FMO DATABASE

FMODB ID: 141QZ

Calculation Name: 4DX9-i-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: i

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	OptHSide
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	118
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-939143.079729
FMO2-HF: Nuclear repulsion	892468.574107
FMO2-HF: Total energy	-46674.505622
FMO2-MP2: Total energy	-46808.421433

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(i:60:CYM)

Summations of interaction energy for fragment #1(i:60:CYM)

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.
31.853	36.242	2.297	-3.333	-3.354	-0.006

Interaction energy analysis for fragmet #1(i:60:CYM)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.973 / q_NPA : -0.981

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	i	62	GLU	-1	-0.906	-0.956	3.636	47.094	49.594	-0.009	-1.328	-1.163	0.002
4	i	63	PHE	0	-0.030	-0.017	6.524	-2.752	-2.752	0.000	0.000	0.000	0.000
5	i	64	ARG	1	0.787	0.885	10.214	-15.928	-15.928	0.000	0.000	0.000	0.000
6	i	65	ILE	0	-0.040	-0.018	12.560	-0.551	-0.551	0.000	0.000	0.000	0.000
7	i	66	LYS	1	0.802	0.906	15.200	-15.059	-15.059	0.000	0.000	0.000	0.000
8	i	67	TYR	0	-0.009	-0.023	17.704	0.426	0.426	0.000	0.000	0.000	0.000
9	i	68	VAL	0	-0.013	0.001	20.198	-0.497	-0.497	0.000	0.000	0.000	0.000
10	i	69	GLY	0	0.023	0.007	22.632	-0.619	-0.619	0.000	0.000	0.000	0.000
11	i	70	ALA	0	-0.041	-0.019	22.439	0.647	0.647	0.000	0.000	0.000	0.000
12	i	71	ILE	0	0.041	0.038	23.866	-0.346	-0.346	0.000	0.000	0.000	0.000
13	i	82	LEU	0	0.058	0.016	27.270	-0.066	-0.066	0.000	0.000	0.000	0.000
14	i	83	GLU	-1	-0.979	-0.989	27.412	10.433	10.433	0.000	0.000	0.000	0.000
15	i	84	GLY	0	0.026	0.011	25.900	-0.100	-0.100	0.000	0.000	0.000	0.000
16	i	85	PRO	0	-0.071	-0.043	23.034	0.215	0.215	0.000	0.000	0.000	0.000
17	i	86	LEU	0	0.058	0.009	24.525	0.117	0.117	0.000	0.000	0.000	0.000
18	i	87	ASP	-1	-0.880	-0.934	27.667	10.136	10.136	0.000	0.000	0.000	0.000
19	i	88	LEU	0	-0.065	-0.031	23.248	-0.141	-0.141	0.000	0.000	0.000	0.000
20	i	89	ILE	0	-0.024	-0.013	24.388	0.071	0.071	0.000	0.000	0.000	0.000
21	i	90	ASN	0	-0.002	0.020	27.326	-0.312	-0.312	0.000	0.000	0.000	0.000
22	i	91	TYR	0	0.012	0.000	27.227	-0.364	-0.364	0.000	0.000	0.000	0.000
23	i	92	ILE	0	0.014	0.015	23.532	0.167	0.167	0.000	0.000	0.000	0.000
24	i	93	ASP	-1	-0.830	-0.929	27.908	9.989	9.989	0.000	0.000	0.000	0.000
25	i	94	VAL	0	-0.047	-0.029	31.020	-0.308	-0.308	0.000	0.000	0.000	0.000
26	i	95	ALA	0	-0.046	-0.031	29.144	-0.218	-0.218	0.000	0.000	0.000	0.000
27	i	96	GLN	0	-0.013	0.007	27.369	-0.347	-0.347	0.000	0.000	0.000	0.000
28	i	97	GLN	0	-0.022	-0.011	31.896	-0.330	-0.330	0.000	0.000	0.000	0.000
29	i	98	ASP	-1	-0.861	-0.943	35.188	7.604	7.604	0.000	0.000	0.000	0.000
30	i	99	GLY	0	-0.049	-0.015	37.222	0.102	0.102	0.000	0.000	0.000	0.000
31	i	100	LYS	1	0.793	0.903	33.915	-8.768	-8.768	0.000	0.000	0.000	0.000
32	i	101	LEU	0	0.080	0.021	31.378	0.052	0.052	0.000	0.000	0.000	0.000
33	i	102	PRO	0	-0.060	0.002	27.511	0.170	0.170	0.000	0.000	0.000	0.000
34	i	103	PHE	0	0.012	-0.001	27.632	0.312	0.312	0.000	0.000	0.000	0.000
35	i	104	VAL	0	-0.002	-0.003	27.081	0.267	0.267	0.000	0.000	0.000	0.000
36	i	105	PRO	0	-0.013	0.003	22.419	-0.024	-0.024	0.000	0.000	0.000	0.000
37	i	106	PRO	0	-0.024	-0.007	23.044	-0.216	-0.216	0.000	0.000	0.000	0.000
38	i	107	GLU	-1	-0.819	-0.907	20.152	15.295	15.295	0.000	0.000	0.000	0.000
39	i	108	GLU	-1	-0.864	-0.961	20.348	13.742	13.742	0.000	0.000	0.000	0.000
40	i	109	GLU	-1	-0.856	-0.917	15.418	17.494	17.494	0.000	0.000	0.000	0.000
41	i	110	PHE	0	0.003	0.014	15.001	0.996	0.996	0.000	0.000	0.000	0.000
42	i	111	ILE	0	0.014	0.004	8.792	0.187	0.187	0.000	0.000	0.000	0.000
43	i	112	MET	0	-0.044	-0.032	8.967	-0.266	-0.266	0.000	0.000	0.000	0.000
44	i	113	GLY	0	0.048	0.045	4.905	0.388	0.388	0.000	0.000	0.000	0.000
45	i	114	VAL	0	-0.036	-0.020	4.037	-3.182	-2.856	0.000	-0.078	-0.248	0.000
46	i	115	SER	0	-0.025	-0.020	2.365	8.201	9.576	2.306	-1.853	-1.829	-0.009
47	i	116	LYS	1	0.975	0.992	4.646	-46.941	-46.753	0.000	-0.074	-0.114	0.001
48	i	117	TYR	0	0.004	-0.030	6.904	-5.307	-5.307	0.000	0.000	0.000	0.000
49	i	118	GLY	0	0.058	0.017	8.385	-3.570	-3.570	0.000	0.000	0.000	0.000
50	i	119	ILE	0	-0.006	0.016	7.138	3.759	3.759	0.000	0.000	0.000	0.000
51	i	120	LYS	1	0.930	0.978	7.208	-36.270	-36.270	0.000	0.000	0.000	0.000
52	i	121	VAL	0	-0.001	0.010	9.171	0.725	0.725	0.000	0.000	0.000	0.000
53	i	122	SER	0	0.007	0.010	11.156	-0.005	-0.005	0.000	0.000	0.000	0.000
54	i	131	HIS	0	-0.005	-0.007	13.767	0.100	0.100	0.000	0.000	0.000	0.000
55	i	132	ARG	1	0.930	0.952	13.065	-18.056	-18.056	0.000	0.000	0.000	0.000
56	i	133	HIS	0	0.068	0.046	12.660	-1.234	-1.234	0.000	0.000	0.000	0.000
57	i	134	ALA	0	0.036	0.012	11.768	2.346	2.346	0.000	0.000	0.000	0.000
58	i	135	LEU	0	0.020	0.002	9.724	-1.467	-1.467	0.000	0.000	0.000	0.000
59	i	136	TYR	0	-0.029	-0.005	13.679	-0.593	-0.593	0.000	0.000	0.000	0.000
60	i	137	LEU	0	0.000	0.007	16.508	-0.920	-0.920	0.000	0.000	0.000	0.000
61	i	138	ILE	0	-0.044	-0.020	12.130	-0.704	-0.704	0.000	0.000	0.000	0.000
62	i	139	ILE	0	0.004	0.022	16.167	0.066	0.066	0.000	0.000	0.000	0.000
63	i	140	ARG	1	0.924	0.947	17.716	-13.701	-13.701	0.000	0.000	0.000	0.000
64	i	141	MET	0	0.002	0.022	13.244	0.543	0.543	0.000	0.000	0.000	0.000
65	i	142	VAL	0	-0.034	-0.027	16.673	-0.439	-0.439	0.000	0.000	0.000	0.000
66	i	143	CYS	0	-0.059	-0.010	16.826	-0.079	-0.079	0.000	0.000	0.000	0.000
67	i	144	TYR	0	0.021	0.002	19.215	-0.096	-0.096	0.000	0.000	0.000	0.000
68	i	145	ASP	-1	-0.870	-0.946	22.618	11.730	11.730	0.000	0.000	0.000	0.000
69	i	146	ASP	-1	-0.867	-0.945	24.769	11.335	11.335	0.000	0.000	0.000	0.000
70	i	147	GLY	0	0.013	0.025	26.562	-0.370	-0.370	0.000	0.000	0.000	0.000
71	i	148	LEU	0	-0.043	-0.018	29.584	-0.333	-0.333	0.000	0.000	0.000	0.000
72	i	149	GLY	0	-0.031	-0.005	28.754	0.319	0.319	0.000	0.000	0.000	0.000
73	i	150	ALA	0	0.065	0.006	28.210	-0.209	-0.209	0.000	0.000	0.000	0.000
74	i	151	GLY	0	-0.042	0.003	24.624	0.250	0.250	0.000	0.000	0.000	0.000
75	i	152	LYS	1	0.818	0.895	22.696	-11.690	-11.690	0.000	0.000	0.000	0.000
76	i	153	SER	0	0.034	0.027	19.568	0.022	0.022	0.000	0.000	0.000	0.000
77	i	154	LEU	0	0.008	0.003	20.698	0.306	0.306	0.000	0.000	0.000	0.000
78	i	155	LEU	0	-0.027	-0.020	14.581	0.481	0.481	0.000	0.000	0.000	0.000
79	i	156	ALA	0	0.034	0.022	18.088	-0.663	-0.663	0.000	0.000	0.000	0.000
80	i	157	LEU	0	-0.021	-0.023	13.504	0.938	0.938	0.000	0.000	0.000	0.000
81	i	158	LYS	1	0.929	0.964	17.686	-12.655	-12.655	0.000	0.000	0.000	0.000
82	i	159	THR	0	-0.020	-0.013	17.043	0.834	0.834	0.000	0.000	0.000	0.000
83	i	160	THR	0	0.046	-0.004	19.921	-0.487	-0.487	0.000	0.000	0.000	0.000
84	i	161	ASP	-1	-0.733	-0.851	22.215	12.513	12.513	0.000	0.000	0.000	0.000
85	i	162	ALA	0	-0.032	-0.021	22.381	0.329	0.329	0.000	0.000	0.000	0.000
86	i	163	SER	0	-0.093	-0.045	24.362	-0.296	-0.296	0.000	0.000	0.000	0.000
87	i	164	ASN	0	-0.139	-0.084	26.380	-0.006	-0.006	0.000	0.000	0.000	0.000
88	i	165	GLU	-1	-0.887	-0.927	27.796	9.978	9.978	0.000	0.000	0.000	0.000
89	i	166	GLU	-1	-0.938	-0.967	26.320	11.319	11.319	0.000	0.000	0.000	0.000
90	i	167	TYR	0	-0.090	-0.046	24.683	0.817	0.817	0.000	0.000	0.000	0.000
91	i	168	SER	0	-0.014	-0.005	22.410	-0.462	-0.462	0.000	0.000	0.000	0.000
92	i	169	LEU	0	-0.054	-0.013	20.959	0.563	0.563	0.000	0.000	0.000	0.000
93	i	170	TRP	0	-0.026	-0.022	17.923	-0.444	-0.444	0.000	0.000	0.000	0.000
94	i	171	VAL	0	0.009	0.014	19.259	0.305	0.305	0.000	0.000	0.000	0.000
95	i	172	TYR	0	0.008	-0.005	15.509	0.215	0.215	0.000	0.000	0.000	0.000
96	i	173	GLN	0	0.005	-0.007	17.869	0.181	0.181	0.000	0.000	0.000	0.000
97	i	174	CYS	0	-0.046	-0.012	14.615	0.990	0.990	0.000	0.000	0.000	0.000
98	i	175	ASN	0	0.045	0.011	18.021	-0.873	-0.873	0.000	0.000	0.000	0.000
99	i	176	SER	0	-0.036	-0.028	19.018	-0.417	-0.417	0.000	0.000	0.000	0.000
100	i	177	LEU	0	0.100	0.051	18.801	0.736	0.736	0.000	0.000	0.000	0.000
101	i	178	GLU	-1	-0.847	-0.924	18.118	14.437	14.437	0.000	0.000	0.000	0.000
102	i	179	GLN	0	-0.034	-0.015	13.858	1.602	1.602	0.000	0.000	0.000	0.000
103	i	180	ALA	0	0.115	0.052	13.648	1.426	1.426	0.000	0.000	0.000	0.000
104	i	181	GLN	0	0.009	-0.013	14.654	1.043	1.043	0.000	0.000	0.000	0.000
105	i	182	ALA	0	-0.018	-0.007	11.765	0.577	0.577	0.000	0.000	0.000	0.000
106	i	183	ILE	0	0.020	0.016	9.528	1.796	1.796	0.000	0.000	0.000	0.000
107	i	184	CYS	0	-0.028	-0.017	10.213	1.254	1.254	0.000	0.000	0.000	0.000
108	i	185	LYS	1	0.900	0.950	11.917	-17.106	-17.106	0.000	0.000	0.000	0.000
109	i	186	VAL	0	0.024	0.019	5.448	0.560	0.560	0.000	0.000	0.000	0.000
110	i	187	LEU	0	0.003	0.011	7.770	2.811	2.811	0.000	0.000	0.000	0.000
111	i	188	SER	0	-0.039	-0.030	9.303	-0.739	-0.739	0.000	0.000	0.000	0.000
112	i	189	THR	0	-0.043	-0.025	6.960	0.624	0.624	0.000	0.000	0.000	0.000
113	i	190	ALA	0	0.007	0.012	7.453	-0.242	-0.242	0.000	0.000	0.000	0.000
114	i	191	PHE	0	0.003	-0.016	9.212	-1.281	-1.281	0.000	0.000	0.000	0.000
115	i	192	ASP	-1	-0.934	-0.950	12.280	19.346	19.346	0.000	0.000	0.000	0.000
116	i	193	SER	0	-0.062	-0.015	10.067	0.692	0.692	0.000	0.000	0.000	0.000
117	i	194	VAL	0	-0.066	-0.045	10.753	-0.631	-0.631	0.000	0.000	0.000	0.000
118	i	195	LEU	0	-0.016	0.015	13.282	-1.440	-1.440	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(i:60:CYM)