FMO DATABASE

FMODB ID: 7KZ2K

Calculation Name: 3D01-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane

Ligand 3-letter code: PG5

Ligand of Interest (LOI):

PDB ID: 3D01

Chain ID: A

ChEMBL ID:

UniProt ID: A9CJ63

Base Structure: X-ray

Registration Date: 2025-10-05

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	163
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1460164.821935
FMO2-HF: Nuclear repulsion	1400846.122504
FMO2-HF: Total energy	-59318.69943
FMO2-MP2: Total energy	-59493.005209

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(A:1:GLY)

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

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.
-137.243	-135.673	17.559	-10.563	-8.565	-0.136

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.803 / q_NPA : 0.883

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	GLU	-1	-0.816	-0.902	1.845	-107.780	-105.664	10.372	-7.193	-5.295	-0.091
4	A	4	ASN	0	0.001	-0.005	1.872	-21.083	-21.837	7.188	-3.317	-3.116	-0.045
5	A	5	LEU	0	0.055	0.034	4.352	8.194	8.402	-0.001	-0.053	-0.154	0.000
6	A	6	TYR	0	-0.016	0.003	6.480	5.976	5.976	0.000	0.000	0.000	0.000
7	A	7	PHE	0	-0.010	-0.010	7.081	3.339	3.339	0.000	0.000	0.000	0.000
8	A	8	GLN	0	0.010	0.019	8.497	1.017	1.017	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.035	0.017	10.483	2.661	2.661	0.000	0.000	0.000	0.000
10	A	10	MET	0	-0.028	-0.024	11.887	1.712	1.712	0.000	0.000	0.000	0.000
11	A	11	SER	0	0.006	-0.002	12.515	2.111	2.111	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.897	-0.947	14.578	-19.867	-19.867	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.056	-0.026	16.316	1.463	1.463	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.031	0.001	16.438	1.145	1.145	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.795	-0.898	18.630	-15.505	-15.505	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.040	-0.012	20.419	0.770	0.770	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.930	0.960	20.248	15.877	15.877	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.020	-0.009	23.591	0.598	0.598	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.938	0.975	22.300	14.508	14.508	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.961	-0.974	25.231	-12.225	-12.225	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.058	-0.027	27.826	0.444	0.444	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.018	0.002	30.004	0.345	0.345	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.045	-0.029	28.643	0.263	0.263	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.033	-0.029	26.389	-0.385	-0.385	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.001	0.003	21.442	0.209	0.209	0.000	0.000	0.000	0.000
26	A	26	PRO	0	-0.009	0.006	25.734	0.046	0.046	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.029	-0.023	25.744	-0.493	-0.493	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.025	0.016	22.509	0.183	0.183	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.011	-0.001	24.643	0.287	0.287	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.019	-0.004	25.971	-0.302	-0.302	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.018	-0.008	27.982	0.217	0.217	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.011	0.016	31.741	-0.103	-0.103	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.013	-0.013	33.668	0.354	0.354	0.000	0.000	0.000	0.000
34	A	34	ASN	0	-0.036	-0.028	34.375	-0.164	-0.164	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.007	0.008	33.665	0.094	0.094	0.000	0.000	0.000	0.000
36	A	36	VAL	0	0.048	0.035	28.367	-0.020	-0.020	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.001	0.004	26.940	0.215	0.215	0.000	0.000	0.000	0.000
38	A	38	PHE	0	0.039	0.011	22.226	-0.102	-0.102	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.019	-0.002	25.755	0.033	0.033	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.040	0.012	19.495	-0.190	-0.190	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.024	-0.005	23.656	0.281	0.281	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.020	0.015	22.328	0.010	0.010	0.000	0.000	0.000	0.000
43	A	43	ASN	0	0.017	0.012	18.813	-0.751	-0.751	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.031	-0.013	20.283	-0.118	-0.118	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.015	0.017	20.269	0.240	0.240	0.000	0.000	0.000	0.000
46	A	46	TYR	0	-0.003	-0.003	23.088	0.417	0.417	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.015	-0.015	25.010	-0.176	-0.176	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.005	-0.024	27.557	0.329	0.329	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.016	0.021	30.959	-0.181	-0.181	0.000	0.000	0.000	0.000
50	A	50	GLN	0	-0.052	-0.027	29.261	-0.082	-0.082	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.061	0.017	32.731	0.196	0.196	0.000	0.000	0.000	0.000
52	A	52	PRO	0	0.002	0.007	34.062	-0.292	-0.292	0.000	0.000	0.000	0.000
53	A	53	MET	0	-0.065	-0.029	33.150	0.329	0.329	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.756	-0.878	33.217	-9.392	-9.392	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.043	-0.031	33.932	0.189	0.189	0.000	0.000	0.000	0.000
56	A	56	GLY	0	-0.010	-0.002	34.414	0.175	0.175	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.920	0.956	35.616	7.999	7.999	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.032	0.012	37.784	-0.190	-0.190	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.003	0.005	38.196	0.230	0.230	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.024	-0.007	39.655	0.157	0.157	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.025	-0.015	41.920	-0.046	-0.046	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.024	0.021	44.738	0.115	0.115	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.037	-0.016	46.272	-0.170	-0.170	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.014	-0.008	43.878	0.068	0.068	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.023	-0.010	47.288	0.072	0.072	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.837	0.925	50.437	6.052	6.052	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.853	-0.920	49.424	-6.218	-6.218	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.012	0.006	44.838	-0.061	-0.061	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.798	-0.885	46.049	-6.974	-6.974	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.035	-0.001	43.099	-0.168	-0.168	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.027	0.024	42.161	-0.219	-0.219	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.010	-0.029	41.155	-0.235	-0.235	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.012	0.001	40.986	-0.194	-0.194	0.000	0.000	0.000	0.000
74	A	74	GLN	0	-0.058	-0.035	38.313	-0.192	-0.192	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.894	0.957	34.997	8.843	8.843	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.024	-0.002	36.288	-0.244	-0.244	0.000	0.000	0.000	0.000
77	A	77	ALA	0	0.016	0.008	35.460	-0.254	-0.254	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.881	-0.955	32.387	-9.625	-9.625	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.003	0.007	31.360	-0.416	-0.416	0.000	0.000	0.000	0.000
80	A	80	CYS	0	-0.084	-0.014	31.673	-0.198	-0.198	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.016	0.004	28.884	-0.336	-0.336	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.005	0.004	27.332	-0.570	-0.570	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.057	-0.042	26.774	-0.511	-0.511	0.000	0.000	0.000	0.000
84	A	84	ILE	0	-0.006	-0.004	25.479	-0.379	-0.379	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.007	0.003	22.169	-0.574	-0.574	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.024	0.020	22.239	-0.761	-0.761	0.000	0.000	0.000	0.000
87	A	87	GLN	0	-0.004	-0.017	22.907	-0.771	-0.771	0.000	0.000	0.000	0.000
88	A	88	VAL	0	-0.009	-0.008	19.374	-0.441	-0.441	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.812	0.889	17.548	15.936	15.936	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.043	-0.022	18.230	-0.854	-0.854	0.000	0.000	0.000	0.000
91	A	91	ALA	0	-0.020	-0.006	19.199	-0.559	-0.559	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.030	-0.005	14.896	-0.617	-0.617	0.000	0.000	0.000	0.000
93	A	93	ASN	0	-0.074	-0.035	13.676	-0.996	-0.996	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.012	0.000	14.396	-0.949	-0.949	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.802	-0.900	10.282	-29.340	-29.340	0.000	0.000	0.000	0.000
96	A	96	LEU	0	0.047	0.004	13.745	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.057	-0.042	11.641	0.072	0.072	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.811	0.909	8.245	31.306	31.306	0.000	0.000	0.000	0.000
99	A	99	ILE	0	-0.007	0.012	13.704	0.845	0.845	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.749	0.850	15.664	17.294	17.294	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.780	0.861	17.836	13.678	13.678	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.016	0.019	21.598	0.056	0.056	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.024	-0.005	24.145	0.409	0.409	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.808	0.897	26.543	9.876	9.876	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.027	0.035	28.274	-0.240	-0.240	0.000	0.000	0.000	0.000
106	A	106	ASN	0	-0.085	-0.063	31.377	0.469	0.469	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.042	0.021	34.794	-0.140	-0.140	0.000	0.000	0.000	0.000
108	A	108	PHE	0	-0.004	-0.010	35.990	0.282	0.282	0.000	0.000	0.000	0.000
109	A	109	VAL	0	0.053	0.011	39.759	-0.109	-0.109	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.019	0.041	42.281	0.184	0.184	0.000	0.000	0.000	0.000
111	A	111	SER	0	-0.013	-0.022	45.284	-0.029	-0.029	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.006	0.017	48.146	0.075	0.075	0.000	0.000	0.000	0.000
113	A	113	PRO	0	-0.024	-0.022	51.203	-0.104	-0.104	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.879	-0.942	53.099	-5.848	-5.848	0.000	0.000	0.000	0.000
115	A	115	PHE	0	-0.049	-0.013	45.101	-0.044	-0.044	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.013	0.011	48.358	-0.071	-0.071	0.000	0.000	0.000	0.000
117	A	117	GLU	-1	-0.893	-0.959	45.460	-6.899	-6.899	0.000	0.000	0.000	0.000
118	A	118	GLN	0	0.016	-0.016	42.228	-0.215	-0.215	0.000	0.000	0.000	0.000
119	A	119	HIS	0	0.006	0.000	40.049	-0.341	-0.341	0.000	0.000	0.000	0.000
120	A	120	LEU	0	0.000	-0.001	39.402	-0.279	-0.279	0.000	0.000	0.000	0.000
121	A	121	VAL	0	0.011	0.019	39.471	-0.158	-0.158	0.000	0.000	0.000	0.000
122	A	122	ILE	0	0.025	0.006	35.130	-0.248	-0.248	0.000	0.000	0.000	0.000
123	A	123	ASN	0	0.004	0.013	34.998	-0.445	-0.445	0.000	0.000	0.000	0.000
124	A	124	GLY	0	0.023	0.030	34.486	-0.228	-0.228	0.000	0.000	0.000	0.000
125	A	125	ALA	0	0.010	0.014	31.806	-0.279	-0.279	0.000	0.000	0.000	0.000
126	A	126	SER	0	-0.040	-0.051	30.431	-0.267	-0.267	0.000	0.000	0.000	0.000
127	A	127	ASN	0	0.002	-0.004	29.884	-0.424	-0.424	0.000	0.000	0.000	0.000
128	A	128	LEU	0	0.041	0.057	27.118	-0.337	-0.337	0.000	0.000	0.000	0.000
129	A	129	ILE	0	0.008	-0.004	24.963	-0.508	-0.508	0.000	0.000	0.000	0.000
130	A	130	ALA	0	-0.014	-0.016	24.965	-0.581	-0.581	0.000	0.000	0.000	0.000
131	A	131	THR	0	-0.047	-0.023	25.875	-0.243	-0.243	0.000	0.000	0.000	0.000
132	A	132	VAL	0	-0.014	-0.010	22.776	-0.425	-0.425	0.000	0.000	0.000	0.000
133	A	133	LEU	0	0.005	0.011	19.568	-0.782	-0.782	0.000	0.000	0.000	0.000
134	A	134	GLY	0	0.027	0.025	20.830	-0.666	-0.666	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.805	-0.893	23.046	-11.896	-11.896	0.000	0.000	0.000	0.000
136	A	136	PRO	0	0.025	0.008	18.989	0.513	0.513	0.000	0.000	0.000	0.000
137	A	137	GLY	0	0.062	0.033	21.773	0.038	0.038	0.000	0.000	0.000	0.000
138	A	138	ARG	1	0.845	0.925	24.300	11.627	11.627	0.000	0.000	0.000	0.000
139	A	139	HIS	0	0.026	0.043	26.677	0.127	0.127	0.000	0.000	0.000	0.000
140	A	140	ALA	0	0.014	0.012	28.851	0.410	0.410	0.000	0.000	0.000	0.000
141	A	141	ARG	1	0.846	0.888	31.699	8.887	8.887	0.000	0.000	0.000	0.000
142	A	142	ALA	0	-0.008	-0.006	34.383	0.184	0.184	0.000	0.000	0.000	0.000
143	A	143	ALA	0	-0.003	0.002	36.995	-0.201	-0.201	0.000	0.000	0.000	0.000
144	A	144	VAL	0	0.002	0.008	39.640	0.187	0.187	0.000	0.000	0.000	0.000
145	A	145	GLY	0	0.024	0.020	42.694	-0.080	-0.080	0.000	0.000	0.000	0.000
146	A	146	MET	0	-0.032	-0.015	42.193	0.060	0.060	0.000	0.000	0.000	0.000
147	A	147	ALA	0	0.031	0.010	45.893	0.056	0.056	0.000	0.000	0.000	0.000
148	A	148	SER	0	-0.031	-0.016	47.047	0.088	0.088	0.000	0.000	0.000	0.000
149	A	149	LEU	0	0.006	0.010	40.560	-0.095	-0.095	0.000	0.000	0.000	0.000
150	A	150	PRO	0	0.035	0.017	40.004	0.188	0.188	0.000	0.000	0.000	0.000
151	A	151	PHE	0	-0.036	-0.029	39.488	-0.072	-0.072	0.000	0.000	0.000	0.000
152	A	152	ASN	0	-0.002	0.007	43.417	0.051	0.051	0.000	0.000	0.000	0.000
153	A	153	ALA	0	0.032	0.027	40.086	0.049	0.049	0.000	0.000	0.000	0.000
154	A	154	SER	0	0.025	-0.013	42.177	0.053	0.053	0.000	0.000	0.000	0.000
155	A	155	VAL	0	-0.073	-0.043	37.033	0.058	0.058	0.000	0.000	0.000	0.000
156	A	156	GLU	-1	-0.846	-0.938	36.147	-8.594	-8.594	0.000	0.000	0.000	0.000
157	A	157	ILE	0	-0.058	-0.026	31.968	0.110	0.110	0.000	0.000	0.000	0.000
158	A	158	ASP	-1	-0.843	-0.882	31.350	-9.847	-9.847	0.000	0.000	0.000	0.000
159	A	159	ALA	0	0.026	-0.012	27.003	-0.034	-0.034	0.000	0.000	0.000	0.000
160	A	160	ILE	0	-0.017	0.006	26.331	-0.067	-0.067	0.000	0.000	0.000	0.000
161	A	161	VAL	0	-0.027	-0.021	20.679	0.065	0.065	0.000	0.000	0.000	0.000
162	A	162	GLU	-1	-0.852	-0.915	19.603	-15.175	-15.175	0.000	0.000	0.000	0.000
163	A	163	ILE	-1	-0.843	-0.907	15.342	-19.992	-19.992	0.000	0.000	0.000	0.000

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