FMO DATABASE

FMODB ID: RLV98

Calculation Name: 3JB9-f-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: f

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	82
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-526170.113963
FMO2-HF: Nuclear repulsion	493203.357273
FMO2-HF: Total energy	-32966.75669
FMO2-MP2: Total energy	-33060.568981

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.
-27.645	-24.253	0.218	-1.662	-1.947	-0.009

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 : 0.884 / q_NPA : 0.935

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	3	LEU	0	0.112	0.062	3.891	-1.995	-0.239	-0.019	-0.887	-0.849	-0.001
5	A	5	ARG	1	0.830	0.898	3.182	59.860	61.252	0.238	-0.686	-0.944	-0.007
82	A	82	ASP	-2	-1.763	-1.857	4.197	-99.574	-99.330	-0.001	-0.089	-0.154	-0.001
4	A	4	VAL	0	0.015	0.006	6.879	2.021	2.021	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.068	0.035	6.430	2.354	2.354	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.004	0.000	8.745	2.671	2.671	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.074	-0.036	9.473	0.561	0.561	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.845	0.931	8.471	32.477	32.477	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.021	-0.001	12.706	1.296	1.296	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.054	-0.034	15.384	1.369	1.369	0.000	0.000	0.000	0.000
12	A	12	ASN	0	0.010	0.007	17.916	0.439	0.439	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.855	-0.922	19.957	-13.970	-13.970	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.067	-0.038	21.948	0.098	0.098	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.020	-0.011	19.690	-0.328	-0.328	0.000	0.000	0.000	0.000
16	A	16	SER	0	0.002	0.006	23.166	0.522	0.522	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.027	-0.021	20.862	-0.441	-0.441	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.792	-0.901	23.127	-10.869	-10.869	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.021	-0.010	23.022	-0.826	-0.826	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.798	0.863	19.107	16.067	16.067	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.062	-0.027	25.578	0.471	0.471	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.009	0.016	28.261	0.422	0.422	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.061	-0.042	27.946	0.430	0.430	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.045	0.041	27.871	-0.472	-0.472	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.019	-0.021	25.798	0.427	0.427	0.000	0.000	0.000	0.000
26	A	26	HIS	0	0.048	0.030	26.148	-0.606	-0.606	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.016	0.002	25.981	0.428	0.428	0.000	0.000	0.000	0.000
28	A	28	THR	0	0.005	0.015	24.169	-0.356	-0.356	0.000	0.000	0.000	0.000
29	A	29	ILE	0	0.008	0.001	17.737	0.085	0.085	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.029	-0.023	21.207	0.066	0.066	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.006	-0.004	17.343	-0.434	-0.434	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.024	0.003	12.988	0.683	0.683	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.831	-0.915	13.609	-22.114	-22.114	0.000	0.000	0.000	0.000
34	A	34	MET	0	-0.019	-0.014	8.411	-3.302	-3.302	0.000	0.000	0.000	0.000
35	A	35	GLN	0	-0.088	-0.042	11.120	-0.751	-0.751	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.012	-0.010	12.213	0.575	0.575	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.006	0.014	14.602	1.317	1.317	0.000	0.000	0.000	0.000
38	A	38	THR	0	0.026	0.021	16.791	-0.625	-0.625	0.000	0.000	0.000	0.000
39	A	39	HIS	0	0.025	0.011	19.018	1.362	1.362	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.010	0.011	21.613	-0.403	-0.403	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.859	0.932	24.204	11.539	11.539	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.019	0.019	27.218	-0.107	-0.107	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.037	0.000	27.369	-0.080	-0.080	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.933	0.955	29.855	9.727	9.727	0.000	0.000	0.000	0.000
45	A	45	MET	0	-0.021	0.009	30.000	-0.202	-0.202	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.051	0.014	31.554	0.400	0.400	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.001	-0.001	32.525	-0.287	-0.287	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.987	0.991	33.254	9.282	9.282	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.018	0.001	35.097	0.153	0.153	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.904	0.943	37.825	8.417	8.417	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.840	-0.914	38.115	-7.832	-7.832	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.057	-0.027	36.105	-0.236	-0.236	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.003	-0.001	35.517	0.239	0.239	0.000	0.000	0.000	0.000
54	A	54	PRO	0	-0.033	-0.013	34.309	-0.343	-0.343	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.008	-0.017	31.147	0.151	0.151	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.795	-0.904	30.874	-10.622	-10.622	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.014	-0.004	28.411	-0.241	-0.241	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.003	0.015	26.575	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.025	0.014	23.535	-0.433	-0.433	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.011	-0.005	21.464	0.427	0.427	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.971	0.990	20.590	13.552	13.552	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.098	0.027	17.635	0.292	0.292	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.066	-0.025	18.598	0.356	0.356	0.000	0.000	0.000	0.000
64	A	64	ASN	0	0.029	0.004	19.691	-0.182	-0.182	0.000	0.000	0.000	0.000
65	A	65	ILE	0	0.033	0.033	18.115	0.737	0.737	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.854	0.945	19.862	12.080	12.080	0.000	0.000	0.000	0.000
67	A	67	TYR	0	0.051	0.007	18.861	-0.698	-0.698	0.000	0.000	0.000	0.000
68	A	68	TYR	0	0.017	0.008	15.320	0.284	0.284	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.014	-0.001	19.532	-0.496	-0.496	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.002	-0.012	15.874	0.197	0.197	0.000	0.000	0.000	0.000
71	A	71	PRO	0	0.033	0.025	20.456	0.335	0.335	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.882	-0.951	21.855	-12.772	-12.772	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.041	-0.017	23.424	0.048	0.048	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.031	-0.004	16.513	-0.184	-0.184	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.006	0.008	18.061	-0.308	-0.308	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.032	-0.002	14.712	-1.206	-1.206	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.880	-0.938	13.512	-20.360	-20.360	0.000	0.000	0.000	0.000
78	A	78	THR	0	-0.027	-0.025	13.201	-0.979	-0.979	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.033	-0.011	11.975	-1.040	-1.040	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.064	-0.039	8.956	-3.109	-3.109	0.000	0.000	0.000	0.000
81	A	81	ILE	0	-0.021	0.009	8.263	-3.077	-3.077	0.000	0.000	0.000	0.000

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