FMO DATABASE

FMODB ID: G87Y1

Calculation Name: 1E8O-B-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate

Ligand 3-letter code: GDP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1E8O

Chain ID: B

ChEMBL ID:

UniProt ID: P49458

Base Structure: X-ray

Registration Date: 2025-09-02

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	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-468529.818048
FMO2-HF: Nuclear repulsion	437980.815905
FMO2-HF: Total energy	-30549.002143
FMO2-MP2: Total energy	-30636.364757

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:2:VAL)

Summations of interaction energy for fragment #1(A:2:VAL)

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.
97.293	99.486	-0.012	-0.927	-1.255	-0.002

Interaction energy analysis for fragmet #1(A:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.863 / q_NPA : 0.920

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	4	LEU	0	-0.011	-0.001	3.798	0.013	1.807	-0.013	-0.740	-1.041	-0.001
48	A	68	SER	0	-0.029	-0.033	3.699	-2.249	-1.850	0.001	-0.187	-0.214	-0.001
4	A	5	GLU	-1	-0.807	-0.897	6.415	-23.668	-23.668	0.000	0.000	0.000	0.000
5	A	6	SER	0	-0.033	-0.038	9.711	-0.838	-0.838	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.912	-0.959	12.610	-16.980	-16.980	0.000	0.000	0.000	0.000
7	A	8	GLN	0	0.011	0.011	9.071	1.584	1.584	0.000	0.000	0.000	0.000
8	A	9	PHE	0	-0.022	-0.022	8.327	-0.213	-0.213	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.042	0.021	10.276	0.553	0.553	0.000	0.000	0.000	0.000
10	A	11	THR	0	0.023	0.034	12.934	1.530	1.530	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.868	-0.949	8.212	-24.964	-24.964	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.019	-0.008	11.456	0.485	0.485	0.000	0.000	0.000	0.000
13	A	14	THR	0	0.013	-0.006	13.360	1.330	1.330	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.891	0.942	12.273	20.970	20.970	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.049	-0.014	10.987	0.574	0.574	0.000	0.000	0.000	0.000
16	A	17	PHE	0	0.068	0.014	14.994	0.562	0.562	0.000	0.000	0.000	0.000
17	A	18	GLN	0	-0.006	0.000	18.509	0.425	0.425	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.905	0.952	14.435	19.038	19.038	0.000	0.000	0.000	0.000
19	A	20	CYS	0	-0.063	-0.030	17.233	0.225	0.225	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.829	0.897	20.146	12.001	12.001	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.014	-0.002	23.569	0.430	0.430	0.000	0.000	0.000	0.000
22	A	23	SER	0	0.033	0.000	23.754	0.577	0.577	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.018	0.025	20.649	-0.387	-0.387	0.000	0.000	0.000	0.000
24	A	25	SER	0	-0.040	-0.030	19.307	0.718	0.718	0.000	0.000	0.000	0.000
25	A	26	VAL	0	-0.010	0.012	15.201	-0.988	-0.988	0.000	0.000	0.000	0.000
26	A	27	TYR	0	0.008	0.013	14.309	0.672	0.672	0.000	0.000	0.000	0.000
27	A	28	ILE	0	0.011	-0.014	13.479	-1.881	-1.881	0.000	0.000	0.000	0.000
28	A	29	THR	0	-0.057	-0.025	11.347	0.540	0.540	0.000	0.000	0.000	0.000
29	A	30	LEU	0	0.057	0.020	12.131	-1.896	-1.896	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.945	0.975	12.386	21.643	21.643	0.000	0.000	0.000	0.000
31	A	32	LYS	1	0.950	0.969	13.416	15.401	15.401	0.000	0.000	0.000	0.000
32	A	33	TYR	0	-0.056	-0.045	7.986	-0.428	-0.428	0.000	0.000	0.000	0.000
33	A	34	ASP	-2	-1.852	-1.903	12.429	-39.943	-39.943	0.000	0.000	0.000	0.000
34	A	54	ASN	0	0.043	0.008	17.938	-0.523	-0.523	0.000	0.000	0.000	0.000
35	A	55	LYS	1	0.945	0.975	12.329	22.841	22.841	0.000	0.000	0.000	0.000
36	A	56	CYS	0	-0.038	0.000	13.761	0.570	0.570	0.000	0.000	0.000	0.000
37	A	57	LEU	0	0.012	0.009	6.132	-1.642	-1.642	0.000	0.000	0.000	0.000
38	A	58	LEU	0	0.013	0.012	9.646	1.968	1.968	0.000	0.000	0.000	0.000
39	A	59	ARG	1	0.922	0.946	6.475	30.546	30.546	0.000	0.000	0.000	0.000
40	A	60	ALA	0	0.023	0.021	8.971	3.340	3.340	0.000	0.000	0.000	0.000
41	A	61	THR	0	-0.048	-0.053	9.379	-3.159	-3.159	0.000	0.000	0.000	0.000
42	A	62	ASP	-1	-0.759	-0.861	11.621	-20.653	-20.653	0.000	0.000	0.000	0.000
43	A	63	GLY	0	0.001	0.011	13.215	1.494	1.494	0.000	0.000	0.000	0.000
44	A	64	LYS	1	0.893	0.942	12.694	16.508	16.508	0.000	0.000	0.000	0.000
45	A	65	LYS	1	0.899	0.945	8.681	24.061	24.061	0.000	0.000	0.000	0.000
46	A	66	LYS	1	0.917	0.975	6.502	30.535	30.535	0.000	0.000	0.000	0.000
47	A	67	ILE	0	0.005	0.015	5.373	-5.636	-5.636	0.000	0.000	0.000	0.000
49	A	69	THR	0	0.045	0.011	6.133	-3.195	-3.195	0.000	0.000	0.000	0.000
50	A	70	VAL	0	-0.002	-0.007	7.725	0.579	0.579	0.000	0.000	0.000	0.000
51	A	71	VAL	0	0.037	0.052	10.178	1.168	1.168	0.000	0.000	0.000	0.000
52	A	72	SER	0	0.045	0.002	13.908	0.925	0.925	0.000	0.000	0.000	0.000
53	A	73	SER	0	0.054	0.000	16.210	0.381	0.381	0.000	0.000	0.000	0.000
54	A	74	LYS	1	0.930	0.968	18.292	14.962	14.962	0.000	0.000	0.000	0.000
55	A	75	GLU	-1	-0.876	-0.914	14.692	-20.379	-20.379	0.000	0.000	0.000	0.000
56	A	76	VAL	0	-0.003	0.002	18.773	0.132	0.132	0.000	0.000	0.000	0.000
57	A	77	ASN	0	0.013	0.010	20.055	0.006	0.006	0.000	0.000	0.000	0.000
58	A	78	LYS	1	1.014	1.004	20.082	15.044	15.044	0.000	0.000	0.000	0.000
59	A	79	PHE	0	0.027	0.011	13.877	0.009	0.009	0.000	0.000	0.000	0.000
60	A	80	GLN	0	0.017	0.007	18.912	-0.451	-0.451	0.000	0.000	0.000	0.000
61	A	81	MET	0	0.003	0.002	21.437	0.257	0.257	0.000	0.000	0.000	0.000
62	A	82	ALA	0	0.031	0.024	19.387	0.255	0.255	0.000	0.000	0.000	0.000
63	A	83	TYR	0	0.023	-0.002	16.250	0.007	0.007	0.000	0.000	0.000	0.000
64	A	84	SER	0	-0.011	-0.003	19.458	0.215	0.215	0.000	0.000	0.000	0.000
65	A	85	ASN	0	0.014	-0.002	23.076	0.541	0.541	0.000	0.000	0.000	0.000
66	A	86	LEU	0	-0.035	0.000	16.423	0.203	0.203	0.000	0.000	0.000	0.000
67	A	87	LEU	0	0.006	-0.011	18.538	0.181	0.181	0.000	0.000	0.000	0.000
68	A	88	ARG	1	0.937	0.961	21.914	11.475	11.475	0.000	0.000	0.000	0.000
69	A	89	ALA	0	-0.005	0.007	23.926	0.377	0.377	0.000	0.000	0.000	0.000
70	A	90	ASN	0	-0.086	-0.053	21.177	0.200	0.200	0.000	0.000	0.000	0.000
71	A	91	MET	0	-0.054	-0.019	21.928	-0.449	-0.449	0.000	0.000	0.000	0.000
72	A	92	ASP	-1	-0.765	-0.846	25.045	-11.145	-11.145	0.000	0.000	0.000	0.000
73	A	93	GLY	0	-0.019	0.000	27.993	0.371	0.371	0.000	0.000	0.000	0.000
74	A	94	LEU	0	-0.078	-0.041	27.571	0.108	0.108	0.000	0.000	0.000	0.000
75	A	95	LYS	0	0.046	0.037	31.351	0.430	0.430	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:VAL)