FMO DATABASE

FMODB ID: JL289

Calculation Name: 4W5X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4W5X

Chain ID: B

ChEMBL ID:

UniProt ID: P08586

Base Structure: X-ray

Registration Date: 2023-06-22

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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1001961.942198
FMO2-HF: Nuclear repulsion	953819.839496
FMO2-HF: Total energy	-48142.102701
FMO2-MP2: Total energy	-48279.440341

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(B:2:GLU)

Summations of interaction energy for fragment #1(B:2:GLU)

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.
-139.936	-139.212	21.35	-12.632	-9.442	0.12

Interaction energy analysis for fragmet #1(B:2:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.815 / q_NPA : -0.893

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	B	4	ASP	-1	-0.752	-0.874	2.934	34.148	36.999	0.250	-1.407	-1.694	-0.001
4	B	5	LYS	1	0.857	0.885	1.647	-119.574	-124.367	20.971	-10.064	-6.113	0.110
5	B	6	ARG	1	0.834	0.926	6.759	-23.566	-23.566	0.000	0.000	0.000	0.000
6	B	7	MET	0	-0.004	0.007	8.983	-1.923	-1.923	0.000	0.000	0.000	0.000
7	B	8	LYS	1	0.848	0.942	8.071	-36.419	-36.419	0.000	0.000	0.000	0.000
8	B	9	SER	0	-0.025	-0.004	10.104	-2.755	-2.755	0.000	0.000	0.000	0.000
9	B	10	LEU	0	-0.032	-0.020	12.523	-2.041	-2.041	0.000	0.000	0.000	0.000
10	B	11	ALA	0	0.010	0.008	13.034	-1.541	-1.541	0.000	0.000	0.000	0.000
11	B	12	MET	0	-0.006	0.021	12.920	-1.106	-1.106	0.000	0.000	0.000	0.000
12	B	13	THR	0	-0.054	-0.030	15.619	-1.321	-1.321	0.000	0.000	0.000	0.000
13	B	14	ALA	0	-0.080	-0.049	18.237	-0.836	-0.836	0.000	0.000	0.000	0.000
14	B	15	PHE	0	-0.013	0.006	18.060	-0.808	-0.808	0.000	0.000	0.000	0.000
15	B	16	PHE	0	0.018	0.020	18.146	0.147	0.147	0.000	0.000	0.000	0.000
16	B	17	GLY	0	0.013	0.006	19.213	-0.792	-0.792	0.000	0.000	0.000	0.000
17	B	18	GLU	-1	-0.932	-0.968	20.742	13.211	13.211	0.000	0.000	0.000	0.000
18	B	19	LEU	0	-0.091	-0.048	16.483	-0.200	-0.200	0.000	0.000	0.000	0.000
19	B	20	SER	0	0.079	0.053	18.828	0.407	0.407	0.000	0.000	0.000	0.000
20	B	21	THR	0	0.048	-0.025	15.328	0.652	0.652	0.000	0.000	0.000	0.000
21	B	22	LEU	0	0.035	0.020	15.851	0.905	0.905	0.000	0.000	0.000	0.000
22	B	23	ASP	-1	-0.786	-0.856	17.703	15.287	15.287	0.000	0.000	0.000	0.000
23	B	24	ILE	0	-0.026	-0.008	11.716	0.528	0.528	0.000	0.000	0.000	0.000
24	B	25	MET	0	-0.040	0.007	13.238	0.991	0.991	0.000	0.000	0.000	0.000
25	B	26	ALA	0	0.059	0.016	14.164	0.084	0.084	0.000	0.000	0.000	0.000
26	B	27	LEU	0	-0.034	-0.031	14.158	-0.269	-0.269	0.000	0.000	0.000	0.000
27	B	28	ILE	0	-0.059	-0.028	8.881	0.654	0.654	0.000	0.000	0.000	0.000
28	B	29	MET	0	0.006	0.023	11.368	-0.241	-0.241	0.000	0.000	0.000	0.000
29	B	30	SER	0	-0.044	-0.016	13.622	-0.717	-0.717	0.000	0.000	0.000	0.000
30	B	31	ILE	0	-0.087	-0.053	11.641	-0.845	-0.845	0.000	0.000	0.000	0.000
31	B	32	PHE	0	-0.036	-0.033	8.479	0.026	0.026	0.000	0.000	0.000	0.000
32	B	33	LYS	1	0.919	0.977	10.530	-16.546	-16.546	0.000	0.000	0.000	0.000
33	B	34	ARG	1	0.864	0.943	3.131	-41.465	-40.115	0.084	-0.731	-0.703	0.009
34	B	35	HIS	0	0.045	0.004	10.351	-0.308	-0.308	0.000	0.000	0.000	0.000
35	B	36	PRO	0	-0.047	-0.015	11.116	1.234	1.234	0.000	0.000	0.000	0.000
36	B	37	ASN	0	-0.010	-0.019	9.885	-1.676	-1.676	0.000	0.000	0.000	0.000
37	B	38	ASN	0	-0.008	-0.007	13.320	-0.576	-0.576	0.000	0.000	0.000	0.000
38	B	39	THR	0	-0.012	0.004	15.110	1.049	1.049	0.000	0.000	0.000	0.000
39	B	40	ILE	0	0.006	0.008	14.635	-0.239	-0.239	0.000	0.000	0.000	0.000
40	B	41	PHE	0	-0.006	0.004	18.575	0.167	0.167	0.000	0.000	0.000	0.000
41	B	42	SER	0	-0.002	0.000	18.925	0.239	0.239	0.000	0.000	0.000	0.000
42	B	43	VAL	0	0.021	0.024	21.327	-0.425	-0.425	0.000	0.000	0.000	0.000
43	B	44	ASP	-1	-0.811	-0.914	21.046	14.563	14.563	0.000	0.000	0.000	0.000
44	B	45	LYS	1	0.823	0.874	20.974	-14.375	-14.375	0.000	0.000	0.000	0.000
45	B	46	ASP	-1	-0.880	-0.911	23.822	12.421	12.421	0.000	0.000	0.000	0.000
46	B	47	GLY	0	-0.001	0.010	25.994	-0.476	-0.476	0.000	0.000	0.000	0.000
47	B	48	GLN	0	-0.058	-0.029	23.751	-0.761	-0.761	0.000	0.000	0.000	0.000
48	B	49	PHE	0	0.025	0.007	23.936	0.614	0.614	0.000	0.000	0.000	0.000
49	B	50	MET	0	-0.049	-0.038	17.903	0.242	0.242	0.000	0.000	0.000	0.000
50	B	51	ILE	0	0.018	0.029	18.521	0.155	0.155	0.000	0.000	0.000	0.000
51	B	52	ASP	-1	-0.762	-0.842	13.854	23.276	23.276	0.000	0.000	0.000	0.000
52	B	53	PHE	0	-0.020	-0.039	13.235	-0.857	-0.857	0.000	0.000	0.000	0.000
53	B	54	GLU	-1	-0.861	-0.937	11.143	24.361	24.361	0.000	0.000	0.000	0.000
54	B	55	TYR	0	0.003	-0.007	7.034	-1.514	-1.514	0.000	0.000	0.000	0.000
55	B	56	ASP	-1	-0.837	-0.913	5.452	29.159	29.159	0.000	0.000	0.000	0.000
56	B	57	ASN	0	-0.062	-0.039	3.761	-0.889	-0.602	0.003	-0.066	-0.224	0.000
57	B	58	TYR	0	-0.016	-0.014	3.456	5.345	6.374	0.042	-0.364	-0.708	0.002
58	B	59	LYS	1	0.985	1.004	6.411	-26.480	-26.480	0.000	0.000	0.000	0.000
59	B	60	ALA	0	0.016	0.000	9.287	2.302	2.302	0.000	0.000	0.000	0.000
60	B	61	SER	0	-0.007	-0.038	11.176	1.020	1.020	0.000	0.000	0.000	0.000
61	B	62	GLN	0	0.070	0.032	6.755	-1.968	-1.968	0.000	0.000	0.000	0.000
62	B	63	TYR	0	-0.045	-0.033	6.238	3.454	3.454	0.000	0.000	0.000	0.000
63	B	64	LEU	0	-0.017	-0.019	10.110	-0.968	-0.968	0.000	0.000	0.000	0.000
64	B	65	ASP	-1	-0.866	-0.919	11.448	26.640	26.640	0.000	0.000	0.000	0.000
65	B	66	LEU	0	-0.006	-0.001	13.136	-1.709	-1.709	0.000	0.000	0.000	0.000
66	B	67	THR	0	-0.035	-0.042	14.457	1.018	1.018	0.000	0.000	0.000	0.000
67	B	68	LEU	0	-0.042	0.003	16.261	-1.056	-1.056	0.000	0.000	0.000	0.000
68	B	69	THR	0	-0.006	-0.002	18.410	0.523	0.523	0.000	0.000	0.000	0.000
69	B	70	PRO	0	-0.020	-0.013	19.775	-0.202	-0.202	0.000	0.000	0.000	0.000
70	B	71	ILE	0	-0.015	0.005	21.774	-0.424	-0.424	0.000	0.000	0.000	0.000
71	B	72	SER	0	-0.011	-0.012	24.977	-0.190	-0.190	0.000	0.000	0.000	0.000
72	B	73	GLY	0	0.009	-0.020	28.082	-0.112	-0.112	0.000	0.000	0.000	0.000
73	B	74	ASP	-1	-0.917	-0.964	31.005	9.301	9.301	0.000	0.000	0.000	0.000
74	B	75	GLU	-1	-0.882	-0.929	27.604	11.534	11.534	0.000	0.000	0.000	0.000
75	B	76	CYS	0	-0.027	-0.009	29.866	0.073	0.073	0.000	0.000	0.000	0.000
76	B	77	LYS	1	0.978	0.975	30.830	-8.359	-8.359	0.000	0.000	0.000	0.000
77	B	78	THR	0	-0.022	-0.013	31.887	-0.248	-0.248	0.000	0.000	0.000	0.000
78	B	79	HIS	0	0.041	0.027	28.365	-0.089	-0.089	0.000	0.000	0.000	0.000
79	B	80	ALA	0	0.017	0.025	29.793	0.231	0.231	0.000	0.000	0.000	0.000
80	B	81	SER	0	-0.004	-0.016	31.309	0.064	0.064	0.000	0.000	0.000	0.000
81	B	82	SER	0	0.046	0.018	27.434	0.014	0.014	0.000	0.000	0.000	0.000
82	B	83	ILE	0	-0.027	-0.007	26.602	0.402	0.402	0.000	0.000	0.000	0.000
83	B	84	ALA	0	-0.004	-0.006	27.116	0.266	0.266	0.000	0.000	0.000	0.000
84	B	85	GLU	-1	-0.905	-0.948	27.671	10.926	10.926	0.000	0.000	0.000	0.000
85	B	86	GLN	0	0.012	-0.011	22.461	0.831	0.831	0.000	0.000	0.000	0.000
86	B	87	LEU	0	-0.009	-0.009	23.926	0.451	0.451	0.000	0.000	0.000	0.000
87	B	88	ALA	0	0.024	0.020	25.288	0.119	0.119	0.000	0.000	0.000	0.000
88	B	89	SER	0	-0.018	-0.016	24.254	-0.008	-0.008	0.000	0.000	0.000	0.000
89	B	90	VAL	0	-0.038	-0.023	20.023	0.334	0.334	0.000	0.000	0.000	0.000
90	B	91	ASP	-1	-0.902	-0.951	22.066	12.063	12.063	0.000	0.000	0.000	0.000
91	B	92	ILE	0	-0.023	-0.004	24.626	-0.113	-0.113	0.000	0.000	0.000	0.000
92	B	93	ILE	0	-0.089	-0.055	18.821	0.174	0.174	0.000	0.000	0.000	0.000
93	B	94	LYS	1	0.876	0.920	19.256	-13.367	-13.367	0.000	0.000	0.000	0.000
94	B	95	GLU	-1	-0.944	-0.941	21.230	10.724	10.724	0.000	0.000	0.000	0.000
95	B	96	ASP	-1	-0.829	-0.912	23.792	11.273	11.273	0.000	0.000	0.000	0.000
96	B	97	ILE	0	0.024	0.007	17.603	0.062	0.062	0.000	0.000	0.000	0.000
97	B	98	SER	0	-0.047	-0.034	20.977	0.280	0.280	0.000	0.000	0.000	0.000
98	B	99	GLU	-1	-0.885	-0.945	22.660	10.330	10.330	0.000	0.000	0.000	0.000
99	B	100	TYR	0	0.031	0.029	21.256	-0.169	-0.169	0.000	0.000	0.000	0.000
100	B	101	ILE	0	-0.037	-0.009	18.311	0.079	0.079	0.000	0.000	0.000	0.000
101	B	102	LYS	1	0.866	0.938	22.323	-10.350	-10.350	0.000	0.000	0.000	0.000
102	B	103	THR	0	-0.054	-0.034	25.641	-0.269	-0.269	0.000	0.000	0.000	0.000
103	B	104	THR	0	0.053	0.027	23.594	-0.262	-0.262	0.000	0.000	0.000	0.000
104	B	105	PRO	0	-0.037	-0.019	24.587	0.523	0.523	0.000	0.000	0.000	0.000
105	B	106	ARG	1	0.888	0.890	22.282	-13.640	-13.640	0.000	0.000	0.000	0.000
106	B	107	LEU	0	0.056	0.038	19.084	0.632	0.632	0.000	0.000	0.000	0.000
107	B	108	LYS	1	0.980	1.002	20.622	-10.580	-10.580	0.000	0.000	0.000	0.000
108	B	109	ARG	1	0.844	0.922	22.683	-12.411	-12.411	0.000	0.000	0.000	0.000
109	B	110	PHE	0	0.055	0.028	13.598	0.085	0.085	0.000	0.000	0.000	0.000
110	B	111	ILE	0	0.051	0.016	17.264	0.522	0.522	0.000	0.000	0.000	0.000
111	B	112	LYS	1	0.909	0.966	18.863	-11.613	-11.613	0.000	0.000	0.000	0.000
112	B	113	LYS	1	0.973	0.991	18.246	-16.315	-16.315	0.000	0.000	0.000	0.000
113	B	114	TYR	0	-0.011	-0.025	9.761	-0.843	-0.843	0.000	0.000	0.000	0.000
114	B	115	ARG	1	0.931	0.967	16.021	-13.757	-13.757	0.000	0.000	0.000	0.000
115	B	116	ASN	0	-0.057	-0.028	18.174	-1.094	-1.094	0.000	0.000	0.000	0.000
116	B	117	ARG	1	0.984	1.003	15.992	-14.394	-14.394	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:GLU)