FMO DATABASE

FMODB ID: G5NR1

Calculation Name: 1GOT-G-Xray372

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-diphosphate

ligand 3-letter code: GDP

PDB ID: 1GOT

Chain ID: G

ChEMBL ID:

UniProt ID: P62871

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	58
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-246635.577925
FMO2-HF: Nuclear repulsion	221855.472728
FMO2-HF: Total energy	-24780.105198
FMO2-MP2: Total energy	-24849.815747

3D Structure

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(G:9:LEU)

Summations of interaction energy for fragment #1(G:9:LEU)

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.
-9.363	-3.523	3.419	-4.023	-5.239	-0.02

Interaction energy analysis for fragmet #1(G:9:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.012

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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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	G	11	GLU	-1	-0.787	-0.869	3.692	-0.749	0.776	0.024	-0.519	-1.030	0.000
4	G	12	LYS	1	0.875	0.923	2.824	-3.661	-1.701	0.376	-0.844	-1.492	0.008
5	G	13	ASP	-1	-0.824	-0.901	2.319	-1.533	0.545	3.021	-2.612	-2.488	-0.028
6	G	14	LYS	1	0.889	0.941	4.701	-0.259	-0.166	-0.001	-0.011	-0.082	0.000
7	G	15	LEU	0	0.013	0.005	7.541	0.003	0.003	0.000	0.000	0.000	0.000
8	G	16	LYS	1	0.831	0.896	3.620	-2.973	-2.789	-0.001	-0.037	-0.147	0.000
9	G	17	MET	0	0.028	0.011	7.249	-0.135	-0.135	0.000	0.000	0.000	0.000
10	G	18	GLU	-1	-0.885	-0.917	10.649	0.203	0.203	0.000	0.000	0.000	0.000
11	G	19	VAL	0	0.038	-0.003	12.246	-0.045	-0.045	0.000	0.000	0.000	0.000
12	G	20	ASP	-1	-0.862	-0.902	12.828	0.339	0.339	0.000	0.000	0.000	0.000
13	G	21	GLN	0	0.036	0.036	14.616	-0.034	-0.034	0.000	0.000	0.000	0.000
14	G	22	LEU	0	-0.001	-0.004	16.391	-0.023	-0.023	0.000	0.000	0.000	0.000
15	G	23	LYS	1	0.798	0.879	14.096	-0.411	-0.411	0.000	0.000	0.000	0.000
16	G	24	LYS	1	0.857	0.933	18.988	-0.130	-0.130	0.000	0.000	0.000	0.000
17	G	25	GLU	-1	-0.834	-0.925	20.719	0.100	0.100	0.000	0.000	0.000	0.000
18	G	26	VAL	0	-0.032	-0.013	22.131	-0.013	-0.013	0.000	0.000	0.000	0.000
19	G	27	THR	0	-0.054	-0.037	23.807	-0.012	-0.012	0.000	0.000	0.000	0.000
20	G	28	LEU	0	-0.004	0.017	25.401	-0.009	-0.009	0.000	0.000	0.000	0.000
21	G	29	GLU	-1	-0.901	-0.948	27.928	0.067	0.067	0.000	0.000	0.000	0.000
22	G	30	ARG	1	0.743	0.856	25.883	-0.102	-0.102	0.000	0.000	0.000	0.000
23	G	31	MET	0	0.024	0.025	33.024	0.000	0.000	0.000	0.000	0.000	0.000
24	G	32	LEU	0	-0.004	-0.010	36.352	0.001	0.001	0.000	0.000	0.000	0.000
25	G	33	VAL	0	0.080	0.028	36.649	-0.002	-0.002	0.000	0.000	0.000	0.000
26	G	34	SER	0	0.004	0.020	39.130	-0.001	-0.001	0.000	0.000	0.000	0.000
27	G	35	LYS	1	1.021	1.013	41.687	-0.039	-0.039	0.000	0.000	0.000	0.000
28	G	36	CYS	0	0.000	0.006	38.200	-0.001	-0.001	0.000	0.000	0.000	0.000
29	G	37	CYS	0	-0.043	-0.029	40.645	-0.002	-0.002	0.000	0.000	0.000	0.000
30	G	38	GLU	-1	-0.974	-0.990	42.733	0.028	0.028	0.000	0.000	0.000	0.000
31	G	39	GLU	-1	-0.869	-0.947	42.580	0.030	0.030	0.000	0.000	0.000	0.000
32	G	40	PHE	0	-0.033	-0.012	41.040	-0.002	-0.002	0.000	0.000	0.000	0.000
33	G	41	ARG	1	0.809	0.867	43.821	-0.024	-0.024	0.000	0.000	0.000	0.000
34	G	42	ASP	-1	-0.786	-0.869	47.130	0.020	0.020	0.000	0.000	0.000	0.000
35	G	43	TYR	0	-0.021	-0.001	44.647	-0.002	-0.002	0.000	0.000	0.000	0.000
36	G	44	VAL	0	0.003	0.003	45.566	-0.002	-0.002	0.000	0.000	0.000	0.000
37	G	45	GLU	-1	-0.860	-0.910	48.147	0.014	0.014	0.000	0.000	0.000	0.000
38	G	46	GLU	-1	-0.916	-0.938	50.567	0.015	0.015	0.000	0.000	0.000	0.000
39	G	47	ARG	1	0.762	0.871	48.461	-0.015	-0.015	0.000	0.000	0.000	0.000
40	G	48	SER	0	-0.012	-0.033	51.217	-0.001	-0.001	0.000	0.000	0.000	0.000
41	G	49	GLY	0	-0.043	-0.031	52.605	-0.001	-0.001	0.000	0.000	0.000	0.000
42	G	50	GLU	-1	-0.975	-0.996	53.762	0.008	0.008	0.000	0.000	0.000	0.000
43	G	51	ASP	-1	-0.844	-0.915	49.697	0.007	0.007	0.000	0.000	0.000	0.000
44	G	52	PRO	0	0.005	-0.023	52.155	0.000	0.000	0.000	0.000	0.000	0.000
45	G	53	LEU	0	-0.059	-0.019	48.547	-0.001	-0.001	0.000	0.000	0.000	0.000
46	G	54	VAL	0	-0.043	-0.016	50.808	0.000	0.000	0.000	0.000	0.000	0.000
47	G	55	LYS	1	0.814	0.922	53.420	-0.009	-0.009	0.000	0.000	0.000	0.000
48	G	56	GLY	0	0.018	0.030	56.010	0.000	0.000	0.000	0.000	0.000	0.000
49	G	57	ILE	0	-0.014	-0.026	55.539	0.000	0.000	0.000	0.000	0.000	0.000
50	G	58	PRO	0	-0.018	-0.008	59.618	0.000	0.000	0.000	0.000	0.000	0.000
51	G	59	GLU	-1	-0.746	-0.882	62.148	0.000	0.000	0.000	0.000	0.000	0.000
52	G	60	ASP	-1	-0.907	-0.935	63.518	0.001	0.001	0.000	0.000	0.000	0.000
53	G	61	LYS	1	0.898	0.934	60.391	-0.004	-0.004	0.000	0.000	0.000	0.000
54	G	62	ASN	0	-0.018	-0.002	58.111	0.000	0.000	0.000	0.000	0.000	0.000
55	G	63	PRO	0	-0.026	-0.008	55.846	0.000	0.000	0.000	0.000	0.000	0.000
56	G	64	PHE	0	-0.059	-0.033	52.224	-0.001	-0.001	0.000	0.000	0.000	0.000
57	G	65	LYS	1	0.825	0.916	57.618	0.001	0.001	0.000	0.000	0.000	0.000
58	G	66	GLU	-1	-0.975	-0.982	61.066	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:9:LEU)