FMO DATABASE

FMODB ID: 9LJL2

Calculation Name: 2CFE-A-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2CFE

Chain ID: A

ChEMBL ID:

UniProt ID: O93970

Base Structure: X-ray

Registration Date: 2025-10-03

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	162
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1560412.38428
FMO2-HF: Nuclear repulsion	1499511.150886
FMO2-HF: Total energy	-60901.233394
FMO2-MP2: Total energy	-61077.287751

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.
-4.248	2.183	2.055	-2.965	-5.519	-0.018

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 : 0.841 / q_NPA : 0.913

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	ASN	0	0.047	0.032	3.839	-1.753	-0.208	-0.016	-0.663	-0.866	0.001
24	A	24	ASP	-1	-0.747	-0.854	2.692	-55.514	-52.687	1.099	-1.307	-2.618	-0.012
25	A	25	ASP	-1	-0.904	-0.950	4.619	-40.522	-40.318	-0.001	-0.017	-0.186	0.000
28	A	28	PRO	0	0.054	0.043	4.224	-1.333	-1.198	-0.001	-0.009	-0.124	0.000
35	A	35	ARG	1	0.787	0.843	2.892	53.898	55.618	0.974	-0.969	-1.725	-0.007
4	A	4	VAL	0	0.021	0.002	6.683	-1.466	-1.466	0.000	0.000	0.000	0.000
5	A	5	PHE	0	-0.037	-0.017	9.052	1.925	1.925	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.011	-0.008	12.866	0.078	0.078	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.773	-0.869	16.187	-16.493	-16.493	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.023	-0.015	19.319	0.261	0.261	0.000	0.000	0.000	0.000
9	A	9	THR	0	-0.009	-0.003	22.061	0.520	0.520	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.879	0.921	25.728	9.504	9.504	0.000	0.000	0.000	0.000
11	A	11	ASN	0	-0.021	-0.028	28.748	0.122	0.122	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.053	0.036	28.681	0.299	0.299	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.006	0.011	29.238	-0.107	-0.107	0.000	0.000	0.000	0.000
14	A	14	PRO	0	-0.023	-0.024	25.784	-0.247	-0.247	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.027	-0.006	24.917	0.355	0.355	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.015	0.005	23.206	0.127	0.127	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.035	-0.035	16.718	0.098	0.098	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.045	-0.010	15.835	0.285	0.285	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.884	0.923	12.691	18.288	18.288	0.000	0.000	0.000	0.000
20	A	20	PHE	0	0.024	-0.004	10.559	1.504	1.504	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.910	0.979	7.319	20.942	20.942	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.023	-0.026	5.378	3.528	3.528	0.000	0.000	0.000	0.000
23	A	23	PHE	0	0.001	-0.001	5.417	-3.340	-3.340	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.067	-0.030	6.100	3.587	3.587	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.047	-0.015	7.860	2.321	2.321	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.943	0.972	5.678	19.605	19.605	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.002	-0.023	8.130	1.184	1.184	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.000	0.011	5.964	0.890	0.890	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.007	-0.004	5.140	-1.237	-1.237	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.008	-0.006	6.935	1.643	1.643	0.000	0.000	0.000	0.000
34	A	34	PHE	0	0.059	0.022	9.362	0.683	0.683	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.011	0.009	7.715	1.034	1.034	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.044	-0.012	10.031	2.266	2.266	0.000	0.000	0.000	0.000
38	A	38	CYS	0	-0.043	-0.016	9.750	1.866	1.866	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.038	-0.032	8.406	1.496	1.496	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.018	0.024	11.494	1.422	1.422	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.832	-0.903	9.381	-28.045	-28.045	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.828	0.903	11.178	24.288	24.288	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.020	0.020	16.184	1.004	1.004	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.032	-0.033	17.166	1.035	1.035	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.029	0.003	16.062	-1.231	-1.231	0.000	0.000	0.000	0.000
46	A	46	TYR	0	-0.055	-0.046	12.822	0.901	0.901	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.045	0.044	17.327	0.661	0.661	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.027	0.024	19.226	0.390	0.390	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.095	-0.057	19.688	0.548	0.548	0.000	0.000	0.000	0.000
50	A	50	HIS	0	0.017	0.006	22.259	-0.308	-0.308	0.000	0.000	0.000	0.000
51	A	51	PHE	0	-0.006	-0.018	18.889	-0.311	-0.311	0.000	0.000	0.000	0.000
52	A	52	HIS	0	-0.017	-0.001	23.054	0.412	0.412	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.878	0.948	25.774	10.934	10.934	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.018	0.011	25.500	-0.489	-0.489	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.051	-0.017	27.622	0.460	0.460	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.008	-0.004	28.476	-0.312	-0.312	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.897	-0.935	29.413	-9.482	-9.482	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.043	-0.034	25.944	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	59	MET	0	-0.034	-0.007	23.121	-0.713	-0.713	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.031	0.023	21.441	0.504	0.504	0.000	0.000	0.000	0.000
61	A	61	GLN	0	0.014	-0.009	21.522	-0.407	-0.407	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.038	0.017	20.891	0.562	0.562	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.048	0.021	18.718	-0.364	-0.364	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.728	-0.854	19.519	-12.344	-12.344	0.000	0.000	0.000	0.000
65	A	65	PHE	0	0.035	-0.002	17.308	0.441	0.441	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.039	-0.019	22.569	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.042	-0.012	25.385	0.409	0.409	0.000	0.000	0.000	0.000
68	A	68	GLY	0	-0.028	0.004	26.040	0.336	0.336	0.000	0.000	0.000	0.000
69	A	69	ASN	0	0.007	-0.001	27.056	-0.073	-0.073	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.017	0.013	25.839	0.236	0.236	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.099	-0.064	26.909	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.009	0.014	25.713	0.060	0.060	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.001	-0.007	21.585	-0.350	-0.350	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.838	0.933	19.681	14.789	14.789	0.000	0.000	0.000	0.000
75	A	75	SER	0	-0.012	-0.011	14.955	-0.829	-0.829	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.016	-0.018	9.729	0.734	0.734	0.000	0.000	0.000	0.000
77	A	77	TYR	0	-0.086	-0.053	9.157	-0.223	-0.223	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.041	0.036	15.164	0.865	0.865	0.000	0.000	0.000	0.000
79	A	79	ALA	0	-0.015	-0.001	18.608	-0.441	-0.441	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.938	0.964	19.329	11.905	11.905	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.015	-0.001	12.990	-0.073	-0.073	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.037	0.006	16.269	0.350	0.350	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.803	-0.895	15.877	-15.412	-15.412	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.811	-0.877	9.406	-24.831	-24.831	0.000	0.000	0.000	0.000
85	A	85	ASN	0	0.008	-0.013	11.703	0.568	0.568	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.004	-0.002	15.515	-0.203	-0.203	0.000	0.000	0.000	0.000
87	A	87	GLN	0	0.007	0.013	13.486	0.727	0.727	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.051	-0.013	11.414	0.366	0.366	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.972	0.988	16.103	13.241	13.241	0.000	0.000	0.000	0.000
90	A	90	HIS	0	0.013	0.001	18.292	-0.891	-0.891	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.027	-0.032	18.443	0.338	0.338	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.917	0.964	16.661	16.883	16.883	0.000	0.000	0.000	0.000
93	A	93	PRO	0	0.020	0.027	20.557	-0.320	-0.320	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.034	0.006	18.182	-0.385	-0.385	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.058	-0.012	14.925	-1.286	-1.286	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.013	0.009	11.875	0.924	0.924	0.000	0.000	0.000	0.000
97	A	97	SER	0	0.013	-0.025	14.447	-0.816	-0.816	0.000	0.000	0.000	0.000
98	A	98	MET	0	-0.008	0.015	15.005	-0.112	-0.112	0.000	0.000	0.000	0.000
99	A	99	ALA	0	-0.017	-0.008	17.451	0.873	0.873	0.000	0.000	0.000	0.000
100	A	100	ASN	0	-0.055	-0.036	20.524	0.178	0.178	0.000	0.000	0.000	0.000
101	A	101	ALA	0	0.006	-0.003	22.818	0.360	0.360	0.000	0.000	0.000	0.000
102	A	102	GLY	0	0.026	0.024	25.440	0.435	0.435	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.016	0.003	23.036	-0.455	-0.455	0.000	0.000	0.000	0.000
104	A	104	ASN	0	-0.035	-0.017	19.931	-0.264	-0.264	0.000	0.000	0.000	0.000
105	A	105	THR	0	-0.026	-0.029	20.986	0.128	0.128	0.000	0.000	0.000	0.000
106	A	106	ASN	0	-0.008	-0.010	16.748	0.441	0.441	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.066	0.026	18.222	0.011	0.011	0.000	0.000	0.000	0.000
108	A	108	SER	0	0.013	0.000	16.414	-0.826	-0.826	0.000	0.000	0.000	0.000
109	A	109	GLN	0	-0.075	-0.038	17.049	-0.542	-0.542	0.000	0.000	0.000	0.000
110	A	110	PHE	0	-0.002	0.011	15.995	-0.497	-0.497	0.000	0.000	0.000	0.000
111	A	111	PHE	0	-0.030	-0.031	17.997	0.893	0.893	0.000	0.000	0.000	0.000
112	A	112	ILE	0	0.020	0.016	16.983	-0.995	-0.995	0.000	0.000	0.000	0.000
113	A	113	THR	0	-0.025	-0.017	19.227	0.580	0.580	0.000	0.000	0.000	0.000
114	A	114	THR	0	-0.048	-0.054	21.223	-0.495	-0.495	0.000	0.000	0.000	0.000
115	A	115	VAL	0	0.010	0.015	23.982	0.228	0.228	0.000	0.000	0.000	0.000
116	A	116	VAL	0	-0.018	-0.002	23.582	-0.547	-0.547	0.000	0.000	0.000	0.000
117	A	117	THR	0	0.018	-0.002	23.184	0.306	0.306	0.000	0.000	0.000	0.000
118	A	118	SER	0	0.037	0.008	24.116	-0.057	-0.057	0.000	0.000	0.000	0.000
119	A	119	TRP	0	0.011	0.021	25.157	-0.068	-0.068	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.043	-0.027	23.196	0.205	0.205	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.768	-0.882	21.766	-14.034	-14.034	0.000	0.000	0.000	0.000
122	A	122	GLY	0	-0.031	-0.019	21.520	0.521	0.521	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.885	0.955	22.669	11.163	11.163	0.000	0.000	0.000	0.000
124	A	124	HIS	1	0.842	0.930	19.965	13.560	13.560	0.000	0.000	0.000	0.000
125	A	125	VAL	0	0.020	0.028	13.499	0.108	0.108	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.027	0.019	13.938	-0.527	-0.527	0.000	0.000	0.000	0.000
127	A	127	PHE	0	0.007	-0.017	9.988	-0.531	-0.531	0.000	0.000	0.000	0.000
128	A	128	GLY	0	0.030	0.009	9.296	-3.333	-3.333	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.877	-0.934	10.696	-17.809	-17.809	0.000	0.000	0.000	0.000
130	A	130	VAL	0	-0.024	-0.011	11.942	-1.610	-1.610	0.000	0.000	0.000	0.000
131	A	131	ILE	0	-0.064	-0.034	10.221	0.387	0.387	0.000	0.000	0.000	0.000
132	A	132	ASP	-1	-0.798	-0.890	14.165	-16.331	-16.331	0.000	0.000	0.000	0.000
133	A	133	GLY	0	0.067	0.040	16.967	-0.395	-0.395	0.000	0.000	0.000	0.000
134	A	134	MET	0	-0.014	-0.007	19.681	0.176	0.176	0.000	0.000	0.000	0.000
135	A	135	ASN	0	0.004	-0.005	20.961	0.045	0.045	0.000	0.000	0.000	0.000
136	A	136	VAL	0	0.019	0.019	21.437	0.512	0.512	0.000	0.000	0.000	0.000
137	A	137	VAL	0	0.007	0.002	19.511	0.295	0.295	0.000	0.000	0.000	0.000
138	A	138	LYS	1	1.004	0.989	22.524	12.056	12.056	0.000	0.000	0.000	0.000
139	A	139	ALA	0	-0.029	-0.004	25.937	0.469	0.469	0.000	0.000	0.000	0.000
140	A	140	ILE	0	-0.009	-0.004	22.093	0.344	0.344	0.000	0.000	0.000	0.000
141	A	141	GLU	-1	-0.806	-0.887	26.246	-11.035	-11.035	0.000	0.000	0.000	0.000
142	A	142	ALA	0	-0.014	-0.001	27.714	0.353	0.353	0.000	0.000	0.000	0.000
143	A	143	GLU	-1	-0.814	-0.865	29.261	-9.236	-9.236	0.000	0.000	0.000	0.000
144	A	144	GLY	0	0.057	0.033	30.548	0.034	0.034	0.000	0.000	0.000	0.000
145	A	145	SER	0	-0.070	-0.062	31.114	0.466	0.466	0.000	0.000	0.000	0.000
146	A	146	GLY	0	0.067	0.029	32.901	-0.213	-0.213	0.000	0.000	0.000	0.000
147	A	147	SER	0	-0.013	-0.003	34.522	-0.080	-0.080	0.000	0.000	0.000	0.000
148	A	148	GLY	0	0.012	-0.003	30.809	-0.131	-0.131	0.000	0.000	0.000	0.000
149	A	149	LYS	1	0.939	0.980	30.404	8.171	8.171	0.000	0.000	0.000	0.000
150	A	150	PRO	0	0.028	0.031	28.820	0.218	0.218	0.000	0.000	0.000	0.000
151	A	151	ARG	1	0.865	0.936	31.414	9.147	9.147	0.000	0.000	0.000	0.000
152	A	152	SER	0	-0.059	-0.055	31.085	0.125	0.125	0.000	0.000	0.000	0.000
153	A	153	ARG	1	0.806	0.884	25.993	11.227	11.227	0.000	0.000	0.000	0.000
154	A	154	ILE	0	0.011	0.013	23.937	-0.072	-0.072	0.000	0.000	0.000	0.000
155	A	155	GLU	-1	-0.822	-0.907	23.503	-12.248	-12.248	0.000	0.000	0.000	0.000
156	A	156	ILE	0	-0.005	0.002	17.219	-0.151	-0.151	0.000	0.000	0.000	0.000
157	A	157	ALA	0	0.024	0.020	20.525	-0.110	-0.110	0.000	0.000	0.000	0.000
158	A	158	LYS	1	0.882	0.935	16.739	17.100	17.100	0.000	0.000	0.000	0.000
159	A	159	CYS	0	-0.073	-0.023	13.959	0.332	0.332	0.000	0.000	0.000	0.000
160	A	160	GLY	0	0.036	0.025	11.607	0.653	0.653	0.000	0.000	0.000	0.000
161	A	161	VAL	0	-0.023	-0.023	5.780	-1.311	-1.311	0.000	0.000	0.000	0.000
162	A	162	CYS	-1	-0.897	-0.941	7.629	-34.745	-34.745	0.000	0.000	0.000	0.000

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