FMO DATABASE

FMODB ID: 7N6QK

Calculation Name: 3JB9-G-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: G

ChEMBL ID:

UniProt ID: P39964

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-04

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	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-661259.888402
FMO2-HF: Nuclear repulsion	622322.877567
FMO2-HF: Total energy	-38937.010834
FMO2-MP2: Total energy	-39049.892647

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:19:ARG)

Summations of interaction energy for fragment #1(A:19:ARG)

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.
70.224	73.991	0.024	-1.4	-2.393	-0.006

Interaction energy analysis for fragmet #1(A:19:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.856 / q_NPA : 1.904

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	21	GLU	-1	-0.792	-0.865	3.327	-67.405	-64.807	0.021	-1.035	-1.585	-0.004
4	A	22	GLU	-1	-0.939	-0.971	3.245	-73.855	-72.869	0.004	-0.347	-0.644	-0.002
5	A	23	TYR	0	0.051	0.034	4.916	9.851	10.034	-0.001	-0.018	-0.164	0.000
6	A	24	GLU	-1	-0.907	-0.964	7.127	-42.409	-42.409	0.000	0.000	0.000	0.000
7	A	25	PHE	0	0.014	0.004	6.919	6.321	6.321	0.000	0.000	0.000	0.000
8	A	26	SER	0	-0.062	-0.026	9.683	5.380	5.380	0.000	0.000	0.000	0.000
9	A	27	ALA	0	0.022	0.021	11.585	3.754	3.754	0.000	0.000	0.000	0.000
10	A	28	GLY	0	0.026	0.027	12.481	2.295	2.295	0.000	0.000	0.000	0.000
11	A	29	PRO	0	0.021	-0.011	13.918	1.394	1.394	0.000	0.000	0.000	0.000
12	A	30	LEU	0	-0.013	0.007	11.739	2.806	2.806	0.000	0.000	0.000	0.000
13	A	31	SER	0	-0.007	0.009	13.736	1.958	1.958	0.000	0.000	0.000	0.000
14	A	32	VAL	0	0.048	0.007	14.941	1.377	1.377	0.000	0.000	0.000	0.000
15	A	33	LEU	0	-0.037	-0.024	17.297	1.692	1.692	0.000	0.000	0.000	0.000
16	A	34	GLN	0	0.017	0.017	11.618	1.987	1.987	0.000	0.000	0.000	0.000
17	A	35	GLN	0	-0.023	-0.005	16.524	1.298	1.298	0.000	0.000	0.000	0.000
18	A	36	ALA	0	0.073	0.036	19.359	0.940	0.940	0.000	0.000	0.000	0.000
19	A	37	VAL	0	-0.051	-0.044	18.984	0.887	0.887	0.000	0.000	0.000	0.000
20	A	38	LYS	1	0.864	0.929	14.512	35.446	35.446	0.000	0.000	0.000	0.000
21	A	39	ASN	0	-0.008	0.008	20.851	0.336	0.336	0.000	0.000	0.000	0.000
22	A	40	HIS	0	-0.071	-0.031	23.821	0.810	0.810	0.000	0.000	0.000	0.000
23	A	41	ASP	-1	-0.812	-0.886	24.793	-20.808	-20.808	0.000	0.000	0.000	0.000
24	A	42	GLN	0	-0.070	-0.047	26.096	-0.046	-0.046	0.000	0.000	0.000	0.000
25	A	43	VAL	0	-0.016	-0.018	23.424	-0.558	-0.558	0.000	0.000	0.000	0.000
26	A	44	LEU	0	-0.019	0.009	26.847	0.649	0.649	0.000	0.000	0.000	0.000
27	A	45	ILE	0	0.009	-0.006	24.762	-0.773	-0.773	0.000	0.000	0.000	0.000
28	A	46	ASN	0	0.015	0.000	27.663	1.173	1.173	0.000	0.000	0.000	0.000
29	A	47	CYS	0	0.019	0.007	27.558	-0.945	-0.945	0.000	0.000	0.000	0.000
30	A	48	ARG	1	0.957	0.972	24.574	23.243	23.243	0.000	0.000	0.000	0.000
31	A	49	ASN	0	0.010	0.002	29.665	0.848	0.848	0.000	0.000	0.000	0.000
32	A	50	ASN	0	-0.026	-0.014	32.531	0.485	0.485	0.000	0.000	0.000	0.000
33	A	51	LYS	1	0.877	0.949	33.172	17.159	17.159	0.000	0.000	0.000	0.000
34	A	52	LYS	1	0.933	0.976	31.729	16.853	16.853	0.000	0.000	0.000	0.000
35	A	53	LEU	0	0.017	0.002	27.618	0.485	0.485	0.000	0.000	0.000	0.000
36	A	54	LEU	0	-0.004	0.005	30.036	-0.363	-0.363	0.000	0.000	0.000	0.000
37	A	55	ALA	0	0.025	0.016	27.734	0.456	0.456	0.000	0.000	0.000	0.000
38	A	56	ARG	1	0.991	1.006	26.782	18.554	18.554	0.000	0.000	0.000	0.000
39	A	57	VAL	0	-0.007	-0.005	20.521	0.132	0.132	0.000	0.000	0.000	0.000
40	A	58	LYS	1	0.809	0.901	22.277	22.125	22.125	0.000	0.000	0.000	0.000
41	A	59	ALA	0	0.045	0.015	17.295	-0.760	-0.760	0.000	0.000	0.000	0.000
42	A	60	PHE	0	-0.023	-0.021	13.179	1.614	1.614	0.000	0.000	0.000	0.000
43	A	61	ASP	-1	-0.826	-0.905	12.504	-43.019	-43.019	0.000	0.000	0.000	0.000
44	A	62	ARG	1	0.893	0.916	6.463	59.678	59.678	0.000	0.000	0.000	0.000
45	A	63	HIS	0	-0.039	-0.011	11.732	1.800	1.800	0.000	0.000	0.000	0.000
46	A	64	SER	0	-0.055	-0.029	14.778	3.018	3.018	0.000	0.000	0.000	0.000
47	A	65	ASN	0	0.012	0.008	16.610	2.553	2.553	0.000	0.000	0.000	0.000
48	A	66	MET	0	-0.016	-0.009	17.646	-1.254	-1.254	0.000	0.000	0.000	0.000
49	A	67	VAL	0	-0.012	0.009	20.232	1.119	1.119	0.000	0.000	0.000	0.000
50	A	68	LEU	0	0.004	-0.005	22.329	-0.238	-0.238	0.000	0.000	0.000	0.000
51	A	69	GLU	-1	-0.852	-0.941	25.346	-19.854	-19.854	0.000	0.000	0.000	0.000
52	A	70	ASN	0	-0.056	-0.029	28.374	0.195	0.195	0.000	0.000	0.000	0.000
53	A	71	VAL	0	0.003	0.010	28.957	-0.110	-0.110	0.000	0.000	0.000	0.000
54	A	72	LYS	1	0.842	0.907	31.686	16.299	16.299	0.000	0.000	0.000	0.000
55	A	73	GLU	-1	-0.906	-0.958	33.681	-17.492	-17.492	0.000	0.000	0.000	0.000
56	A	74	MET	0	0.000	0.000	35.290	0.574	0.574	0.000	0.000	0.000	0.000
57	A	75	TRP	0	-0.061	-0.028	36.482	-0.117	-0.117	0.000	0.000	0.000	0.000
58	A	76	THR	0	0.025	0.025	38.952	0.267	0.267	0.000	0.000	0.000	0.000
59	A	77	GLU	-1	-0.811	-0.900	41.795	-13.726	-13.726	0.000	0.000	0.000	0.000
60	A	78	LYS	0	0.003	0.015	44.540	0.398	0.398	0.000	0.000	0.000	0.000
61	A	79	LYS	1	0.967	0.978	47.895	11.450	11.450	0.000	0.000	0.000	0.000
62	A	80	ARG	1	0.960	0.974	43.018	13.827	13.827	0.000	0.000	0.000	0.000
63	A	81	THR	0	-0.044	0.009	50.868	0.135	0.135	0.000	0.000	0.000	0.000
64	A	82	ALA	0	0.074	0.054	54.124	0.220	0.220	0.000	0.000	0.000	0.000
65	A	83	SER	0	0.035	0.016	55.471	0.209	0.209	0.000	0.000	0.000	0.000
66	A	84	GLY	0	0.006	-0.004	57.233	0.023	0.023	0.000	0.000	0.000	0.000
67	A	85	LYS	1	1.009	1.004	57.542	10.402	10.402	0.000	0.000	0.000	0.000
68	A	86	LYS	1	0.903	0.916	50.675	11.984	11.984	0.000	0.000	0.000	0.000
69	A	87	GLY	0	-0.003	-0.003	50.179	0.055	0.055	0.000	0.000	0.000	0.000
70	A	88	LYS	1	0.903	0.933	51.219	10.948	10.948	0.000	0.000	0.000	0.000
71	A	89	ALA	0	0.071	0.028	49.192	-0.082	-0.082	0.000	0.000	0.000	0.000
72	A	90	ILE	0	-0.009	0.004	46.432	0.260	0.260	0.000	0.000	0.000	0.000
73	A	91	ASN	0	0.052	0.025	42.825	-0.169	-0.169	0.000	0.000	0.000	0.000
74	A	92	LYS	1	0.777	0.881	41.806	13.805	13.805	0.000	0.000	0.000	0.000
75	A	93	ASP	-1	-0.723	-0.842	39.357	-15.415	-15.415	0.000	0.000	0.000	0.000
76	A	94	ARG	1	0.907	0.938	37.621	15.247	15.247	0.000	0.000	0.000	0.000
77	A	95	PHE	0	0.063	0.035	36.182	-0.374	-0.374	0.000	0.000	0.000	0.000
78	A	96	ILE	0	0.001	0.004	31.661	0.250	0.250	0.000	0.000	0.000	0.000
79	A	97	SER	0	-0.011	0.004	32.642	-0.469	-0.469	0.000	0.000	0.000	0.000
80	A	98	LYS	1	1.006	0.992	28.156	18.870	18.870	0.000	0.000	0.000	0.000
81	A	99	MET	0	0.006	0.008	27.202	0.532	0.532	0.000	0.000	0.000	0.000
82	A	100	PHE	0	0.015	0.018	19.595	-0.705	-0.705	0.000	0.000	0.000	0.000
83	A	101	LEU	0	-0.016	-0.005	23.226	0.813	0.813	0.000	0.000	0.000	0.000
84	A	102	ARG	1	0.883	0.926	20.073	25.596	25.596	0.000	0.000	0.000	0.000
85	A	103	GLY	0	0.083	0.032	19.371	0.935	0.935	0.000	0.000	0.000	0.000
86	A	104	ASP	-1	-0.796	-0.888	20.411	-25.834	-25.834	0.000	0.000	0.000	0.000
87	A	105	GLY	0	-0.054	-0.027	22.667	0.935	0.935	0.000	0.000	0.000	0.000
88	A	106	VAL	0	-0.010	-0.003	22.252	1.194	1.194	0.000	0.000	0.000	0.000
89	A	107	VAL	0	-0.035	-0.025	24.060	-0.277	-0.277	0.000	0.000	0.000	0.000
90	A	108	LEU	0	-0.006	0.001	24.979	-0.203	-0.203	0.000	0.000	0.000	0.000
91	A	109	VAL	0	-0.023	-0.008	21.717	0.465	0.465	0.000	0.000	0.000	0.000
92	A	110	VAL	0	-0.003	0.001	24.431	-0.491	-0.491	0.000	0.000	0.000	0.000
93	A	111	ARG	1	0.882	0.922	18.353	29.261	29.261	0.000	0.000	0.000	0.000
94	A	112	ILE	0	-0.028	-0.009	25.357	-0.058	-0.058	0.000	0.000	0.000	0.000
95	A	113	PRO	0	0.075	0.054	27.649	0.090	0.090	0.000	0.000	0.000	0.000
96	A	114	SER	0	-0.058	-0.047	29.191	0.394	0.394	0.000	0.000	0.000	0.000
97	A	115	ALA	-1	-0.944	-0.952	31.524	-18.076	-18.076	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:19:ARG)