FMO DATABASE

FMODB ID: KVYY3

Calculation Name: 5FEF-A-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5FEF

Chain ID: A

ChEMBL ID:

UniProt ID: Q9FR39

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	132
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1114755.162798
FMO2-HF: Nuclear repulsion	1063894.399486
FMO2-HF: Total energy	-50860.763312
FMO2-MP2: Total energy	-51005.133335

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:0:GLY)

Summations of interaction energy for fragment #1(A:0: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.
-132.534	-131.779	-0.003	-0.318	-0.434	-0.001

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.831 / q_NPA : 0.900

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	2	SER	0	0.020	0.000	3.836	-0.751	0.004	-0.003	-0.318	-0.434	-0.001
4	A	3	TRP	0	0.088	0.042	6.677	0.826	0.826	0.000	0.000	0.000	0.000
5	A	4	GLN	0	-0.033	-0.024	10.159	1.636	1.636	0.000	0.000	0.000	0.000
6	A	5	ALA	0	0.045	0.026	7.741	1.479	1.479	0.000	0.000	0.000	0.000
7	A	6	TYR	0	-0.037	-0.039	8.438	0.138	0.138	0.000	0.000	0.000	0.000
8	A	7	VAL	0	0.013	0.011	11.519	2.024	2.024	0.000	0.000	0.000	0.000
9	A	8	ASP	-1	-0.835	-0.929	12.921	-20.981	-20.981	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.924	-0.972	10.329	-27.814	-27.814	0.000	0.000	0.000	0.000
11	A	10	HIS	0	-0.106	-0.056	10.126	2.177	2.177	0.000	0.000	0.000	0.000
12	A	11	LEU	0	-0.021	-0.011	14.840	1.416	1.416	0.000	0.000	0.000	0.000
13	A	12	LEU	0	-0.005	-0.012	17.276	1.194	1.194	0.000	0.000	0.000	0.000
14	A	13	CYS	0	-0.046	-0.003	16.777	0.538	0.538	0.000	0.000	0.000	0.000
15	A	14	ASP	-1	-0.887	-0.949	18.576	-12.552	-12.552	0.000	0.000	0.000	0.000
16	A	15	ILE	0	0.002	0.003	21.552	-0.439	-0.439	0.000	0.000	0.000	0.000
17	A	16	GLU	-1	-0.897	-0.930	24.222	-10.756	-10.756	0.000	0.000	0.000	0.000
18	A	17	GLY	0	-0.001	0.005	26.279	0.544	0.544	0.000	0.000	0.000	0.000
19	A	18	GLN	0	-0.080	-0.039	26.826	0.153	0.153	0.000	0.000	0.000	0.000
20	A	19	HIS	1	0.855	0.912	21.787	13.029	13.029	0.000	0.000	0.000	0.000
21	A	20	LEU	0	0.006	0.008	20.917	0.621	0.621	0.000	0.000	0.000	0.000
22	A	21	SER	0	-0.014	-0.010	23.708	-0.297	-0.297	0.000	0.000	0.000	0.000
23	A	22	ALA	0	-0.013	-0.002	22.969	-0.052	-0.052	0.000	0.000	0.000	0.000
24	A	23	ALA	0	-0.006	-0.012	19.272	0.284	0.284	0.000	0.000	0.000	0.000
25	A	24	ALA	0	0.009	0.009	18.315	-0.339	-0.339	0.000	0.000	0.000	0.000
26	A	25	ILE	0	-0.011	0.006	13.485	0.066	0.066	0.000	0.000	0.000	0.000
27	A	26	VAL	0	0.010	0.006	17.158	-0.326	-0.326	0.000	0.000	0.000	0.000
28	A	27	GLY	0	0.085	0.049	19.034	-0.063	-0.063	0.000	0.000	0.000	0.000
29	A	28	HIS	0	-0.066	-0.038	19.743	0.951	0.951	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.872	-0.906	21.656	-13.993	-13.993	0.000	0.000	0.000	0.000
31	A	30	GLY	0	-0.022	-0.009	23.181	0.436	0.436	0.000	0.000	0.000	0.000
32	A	31	SER	0	-0.097	-0.065	19.555	-0.385	-0.385	0.000	0.000	0.000	0.000
33	A	32	VAL	0	0.015	0.003	17.839	-0.537	-0.537	0.000	0.000	0.000	0.000
34	A	33	TRP	0	-0.067	-0.033	13.648	-0.879	-0.879	0.000	0.000	0.000	0.000
35	A	34	ALA	0	-0.020	-0.015	13.084	-1.836	-1.836	0.000	0.000	0.000	0.000
36	A	35	GLN	0	-0.023	-0.020	15.195	0.948	0.948	0.000	0.000	0.000	0.000
37	A	36	SER	0	0.033	0.029	17.356	-0.502	-0.502	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.943	-0.982	19.264	-13.474	-13.474	0.000	0.000	0.000	0.000
39	A	38	ASN	0	-0.016	-0.007	21.417	0.690	0.690	0.000	0.000	0.000	0.000
40	A	39	PHE	0	-0.015	-0.006	21.933	0.486	0.486	0.000	0.000	0.000	0.000
41	A	40	PRO	0	-0.034	-0.015	23.953	0.201	0.201	0.000	0.000	0.000	0.000
42	A	41	GLU	-1	-0.846	-0.911	24.009	-13.586	-13.586	0.000	0.000	0.000	0.000
43	A	42	LEU	0	-0.010	-0.013	24.352	0.647	0.647	0.000	0.000	0.000	0.000
44	A	43	LYS	1	0.798	0.896	27.923	10.417	10.417	0.000	0.000	0.000	0.000
45	A	44	PRO	0	0.013	-0.007	30.396	-0.190	-0.190	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.897	-0.962	31.818	-9.248	-9.248	0.000	0.000	0.000	0.000
47	A	46	GLU	-1	-0.770	-0.863	29.875	-10.463	-10.463	0.000	0.000	0.000	0.000
48	A	47	VAL	0	0.053	0.011	25.096	0.036	0.036	0.000	0.000	0.000	0.000
49	A	48	ALA	0	0.027	0.027	28.225	-0.073	-0.073	0.000	0.000	0.000	0.000
50	A	49	GLY	0	-0.002	-0.005	30.787	0.161	0.161	0.000	0.000	0.000	0.000
51	A	50	MET	0	-0.044	-0.012	26.989	-0.043	-0.043	0.000	0.000	0.000	0.000
52	A	51	ILE	0	0.024	0.018	25.288	0.018	0.018	0.000	0.000	0.000	0.000
53	A	52	LYS	1	0.851	0.922	29.313	8.618	8.618	0.000	0.000	0.000	0.000
54	A	53	ASP	-1	-0.852	-0.928	32.387	-9.050	-9.050	0.000	0.000	0.000	0.000
55	A	54	PHE	0	-0.033	-0.028	26.460	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	55	ASP	-1	-0.899	-0.951	30.180	-10.459	-10.459	0.000	0.000	0.000	0.000
57	A	56	GLU	-1	-0.908	-0.953	32.601	-8.058	-8.058	0.000	0.000	0.000	0.000
58	A	57	PRO	0	-0.010	-0.007	33.934	0.104	0.104	0.000	0.000	0.000	0.000
59	A	58	GLY	0	-0.009	0.004	36.036	0.280	0.280	0.000	0.000	0.000	0.000
60	A	59	THR	0	-0.059	-0.034	36.643	0.181	0.181	0.000	0.000	0.000	0.000
61	A	60	LEU	0	0.002	0.001	32.930	0.149	0.149	0.000	0.000	0.000	0.000
62	A	61	ALA	0	-0.012	-0.008	36.997	0.084	0.084	0.000	0.000	0.000	0.000
63	A	62	PRO	0	-0.043	-0.025	39.128	0.103	0.103	0.000	0.000	0.000	0.000
64	A	63	THR	0	-0.027	0.009	38.594	0.193	0.193	0.000	0.000	0.000	0.000
65	A	64	GLY	0	-0.045	-0.037	38.199	0.103	0.103	0.000	0.000	0.000	0.000
66	A	65	LEU	0	0.041	0.020	30.326	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	66	PHE	0	-0.041	-0.031	33.705	0.174	0.174	0.000	0.000	0.000	0.000
68	A	67	VAL	0	0.066	0.027	27.500	-0.223	-0.223	0.000	0.000	0.000	0.000
69	A	68	GLY	0	0.063	0.030	29.848	0.063	0.063	0.000	0.000	0.000	0.000
70	A	69	GLY	0	-0.091	-0.040	30.315	0.198	0.198	0.000	0.000	0.000	0.000
71	A	70	THR	0	-0.074	-0.032	32.404	0.469	0.469	0.000	0.000	0.000	0.000
72	A	71	LYS	1	0.881	0.962	33.778	7.819	7.819	0.000	0.000	0.000	0.000
73	A	72	TYR	0	0.007	-0.001	30.404	0.058	0.058	0.000	0.000	0.000	0.000
74	A	73	MET	0	-0.053	-0.029	35.727	0.235	0.235	0.000	0.000	0.000	0.000
75	A	74	VAL	0	0.055	0.030	34.914	-0.227	-0.227	0.000	0.000	0.000	0.000
76	A	75	ILE	0	-0.063	-0.029	33.467	0.322	0.322	0.000	0.000	0.000	0.000
77	A	76	GLN	0	-0.038	-0.024	35.124	0.078	0.078	0.000	0.000	0.000	0.000
78	A	77	GLY	0	0.062	0.045	32.021	-0.264	-0.264	0.000	0.000	0.000	0.000
79	A	78	GLU	-1	-0.902	-0.945	29.173	-10.523	-10.523	0.000	0.000	0.000	0.000
80	A	79	PRO	0	0.007	0.003	30.856	-0.251	-0.251	0.000	0.000	0.000	0.000
81	A	80	GLY	0	0.060	0.028	29.884	-0.053	-0.053	0.000	0.000	0.000	0.000
82	A	81	VAL	0	-0.060	-0.018	25.641	-0.437	-0.437	0.000	0.000	0.000	0.000
83	A	82	VAL	0	-0.019	-0.019	25.988	-0.549	-0.549	0.000	0.000	0.000	0.000
84	A	83	ILE	0	0.018	0.031	27.962	0.525	0.525	0.000	0.000	0.000	0.000
85	A	84	ARG	1	0.760	0.837	28.384	10.442	10.442	0.000	0.000	0.000	0.000
86	A	85	GLY	0	0.029	0.004	31.090	0.374	0.374	0.000	0.000	0.000	0.000
87	A	86	LYS	1	0.891	0.949	32.599	8.458	8.458	0.000	0.000	0.000	0.000
88	A	87	LYS	1	0.924	0.955	34.992	9.327	9.327	0.000	0.000	0.000	0.000
89	A	88	GLY	0	-0.002	0.010	36.353	-0.088	-0.088	0.000	0.000	0.000	0.000
90	A	89	THR	0	-0.052	-0.051	36.083	0.161	0.161	0.000	0.000	0.000	0.000
91	A	90	GLY	0	0.069	0.059	33.030	-0.159	-0.159	0.000	0.000	0.000	0.000
92	A	91	GLY	0	-0.060	-0.053	31.468	0.392	0.392	0.000	0.000	0.000	0.000
93	A	92	ILE	0	-0.042	-0.001	27.000	-0.277	-0.277	0.000	0.000	0.000	0.000
94	A	93	THR	0	0.009	0.005	25.420	0.490	0.490	0.000	0.000	0.000	0.000
95	A	94	ILE	0	0.022	0.002	24.438	-0.518	-0.518	0.000	0.000	0.000	0.000
96	A	95	LYS	1	0.834	0.919	21.569	13.946	13.946	0.000	0.000	0.000	0.000
97	A	96	LYS	1	0.908	0.973	21.982	10.986	10.986	0.000	0.000	0.000	0.000
98	A	97	THR	0	-0.036	-0.039	17.873	0.051	0.051	0.000	0.000	0.000	0.000
99	A	98	GLY	0	-0.019	-0.022	19.599	0.658	0.658	0.000	0.000	0.000	0.000
100	A	99	MET	0	-0.096	-0.052	16.493	0.211	0.211	0.000	0.000	0.000	0.000
101	A	100	SER	0	-0.037	-0.023	16.863	-0.220	-0.220	0.000	0.000	0.000	0.000
102	A	101	LEU	0	-0.023	-0.011	19.004	0.875	0.875	0.000	0.000	0.000	0.000
103	A	102	ILE	0	0.009	0.011	16.463	-0.715	-0.715	0.000	0.000	0.000	0.000
104	A	103	ILE	0	0.008	-0.002	19.805	1.034	1.034	0.000	0.000	0.000	0.000
105	A	104	GLY	0	0.038	0.009	21.169	-0.776	-0.776	0.000	0.000	0.000	0.000
106	A	105	ILE	0	-0.021	-0.015	23.270	0.690	0.690	0.000	0.000	0.000	0.000
107	A	106	TYR	0	0.022	0.002	25.918	-0.334	-0.334	0.000	0.000	0.000	0.000
108	A	107	ASP	-1	-0.801	-0.911	28.311	-9.213	-9.213	0.000	0.000	0.000	0.000
109	A	108	GLU	-1	-0.956	-0.964	31.051	-9.222	-9.222	0.000	0.000	0.000	0.000
110	A	109	PRO	0	-0.008	-0.004	31.762	-0.047	-0.047	0.000	0.000	0.000	0.000
111	A	110	MET	0	-0.039	0.001	24.456	-0.085	-0.085	0.000	0.000	0.000	0.000
112	A	111	THR	0	-0.021	-0.029	30.373	0.314	0.314	0.000	0.000	0.000	0.000
113	A	112	PRO	0	0.022	0.000	29.662	-0.326	-0.326	0.000	0.000	0.000	0.000
114	A	113	GLY	0	0.005	0.005	29.356	-0.252	-0.252	0.000	0.000	0.000	0.000
115	A	114	GLN	0	0.052	0.010	26.714	-0.285	-0.285	0.000	0.000	0.000	0.000
116	A	115	CYS	0	-0.015	0.004	25.182	-0.682	-0.682	0.000	0.000	0.000	0.000
117	A	116	ASN	0	0.024	0.014	24.505	-0.621	-0.621	0.000	0.000	0.000	0.000
118	A	117	MET	0	-0.041	-0.014	24.367	-0.444	-0.444	0.000	0.000	0.000	0.000
119	A	118	VAL	0	-0.047	-0.015	19.680	-0.597	-0.597	0.000	0.000	0.000	0.000
120	A	119	VAL	0	0.020	0.008	19.761	-0.865	-0.865	0.000	0.000	0.000	0.000
121	A	120	GLU	-1	-0.796	-0.901	20.369	-12.360	-12.360	0.000	0.000	0.000	0.000
122	A	121	ARG	1	0.938	0.980	18.254	16.092	16.092	0.000	0.000	0.000	0.000
123	A	122	LEU	0	-0.011	0.005	13.348	-0.692	-0.692	0.000	0.000	0.000	0.000
124	A	123	GLY	0	0.039	0.008	16.273	-0.815	-0.815	0.000	0.000	0.000	0.000
125	A	124	ASP	-1	-0.822	-0.898	18.436	-13.973	-13.973	0.000	0.000	0.000	0.000
126	A	125	TYR	0	-0.053	-0.023	9.793	-0.216	-0.216	0.000	0.000	0.000	0.000
127	A	126	LEU	0	-0.002	-0.012	11.854	-0.934	-0.934	0.000	0.000	0.000	0.000
128	A	127	ILE	0	0.001	0.011	14.910	-0.201	-0.201	0.000	0.000	0.000	0.000
129	A	128	GLU	-1	-0.969	-0.978	16.524	-15.058	-15.058	0.000	0.000	0.000	0.000
130	A	129	GLN	0	-0.098	-0.043	8.946	-0.265	-0.265	0.000	0.000	0.000	0.000
131	A	130	GLY	0	-0.027	-0.002	13.591	-0.805	-0.805	0.000	0.000	0.000	0.000
132	A	131	PHE	-1	-0.752	-0.850	10.074	-17.177	-17.177	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)