FMO DATABASE

FMODB ID: MLJVZ

Calculation Name: 3JB9-k-Other547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate | adenosine-5'-diphosphate

Ligand 3-letter code: GDP | ADP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3JB9

Chain ID: k

ChEMBL ID:

UniProt ID: P39964

Base Structure: ElectronMicroscopy

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	89
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-625131.700835
FMO2-HF: Nuclear repulsion	589832.092044
FMO2-HF: Total energy	-35299.608792
FMO2-MP2: Total energy	-35402.116125

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:5:THR)

Summations of interaction energy for fragment #1(A:5: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.
61.527	68.124	20.74	-11.575	-15.763	-0.087

Interaction energy analysis for fragmet #1(A:5:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.807 / q_NPA : 0.880

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

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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	7	TYR	0	-0.034	-0.029	2.630	-1.841	0.461	0.887	-1.299	-1.891	-0.015
4	A	8	VAL	0	0.035	0.020	4.757	2.593	2.613	-0.001	-0.006	-0.012	0.000
46	A	50	HIS	0	-0.002	0.006	2.782	-8.348	-7.336	0.479	-0.408	-1.083	-0.003
47	A	51	VAL	0	0.016	0.010	3.132	4.430	5.136	0.076	-0.240	-0.543	-0.001
48	A	52	VAL	0	-0.031	-0.018	2.379	-25.719	-21.296	5.380	-4.380	-5.423	-0.032
49	A	53	PHE	0	0.035	0.016	2.894	7.261	7.640	0.060	0.075	-0.513	-0.001
50	A	54	PHE	0	-0.010	-0.009	4.614	-5.625	-5.524	-0.001	-0.007	-0.093	0.000
52	A	56	PRO	0	-0.008	-0.013	4.681	-6.311	-6.264	-0.001	-0.001	-0.044	0.000
55	A	59	ALA	0	-0.022	-0.015	3.189	-2.154	-1.829	0.009	-0.130	-0.203	-0.001
56	A	60	ALA	0	0.037	0.015	5.242	3.066	3.091	-0.001	-0.001	-0.024	0.000
76	A	80	TYR	0	0.092	0.033	4.689	-5.755	-5.611	-0.001	-0.024	-0.119	0.000
77	A	81	ALA	0	-0.062	-0.023	2.317	6.166	6.745	1.560	-0.701	-1.438	-0.004
78	A	82	HIS	0	0.055	0.031	4.403	-0.031	0.082	-0.001	-0.019	-0.093	0.000
80	A	84	LYS	1	0.931	0.956	4.061	21.650	21.920	0.000	-0.051	-0.219	0.000
81	A	85	SER	0	0.035	0.017	1.749	-10.646	-15.423	12.260	-4.026	-3.457	-0.029
82	A	86	LYS	1	0.929	0.939	3.815	26.435	26.730	0.000	-0.168	-0.128	-0.001
84	A	88	ILE	0	0.015	0.000	3.389	0.045	0.678	0.035	-0.189	-0.480	0.000
5	A	9	ASN	0	0.000	-0.012	8.012	1.669	1.669	0.000	0.000	0.000	0.000
6	A	10	ASN	0	0.014	-0.010	11.300	0.921	0.921	0.000	0.000	0.000	0.000
7	A	11	LEU	0	0.034	0.026	10.620	0.899	0.899	0.000	0.000	0.000	0.000
8	A	12	ASN	0	0.016	-0.002	14.933	0.815	0.815	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.835	-0.912	17.258	-14.607	-14.607	0.000	0.000	0.000	0.000
10	A	14	LYS	1	0.955	0.979	18.194	11.619	11.619	0.000	0.000	0.000	0.000
11	A	15	ILE	0	0.028	0.048	17.942	0.474	0.474	0.000	0.000	0.000	0.000
12	A	16	ASN	0	0.040	0.031	18.740	-0.898	-0.898	0.000	0.000	0.000	0.000
13	A	17	LYS	1	0.971	0.963	14.433	16.724	16.724	0.000	0.000	0.000	0.000
14	A	18	ASN	0	0.008	0.010	14.736	-1.740	-1.740	0.000	0.000	0.000	0.000
15	A	19	ASP	-1	-0.855	-0.933	16.027	-15.257	-15.257	0.000	0.000	0.000	0.000
16	A	20	LEU	0	0.002	0.007	12.711	-0.519	-0.519	0.000	0.000	0.000	0.000
17	A	21	ARG	1	0.852	0.902	10.003	22.730	22.730	0.000	0.000	0.000	0.000
18	A	22	THR	0	0.007	0.008	12.480	-1.151	-1.151	0.000	0.000	0.000	0.000
19	A	23	ALA	0	0.061	0.027	15.082	-0.351	-0.351	0.000	0.000	0.000	0.000
20	A	24	LEU	0	-0.026	-0.022	9.379	-0.487	-0.487	0.000	0.000	0.000	0.000
21	A	25	TYR	0	0.007	-0.001	10.485	-0.921	-0.921	0.000	0.000	0.000	0.000
22	A	26	MET	0	-0.017	0.009	11.930	-0.331	-0.331	0.000	0.000	0.000	0.000
23	A	27	LEU	0	0.005	0.008	13.029	0.031	0.031	0.000	0.000	0.000	0.000
24	A	28	PHE	0	-0.006	-0.021	8.654	-0.689	-0.689	0.000	0.000	0.000	0.000
25	A	29	SER	0	-0.052	-0.020	10.770	-0.575	-0.575	0.000	0.000	0.000	0.000
26	A	30	THR	0	-0.032	-0.024	12.551	0.288	0.288	0.000	0.000	0.000	0.000
27	A	31	TYR	0	-0.113	-0.048	9.532	1.683	1.683	0.000	0.000	0.000	0.000
28	A	32	GLY	0	0.050	0.027	10.882	-1.614	-1.614	0.000	0.000	0.000	0.000
29	A	33	THR	0	-0.004	-0.018	10.692	-0.255	-0.255	0.000	0.000	0.000	0.000
30	A	34	VAL	0	-0.011	0.007	6.942	-3.794	-3.794	0.000	0.000	0.000	0.000
31	A	35	VAL	0	-0.018	-0.010	7.153	3.088	3.088	0.000	0.000	0.000	0.000
32	A	36	ASP	-1	-0.801	-0.899	6.643	-24.996	-24.996	0.000	0.000	0.000	0.000
33	A	37	ILE	0	-0.044	-0.009	5.600	-4.745	-4.745	0.000	0.000	0.000	0.000
34	A	38	VAL	0	-0.019	0.002	5.673	3.589	3.589	0.000	0.000	0.000	0.000
35	A	39	ALA	0	0.062	0.030	7.312	-1.116	-1.116	0.000	0.000	0.000	0.000
36	A	40	LEU	0	-0.034	-0.026	10.165	1.552	1.552	0.000	0.000	0.000	0.000
37	A	41	LYS	1	0.864	0.896	13.294	15.430	15.430	0.000	0.000	0.000	0.000
38	A	42	THR	0	0.034	0.023	15.519	0.593	0.593	0.000	0.000	0.000	0.000
39	A	43	PRO	0	0.048	0.004	16.912	-0.681	-0.681	0.000	0.000	0.000	0.000
40	A	44	LYS	1	0.989	1.002	13.019	19.155	19.155	0.000	0.000	0.000	0.000
41	A	45	MET	0	0.001	0.000	9.353	-0.481	-0.481	0.000	0.000	0.000	0.000
42	A	46	ARG	1	0.864	0.942	12.480	13.383	13.383	0.000	0.000	0.000	0.000
43	A	47	GLY	0	0.033	0.013	14.320	-0.187	-0.187	0.000	0.000	0.000	0.000
44	A	48	GLN	0	-0.047	-0.013	9.398	-1.637	-1.637	0.000	0.000	0.000	0.000
45	A	49	ALA	0	-0.024	-0.016	7.970	1.366	1.366	0.000	0.000	0.000	0.000
51	A	55	ASP	-1	-0.781	-0.881	7.073	-30.200	-30.200	0.000	0.000	0.000	0.000
53	A	57	SER	0	0.073	0.028	5.759	-0.679	-0.679	0.000	0.000	0.000	0.000
54	A	58	ALA	0	0.012	0.008	7.077	0.606	0.606	0.000	0.000	0.000	0.000
57	A	61	ILE	0	-0.025	-0.018	8.130	2.231	2.231	0.000	0.000	0.000	0.000
58	A	62	ALA	0	0.042	0.032	7.868	2.002	2.002	0.000	0.000	0.000	0.000
59	A	63	MET	0	-0.054	-0.027	8.102	0.794	0.794	0.000	0.000	0.000	0.000
60	A	64	LYS	1	0.904	0.946	9.939	21.199	21.199	0.000	0.000	0.000	0.000
61	A	65	ALA	0	-0.017	-0.001	12.978	1.510	1.510	0.000	0.000	0.000	0.000
62	A	66	LEU	0	0.036	0.018	11.573	1.119	1.119	0.000	0.000	0.000	0.000
63	A	67	LYS	1	0.947	0.976	13.629	19.253	19.253	0.000	0.000	0.000	0.000
64	A	68	ASN	0	-0.042	-0.033	14.449	1.087	1.087	0.000	0.000	0.000	0.000
65	A	69	PHE	0	0.056	0.039	15.573	1.086	1.086	0.000	0.000	0.000	0.000
66	A	70	ILE	0	0.013	0.009	16.880	-0.551	-0.551	0.000	0.000	0.000	0.000
67	A	71	PHE	0	0.014	-0.009	14.246	-0.053	-0.053	0.000	0.000	0.000	0.000
68	A	72	PHE	0	-0.011	-0.020	16.599	0.082	0.082	0.000	0.000	0.000	0.000
69	A	73	GLY	0	0.038	0.022	20.194	0.363	0.363	0.000	0.000	0.000	0.000
70	A	74	LYS	1	0.885	0.961	18.170	15.681	15.681	0.000	0.000	0.000	0.000
71	A	75	GLU	-1	-0.874	-0.924	18.023	-15.025	-15.025	0.000	0.000	0.000	0.000
72	A	76	MET	0	-0.025	0.017	12.269	-0.937	-0.937	0.000	0.000	0.000	0.000
73	A	77	LYS	1	0.858	0.929	12.784	17.154	17.154	0.000	0.000	0.000	0.000
74	A	78	ILE	0	0.022	0.013	7.805	-1.399	-1.399	0.000	0.000	0.000	0.000
75	A	79	GLN	0	0.002	-0.006	7.733	3.125	3.125	0.000	0.000	0.000	0.000
79	A	83	SER	0	-0.065	-0.039	5.442	-2.021	-2.021	0.000	0.000	0.000	0.000
83	A	87	ILE	0	-0.006	0.005	5.639	1.734	1.734	0.000	0.000	0.000	0.000
85	A	89	GLU	-1	-0.824	-0.883	6.343	-24.344	-24.344	0.000	0.000	0.000	0.000
86	A	90	ARG	1	0.989	0.987	9.168	20.619	20.619	0.000	0.000	0.000	0.000
87	A	91	ILE	0	-0.032	0.006	8.385	1.013	1.013	0.000	0.000	0.000	0.000
88	A	92	VAL	0	-0.073	-0.039	9.062	-0.048	-0.048	0.000	0.000	0.000	0.000
89	A	93	ALA	-1	-0.928	-0.944	12.013	-18.067	-18.067	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:THR)