FMO DATABASE

FMODB ID: 3MKML

Calculation Name: 2FBD-A-Xray547

Preferred Name:

Target Type:

Ligand Name: di(hydroxyethyl)ether

Ligand 3-letter code: PEG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FBD

Chain ID: A

ChEMBL ID:

UniProt ID: Q7YT16

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
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	118
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1059883.145699
FMO2-HF: Nuclear repulsion	1009666.757399
FMO2-HF: Total energy	-50216.3883
FMO2-MP2: Total energy	-50357.353172

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:LYS)

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

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.
-141.883	-134.731	14.935	-11.579	-10.51	-0.135

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.769 / q_NPA : 1.878

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	PHE	0	-0.028	0.005	3.215	-8.954	-6.320	0.052	-1.105	-1.581	-0.007
36	A	36	ARG	1	0.884	0.939	4.763	50.804	50.918	-0.001	-0.042	-0.071	0.000
37	A	37	THR	0	0.040	0.021	1.964	-15.024	-12.998	4.992	-3.600	-3.418	-0.048
38	A	38	ASN	0	-0.002	0.001	3.912	16.793	17.036	-0.001	-0.039	-0.203	0.000
83	A	84	ASP	-1	-0.876	-0.948	1.954	-157.599	-155.490	9.893	-6.768	-5.235	-0.080
84	A	85	ASN	0	0.015	0.014	4.053	2.124	2.150	0.000	-0.025	-0.002	0.000
4	A	4	THR	0	0.017	0.002	5.934	1.666	1.666	0.000	0.000	0.000	0.000
5	A	5	ARG	1	0.902	0.935	8.095	35.908	35.908	0.000	0.000	0.000	0.000
6	A	6	CYS	0	-0.024	-0.006	11.537	-0.164	-0.164	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.019	0.012	7.590	2.165	2.165	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.023	0.017	9.163	1.365	1.365	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.012	0.001	10.692	2.741	2.741	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.890	0.936	12.934	41.483	41.483	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.863	-0.944	7.999	-60.115	-60.115	0.000	0.000	0.000	0.000
12	A	12	MET	0	-0.023	-0.009	12.147	1.547	1.547	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.027	-0.007	14.254	2.647	2.647	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.015	-0.006	14.554	1.793	1.793	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.037	-0.008	12.018	1.091	1.091	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.028	0.022	16.417	1.079	1.079	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.069	-0.029	16.529	1.443	1.443	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.015	0.014	19.433	-0.201	-0.201	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.985	0.975	20.849	27.109	27.109	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.020	-0.010	21.976	-0.769	-0.769	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.809	-0.886	20.641	-26.934	-26.934	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.011	0.017	16.150	-1.037	-1.037	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.000	0.016	17.716	-2.105	-2.105	0.000	0.000	0.000	0.000
24	A	24	GLN	0	0.054	0.036	18.943	-1.903	-1.903	0.000	0.000	0.000	0.000
25	A	25	TRP	0	-0.007	-0.020	15.328	-1.543	-1.543	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.064	-0.042	13.626	-2.055	-2.055	0.000	0.000	0.000	0.000
27	A	27	CYS	0	-0.067	-0.017	14.607	-2.829	-2.829	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.027	0.009	15.244	-0.680	-0.680	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.015	0.010	10.766	-0.937	-0.937	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.924	-0.935	11.879	-45.396	-45.396	0.000	0.000	0.000	0.000
31	A	31	HIS	1	0.861	0.908	13.087	33.697	33.697	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.791	-0.862	13.552	-33.945	-33.945	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.000	-0.011	8.890	-2.362	-2.362	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.058	-0.012	8.890	-4.842	-4.842	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.041	-0.049	7.404	-7.479	-7.479	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.017	-0.009	5.778	3.613	3.613	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.036	0.020	8.732	1.990	1.990	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.025	0.018	12.277	-0.520	-0.520	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.024	-0.021	14.759	1.055	1.055	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.024	-0.016	17.788	-0.191	-0.191	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.032	-0.017	19.688	0.761	0.761	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.002	-0.013	22.953	0.419	0.419	0.000	0.000	0.000	0.000
46	A	46	ASN	0	0.040	0.043	24.648	0.058	0.058	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.006	0.006	24.890	0.343	0.343	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.069	-0.039	21.521	-0.691	-0.691	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.037	-0.034	16.861	1.010	1.010	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.775	-0.855	15.677	-31.032	-31.032	0.000	0.000	0.000	0.000
51	A	51	TYR	0	0.035	0.006	11.883	-0.974	-0.974	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.066	0.051	8.142	1.421	1.421	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.034	-0.015	6.196	2.208	2.208	0.000	0.000	0.000	0.000
54	A	54	PHE	0	-0.030	-0.022	8.579	1.030	1.030	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.035	-0.015	11.002	4.765	4.765	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.017	0.007	12.827	2.705	2.705	0.000	0.000	0.000	0.000
57	A	57	ASN	0	0.024	-0.020	15.472	0.491	0.491	0.000	0.000	0.000	0.000
58	A	58	ASN	0	0.019	-0.013	17.667	1.645	1.645	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.026	0.022	19.327	0.924	0.924	0.000	0.000	0.000	0.000
60	A	60	TYR	0	-0.002	0.000	21.876	1.300	1.300	0.000	0.000	0.000	0.000
61	A	61	TRP	0	0.042	0.016	18.575	0.512	0.512	0.000	0.000	0.000	0.000
62	A	62	CYS	0	-0.024	0.012	14.859	-1.306	-1.306	0.000	0.000	0.000	0.000
63	A	63	GLN	0	0.003	-0.002	18.646	1.200	1.200	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.002	-0.004	18.820	-1.662	-1.662	0.000	0.000	0.000	0.000
65	A	65	SER	0	0.011	0.015	17.387	1.780	1.780	0.000	0.000	0.000	0.000
66	A	66	ASN	0	-0.037	-0.021	20.036	1.396	1.396	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.035	0.022	22.872	0.937	0.937	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.910	0.964	23.219	25.116	25.116	0.000	0.000	0.000	0.000
69	A	69	PHE	0	-0.001	-0.001	24.663	-0.677	-0.677	0.000	0.000	0.000	0.000
70	A	70	SER	0	0.010	-0.015	21.584	-0.293	-0.293	0.000	0.000	0.000	0.000
71	A	71	TYR	0	-0.029	-0.013	24.714	0.724	0.724	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.014	0.000	20.825	-0.762	-0.762	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.706	-0.839	22.716	-22.459	-22.459	0.000	0.000	0.000	0.000
74	A	74	CYS	0	-0.128	-0.057	15.094	2.021	2.021	0.000	0.000	0.000	0.000
75	A	75	HIS	0	-0.065	-0.026	19.724	-0.210	-0.210	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.002	0.006	14.602	-0.412	-0.412	0.000	0.000	0.000	0.000
77	A	77	SER	0	0.036	0.019	16.031	0.167	0.167	0.000	0.000	0.000	0.000
78	A	79	ASP	-1	-0.811	-0.919	12.038	-39.390	-39.390	0.000	0.000	0.000	0.000
79	A	80	ALA	0	-0.053	-0.014	10.753	-3.874	-3.874	0.000	0.000	0.000	0.000
80	A	81	LEU	0	0.004	-0.001	10.455	-1.239	-1.239	0.000	0.000	0.000	0.000
81	A	82	LEU	0	-0.040	-0.010	7.296	-3.354	-3.354	0.000	0.000	0.000	0.000
82	A	83	THR	0	-0.039	-0.026	5.427	-8.902	-8.902	0.000	0.000	0.000	0.000
85	A	86	ILE	0	0.067	0.035	6.316	2.702	2.702	0.000	0.000	0.000	0.000
86	A	87	SER	0	0.022	0.014	8.315	4.211	4.211	0.000	0.000	0.000	0.000
87	A	88	ASN	0	0.011	0.013	11.430	4.416	4.416	0.000	0.000	0.000	0.000
88	A	89	SER	0	0.031	0.005	9.217	3.653	3.653	0.000	0.000	0.000	0.000
89	A	90	VAL	0	0.001	0.001	11.333	1.936	1.936	0.000	0.000	0.000	0.000
90	A	91	THR	0	-0.012	-0.014	13.646	2.770	2.770	0.000	0.000	0.000	0.000
91	A	93	ALA	0	0.049	0.025	14.860	1.710	1.710	0.000	0.000	0.000	0.000
92	A	94	ARG	1	0.907	0.937	16.809	30.466	30.466	0.000	0.000	0.000	0.000
93	A	95	LYS	1	0.815	0.921	19.472	25.355	25.355	0.000	0.000	0.000	0.000
94	A	96	ILE	0	0.030	0.013	17.594	1.140	1.140	0.000	0.000	0.000	0.000
95	A	97	LYS	1	0.848	0.916	20.758	26.583	26.583	0.000	0.000	0.000	0.000
96	A	98	SER	0	-0.097	-0.042	22.506	1.264	1.264	0.000	0.000	0.000	0.000
97	A	99	GLN	0	-0.023	-0.031	24.688	0.519	0.519	0.000	0.000	0.000	0.000
98	A	100	GLN	0	-0.044	-0.019	24.294	0.756	0.756	0.000	0.000	0.000	0.000
99	A	101	GLY	0	0.022	0.026	25.668	0.220	0.220	0.000	0.000	0.000	0.000
100	A	102	TRP	0	0.006	-0.031	19.073	-0.779	-0.779	0.000	0.000	0.000	0.000
101	A	103	THR	0	-0.019	-0.017	22.702	-0.830	-0.830	0.000	0.000	0.000	0.000
102	A	104	ALA	0	0.003	0.026	21.590	0.334	0.334	0.000	0.000	0.000	0.000
103	A	105	TRP	0	-0.029	-0.011	16.040	0.146	0.146	0.000	0.000	0.000	0.000
104	A	106	SER	0	0.048	0.014	20.683	1.295	1.295	0.000	0.000	0.000	0.000
105	A	107	THR	0	-0.099	-0.090	17.796	0.890	0.890	0.000	0.000	0.000	0.000
106	A	108	TRP	0	0.061	0.027	20.845	-0.121	-0.121	0.000	0.000	0.000	0.000
107	A	109	LYS	1	0.925	0.964	22.741	25.811	25.811	0.000	0.000	0.000	0.000
108	A	110	TYR	0	-0.044	-0.025	20.972	0.502	0.502	0.000	0.000	0.000	0.000
109	A	112	SER	0	0.038	0.020	22.833	-0.022	-0.022	0.000	0.000	0.000	0.000
110	A	113	GLY	0	0.015	0.020	26.091	0.939	0.939	0.000	0.000	0.000	0.000
111	A	114	SER	0	-0.026	-0.024	26.184	-0.420	-0.420	0.000	0.000	0.000	0.000
112	A	115	LEU	0	-0.003	0.011	20.568	-0.804	-0.804	0.000	0.000	0.000	0.000
113	A	116	PRO	0	0.013	0.005	19.207	0.858	0.858	0.000	0.000	0.000	0.000
114	A	117	SER	0	0.048	0.018	20.838	-1.296	-1.296	0.000	0.000	0.000	0.000
115	A	118	ILE	0	0.022	0.001	16.752	-0.606	-0.606	0.000	0.000	0.000	0.000
116	A	119	ASN	0	-0.016	-0.019	19.474	-1.491	-1.491	0.000	0.000	0.000	0.000
117	A	120	ASP	-1	-0.805	-0.890	17.248	-33.112	-33.112	0.000	0.000	0.000	0.000
118	A	122	PHE	-1	-0.922	-0.950	17.056	-31.103	-31.103	0.000	0.000	0.000	0.000

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