FMO DATABASE

FMODB ID: Q5G7Y

Calculation Name: 1E8O-A-Xray549

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: A

ChEMBL ID:

UniProt ID: P49458

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	74
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-481424.292314
FMO2-HF: Nuclear repulsion	450355.313639
FMO2-HF: Total energy	-31068.978675
FMO2-MP2: Total energy	-31157.189155

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:PRO)

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

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.
-27.572	-19.755	6.597	-6.173	-8.242	-0.061

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.853 / q_NPA : 0.915

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	TYR	0	-0.011	-0.003	2.902	-8.468	-4.332	0.471	-1.841	-2.766	-0.012
4	A	5	GLN	0	0.041	0.007	5.113	4.018	4.043	-0.001	-0.003	-0.020	0.000
46	A	47	VAL	0	-0.003	0.016	3.692	-4.104	-3.909	0.001	-0.031	-0.165	0.000
47	A	48	CYS	0	-0.036	-0.019	4.005	6.055	6.400	-0.001	-0.100	-0.244	0.000
48	A	49	LEU	0	-0.034	-0.001	2.190	-42.393	-39.875	6.125	-4.038	-4.606	-0.048
49	A	50	VAL	0	0.007	-0.011	3.367	12.645	13.243	0.002	-0.160	-0.441	-0.001
5	A	6	THR	0	0.008	0.001	8.428	2.175	2.175	0.000	0.000	0.000	0.000
6	A	7	TRP	0	0.028	0.014	9.287	-2.468	-2.468	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.911	-0.948	11.356	-20.154	-20.154	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.848	-0.905	7.584	-26.487	-26.487	0.000	0.000	0.000	0.000
9	A	10	PHE	0	-0.010	-0.006	6.149	-1.799	-1.799	0.000	0.000	0.000	0.000
10	A	11	SER	0	0.019	0.015	7.787	-0.220	-0.220	0.000	0.000	0.000	0.000
11	A	12	ARG	1	0.912	0.927	10.016	23.256	23.256	0.000	0.000	0.000	0.000
12	A	13	ALA	0	-0.051	-0.023	5.421	0.289	0.289	0.000	0.000	0.000	0.000
13	A	14	ALA	0	-0.013	-0.019	7.559	-0.576	-0.576	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.940	-0.960	8.848	-18.093	-18.093	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.950	0.971	9.450	27.222	27.222	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.051	-0.022	6.191	0.212	0.212	0.000	0.000	0.000	0.000
17	A	18	TYR	0	0.050	0.007	10.104	1.216	1.216	0.000	0.000	0.000	0.000
18	A	19	LEU	0	-0.023	-0.018	13.231	1.332	1.332	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.065	-0.028	12.216	1.168	1.168	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.793	-0.893	13.378	-19.050	-19.050	0.000	0.000	0.000	0.000
21	A	22	PRO	0	-0.016	0.013	14.844	-0.813	-0.813	0.000	0.000	0.000	0.000
22	A	23	MET	0	-0.052	-0.024	16.824	1.106	1.106	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.804	0.881	12.807	22.287	22.287	0.000	0.000	0.000	0.000
24	A	25	ALA	0	-0.040	0.004	12.134	-0.940	-0.940	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.872	0.935	11.878	22.281	22.281	0.000	0.000	0.000	0.000
26	A	27	VAL	0	0.008	0.004	11.332	-2.686	-2.686	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.035	-0.023	11.276	1.760	1.760	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.001	-0.003	12.344	-1.638	-1.638	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.950	0.973	14.486	20.306	20.306	0.000	0.000	0.000	0.000
30	A	31	TYR	0	0.028	-0.002	16.077	-0.727	-0.727	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.828	0.902	18.904	14.498	14.498	0.000	0.000	0.000	0.000
32	A	33	HIS	0	0.080	0.045	20.982	-0.296	-0.296	0.000	0.000	0.000	0.000
33	A	34	SER	0	-0.052	-0.050	24.053	0.174	0.174	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.827	-0.881	20.635	-14.142	-14.142	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.005	0.017	21.107	-0.463	-0.463	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.068	-0.031	16.735	-1.027	-1.027	0.000	0.000	0.000	0.000
37	A	38	LEU	0	-0.003	-0.007	15.425	0.733	0.733	0.000	0.000	0.000	0.000
38	A	39	CYS	-1	-0.815	-0.829	11.109	-29.687	-29.687	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.025	0.012	10.714	1.620	1.620	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.936	0.961	6.793	27.935	27.935	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.040	0.024	6.931	3.660	3.660	0.000	0.000	0.000	0.000
42	A	43	THR	0	-0.098	-0.063	6.537	-6.709	-6.709	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.762	-0.893	8.572	-24.497	-24.497	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.838	-0.915	10.160	-22.033	-22.033	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.007	0.005	8.920	0.823	0.823	0.000	0.000	0.000	0.000
50	A	51	TYR	0	-0.007	-0.026	5.503	-3.731	-3.731	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.769	0.813	8.646	30.029	30.029	0.000	0.000	0.000	0.000
52	A	53	THR	0	-0.014	-0.009	11.491	-0.468	-0.468	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.810	-0.897	14.808	-16.611	-16.611	0.000	0.000	0.000	0.000
54	A	55	GLN	0	-0.036	-0.023	17.322	1.488	1.488	0.000	0.000	0.000	0.000
55	A	56	ALA	0	0.041	0.005	19.067	-0.442	-0.442	0.000	0.000	0.000	0.000
56	A	57	GLN	0	-0.034	-0.013	17.855	0.625	0.625	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.762	-0.878	15.188	-19.270	-19.270	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.005	0.010	18.023	-0.544	-0.544	0.000	0.000	0.000	0.000
59	A	60	LYS	1	0.990	0.992	20.010	12.324	12.324	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.861	0.932	16.120	18.103	18.103	0.000	0.000	0.000	0.000
61	A	62	ILE	0	0.027	0.024	14.476	-0.562	-0.562	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.903	-0.953	16.977	-13.792	-13.792	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.917	0.964	19.538	14.388	14.388	0.000	0.000	0.000	0.000
64	A	65	PHE	0	0.041	0.025	11.856	0.064	0.064	0.000	0.000	0.000	0.000
65	A	66	HIS	0	0.022	0.007	14.958	-0.439	-0.439	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.005	-0.002	18.247	0.410	0.410	0.000	0.000	0.000	0.000
67	A	68	GLN	0	-0.060	-0.033	17.636	-0.029	-0.029	0.000	0.000	0.000	0.000
68	A	69	LEU	0	0.027	0.009	13.505	0.255	0.255	0.000	0.000	0.000	0.000
69	A	70	MET	0	-0.006	-0.007	18.192	0.605	0.605	0.000	0.000	0.000	0.000
70	A	71	ARG	1	0.936	0.965	21.450	13.057	13.057	0.000	0.000	0.000	0.000
71	A	72	LEU	0	-0.021	-0.016	17.587	0.390	0.390	0.000	0.000	0.000	0.000
72	A	73	MET	0	-0.068	-0.023	17.282	0.212	0.212	0.000	0.000	0.000	0.000
73	A	74	VAL	0	-0.075	-0.027	22.255	0.398	0.398	0.000	0.000	0.000	0.000
74	A	75	ALA	-1	-0.939	-0.949	25.473	-11.333	-11.333	0.000	0.000	0.000	0.000

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