-0.013	0.000	0.000	0.000	0.000
27	s	98	ASP	-1	-0.941	-0.967	34.185	0.117	0.117	0.000	0.000	0.000	0.000
28	s	99	GLY	0	-0.036	-0.009	34.213	-0.004	-0.004	0.000	0.000	0.000	0.000
29	s	100	LYS	1	0.865	0.942	30.383	-0.150	-0.150	0.000	0.000	0.000	0.000
30	s	101	LEU	0	-0.012	-0.003	25.098	0.009	0.009	0.000	0.000	0.000	0.000
31	s	102	PRO	0	0.015	0.019	27.266	-0.010	-0.010	0.000	0.000	0.000	0.000
32	s	103	PHE	0	0.026	-0.003	27.882	0.007	0.007	0.000	0.000	0.000	0.000
33	s	104	VAL	0	-0.051	-0.019	28.070	-0.004	-0.004	0.000	0.000	0.000	0.000
34	s	105	PRO	0	-0.018	0.002	23.638	0.002	0.002	0.000	0.000	0.000	0.000
35	s	106	PRO	0	0.029	0.008	24.801	-0.017	-0.017	0.000	0.000	0.000	0.000
36	s	107	GLU	-1	-0.950	-0.960	24.523	0.060	0.060	0.000	0.000	0.000	0.000
37	s	108	GLU	-1	-0.961	-0.991	21.658	0.182	0.182	0.000	0.000	0.000	0.000
38	s	109	GLU	-1	-0.931	-0.984	18.088	0.088	0.088	0.000	0.000	0.000	0.000
39	s	110	PHE	0	-0.053	-0.028	15.526	0.013	0.013	0.000	0.000	0.000	0.000
40	s	111	ILE	0	0.006	-0.003	9.586	-0.039	-0.039	0.000	0.000	0.000	0.000
41	s	112	MET	0	-0.052	-0.009	9.061	0.120	0.120	0.000	0.000	0.000	0.000
42	s	113	GLY	0	0.042	0.013	6.254	-0.229	-0.229	0.000	0.000	0.000	0.000
43	s	114	VAL	0	0.001	0.012	4.436	0.212	0.512	-0.001	-0.083	-0.217	0.000
44	s	115	SER	0	-0.003	-0.018	2.343	-3.096	-1.300	5.000	-3.674	-3.123	-0.028
45	s	116	LYS	1	0.975	0.963	3.388	-1.091	-1.349	0.019	0.734	-0.496	0.000
46	s	117	TYR	0	0.007	0.020	5.562	-0.635	-0.635	0.000	0.000	0.000	0.000
47	s	118	GLY	0	0.041	0.033	8.062	-0.163	-0.163	0.000	0.000	0.000	0.000
48	s	119	ILE	0	-0.011	-0.005	6.841	0.658	0.658	0.000	0.000	0.000	0.000
49	s	120	LYS	1	0.962	0.982	7.058	-1.674	-1.674	0.000	0.000	0.000	0.000
50	s	130	LEU	0	0.010	-0.001	16.195	0.035	0.035	0.000	0.000	0.000	0.000
51	s	131	HIS	1	0.927	0.952	15.112	-0.486	-0.486	0.000	0.000	0.000	0.000
52	s	132	ARG	1	0.955	0.984	11.646	-0.710	-0.710	0.000	0.000	0.000	0.000
53	s	133	HIS	0	0.031	0.033	12.309	-0.053	-0.053	0.000	0.000	0.000	0.000
54	s	134	ALA	0	0.058	0.025	11.499	0.223	0.223	0.000	0.000	0.000	0.000
55	s	135	LEU	0	0.048	-0.009	8.965	-0.044	-0.044	0.000	0.000	0.000	0.000
56	s	136	TYR	0	-0.041	-0.012	12.204	-0.063	-0.063	0.000	0.000	0.000	0.000
57	s	137	LEU	0	0.020	0.012	15.385	-0.049	-0.049	0.000	0.000	0.000	0.000
58	s	138	ILE	0	-0.051	-0.009	11.416	-0.018	-0.018	0.000	0.000	0.000	0.000
59	s	139	ILE	0	0.025	0.048	15.504	-0.005	-0.005	0.000	0.000	0.000	0.000
60	s	140	ARG	1	0.911	0.951	17.264	-0.309	-0.309	0.000	0.000	0.000	0.000
61	s	141	MET	0	-0.008	0.007	11.538	0.040	0.040	0.000	0.000	0.000	0.000
62	s	142	VAL	0	-0.024	-0.012	16.142	-0.032	-0.032	0.000	0.000	0.000	0.000
63	s	143	CYS	0	-0.032	-0.016	16.842	0.001	0.001	0.000	0.000	0.000	0.000
64	s	144	TYR	0	0.042	0.012	18.933	-0.007	-0.007	0.000	0.000	0.000	0.000
65	s	145	ASP	-1	-0.869	-0.947	22.320	0.071	0.071	0.000	0.000	0.000	0.000
66	s	146	ASP	-1	-0.808	-0.899	24.605	0.091	0.091	0.000	0.000	0.000	0.000
67	s	147	GLY	0	0.050	0.024	26.563	0.000	0.000	0.000	0.000	0.000	0.000
68	s	148	LEU	0	-0.082	-0.035	29.635	-0.007	-0.007	0.000	0.000	0.000	0.000
69	s	149	GLY	0	-0.038	-0.027	31.679	-0.006	-0.006	0.000	0.000	0.000	0.000
70	s	150	ALA	0	-0.071	-0.030	28.356	-0.009	-0.009	0.000	0.000	0.000	0.000
71	s	151	GLY	0	0.086	0.047	25.200	-0.011	-0.011	0.000	0.000	0.000	0.000
72	s	152	LYS	1	0.753	0.876	22.760	-0.046	-0.046	0.000	0.000	0.000	0.000
73	s	153	SER	0	0.016	0.001	19.719	-0.002	-0.002	0.000	0.000	0.000	0.000
74	s	154	LEU	0	-0.005	-0.005	20.186	0.005	0.005	0.000	0.000	0.000	0.000
75	s	155	LEU	0	-0.036	-0.019	13.659	0.009	0.009	0.000	0.000	0.000	0.000
76	s	156	ALA	0	0.034	0.029	17.663	-0.002	-0.002	0.000	0.000	0.000	0.000
77	s	157	LEU	0	-0.048	-0.041	13.102	0.036	0.036	0.000	0.000	0.000	0.000
78	s	158	LYN	0	0.019	0.015	17.233	-0.013	-0.013	0.000	0.000	0.000	0.000
79	s	159	THR	0	-0.105	-0.124	17.384	0.044	0.044	0.000	0.000	0.000	0.000
80	s	160	THR	0	0.144	0.085	20.015	-0.009	-0.009	0.000	0.000	0.000	0.000
81	s	161	ASP	-1	-0.882	-0.960	22.554	0.330	0.330	0.000	0.000	0.000	0.000
82	s	162	ALA	0	-0.027	-0.016	25.032	-0.020	-0.020	0.000	0.000	0.000	0.000
83	s	163	SER	0	-0.067	-0.038	27.527	-0.013	-0.013	0.000	0.000	0.000	0.000
84	s	164	ASN	0	-0.127	-0.090	26.861	-0.022	-0.022	0.000	0.000	0.000	0.000
85	s	165	GLU	-1	-0.910	-0.940	28.953	0.198	0.198	0.000	0.000	0.000	0.000
86	s	166	GLU	-1	-0.942	-0.941	24.464	0.302	0.302	0.000	0.000	0.000	0.000
87	s	167	TYR	-1	-0.913	-0.913	23.668	0.309	0.309	0.000	0.000	0.000	0.000
88	s	168	SER	0	-0.044	-0.014	21.887	-0.029	-0.029	0.000	0.000	0.000	0.000
89	s	169	LEU	0	-0.007	0.003	20.507	0.039	0.039	0.000	0.000	0.000	0.000
90	s	170	TRP	0	-0.054	-0.041	17.565	-0.028	-0.028	0.000	0.000	0.000	0.000
91	s	171	VAL	0	0.047	0.019	18.645	0.024	0.024	0.000	0.000	0.000	0.000
92	s	172	TYR	0	-0.022	-0.016	15.436	0.009	0.009	0.000	0.000	0.000	0.000
93	s	173	GLN	0	0.059	0.020	18.361	-0.026	-0.026	0.000	0.000	0.000	0.000
94	s	174	CYS	0	-0.044	-0.002	15.298	0.020	0.020	0.000	0.000	0.000	0.000
95	s	175	ASN	0	0.050	0.022	18.202	0.009	0.009	0.000	0.000	0.000	0.000
96	s	176	SER	0	-0.013	-0.005	19.079	-0.023	-0.023	0.000	0.000	0.000	0.000
97	s	177	LEU	0	0.102	0.055	19.025	0.019	0.019	0.000	0.000	0.000	0.000
98	s	178	GLU	-1	-0.906	-0.972	17.679	-0.002	-0.002	0.000	0.000	0.000	0.000
99	s	179	GLN	0	-0.024	-0.018	13.652	0.023	0.023	0.000	0.000	0.000	0.000
100	s	180	ALA	0	0.052	0.018	13.465	0.034	0.034	0.000	0.000	0.000	0.000
101	s	181	GLN	0	0.021	0.004	14.258	0.089	0.089	0.000	0.000	0.000	0.000
102	s	182	ALA	0	-0.040	-0.017	11.118	0.053	0.053	0.000	0.000	0.000	0.000
103	s	183	ILE	0	0.005	0.000	8.977	0.085	0.085	0.000	0.000	0.000	0.000
104	s	184	CYS	0	-0.004	-0.007	9.374	0.256	0.256	0.000	0.000	0.000	0.000
105	s	185	LYS	1	0.940	0.971	10.287	-0.064	-0.064	0.000	0.000	0.000	0.000
106	s	186	VAL	0	-0.013	-0.003	4.290	-0.071	0.078	0.000	-0.026	-0.124	0.000
107	s	187	LEU	0	0.033	-0.005	6.675	0.745	0.745	0.000	0.000	0.000	0.000
108	s	188	SER	0	-0.064	-0.018	8.753	-0.096	-0.096	0.000	0.000	0.000	0.000
109	s	189	THR	0	0.004	0.006	7.163	0.071	0.071	0.000	0.000	0.000	0.000
110	s	190	ALA	0	-0.033	-0.010	6.167	-0.019	-0.019	0.000	0.000	0.000	0.000
111	s	191	PHE	0	0.019	0.018	7.429	-0.210	-0.210	0.000	0.000	0.000	0.000
112	s	192	ASP	-1	-0.895	-0.934	11.096	0.399	0.399	0.000	0.000	0.000	0.000
113	s	193	SER	0	-0.128	-0.081	8.618	-0.067	-0.067	0.000	0.000	0.000	0.000
114	s	194	VAL	0	-0.045	-0.022	10.560	-0.115	-0.115	0.000	0.000	0.000	0.000
115	s	195	LEU	0	-0.013	0.018	12.604	-0.098	-0.098	0.000	0.000	0.000	0.000

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