FMO DATABASE

FMODB ID: 3M89L

Calculation Name: 3JB9-J-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: J

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	73
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-430356.879917
FMO2-HF: Nuclear repulsion	402250.821198
FMO2-HF: Total energy	-28106.058719
FMO2-MP2: Total energy	-28189.316823

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:3:LYS)

Summations of interaction energy for fragment #1(A:3:LYS)

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.
-1.613	0.44400000000002	-0.001	-0.893	-1.162	-0.005

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.833 / q_NPA : 1.901

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	5	GLY	0	0.040	0.042	3.772	3.873	5.930	-0.001	-0.893	-1.162	-0.005
4	A	6	ALA	0	0.024	0.008	5.535	4.891	4.891	0.000	0.000	0.000	0.000
5	A	7	PRO	0	0.049	0.037	9.179	1.954	1.954	0.000	0.000	0.000	0.000
6	A	8	ASP	-1	-0.907	-0.951	10.958	-39.782	-39.782	0.000	0.000	0.000	0.000
7	A	9	LEU	0	0.016	-0.003	14.185	2.346	2.346	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.887	0.933	13.757	41.219	41.219	0.000	0.000	0.000	0.000
9	A	11	LYS	1	0.949	0.972	18.334	30.255	30.255	0.000	0.000	0.000	0.000
10	A	12	TYR	0	0.007	-0.001	18.562	1.307	1.307	0.000	0.000	0.000	0.000
11	A	13	LEU	0	-0.017	0.001	19.513	0.417	0.417	0.000	0.000	0.000	0.000
12	A	14	ASP	-1	-0.883	-0.927	22.652	-22.738	-22.738	0.000	0.000	0.000	0.000
13	A	15	ARG	1	0.828	0.904	25.297	23.380	23.380	0.000	0.000	0.000	0.000
14	A	16	GLN	0	0.008	-0.003	26.139	-0.333	-0.333	0.000	0.000	0.000	0.000
15	A	17	VAL	0	-0.056	-0.022	22.427	-0.393	-0.393	0.000	0.000	0.000	0.000
16	A	18	PHE	0	-0.017	-0.011	25.240	0.784	0.784	0.000	0.000	0.000	0.000
17	A	19	VAL	0	0.016	0.011	20.757	-0.791	-0.791	0.000	0.000	0.000	0.000
18	A	20	GLN	0	-0.026	-0.023	22.263	1.023	1.023	0.000	0.000	0.000	0.000
19	A	21	LEU	0	-0.005	-0.010	20.639	-1.531	-1.531	0.000	0.000	0.000	0.000
20	A	22	ASN	0	0.042	0.012	20.863	1.716	1.716	0.000	0.000	0.000	0.000
21	A	23	GLY	0	-0.016	-0.010	22.777	0.408	0.408	0.000	0.000	0.000	0.000
22	A	24	SER	0	-0.051	-0.018	25.968	1.017	1.017	0.000	0.000	0.000	0.000
23	A	25	ARG	1	0.971	0.989	25.330	22.568	22.568	0.000	0.000	0.000	0.000
24	A	26	LYS	1	0.890	0.954	26.040	19.713	19.713	0.000	0.000	0.000	0.000
25	A	27	VAL	0	-0.002	0.003	25.546	0.597	0.597	0.000	0.000	0.000	0.000
26	A	28	TYR	0	0.044	0.028	26.514	-0.362	-0.362	0.000	0.000	0.000	0.000
27	A	29	GLY	0	0.040	0.009	27.229	0.080	0.080	0.000	0.000	0.000	0.000
28	A	30	VAL	0	-0.006	0.006	26.875	-0.333	-0.333	0.000	0.000	0.000	0.000
29	A	31	LEU	0	-0.033	-0.013	19.280	-0.587	-0.587	0.000	0.000	0.000	0.000
30	A	32	ARG	1	0.884	0.917	23.192	22.509	22.509	0.000	0.000	0.000	0.000
31	A	33	GLY	0	0.004	0.001	19.256	-0.286	-0.286	0.000	0.000	0.000	0.000
32	A	34	TYR	0	-0.034	-0.017	13.048	-0.136	-0.136	0.000	0.000	0.000	0.000
33	A	35	ASP	-1	-0.802	-0.902	11.447	-48.887	-48.887	0.000	0.000	0.000	0.000
34	A	36	ILE	0	-0.033	-0.018	5.954	-2.458	-2.458	0.000	0.000	0.000	0.000
35	A	37	PHE	0	-0.108	-0.054	6.318	-5.590	-5.590	0.000	0.000	0.000	0.000
36	A	38	LEU	0	0.025	0.010	9.445	2.971	2.971	0.000	0.000	0.000	0.000
37	A	39	ASN	0	0.011	0.014	12.312	3.281	3.281	0.000	0.000	0.000	0.000
38	A	40	ILE	0	-0.003	-0.002	14.993	-1.010	-1.010	0.000	0.000	0.000	0.000
39	A	41	VAL	0	-0.008	0.000	18.184	0.793	0.793	0.000	0.000	0.000	0.000
40	A	42	LEU	0	-0.012	-0.005	21.347	-0.104	-0.104	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.822	-0.909	24.613	-21.528	-21.528	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.929	-0.962	28.168	-19.146	-19.146	0.000	0.000	0.000	0.000
43	A	45	SER	0	-0.055	-0.041	27.873	0.351	0.351	0.000	0.000	0.000	0.000
44	A	46	ILE	0	-0.019	-0.027	29.797	0.785	0.785	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.918	-0.960	30.480	-18.938	-18.938	0.000	0.000	0.000	0.000
46	A	48	GLU	-1	-0.946	-0.987	30.859	-17.902	-17.902	0.000	0.000	0.000	0.000
47	A	49	LYS	1	0.898	0.952	31.840	15.528	15.528	0.000	0.000	0.000	0.000
48	A	50	VAL	0	-0.010	-0.025	33.161	0.210	0.210	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.905	-0.947	35.415	-14.654	-14.654	0.000	0.000	0.000	0.000
50	A	52	GLY	0	0.009	0.016	37.245	0.295	0.295	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.931	-0.954	38.176	-15.178	-15.178	0.000	0.000	0.000	0.000
52	A	54	LYS	1	0.882	0.941	34.669	16.641	16.641	0.000	0.000	0.000	0.000
53	A	55	VAL	0	0.032	0.022	34.978	0.345	0.345	0.000	0.000	0.000	0.000
54	A	56	LYS	1	0.941	0.967	34.235	15.552	15.552	0.000	0.000	0.000	0.000
55	A	57	ILE	0	-0.024	-0.005	30.139	0.255	0.255	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.035	0.028	31.652	0.240	0.240	0.000	0.000	0.000	0.000
57	A	59	SER	0	-0.021	0.008	27.640	-0.383	-0.383	0.000	0.000	0.000	0.000
58	A	60	VAL	0	0.002	0.001	24.323	0.125	0.125	0.000	0.000	0.000	0.000
59	A	61	ALA	0	-0.005	0.004	20.393	-0.736	-0.736	0.000	0.000	0.000	0.000
60	A	62	ILE	0	0.008	0.004	19.140	0.484	0.484	0.000	0.000	0.000	0.000
61	A	63	ARG	1	0.941	0.962	14.023	34.279	34.279	0.000	0.000	0.000	0.000
62	A	64	GLY	0	0.081	0.025	13.652	1.072	1.072	0.000	0.000	0.000	0.000
63	A	65	ASN	0	-0.107	-0.056	13.742	1.810	1.810	0.000	0.000	0.000	0.000
64	A	66	SER	0	0.021	0.008	14.601	0.331	0.331	0.000	0.000	0.000	0.000
65	A	67	VAL	0	-0.017	0.001	16.055	1.799	1.799	0.000	0.000	0.000	0.000
66	A	68	ILE	0	-0.032	0.000	16.762	-1.197	-1.197	0.000	0.000	0.000	0.000
67	A	69	MET	0	-0.028	-0.017	18.266	-0.656	-0.656	0.000	0.000	0.000	0.000
68	A	70	ILE	0	-0.011	-0.013	16.884	0.376	0.376	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.839	-0.907	20.560	-22.632	-22.632	0.000	0.000	0.000	0.000
70	A	72	THR	0	-0.017	-0.023	23.831	-0.409	-0.409	0.000	0.000	0.000	0.000
71	A	73	LEU	0	-0.032	-0.005	26.211	0.316	0.316	0.000	0.000	0.000	0.000
72	A	74	ASP	-1	-0.913	-0.949	29.946	-17.518	-17.518	0.000	0.000	0.000	0.000
73	A	75	LYS	0	0.093	0.064	28.886	-3.311	-3.311	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)