FMO DATABASE

FMODB ID: NLLLQ

Calculation Name: 2PKP-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: 2PKP

Chain ID: A

ChEMBL ID:

UniProt ID: Q58667

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	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1633828.366981
FMO2-HF: Nuclear repulsion	1569497.845974
FMO2-HF: Total energy	-64330.521007
FMO2-MP2: Total energy	-64517.74716

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:MET)

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

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.
-100.305	-95.013	22.369	-14.089	-13.572	-0.135

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.757 / q_NPA : 0.871

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	ILE	0	-0.027	-0.004	2.326	-0.947	1.899	1.780	-1.621	-3.005	-0.008
4	A	4	LYS	1	0.844	0.907	4.365	27.036	27.147	0.000	-0.034	-0.077	0.000
80	A	80	LYS	1	0.876	0.923	3.269	28.982	29.590	0.047	-0.120	-0.535	0.001
101	A	101	ILE	0	0.005	-0.013	4.581	0.308	0.542	0.008	-0.052	-0.190	0.000
119	A	119	ASP	-1	-0.787	-0.889	4.556	-65.623	-65.519	-0.001	-0.036	-0.067	0.000
120	A	120	LEU	0	-0.017	-0.036	2.191	5.165	6.096	3.222	-1.147	-3.006	-0.006
121	A	121	ASP	-1	-0.877	-0.924	1.762	-135.920	-135.646	17.314	-11.020	-6.568	-0.122
122	A	122	LYS	1	0.846	0.910	4.188	46.173	46.357	-0.001	-0.059	-0.124	0.000
5	A	5	GLY	0	0.063	0.047	8.034	0.696	0.696	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.850	0.919	10.745	15.628	15.628	0.000	0.000	0.000	0.000
7	A	7	ALA	0	-0.007	-0.001	13.387	-0.524	-0.524	0.000	0.000	0.000	0.000
8	A	8	HIS	0	-0.060	-0.036	14.896	1.576	1.576	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.822	0.904	17.235	13.685	13.685	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.004	0.002	18.342	0.652	0.652	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.025	0.003	21.826	-0.279	-0.279	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.841	-0.924	22.797	-12.612	-12.612	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.864	-0.911	24.802	-10.552	-10.552	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.008	0.018	21.450	0.239	0.239	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.791	-0.893	22.682	-11.110	-11.110	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.076	-0.065	22.296	-0.149	-0.149	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.896	-0.936	24.192	-9.930	-9.930	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.007	-0.014	24.819	0.070	0.070	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.046	-0.025	19.401	-0.248	-0.248	0.000	0.000	0.000	0.000
20	A	20	ILE	0	-0.048	-0.033	21.823	-0.242	-0.242	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.037	0.039	23.905	0.240	0.240	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.044	0.018	27.773	0.061	0.061	0.000	0.000	0.000	0.000
23	A	23	PRO	0	-0.065	-0.035	29.902	0.047	0.047	0.000	0.000	0.000	0.000
24	A	24	TYR	0	0.028	-0.001	26.391	0.104	0.104	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.032	-0.009	25.403	-0.228	-0.228	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.887	0.951	27.558	8.123	8.123	0.000	0.000	0.000	0.000
27	A	27	THR	0	0.023	0.010	24.930	0.252	0.252	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.008	-0.006	25.009	-0.080	-0.080	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.837	-0.904	22.150	-11.777	-11.777	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.005	-0.006	17.724	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	31	TYR	0	0.042	0.001	15.792	-0.716	-0.716	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.924	-0.953	19.978	-9.961	-9.961	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.028	-0.006	20.568	0.114	0.114	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.013	0.000	17.410	0.029	0.029	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.060	-0.028	19.242	0.023	0.023	0.000	0.000	0.000	0.000
36	A	36	HIS	1	0.816	0.899	22.014	10.779	10.779	0.000	0.000	0.000	0.000
37	A	37	CYS	0	0.000	0.016	18.347	-0.090	-0.090	0.000	0.000	0.000	0.000
38	A	38	MET	0	-0.023	-0.010	19.157	-0.091	-0.091	0.000	0.000	0.000	0.000
39	A	39	ALA	0	0.002	0.009	21.981	0.300	0.300	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.022	0.000	25.413	0.410	0.410	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.063	-0.038	22.869	0.205	0.205	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.763	-0.867	23.527	-11.363	-11.363	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.859	-0.914	24.476	-10.148	-10.148	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.100	-0.069	25.407	0.126	0.126	0.000	0.000	0.000	0.000
45	A	45	PHE	0	0.028	0.020	15.953	-0.363	-0.363	0.000	0.000	0.000	0.000
46	A	46	PRO	0	-0.010	-0.009	20.124	-0.452	-0.452	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.889	0.950	21.190	10.659	10.659	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.827	0.898	20.486	11.509	11.509	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.034	-0.003	14.835	-0.332	-0.332	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.843	0.919	14.566	14.484	14.484	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.907	-0.953	9.630	-20.055	-20.055	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.017	-0.010	7.876	-0.311	-0.311	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.822	-0.886	8.696	-19.223	-19.223	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.039	-0.032	8.530	-1.106	-1.106	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.005	0.009	11.208	1.142	1.142	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.008	-0.013	13.623	-1.114	-1.114	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.009	0.009	16.082	0.946	0.946	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.040	0.037	19.090	-0.579	-0.579	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.849	-0.923	20.717	-14.088	-14.088	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.088	-0.067	22.707	-0.078	-0.078	0.000	0.000	0.000	0.000
61	A	61	PHE	0	0.071	0.035	16.867	0.230	0.230	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.008	-0.017	20.071	-0.461	-0.461	0.000	0.000	0.000	0.000
63	A	63	CYS	0	-0.043	-0.029	21.095	0.283	0.283	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.082	0.038	24.820	0.089	0.089	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.003	-0.003	26.974	0.052	0.052	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.022	-0.021	24.942	-0.345	-0.345	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.946	0.981	23.301	10.434	10.434	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.899	-0.954	19.917	-12.385	-12.385	0.000	0.000	0.000	0.000
69	A	69	GLN	0	0.049	0.010	19.176	-0.799	-0.799	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.044	0.029	19.885	-0.223	-0.223	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.029	-0.012	15.034	-0.477	-0.477	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.030	-0.009	14.834	-0.833	-0.833	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.040	0.014	15.942	-0.392	-0.392	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.093	0.033	12.647	-0.187	-0.187	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.898	0.963	10.545	17.564	17.564	0.000	0.000	0.000	0.000
76	A	76	TYR	0	-0.068	-0.047	11.710	-0.941	-0.941	0.000	0.000	0.000	0.000
77	A	77	CYS	0	-0.029	-0.002	14.287	0.829	0.829	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.023	0.020	10.617	-0.080	-0.080	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.026	0.013	9.309	-1.505	-1.505	0.000	0.000	0.000	0.000
81	A	81	ALA	0	-0.004	-0.022	6.338	-1.025	-1.025	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.001	0.007	8.146	1.393	1.393	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.009	0.002	11.106	-0.983	-0.983	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.002	0.002	13.402	1.184	1.184	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.858	0.939	16.844	12.272	12.272	0.000	0.000	0.000	0.000
86	A	86	SER	0	0.003	-0.033	19.397	-0.113	-0.113	0.000	0.000	0.000	0.000
87	A	87	PHE	0	-0.007	-0.009	14.152	0.036	0.036	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.046	0.048	19.744	0.375	0.375	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.954	0.954	20.808	11.788	11.788	0.000	0.000	0.000	0.000
90	A	90	ILE	0	-0.019	-0.006	21.008	-0.387	-0.387	0.000	0.000	0.000	0.000
91	A	91	PHE	0	0.057	0.045	15.549	-0.235	-0.235	0.000	0.000	0.000	0.000
92	A	92	TYR	0	0.009	-0.013	14.251	-0.686	-0.686	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.930	0.962	16.148	12.479	12.479	0.000	0.000	0.000	0.000
94	A	94	ASN	0	0.011	-0.002	17.337	-0.227	-0.227	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.027	0.023	13.364	-0.206	-0.206	0.000	0.000	0.000	0.000
96	A	96	ILE	0	0.035	0.022	11.953	-0.881	-0.881	0.000	0.000	0.000	0.000
97	A	97	ASN	0	-0.049	-0.042	12.566	-0.628	-0.628	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.011	0.004	12.679	0.388	0.388	0.000	0.000	0.000	0.000
99	A	99	GLY	0	-0.009	-0.006	9.656	-0.289	-0.289	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.039	0.001	8.057	-1.975	-1.975	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.018	0.003	9.033	0.004	0.004	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.020	-0.021	7.366	-1.451	-1.451	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.027	0.027	11.767	1.355	1.355	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.036	-0.002	14.129	-1.293	-1.293	0.000	0.000	0.000	0.000
106	A	106	ASN	0	0.037	0.019	16.157	1.052	1.052	0.000	0.000	0.000	0.000
107	A	107	THR	0	0.019	-0.023	16.688	-0.123	-0.123	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.884	-0.919	19.035	-12.747	-12.747	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.911	-0.941	19.043	-14.266	-14.266	0.000	0.000	0.000	0.000
110	A	110	ILE	0	-0.006	0.000	15.084	-0.110	-0.110	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.879	0.929	19.265	13.322	13.322	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.776	-0.896	19.273	-14.305	-14.305	0.000	0.000	0.000	0.000
113	A	113	GLY	0	0.013	0.013	19.117	0.379	0.379	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.768	-0.852	17.295	-15.185	-15.185	0.000	0.000	0.000	0.000
115	A	115	ILE	0	-0.029	-0.013	13.456	-0.446	-0.446	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.008	0.013	10.544	-0.060	-0.060	0.000	0.000	0.000	0.000
117	A	117	GLU	-1	-0.833	-0.919	8.882	-31.020	-31.020	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.010	0.000	6.029	1.126	1.126	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.826	-0.871	6.739	-24.994	-24.994	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.911	-0.962	8.154	-22.633	-22.633	0.000	0.000	0.000	0.000
125	A	125	ILE	0	-0.008	-0.018	8.994	-3.683	-3.683	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.023	0.015	11.118	2.642	2.642	0.000	0.000	0.000	0.000
127	A	127	ILE	0	0.022	0.003	13.213	-0.427	-0.427	0.000	0.000	0.000	0.000
128	A	128	THR	0	-0.026	-0.028	13.805	1.473	1.473	0.000	0.000	0.000	0.000
129	A	129	ASN	0	-0.014	-0.019	16.610	0.047	0.047	0.000	0.000	0.000	0.000
130	A	130	LYS	1	0.800	0.884	19.331	15.203	15.203	0.000	0.000	0.000	0.000
131	A	131	ASN	0	-0.035	-0.004	19.911	-0.093	-0.093	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.842	0.922	18.825	15.678	15.678	0.000	0.000	0.000	0.000
133	A	133	THR	0	0.017	0.008	12.939	-0.542	-0.542	0.000	0.000	0.000	0.000
134	A	134	ILE	0	-0.022	0.003	14.718	1.361	1.361	0.000	0.000	0.000	0.000
135	A	135	LYS	1	0.992	0.988	13.116	17.545	17.545	0.000	0.000	0.000	0.000
136	A	136	CYS	0	-0.083	-0.036	9.662	0.324	0.324	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.921	-0.944	11.838	-20.323	-20.323	0.000	0.000	0.000	0.000
138	A	138	THR	0	-0.060	-0.052	6.424	-0.531	-0.531	0.000	0.000	0.000	0.000
139	A	139	PRO	0	0.044	0.017	8.835	1.246	1.246	0.000	0.000	0.000	0.000
140	A	140	LYS	1	0.844	0.918	10.113	24.238	24.238	0.000	0.000	0.000	0.000
141	A	141	GLY	0	0.017	0.002	12.580	1.059	1.059	0.000	0.000	0.000	0.000
142	A	142	LEU	0	0.040	0.012	12.993	-1.404	-1.404	0.000	0.000	0.000	0.000
143	A	143	GLU	-1	-0.837	-0.909	13.105	-19.169	-19.169	0.000	0.000	0.000	0.000
144	A	144	ARG	1	0.987	0.997	7.488	30.289	30.289	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.877	-0.942	8.955	-21.338	-21.338	0.000	0.000	0.000	0.000
146	A	146	ILE	0	-0.043	-0.022	11.209	0.002	0.002	0.000	0.000	0.000	0.000
147	A	147	LEU	0	-0.010	0.009	7.381	0.114	0.114	0.000	0.000	0.000	0.000
148	A	148	ALA	0	-0.025	-0.003	6.377	-0.583	-0.583	0.000	0.000	0.000	0.000
149	A	149	ALA	0	-0.071	-0.031	7.443	0.846	0.846	0.000	0.000	0.000	0.000
150	A	150	GLY	0	0.026	0.007	8.713	1.156	1.156	0.000	0.000	0.000	0.000
151	A	151	GLY	0	0.043	0.022	9.618	1.068	1.068	0.000	0.000	0.000	0.000
152	A	152	LEU	0	-0.009	-0.015	12.686	0.188	0.188	0.000	0.000	0.000	0.000
153	A	153	VAL	0	0.030	0.009	16.085	0.320	0.320	0.000	0.000	0.000	0.000
154	A	154	ASN	0	-0.029	-0.016	12.183	1.372	1.372	0.000	0.000	0.000	0.000
155	A	155	TYR	0	0.009	0.010	14.027	0.621	0.621	0.000	0.000	0.000	0.000
156	A	156	LEU	0	0.000	-0.004	15.428	0.520	0.520	0.000	0.000	0.000	0.000
157	A	157	LYS	1	0.895	0.953	16.293	15.920	15.920	0.000	0.000	0.000	0.000
158	A	158	LYS	1	0.908	0.964	11.870	20.495	20.495	0.000	0.000	0.000	0.000
159	A	159	ARG	1	0.997	0.994	17.670	13.620	13.620	0.000	0.000	0.000	0.000
160	A	160	LYS	1	0.938	0.962	20.210	12.071	12.071	0.000	0.000	0.000	0.000
161	A	161	LEU	0	0.006	0.008	18.833	0.408	0.408	0.000	0.000	0.000	0.000
162	A	162	ILE	0	-0.009	-0.014	18.213	0.264	0.264	0.000	0.000	0.000	0.000
163	A	163	GLN	0	-0.002	-0.002	22.518	0.710	0.710	0.000	0.000	0.000	0.000
164	A	164	SER	0	-0.008	0.001	25.185	0.436	0.436	0.000	0.000	0.000	0.000
165	A	165	LYS	1	0.911	0.957	20.785	13.942	13.942	0.000	0.000	0.000	0.000
166	A	166	LYS	1	0.879	0.944	26.831	10.793	10.793	0.000	0.000	0.000	0.000
167	A	167	GLY	-1	-0.908	-0.930	28.664	-9.384	-9.384	0.000	0.000	0.000	0.000

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