FMO DATABASE

FMODB ID: RK948

Calculation Name: 3GE2-A-Xray549

Preferred Name:

Target Type:

Ligand Name: glycerol | chloride ion | potassium ion

Ligand 3-letter code: GOL | CL | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3GE2

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

Base Structure: X-ray

Registration Date: 2025-10-12

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	89
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-594070.8117
FMO2-HF: Nuclear repulsion	559553.641066
FMO2-HF: Total energy	-34517.170634
FMO2-MP2: Total energy	-34617.456229

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:65:GLN)

Summations of interaction energy for fragment #1(A:65:GLN)

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.
-146.255	-144.83	-0.016	-0.532	-0.877	-0.001

Interaction energy analysis for fragmet #1(A:65:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.840 / q_NPA : 0.894

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	67	VAL	0	0.002	0.000	3.865	1.250	2.620	-0.015	-0.529	-0.826	-0.001
55	A	119	ARG	1	0.889	0.950	4.568	41.781	41.836	-0.001	-0.003	-0.051	0.000
4	A	68	ALA	0	0.010	0.015	6.465	2.444	2.444	0.000	0.000	0.000	0.000
5	A	69	GLN	0	-0.014	-0.012	9.738	2.726	2.726	0.000	0.000	0.000	0.000
6	A	70	PRO	0	0.001	-0.010	12.934	0.549	0.549	0.000	0.000	0.000	0.000
7	A	71	THR	0	-0.021	-0.021	16.732	-0.324	-0.324	0.000	0.000	0.000	0.000
8	A	72	ASP	-1	-0.933	-0.948	18.546	-12.482	-12.482	0.000	0.000	0.000	0.000
9	A	73	ILE	0	0.016	-0.005	17.818	-0.424	-0.424	0.000	0.000	0.000	0.000
10	A	74	ASP	-1	-0.788	-0.854	21.514	-12.356	-12.356	0.000	0.000	0.000	0.000
11	A	75	GLY	0	-0.042	-0.019	25.001	0.129	0.129	0.000	0.000	0.000	0.000
12	A	76	THR	0	-0.049	-0.035	26.511	-0.019	-0.019	0.000	0.000	0.000	0.000
13	A	77	TYR	0	-0.032	-0.034	22.491	0.124	0.124	0.000	0.000	0.000	0.000
14	A	78	THR	0	-0.052	-0.030	25.748	0.246	0.246	0.000	0.000	0.000	0.000
15	A	79	GLY	0	0.034	0.007	24.720	-0.337	-0.337	0.000	0.000	0.000	0.000
16	A	80	GLN	0	-0.087	-0.043	25.196	0.460	0.460	0.000	0.000	0.000	0.000
17	A	81	ASP	-1	-0.854	-0.941	22.687	-14.251	-14.251	0.000	0.000	0.000	0.000
18	A	82	ASP	-1	-0.851	-0.921	24.675	-11.665	-11.665	0.000	0.000	0.000	0.000
19	A	83	GLY	0	-0.124	-0.051	26.715	0.467	0.467	0.000	0.000	0.000	0.000
20	A	84	ASP	-1	-0.827	-0.905	28.277	-9.880	-9.880	0.000	0.000	0.000	0.000
21	A	85	ARG	1	0.868	0.935	28.108	9.359	9.359	0.000	0.000	0.000	0.000
22	A	86	ILE	0	0.013	0.018	23.008	0.136	0.136	0.000	0.000	0.000	0.000
23	A	87	THR	0	-0.048	-0.040	26.401	0.260	0.260	0.000	0.000	0.000	0.000
24	A	88	LEU	0	-0.004	0.004	20.252	-0.085	-0.085	0.000	0.000	0.000	0.000
25	A	89	VAL	0	-0.020	-0.007	24.780	0.069	0.069	0.000	0.000	0.000	0.000
26	A	90	VAL	0	0.002	-0.006	21.204	-0.346	-0.346	0.000	0.000	0.000	0.000
27	A	91	THR	0	-0.007	-0.007	23.959	0.600	0.600	0.000	0.000	0.000	0.000
28	A	92	GLY	0	-0.005	-0.003	23.293	-0.056	-0.056	0.000	0.000	0.000	0.000
29	A	93	THR	0	-0.038	-0.023	18.995	-0.246	-0.246	0.000	0.000	0.000	0.000
30	A	94	THR	0	-0.035	-0.024	19.721	-0.348	-0.348	0.000	0.000	0.000	0.000
31	A	95	GLY	0	0.072	0.027	22.061	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	96	THR	0	-0.068	-0.031	23.839	0.189	0.189	0.000	0.000	0.000	0.000
33	A	97	TRP	0	0.010	-0.015	19.664	-0.250	-0.250	0.000	0.000	0.000	0.000
34	A	98	THR	0	-0.017	-0.021	24.332	0.296	0.296	0.000	0.000	0.000	0.000
35	A	99	GLU	-1	-0.784	-0.877	24.399	-12.495	-12.495	0.000	0.000	0.000	0.000
36	A	100	LEU	0	-0.073	-0.046	28.080	0.377	0.377	0.000	0.000	0.000	0.000
37	A	101	GLU	-1	-0.874	-0.931	31.194	-10.012	-10.012	0.000	0.000	0.000	0.000
38	A	102	SER	0	-0.044	-0.030	33.058	0.370	0.370	0.000	0.000	0.000	0.000
39	A	103	ASP	-1	-0.940	-0.970	35.632	-8.292	-8.292	0.000	0.000	0.000	0.000
40	A	104	GLY	0	-0.076	-0.037	36.894	0.258	0.258	0.000	0.000	0.000	0.000
41	A	105	ASP	-1	-0.923	-0.943	35.328	-8.333	-8.333	0.000	0.000	0.000	0.000
42	A	106	GLN	0	-0.051	-0.049	32.466	-0.377	-0.377	0.000	0.000	0.000	0.000
43	A	107	LYS	1	0.952	0.990	26.748	11.317	11.317	0.000	0.000	0.000	0.000
44	A	108	VAL	0	-0.023	-0.006	28.042	-0.347	-0.347	0.000	0.000	0.000	0.000
45	A	109	LYS	1	0.840	0.923	21.500	13.823	13.823	0.000	0.000	0.000	0.000
46	A	110	GLN	0	-0.009	-0.011	24.306	0.099	0.099	0.000	0.000	0.000	0.000
47	A	111	VAL	0	0.018	0.017	19.036	-0.446	-0.446	0.000	0.000	0.000	0.000
48	A	112	THR	0	-0.059	-0.027	18.032	0.241	0.241	0.000	0.000	0.000	0.000
49	A	113	PHE	0	0.039	0.010	15.489	-0.794	-0.794	0.000	0.000	0.000	0.000
50	A	114	ASP	-1	-0.819	-0.881	11.530	-25.498	-25.498	0.000	0.000	0.000	0.000
51	A	115	SER	0	0.050	0.014	11.799	-1.911	-1.911	0.000	0.000	0.000	0.000
52	A	116	ALA	0	-0.028	-0.006	10.568	-1.184	-1.184	0.000	0.000	0.000	0.000
53	A	117	ASN	0	-0.101	-0.093	7.219	-6.830	-6.830	0.000	0.000	0.000	0.000
54	A	118	GLN	0	-0.027	-0.012	6.550	-10.694	-10.694	0.000	0.000	0.000	0.000
56	A	120	MET	0	-0.001	0.016	10.768	1.489	1.489	0.000	0.000	0.000	0.000
57	A	121	ILE	0	-0.028	-0.007	14.333	-0.594	-0.594	0.000	0.000	0.000	0.000
58	A	122	ILE	0	0.047	0.018	16.312	0.798	0.798	0.000	0.000	0.000	0.000
59	A	123	GLY	0	-0.020	-0.013	19.557	0.378	0.378	0.000	0.000	0.000	0.000
60	A	124	ASP	-1	-0.951	-0.981	19.303	-14.165	-14.165	0.000	0.000	0.000	0.000
61	A	125	ASP	-1	-0.857	-0.910	17.523	-15.785	-15.785	0.000	0.000	0.000	0.000
62	A	126	VAL	0	-0.067	-0.046	11.212	-0.457	-0.457	0.000	0.000	0.000	0.000
63	A	127	LYS	1	0.882	0.936	12.548	17.891	17.891	0.000	0.000	0.000	0.000
64	A	128	ILE	0	-0.060	-0.035	6.491	-2.406	-2.406	0.000	0.000	0.000	0.000
65	A	129	TYR	0	0.037	0.022	10.324	1.960	1.960	0.000	0.000	0.000	0.000
66	A	130	THR	0	-0.050	-0.032	10.788	-3.744	-3.744	0.000	0.000	0.000	0.000
67	A	131	VAL	0	-0.010	0.009	12.753	1.512	1.512	0.000	0.000	0.000	0.000
68	A	132	ASN	0	-0.034	-0.021	15.298	-0.877	-0.877	0.000	0.000	0.000	0.000
69	A	133	GLY	0	-0.019	-0.017	17.776	0.918	0.918	0.000	0.000	0.000	0.000
70	A	134	ASN	0	-0.023	-0.024	20.880	-0.257	-0.257	0.000	0.000	0.000	0.000
71	A	135	GLN	0	0.025	0.024	18.620	-0.426	-0.426	0.000	0.000	0.000	0.000
72	A	136	ILE	0	-0.018	-0.008	16.690	-0.855	-0.855	0.000	0.000	0.000	0.000
73	A	137	VAL	0	-0.001	0.010	14.445	0.715	0.715	0.000	0.000	0.000	0.000
74	A	138	VAL	0	-0.013	-0.020	14.444	-1.446	-1.446	0.000	0.000	0.000	0.000
75	A	139	ASP	-1	-0.761	-0.855	11.011	-23.970	-23.970	0.000	0.000	0.000	0.000
76	A	140	ASP	-1	-0.686	-0.826	12.479	-19.821	-19.821	0.000	0.000	0.000	0.000
77	A	141	MET	0	-0.071	-0.059	8.617	-3.427	-3.427	0.000	0.000	0.000	0.000
78	A	142	ASP	-1	-0.934	-0.961	7.890	-26.708	-26.708	0.000	0.000	0.000	0.000
79	A	143	ARG	1	0.760	0.864	5.948	34.049	34.049	0.000	0.000	0.000	0.000
80	A	144	ASP	-1	-0.765	-0.850	10.778	-16.632	-16.632	0.000	0.000	0.000	0.000
81	A	145	PRO	0	-0.084	-0.049	14.365	0.291	0.291	0.000	0.000	0.000	0.000
82	A	146	SER	0	-0.153	-0.101	16.257	1.006	1.006	0.000	0.000	0.000	0.000
83	A	147	ASP	-1	-0.836	-0.905	16.465	-15.575	-15.575	0.000	0.000	0.000	0.000
84	A	148	GLN	0	-0.173	-0.094	13.559	0.624	0.624	0.000	0.000	0.000	0.000
85	A	149	ILE	0	0.027	0.027	16.813	0.910	0.910	0.000	0.000	0.000	0.000
86	A	150	VAL	0	-0.063	-0.040	17.975	-0.876	-0.876	0.000	0.000	0.000	0.000
87	A	151	LEU	0	-0.012	0.003	20.251	0.847	0.847	0.000	0.000	0.000	0.000
88	A	152	THR	0	-0.056	-0.045	21.780	-0.622	-0.622	0.000	0.000	0.000	0.000
89	A	153	LYS	0	0.000	0.035	23.917	1.733	1.733	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:65:GLN)