FMO DATABASE

FMODB ID: G8VK1

Calculation Name: 1D1J-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane | 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane

Ligand 3-letter code: PG6 | PG5

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1D1J

Chain ID: A

ChEMBL ID:

UniProt ID: P35080

Base Structure: X-ray

Registration Date: 2025-09-02

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	138
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1199513.523769
FMO2-HF: Nuclear repulsion	1145643.314843
FMO2-HF: Total energy	-53870.208926
FMO2-MP2: Total energy	-54021.22974

3D Structure Molmil

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(A:1:ALA)

Summations of interaction energy for fragment #1(A:1:ALA)

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.
-24.563	-22.773	-0.023	-0.848	-0.919	-0.002

Interaction energy analysis for fragmet #1(A:1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.872 / q_NPA : 0.921

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	A	3	TRP	0	0.070	0.027	3.853	1.382	3.172	-0.023	-0.848	-0.919	-0.002
4	A	4	GLN	0	0.056	0.022	6.758	4.009	4.009	0.000	0.000	0.000	0.000
5	A	5	SER	0	0.022	0.030	6.446	2.255	2.255	0.000	0.000	0.000	0.000
6	A	6	TYR	0	0.037	-0.001	5.840	3.586	3.586	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.017	0.005	9.902	2.377	2.377	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.860	-0.931	11.090	-23.899	-23.899	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.006	-0.016	10.381	2.780	2.780	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.041	-0.007	13.756	1.598	1.598	0.000	0.000	0.000	0.000
11	A	11	MET	0	-0.021	-0.012	15.986	1.519	1.519	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.046	-0.010	16.037	0.882	0.882	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.779	-0.852	18.806	-13.836	-13.836	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.009	0.020	21.513	0.728	0.728	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.044	-0.022	22.689	0.512	0.512	0.000	0.000	0.000	0.000
16	A	16	CYS	0	-0.012	-0.021	20.802	0.318	0.318	0.000	0.000	0.000	0.000
17	A	17	GLN	0	-0.085	-0.060	22.931	0.055	0.055	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.795	-0.890	20.316	-14.426	-14.426	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.016	0.002	16.138	0.390	0.390	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.007	-0.017	14.616	-0.511	-0.511	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.026	0.004	9.604	0.161	0.161	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.021	0.008	12.665	-0.684	-0.684	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.042	0.023	12.994	0.050	0.050	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.021	-0.041	13.482	1.521	1.521	0.000	0.000	0.000	0.000
25	A	25	CYS	0	-0.012	0.004	15.039	0.708	0.708	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.777	-0.888	14.175	-18.195	-18.195	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.041	-0.013	11.856	0.372	0.372	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.804	0.904	13.735	13.157	13.157	0.000	0.000	0.000	0.000
29	A	29	TYR	0	0.041	0.004	11.036	1.215	1.215	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.017	0.015	13.970	-1.123	-1.123	0.000	0.000	0.000	0.000
31	A	31	TRP	0	-0.098	-0.044	8.322	-1.685	-1.685	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.018	-0.010	9.736	-3.035	-3.035	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.021	0.005	11.709	1.322	1.322	0.000	0.000	0.000	0.000
34	A	34	THR	0	0.025	0.025	15.180	-0.462	-0.462	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.024	0.013	17.143	0.580	0.580	0.000	0.000	0.000	0.000
36	A	36	GLY	0	-0.037	-0.025	18.569	0.641	0.641	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.007	0.017	20.924	0.696	0.696	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.021	-0.037	22.312	-0.052	-0.052	0.000	0.000	0.000	0.000
39	A	39	PHE	0	-0.010	-0.031	18.769	-0.077	-0.077	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.017	0.011	17.745	-1.228	-1.228	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.029	-0.015	18.887	-0.272	-0.272	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.064	-0.008	19.151	0.661	0.661	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.002	-0.018	19.745	-0.542	-0.542	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.032	-0.006	19.968	0.033	0.033	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.028	0.019	21.495	0.106	0.106	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.724	-0.818	23.217	-12.386	-12.386	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.007	0.000	17.423	0.039	0.039	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.836	-0.902	21.309	-12.988	-12.988	0.000	0.000	0.000	0.000
49	A	49	MET	0	-0.049	-0.019	23.865	0.338	0.338	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.002	0.007	21.383	0.220	0.220	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.001	0.003	19.778	0.197	0.197	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.039	0.046	23.240	0.087	0.087	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.950	0.955	26.344	10.497	10.497	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.849	-0.904	28.991	-8.998	-8.998	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.734	0.806	25.779	10.945	10.945	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.840	-0.893	31.499	-8.299	-8.299	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.059	0.030	33.815	0.067	0.067	0.000	0.000	0.000	0.000
58	A	58	PHE	0	0.001	-0.008	28.499	0.093	0.093	0.000	0.000	0.000	0.000
59	A	59	PHE	0	-0.084	-0.037	32.243	-0.131	-0.131	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.061	-0.045	34.884	0.192	0.192	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.085	-0.051	34.970	0.330	0.330	0.000	0.000	0.000	0.000
62	A	62	GLY	0	-0.059	-0.013	33.053	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.000	-0.002	26.636	-0.055	-0.055	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.076	-0.062	27.449	0.311	0.311	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.000	-0.003	22.633	-0.408	-0.408	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.042	0.032	24.170	0.007	0.007	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.037	-0.036	24.622	0.317	0.317	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.936	0.980	27.457	11.780	11.780	0.000	0.000	0.000	0.000
69	A	69	LYS	1	1.007	1.004	28.949	8.461	8.461	0.000	0.000	0.000	0.000
70	A	70	CYS	0	-0.026	-0.012	28.698	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.008	-0.008	31.055	0.432	0.432	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.013	0.032	28.801	-0.283	-0.283	0.000	0.000	0.000	0.000
73	A	73	ILE	0	-0.083	-0.041	30.826	0.390	0.390	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.956	0.967	29.979	9.999	9.999	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.739	-0.853	27.385	-11.489	-11.489	0.000	0.000	0.000	0.000
76	A	76	SER	0	-0.018	-0.021	26.803	0.524	0.524	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.032	0.010	21.238	-0.350	-0.350	0.000	0.000	0.000	0.000
78	A	78	TYR	0	-0.077	-0.067	22.439	-0.820	-0.820	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.011	0.028	25.956	0.323	0.323	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.873	-0.938	27.085	-10.420	-10.420	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.051	-0.026	26.700	0.184	0.184	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.800	-0.875	25.228	-12.086	-12.086	0.000	0.000	0.000	0.000
83	A	83	CYS	0	-0.072	-0.032	20.704	-0.499	-0.499	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.017	-0.031	21.728	-0.464	-0.464	0.000	0.000	0.000	0.000
85	A	85	MET	0	-0.037	-0.006	23.786	0.260	0.260	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.850	-0.894	25.226	-11.486	-11.486	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.001	-0.009	25.068	0.359	0.359	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.925	0.955	28.574	9.360	9.360	0.000	0.000	0.000	0.000
89	A	89	THR	0	0.037	0.016	28.621	0.090	0.090	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.838	0.898	31.111	9.276	9.276	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.032	-0.023	34.239	-0.123	-0.123	0.000	0.000	0.000	0.000
92	A	92	GLN	0	-0.092	-0.063	35.106	0.164	0.164	0.000	0.000	0.000	0.000
93	A	93	GLY	0	-0.001	-0.007	39.198	0.221	0.221	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.014	0.006	40.394	0.184	0.184	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.804	-0.885	35.177	-8.741	-8.741	0.000	0.000	0.000	0.000
96	A	96	PRO	0	0.013	0.021	34.402	0.008	0.008	0.000	0.000	0.000	0.000
97	A	97	THR	0	-0.051	-0.017	33.428	-0.179	-0.179	0.000	0.000	0.000	0.000
98	A	98	TYR	0	0.031	0.004	28.448	-0.109	-0.109	0.000	0.000	0.000	0.000
99	A	99	ASN	0	-0.032	-0.022	28.686	0.193	0.193	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.026	-0.009	23.407	-0.334	-0.334	0.000	0.000	0.000	0.000
101	A	101	ALA	0	-0.029	0.004	22.821	0.476	0.476	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.016	0.009	19.656	-0.714	-0.714	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.044	0.015	19.117	0.722	0.722	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.817	0.910	17.363	12.924	12.924	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.070	0.032	13.429	0.505	0.505	0.000	0.000	0.000	0.000
106	A	106	GLY	0	0.061	0.028	13.630	0.890	0.890	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.868	0.923	9.382	24.747	24.747	0.000	0.000	0.000	0.000
108	A	108	ALA	0	-0.003	-0.010	10.860	-0.502	-0.502	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.007	-0.001	13.012	1.055	1.055	0.000	0.000	0.000	0.000
110	A	110	VAL	0	0.019	0.018	13.587	-1.309	-1.309	0.000	0.000	0.000	0.000
111	A	111	ILE	0	-0.009	-0.008	15.698	1.314	1.314	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.023	0.004	17.810	-0.728	-0.728	0.000	0.000	0.000	0.000
113	A	113	MET	0	-0.009	0.014	20.311	0.942	0.942	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.047	0.023	23.627	-0.282	-0.282	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.875	0.928	25.002	12.664	12.664	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.860	-0.953	28.130	-9.023	-9.023	0.000	0.000	0.000	0.000
117	A	117	GLY	0	-0.020	0.000	31.886	-0.023	-0.023	0.000	0.000	0.000	0.000
118	A	118	VAL	0	-0.057	-0.007	26.520	0.070	0.070	0.000	0.000	0.000	0.000
119	A	119	HIS	0	0.042	0.026	29.814	-0.120	-0.120	0.000	0.000	0.000	0.000
120	A	120	GLY	0	0.052	0.014	28.036	-0.376	-0.376	0.000	0.000	0.000	0.000
121	A	121	GLY	0	0.017	0.011	27.175	-0.362	-0.362	0.000	0.000	0.000	0.000
122	A	122	THR	0	0.017	0.002	25.032	-0.087	-0.087	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.005	0.004	23.227	-0.491	-0.491	0.000	0.000	0.000	0.000
124	A	124	ASN	0	-0.011	-0.017	22.410	-0.678	-0.678	0.000	0.000	0.000	0.000
125	A	125	LYS	1	0.933	0.959	22.803	11.046	11.046	0.000	0.000	0.000	0.000
126	A	126	LYS	1	0.802	0.884	18.861	15.230	15.230	0.000	0.000	0.000	0.000
127	A	127	ALA	0	-0.012	-0.003	18.162	-0.973	-0.973	0.000	0.000	0.000	0.000
128	A	128	TYR	0	-0.022	-0.007	18.065	-0.880	-0.880	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.882	-0.951	18.909	-14.604	-14.604	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.020	0.001	11.399	-0.820	-0.820	0.000	0.000	0.000	0.000
131	A	131	ALA	0	-0.001	-0.008	14.269	-1.209	-1.209	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.003	0.001	16.210	-0.323	-0.323	0.000	0.000	0.000	0.000
133	A	133	TYR	0	-0.025	-0.023	9.833	0.613	0.613	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.022	-0.019	9.349	-0.852	-0.852	0.000	0.000	0.000	0.000
135	A	135	ARG	1	0.852	0.922	12.702	15.708	15.708	0.000	0.000	0.000	0.000
136	A	136	ARG	1	0.878	0.949	15.597	15.986	15.986	0.000	0.000	0.000	0.000
137	A	137	SER	0	-0.111	-0.055	11.045	0.353	0.353	0.000	0.000	0.000	0.000
138	A	138	ASP	-2	-1.900	-1.927	11.012	-44.224	-44.224	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:ALA)