FMO DATABASE

FMODB ID: N6Z1Q

Calculation Name: 7B9V-Y-Other547

Preferred Name:

Target Type:

Ligand Name: d-chiro inositol hexakisphosphate | guanosine-5'-triphosphate | phosphoserine | potassium ion

Ligand 3-letter code: KGN | GTP | SEP | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7B9V

Chain ID: Y

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-640324.833439
FMO2-HF: Nuclear repulsion	604981.888173
FMO2-HF: Total energy	-35342.945265
FMO2-MP2: Total energy	-35446.182771

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:24:THR)

Summations of interaction energy for fragment #1(A:24:THR)

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.
106.88	110.521	0.23	-1.42	-2.452	-0.008

Interaction energy analysis for fragmet #1(A:24:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.833 / q_NPA : 0.897

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	26	ALA	0	0.025	0.026	3.329	-0.242	1.945	0.018	-1.055	-1.150	-0.007
80	A	103	PHE	0	0.080	0.031	3.176	2.069	2.403	0.037	-0.065	-0.306	0.000
81	A	104	SER	0	-0.039	-0.008	3.669	-4.016	-3.581	0.009	-0.161	-0.283	-0.001
82	A	105	LYS	1	0.924	0.955	2.729	33.959	34.627	0.167	-0.133	-0.703	0.000
83	A	106	SER	0	-0.048	-0.022	4.646	2.610	2.627	-0.001	-0.006	-0.010	0.000
4	A	27	LYS	1	0.877	0.929	5.873	40.724	40.724	0.000	0.000	0.000	0.000
5	A	28	ASN	0	0.029	-0.002	7.664	0.765	0.765	0.000	0.000	0.000	0.000
6	A	29	THR	0	-0.043	0.000	8.999	2.304	2.304	0.000	0.000	0.000	0.000
7	A	30	LEU	0	0.017	0.020	7.556	-3.550	-3.550	0.000	0.000	0.000	0.000
8	A	31	TYR	0	-0.068	-0.056	6.810	2.077	2.077	0.000	0.000	0.000	0.000
9	A	32	VAL	0	0.037	0.015	9.004	-0.628	-0.628	0.000	0.000	0.000	0.000
10	A	33	SER	0	0.031	0.012	10.192	1.910	1.910	0.000	0.000	0.000	0.000
11	A	34	GLN	0	-0.029	-0.026	12.467	1.429	1.429	0.000	0.000	0.000	0.000
12	A	35	LEU	0	0.029	0.026	15.904	0.825	0.825	0.000	0.000	0.000	0.000
13	A	36	ASN	0	-0.047	-0.038	18.669	0.343	0.343	0.000	0.000	0.000	0.000
14	A	37	GLU	-1	-0.778	-0.899	21.758	-12.743	-12.743	0.000	0.000	0.000	0.000
15	A	38	LYS	1	0.933	0.966	23.967	9.873	9.873	0.000	0.000	0.000	0.000
16	A	39	ILE	0	-0.028	0.008	24.569	0.466	0.466	0.000	0.000	0.000	0.000
17	A	40	ASN	0	0.041	0.012	25.941	-0.505	-0.505	0.000	0.000	0.000	0.000
18	A	41	MET	0	0.073	0.030	21.778	-0.083	-0.083	0.000	0.000	0.000	0.000
19	A	42	GLN	0	0.034	0.027	24.382	-0.599	-0.599	0.000	0.000	0.000	0.000
20	A	43	ARG	1	0.966	0.977	26.365	9.699	9.699	0.000	0.000	0.000	0.000
21	A	44	LEU	0	0.015	0.027	21.187	-0.159	-0.159	0.000	0.000	0.000	0.000
22	A	45	ARG	1	0.911	0.944	20.717	12.443	12.443	0.000	0.000	0.000	0.000
23	A	46	VAL	0	0.005	0.010	22.377	-0.289	-0.289	0.000	0.000	0.000	0.000
24	A	47	ASN	0	-0.034	-0.042	24.017	0.013	0.013	0.000	0.000	0.000	0.000
25	A	48	LEU	0	-0.004	0.002	17.143	-0.269	-0.269	0.000	0.000	0.000	0.000
26	A	49	PHE	0	0.015	0.008	19.626	-0.508	-0.508	0.000	0.000	0.000	0.000
27	A	50	LEU	0	-0.015	-0.013	21.521	-0.173	-0.173	0.000	0.000	0.000	0.000
28	A	51	LEU	0	-0.016	-0.001	18.692	0.029	0.029	0.000	0.000	0.000	0.000
29	A	52	PHE	0	0.019	-0.009	13.316	-0.516	-0.516	0.000	0.000	0.000	0.000
30	A	53	ALA	0	0.032	0.021	18.634	-0.355	-0.355	0.000	0.000	0.000	0.000
31	A	54	THR	0	-0.040	-0.016	21.402	0.228	0.228	0.000	0.000	0.000	0.000
32	A	55	PHE	0	-0.024	-0.009	17.220	-0.053	-0.053	0.000	0.000	0.000	0.000
33	A	56	GLY	0	0.017	-0.017	17.291	-0.884	-0.884	0.000	0.000	0.000	0.000
34	A	57	GLU	-1	-0.836	-0.891	18.352	-12.537	-12.537	0.000	0.000	0.000	0.000
35	A	58	VAL	0	-0.027	-0.025	17.236	-0.634	-0.634	0.000	0.000	0.000	0.000
36	A	59	LEU	0	0.006	0.013	17.438	0.737	0.737	0.000	0.000	0.000	0.000
37	A	60	LYS	1	0.855	0.921	17.302	14.198	14.198	0.000	0.000	0.000	0.000
38	A	61	VAL	0	0.037	0.022	16.931	-0.878	-0.878	0.000	0.000	0.000	0.000
39	A	62	SER	0	0.002	0.000	15.717	1.285	1.285	0.000	0.000	0.000	0.000
40	A	63	MET	0	0.012	-0.004	16.463	-0.525	-0.525	0.000	0.000	0.000	0.000
41	A	64	ASN	0	0.020	0.008	17.729	1.168	1.168	0.000	0.000	0.000	0.000
42	A	65	PHE	0	0.057	0.013	18.924	-0.061	-0.061	0.000	0.000	0.000	0.000
43	A	66	LYS	1	0.958	0.987	21.360	10.479	10.479	0.000	0.000	0.000	0.000
44	A	67	LYS	1	0.940	0.965	18.868	13.203	13.203	0.000	0.000	0.000	0.000
45	A	68	GLN	0	0.040	0.015	14.528	-0.676	-0.676	0.000	0.000	0.000	0.000
46	A	69	ARG	1	0.877	0.944	17.354	12.129	12.129	0.000	0.000	0.000	0.000
47	A	70	GLY	0	0.074	0.046	17.398	-0.713	-0.713	0.000	0.000	0.000	0.000
48	A	71	GLN	0	-0.061	-0.012	12.854	-1.879	-1.879	0.000	0.000	0.000	0.000
49	A	72	ALA	0	-0.018	-0.022	14.055	1.106	1.106	0.000	0.000	0.000	0.000
50	A	73	PHE	0	-0.008	0.002	8.733	-1.183	-1.183	0.000	0.000	0.000	0.000
51	A	74	ILE	0	-0.006	0.001	12.213	1.563	1.563	0.000	0.000	0.000	0.000
52	A	75	THR	0	-0.024	-0.006	12.250	-1.423	-1.423	0.000	0.000	0.000	0.000
53	A	76	MET	0	-0.010	0.019	13.272	1.624	1.624	0.000	0.000	0.000	0.000
54	A	77	ARG	1	0.882	0.924	15.049	12.760	12.760	0.000	0.000	0.000	0.000
55	A	78	THR	0	0.009	-0.005	15.297	0.036	0.036	0.000	0.000	0.000	0.000
56	A	79	ILE	0	0.042	0.011	9.565	-0.620	-0.620	0.000	0.000	0.000	0.000
57	A	80	ASP	-1	-0.876	-0.938	11.907	-20.959	-20.959	0.000	0.000	0.000	0.000
58	A	81	GLN	0	0.024	0.031	14.547	0.078	0.078	0.000	0.000	0.000	0.000
59	A	82	ALA	0	-0.018	-0.001	9.950	-0.056	-0.056	0.000	0.000	0.000	0.000
60	A	83	SER	0	-0.006	-0.017	10.180	-1.417	-1.417	0.000	0.000	0.000	0.000
61	A	84	LEU	0	0.033	0.032	11.120	-0.152	-0.152	0.000	0.000	0.000	0.000
62	A	85	ALA	0	0.026	0.000	13.439	0.459	0.459	0.000	0.000	0.000	0.000
63	A	86	GLN	0	-0.099	-0.062	7.651	-0.323	-0.323	0.000	0.000	0.000	0.000
64	A	87	ILE	0	-0.025	-0.012	10.933	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	88	SER	0	-0.045	-0.014	12.606	0.971	0.971	0.000	0.000	0.000	0.000
66	A	89	LEU	0	0.033	0.012	14.831	0.921	0.921	0.000	0.000	0.000	0.000
67	A	90	ASN	0	-0.109	-0.057	10.393	1.533	1.533	0.000	0.000	0.000	0.000
68	A	91	GLY	0	0.030	0.014	14.069	0.416	0.416	0.000	0.000	0.000	0.000
69	A	92	GLU	-1	-0.857	-0.907	17.087	-12.674	-12.674	0.000	0.000	0.000	0.000
70	A	93	ARG	1	0.884	0.928	19.341	12.680	12.680	0.000	0.000	0.000	0.000
71	A	94	PHE	0	0.053	0.024	19.983	0.441	0.441	0.000	0.000	0.000	0.000
72	A	95	PHE	0	-0.052	-0.041	22.063	0.148	0.148	0.000	0.000	0.000	0.000
73	A	96	GLY	0	0.037	0.021	25.083	0.161	0.161	0.000	0.000	0.000	0.000
74	A	97	LYS	1	0.867	0.955	18.912	14.778	14.778	0.000	0.000	0.000	0.000
75	A	98	PRO	0	-0.024	-0.003	18.775	-0.057	-0.057	0.000	0.000	0.000	0.000
76	A	99	LEU	0	-0.001	0.007	15.030	-0.297	-0.297	0.000	0.000	0.000	0.000
77	A	100	LYS	1	0.967	0.981	11.388	20.762	20.762	0.000	0.000	0.000	0.000
78	A	101	VAL	0	0.027	0.014	10.275	0.428	0.428	0.000	0.000	0.000	0.000
79	A	102	GLU	-1	-0.917	-0.941	5.125	-37.044	-37.044	0.000	0.000	0.000	0.000
84	A	107	GLU	-1	-0.775	-0.896	8.067	-25.193	-25.193	0.000	0.000	0.000	0.000
85	A	108	THR	0	-0.076	-0.044	10.729	0.737	0.737	0.000	0.000	0.000	0.000
86	A	109	LYS	1	0.981	0.980	13.896	17.831	17.831	0.000	0.000	0.000	0.000
87	A	110	THR	0	-0.067	-0.042	16.706	0.641	0.641	0.000	0.000	0.000	0.000
88	A	111	LEU	-1	-0.768	-0.847	16.511	-13.281	-13.281	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:24:THR)