FMO DATABASE

FMODB ID: N81YQ

Calculation Name: 3B8L-A-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol | di(hydroxyethyl)ether | chloride ion

Ligand 3-letter code: GOL | PEG | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3B8L

Chain ID: A

ChEMBL ID:

UniProt ID: A4XEN7

Base Structure: X-ray

Registration Date: 2025-10-04

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	147
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1352233.290573
FMO2-HF: Nuclear repulsion	1294165.998288
FMO2-HF: Total energy	-58067.292285
FMO2-MP2: Total energy	-58233.367423

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:-2:PHE)

Summations of interaction energy for fragment #1(A:-2:PHE)

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.
-59.774	-58.193	-0.006	-0.692	-0.884	-0.001

Interaction energy analysis for fragmet #1(A:-2:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.847 / q_NPA : 0.907

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	0	GLY	0	0.042	0.025	3.689	-1.781	-0.200	-0.006	-0.692	-0.884	-0.001
4	A	1	MET	0	-0.002	0.005	6.190	0.461	0.461	0.000	0.000	0.000	0.000
5	A	2	GLN	0	0.007	0.001	8.699	-1.391	-1.391	0.000	0.000	0.000	0.000
6	A	3	CYS	0	0.019	0.019	11.445	1.254	1.254	0.000	0.000	0.000	0.000
7	A	4	PRO	0	-0.025	-0.002	14.887	0.064	0.064	0.000	0.000	0.000	0.000
8	A	5	ILE	0	0.025	0.010	17.778	0.099	0.099	0.000	0.000	0.000	0.000
9	A	6	GLU	-1	-0.844	-0.932	20.777	-12.747	-12.747	0.000	0.000	0.000	0.000
10	A	7	ASP	-1	-0.764	-0.834	19.154	-14.616	-14.616	0.000	0.000	0.000	0.000
11	A	8	ARG	1	0.923	0.947	18.837	15.884	15.884	0.000	0.000	0.000	0.000
12	A	9	LEU	0	-0.055	-0.023	20.992	0.314	0.314	0.000	0.000	0.000	0.000
13	A	10	ALA	0	0.065	0.035	24.306	0.383	0.383	0.000	0.000	0.000	0.000
14	A	11	ILE	0	0.011	0.004	20.220	0.366	0.366	0.000	0.000	0.000	0.000
15	A	12	GLN	0	-0.023	-0.025	23.321	-0.361	-0.361	0.000	0.000	0.000	0.000
16	A	13	ASP	-1	-0.883	-0.946	25.919	-10.535	-10.535	0.000	0.000	0.000	0.000
17	A	14	LEU	0	-0.052	-0.003	26.107	0.419	0.419	0.000	0.000	0.000	0.000
18	A	15	MET	0	-0.036	-0.016	25.401	0.129	0.129	0.000	0.000	0.000	0.000
19	A	16	ILE	0	-0.015	-0.009	28.975	0.334	0.334	0.000	0.000	0.000	0.000
20	A	17	ALA	0	-0.003	0.005	31.789	0.364	0.364	0.000	0.000	0.000	0.000
21	A	18	TYR	0	0.033	0.009	31.222	0.356	0.356	0.000	0.000	0.000	0.000
22	A	19	ALA	0	-0.031	-0.015	33.060	0.263	0.263	0.000	0.000	0.000	0.000
23	A	20	HIS	0	0.008	0.001	34.765	0.206	0.206	0.000	0.000	0.000	0.000
24	A	21	ALA	0	0.027	0.014	36.700	0.259	0.259	0.000	0.000	0.000	0.000
25	A	22	VAL	0	0.011	0.016	36.114	0.265	0.265	0.000	0.000	0.000	0.000
26	A	23	ASP	-1	-0.772	-0.863	38.729	-8.109	-8.109	0.000	0.000	0.000	0.000
27	A	24	THR	0	-0.031	-0.019	40.859	0.254	0.254	0.000	0.000	0.000	0.000
28	A	25	VAL	0	-0.083	-0.034	42.785	0.199	0.199	0.000	0.000	0.000	0.000
29	A	26	SER	0	-0.033	-0.029	43.986	0.176	0.176	0.000	0.000	0.000	0.000
30	A	27	ASP	-1	-0.842	-0.919	42.145	-7.489	-7.489	0.000	0.000	0.000	0.000
31	A	28	ILE	0	-0.002	-0.011	40.862	-0.220	-0.220	0.000	0.000	0.000	0.000
32	A	29	ASP	-1	-0.849	-0.904	39.763	-7.558	-7.558	0.000	0.000	0.000	0.000
33	A	30	ALA	0	-0.024	-0.022	38.369	-0.251	-0.251	0.000	0.000	0.000	0.000
34	A	31	VAL	0	-0.034	-0.016	35.773	-0.322	-0.322	0.000	0.000	0.000	0.000
35	A	32	LEU	0	-0.028	-0.014	35.016	-0.311	-0.311	0.000	0.000	0.000	0.000
36	A	33	ASP	-1	-0.832	-0.903	34.414	-9.275	-9.275	0.000	0.000	0.000	0.000
37	A	34	VAL	0	-0.012	0.008	30.095	-0.328	-0.328	0.000	0.000	0.000	0.000
38	A	35	PHE	0	-0.015	-0.013	29.794	-0.550	-0.550	0.000	0.000	0.000	0.000
39	A	36	THR	0	-0.031	-0.023	27.050	0.192	0.192	0.000	0.000	0.000	0.000
40	A	37	GLU	-1	-0.899	-0.962	30.275	-8.523	-8.523	0.000	0.000	0.000	0.000
41	A	38	ASP	-1	-0.861	-0.944	27.908	-10.657	-10.657	0.000	0.000	0.000	0.000
42	A	39	ALA	0	-0.023	0.009	28.639	-0.180	-0.180	0.000	0.000	0.000	0.000
43	A	40	VAL	0	-0.018	-0.012	27.382	0.346	0.346	0.000	0.000	0.000	0.000
44	A	41	PHE	0	0.035	0.014	28.756	-0.368	-0.368	0.000	0.000	0.000	0.000
45	A	42	ASP	-1	-0.824	-0.900	28.601	-10.201	-10.201	0.000	0.000	0.000	0.000
46	A	43	LEU	0	0.031	0.002	29.801	-0.318	-0.318	0.000	0.000	0.000	0.000
47	A	44	SER	0	-0.014	-0.018	30.897	0.158	0.158	0.000	0.000	0.000	0.000
48	A	45	GLY	0	-0.020	-0.005	29.873	0.153	0.153	0.000	0.000	0.000	0.000
49	A	46	ILE	0	-0.064	-0.045	30.886	-0.043	-0.043	0.000	0.000	0.000	0.000
50	A	47	GLY	0	-0.026	-0.009	33.912	0.285	0.285	0.000	0.000	0.000	0.000
51	A	48	LEU	0	-0.050	-0.029	35.597	0.292	0.292	0.000	0.000	0.000	0.000
52	A	49	THR	0	0.011	-0.005	35.639	-0.250	-0.250	0.000	0.000	0.000	0.000
53	A	50	PRO	0	-0.036	-0.014	32.567	0.035	0.035	0.000	0.000	0.000	0.000
54	A	51	GLN	0	-0.022	0.005	33.844	0.337	0.337	0.000	0.000	0.000	0.000
55	A	52	VAL	0	-0.017	-0.024	31.928	-0.357	-0.357	0.000	0.000	0.000	0.000
56	A	53	GLY	0	0.052	0.030	32.892	0.299	0.299	0.000	0.000	0.000	0.000
57	A	54	HIS	0	-0.012	-0.019	33.499	0.323	0.323	0.000	0.000	0.000	0.000
58	A	55	ALA	0	-0.022	-0.004	36.850	0.168	0.168	0.000	0.000	0.000	0.000
59	A	56	GLY	0	0.061	0.026	37.784	0.159	0.159	0.000	0.000	0.000	0.000
60	A	57	ILE	0	-0.015	-0.005	32.824	0.077	0.077	0.000	0.000	0.000	0.000
61	A	58	ARG	1	0.903	0.937	37.301	7.481	7.481	0.000	0.000	0.000	0.000
62	A	59	GLU	-1	-0.924	-0.938	40.816	-6.864	-6.864	0.000	0.000	0.000	0.000
63	A	60	PHE	0	0.000	-0.002	37.514	0.077	0.077	0.000	0.000	0.000	0.000
64	A	61	PHE	0	0.016	-0.011	36.013	0.043	0.043	0.000	0.000	0.000	0.000
65	A	62	THR	0	-0.029	-0.021	41.455	0.182	0.182	0.000	0.000	0.000	0.000
66	A	63	ASN	0	-0.028	-0.022	43.722	0.292	0.292	0.000	0.000	0.000	0.000
67	A	64	VAL	0	0.005	0.007	40.419	0.114	0.114	0.000	0.000	0.000	0.000
68	A	65	PHE	0	-0.006	-0.006	40.806	0.066	0.066	0.000	0.000	0.000	0.000
69	A	66	ALA	0	-0.017	0.010	45.851	0.173	0.173	0.000	0.000	0.000	0.000
70	A	67	ASN	0	-0.042	-0.026	46.203	0.289	0.289	0.000	0.000	0.000	0.000
71	A	68	MET	0	-0.055	-0.012	43.263	0.135	0.135	0.000	0.000	0.000	0.000
72	A	69	SER	0	-0.067	-0.033	47.123	0.145	0.145	0.000	0.000	0.000	0.000
73	A	70	HIS	0	-0.013	-0.004	46.389	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	71	HIS	0	-0.046	-0.044	40.787	-0.029	-0.029	0.000	0.000	0.000	0.000
75	A	72	ALA	0	0.019	0.018	40.245	0.107	0.107	0.000	0.000	0.000	0.000
76	A	73	HIS	1	0.780	0.876	34.885	8.459	8.459	0.000	0.000	0.000	0.000
77	A	74	TYR	0	0.033	0.024	34.778	-0.196	-0.196	0.000	0.000	0.000	0.000
78	A	75	LEU	0	0.016	0.008	29.270	-0.184	-0.184	0.000	0.000	0.000	0.000
79	A	76	THR	0	-0.009	-0.020	28.671	0.104	0.104	0.000	0.000	0.000	0.000
80	A	77	ASN	0	-0.049	-0.021	24.380	0.009	0.009	0.000	0.000	0.000	0.000
81	A	78	PHE	0	0.046	0.029	23.210	-0.540	-0.540	0.000	0.000	0.000	0.000
82	A	79	ALA	0	-0.056	-0.032	18.136	-0.378	-0.378	0.000	0.000	0.000	0.000
83	A	80	VAL	0	0.013	0.012	14.982	0.360	0.360	0.000	0.000	0.000	0.000
84	A	81	THR	0	-0.091	-0.072	14.946	-0.604	-0.604	0.000	0.000	0.000	0.000
85	A	82	GLY	0	0.002	0.012	12.505	-1.402	-1.402	0.000	0.000	0.000	0.000
86	A	83	TYR	0	0.033	0.000	12.070	1.945	1.945	0.000	0.000	0.000	0.000
87	A	84	GLU	-1	-0.882	-0.922	11.357	-23.755	-23.755	0.000	0.000	0.000	0.000
88	A	85	GLY	0	-0.004	0.000	12.742	0.450	0.450	0.000	0.000	0.000	0.000
89	A	86	ASP	-1	-0.867	-0.935	14.987	-14.461	-14.461	0.000	0.000	0.000	0.000
90	A	87	THR	0	-0.056	-0.041	15.798	1.137	1.137	0.000	0.000	0.000	0.000
91	A	88	ALA	0	0.030	0.008	16.128	-1.106	-1.106	0.000	0.000	0.000	0.000
92	A	89	SER	0	0.025	0.045	16.091	0.809	0.809	0.000	0.000	0.000	0.000
93	A	90	MET	0	-0.057	-0.018	17.575	-0.915	-0.915	0.000	0.000	0.000	0.000
94	A	91	ARG	1	0.951	0.991	18.071	16.599	16.599	0.000	0.000	0.000	0.000
95	A	92	ALA	0	0.038	0.015	21.952	-0.173	-0.173	0.000	0.000	0.000	0.000
96	A	93	TYR	0	-0.033	-0.037	23.863	-0.243	-0.243	0.000	0.000	0.000	0.000
97	A	94	VAL	0	0.010	0.000	27.717	0.098	0.098	0.000	0.000	0.000	0.000
98	A	95	ILE	0	-0.002	0.011	31.348	0.058	0.058	0.000	0.000	0.000	0.000
99	A	96	GLY	0	0.017	-0.004	34.864	0.106	0.106	0.000	0.000	0.000	0.000
100	A	97	MET	0	-0.031	-0.012	36.621	0.099	0.099	0.000	0.000	0.000	0.000
101	A	98	GLY	0	0.047	0.009	40.376	-0.061	-0.061	0.000	0.000	0.000	0.000
102	A	99	VAL	0	-0.053	-0.012	43.375	0.035	0.035	0.000	0.000	0.000	0.000
103	A	100	GLY	0	0.102	0.048	46.971	-0.021	-0.021	0.000	0.000	0.000	0.000
104	A	101	LYS	1	0.828	0.903	48.777	6.509	6.509	0.000	0.000	0.000	0.000
105	A	102	ASP	-1	-0.812	-0.874	50.580	-6.332	-6.332	0.000	0.000	0.000	0.000
106	A	103	GLY	0	-0.005	0.002	52.193	0.075	0.075	0.000	0.000	0.000	0.000
107	A	104	ARG	1	0.774	0.874	48.531	6.518	6.518	0.000	0.000	0.000	0.000
108	A	105	ALA	0	0.015	0.008	46.315	-0.099	-0.099	0.000	0.000	0.000	0.000
109	A	106	VAL	0	-0.001	-0.004	40.782	-0.018	-0.018	0.000	0.000	0.000	0.000
110	A	107	THR	0	-0.052	-0.043	38.072	-0.016	-0.016	0.000	0.000	0.000	0.000
111	A	108	VAL	0	0.015	0.018	33.784	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	109	ASN	0	0.028	0.020	33.884	-0.161	-0.161	0.000	0.000	0.000	0.000
113	A	110	GLY	0	0.054	0.011	30.504	-0.021	-0.021	0.000	0.000	0.000	0.000
114	A	111	ARG	1	0.759	0.848	23.598	12.570	12.570	0.000	0.000	0.000	0.000
115	A	112	TYR	0	0.043	0.018	27.014	0.409	0.409	0.000	0.000	0.000	0.000
116	A	113	PHE	0	-0.046	-0.030	21.194	-0.649	-0.649	0.000	0.000	0.000	0.000
117	A	114	PHE	0	0.063	0.020	22.947	0.526	0.526	0.000	0.000	0.000	0.000
118	A	115	GLU	-1	-0.888	-0.948	18.456	-17.073	-17.073	0.000	0.000	0.000	0.000
119	A	116	VAL	0	-0.009	-0.011	20.734	0.889	0.889	0.000	0.000	0.000	0.000
120	A	117	ARG	1	0.894	0.941	20.665	11.116	11.116	0.000	0.000	0.000	0.000
121	A	118	ARG	1	0.780	0.866	17.838	15.729	15.729	0.000	0.000	0.000	0.000
122	A	119	THR	0	-0.072	-0.053	23.374	0.321	0.321	0.000	0.000	0.000	0.000
123	A	120	GLU	-1	-0.919	-0.962	26.987	-9.452	-9.452	0.000	0.000	0.000	0.000
124	A	121	LYS	1	0.838	0.911	29.674	9.062	9.062	0.000	0.000	0.000	0.000
125	A	122	GLY	0	0.050	0.030	26.887	0.036	0.036	0.000	0.000	0.000	0.000
126	A	123	TRP	0	-0.064	-0.041	18.168	0.063	0.063	0.000	0.000	0.000	0.000
127	A	124	LYS	1	0.834	0.926	25.298	10.367	10.367	0.000	0.000	0.000	0.000
128	A	125	ALA	0	0.033	0.019	25.438	-0.513	-0.513	0.000	0.000	0.000	0.000
129	A	126	THR	0	-0.008	-0.003	22.688	0.406	0.406	0.000	0.000	0.000	0.000
130	A	127	ARG	1	0.951	0.979	22.836	12.937	12.937	0.000	0.000	0.000	0.000
131	A	128	TYR	0	-0.019	0.016	24.590	-0.375	-0.375	0.000	0.000	0.000	0.000
132	A	129	THR	0	-0.010	-0.008	24.789	0.090	0.090	0.000	0.000	0.000	0.000
133	A	130	MET	0	-0.024	-0.006	27.040	-0.078	-0.078	0.000	0.000	0.000	0.000
134	A	131	ASP	-1	-0.784	-0.844	26.023	-12.265	-12.265	0.000	0.000	0.000	0.000
135	A	132	PHE	0	0.028	0.011	29.117	0.119	0.119	0.000	0.000	0.000	0.000
136	A	133	LEU	0	-0.081	-0.035	26.495	-0.382	-0.382	0.000	0.000	0.000	0.000
137	A	134	MET	0	-0.027	-0.019	30.320	0.018	0.018	0.000	0.000	0.000	0.000
138	A	135	PRO	0	0.003	-0.007	34.030	-0.034	-0.034	0.000	0.000	0.000	0.000
139	A	136	LEU	0	-0.016	0.007	36.873	0.013	0.013	0.000	0.000	0.000	0.000
140	A	137	SER	0	-0.022	0.004	38.694	0.198	0.198	0.000	0.000	0.000	0.000
141	A	138	GLY	0	0.031	0.017	41.630	-0.022	-0.022	0.000	0.000	0.000	0.000
142	A	139	THR	0	-0.037	-0.035	43.520	-0.079	-0.079	0.000	0.000	0.000	0.000
143	A	140	LEU	0	0.045	0.015	37.549	0.001	0.001	0.000	0.000	0.000	0.000
144	A	141	ASP	-1	-0.808	-0.914	42.012	-7.070	-7.070	0.000	0.000	0.000	0.000
145	A	142	ASN	0	-0.034	-0.016	45.075	0.116	0.116	0.000	0.000	0.000	0.000
146	A	143	ALA	0	-0.011	-0.012	40.350	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	144	LYS	0	-0.010	0.028	41.305	0.220	0.220	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:-2:PHE)