FMO DATABASE

FMODB ID: 1N4YZ

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	OptHSide
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	-246489.91033
FMO2-HF: Nuclear repulsion	221710.178222
FMO2-HF: Total energy	-24779.732108
FMO2-MP2: Total energy	-24849.496528

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.
-7.398	-1.689	4.747	-4.7	-5.754	-0.018

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 : 0.029 / q_NPA : 0.009

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	-0.822	-0.883	3.832	-0.126	1.422	0.004	-0.487	-1.065	0.002
4	G	12	LYS	1	0.895	0.935	2.930	-3.948	-2.152	0.550	-0.837	-1.508	0.010
5	G	13	ASP	-1	-0.783	-0.883	2.310	1.379	3.414	4.193	-3.308	-2.920	-0.030
6	G	14	LYS	1	0.867	0.944	4.229	-0.761	-0.615	0.001	-0.032	-0.115	0.000
7	G	15	LEU	0	0.028	-0.001	7.291	-0.035	-0.035	0.000	0.000	0.000	0.000
8	G	16	LYS	1	0.824	0.884	3.937	-3.634	-3.450	-0.001	-0.036	-0.146	0.000
9	G	17	MET	0	-0.003	-0.001	6.878	-0.205	-0.205	0.000	0.000	0.000	0.000
10	G	18	GLU	-1	-0.878	-0.909	10.158	0.263	0.263	0.000	0.000	0.000	0.000
11	G	19	VAL	0	0.017	-0.014	12.059	-0.069	-0.069	0.000	0.000	0.000	0.000
12	G	20	ASP	-1	-0.876	-0.930	11.955	0.379	0.379	0.000	0.000	0.000	0.000
13	G	21	GLN	0	-0.052	-0.020	13.919	-0.047	-0.047	0.000	0.000	0.000	0.000
14	G	22	LEU	0	0.004	0.000	16.264	-0.031	-0.031	0.000	0.000	0.000	0.000
15	G	23	LYS	1	0.846	0.912	13.870	-0.491	-0.491	0.000	0.000	0.000	0.000
16	G	24	LYS	1	0.997	1.009	18.756	-0.156	-0.156	0.000	0.000	0.000	0.000
17	G	25	GLU	-1	-0.856	-0.916	20.415	0.134	0.134	0.000	0.000	0.000	0.000
18	G	26	VAL	0	-0.065	-0.038	21.847	-0.017	-0.017	0.000	0.000	0.000	0.000
19	G	27	THR	0	-0.076	-0.044	23.615	-0.011	-0.011	0.000	0.000	0.000	0.000
20	G	28	LEU	0	-0.022	-0.007	25.211	-0.011	-0.011	0.000	0.000	0.000	0.000
21	G	29	GLU	-1	-0.924	-0.951	27.433	0.084	0.084	0.000	0.000	0.000	0.000
22	G	30	ARG	1	0.813	0.905	25.679	-0.123	-0.123	0.000	0.000	0.000	0.000
23	G	31	MET	0	0.010	0.015	32.671	-0.001	-0.001	0.000	0.000	0.000	0.000
24	G	32	LEU	0	-0.003	-0.011	36.102	0.002	0.002	0.000	0.000	0.000	0.000
25	G	33	VAL	0	0.088	0.034	36.683	-0.002	-0.002	0.000	0.000	0.000	0.000
26	G	34	SER	0	0.041	0.034	39.015	-0.001	-0.001	0.000	0.000	0.000	0.000
27	G	35	LYS	1	1.007	1.018	41.202	-0.049	-0.049	0.000	0.000	0.000	0.000
28	G	36	CYS	0	0.024	0.012	37.799	-0.001	-0.001	0.000	0.000	0.000	0.000
29	G	37	CYS	0	-0.067	-0.045	40.261	-0.002	-0.002	0.000	0.000	0.000	0.000
30	G	38	GLU	-1	-0.980	-0.994	42.322	0.034	0.034	0.000	0.000	0.000	0.000
31	G	39	GLU	-1	-0.864	-0.936	42.400	0.038	0.038	0.000	0.000	0.000	0.000
32	G	40	PHE	0	-0.057	-0.023	40.267	-0.002	-0.002	0.000	0.000	0.000	0.000
33	G	41	ARG	1	0.789	0.840	43.169	-0.031	-0.031	0.000	0.000	0.000	0.000
34	G	42	ASP	-1	-0.774	-0.863	46.579	0.026	0.026	0.000	0.000	0.000	0.000
35	G	43	TYR	0	-0.014	0.011	44.673	-0.002	-0.002	0.000	0.000	0.000	0.000
36	G	44	VAL	0	0.016	0.003	45.186	-0.002	-0.002	0.000	0.000	0.000	0.000
37	G	45	GLU	-1	-0.904	-0.951	47.784	0.019	0.019	0.000	0.000	0.000	0.000
38	G	46	GLU	-1	-0.912	-0.927	50.372	0.021	0.021	0.000	0.000	0.000	0.000
39	G	47	ARG	1	0.773	0.862	47.784	-0.021	-0.021	0.000	0.000	0.000	0.000
40	G	48	SER	0	-0.010	0.001	50.633	-0.001	-0.001	0.000	0.000	0.000	0.000
41	G	49	GLY	0	-0.046	-0.028	51.988	-0.001	-0.001	0.000	0.000	0.000	0.000
42	G	50	GLU	-1	-0.980	-0.999	53.282	0.012	0.012	0.000	0.000	0.000	0.000
43	G	51	ASP	-1	-0.837	-0.915	49.178	0.012	0.012	0.000	0.000	0.000	0.000
44	G	52	PRO	0	-0.021	-0.025	51.765	0.000	0.000	0.000	0.000	0.000	0.000
45	G	53	LEU	0	-0.032	-0.016	48.111	-0.001	-0.001	0.000	0.000	0.000	0.000
46	G	54	VAL	0	-0.055	-0.016	50.755	0.000	0.000	0.000	0.000	0.000	0.000
47	G	55	LYS	1	0.842	0.929	53.168	-0.013	-0.013	0.000	0.000	0.000	0.000
48	G	56	GLY	0	0.027	0.039	55.903	0.000	0.000	0.000	0.000	0.000	0.000
49	G	57	ILE	0	-0.017	-0.032	54.862	0.000	0.000	0.000	0.000	0.000	0.000
50	G	58	PRO	0	-0.021	-0.006	59.094	0.000	0.000	0.000	0.000	0.000	0.000
51	G	59	GLU	-1	-0.746	-0.883	61.610	0.003	0.003	0.000	0.000	0.000	0.000
52	G	60	ASP	-1	-0.883	-0.931	63.138	0.003	0.003	0.000	0.000	0.000	0.000
53	G	61	LYS	1	0.857	0.920	60.297	-0.007	-0.007	0.000	0.000	0.000	0.000
54	G	62	ASN	0	-0.009	-0.007	57.647	0.000	0.000	0.000	0.000	0.000	0.000
55	G	63	PRO	0	-0.027	-0.007	55.666	0.000	0.000	0.000	0.000	0.000	0.000
56	G	64	PHE	0	-0.039	-0.025	51.958	-0.001	-0.001	0.000	0.000	0.000	0.000
57	G	65	LYS	1	0.819	0.931	57.462	-0.002	-0.002	0.000	0.000	0.000	0.000
58	G	66	GLU	-1	-0.984	-0.995	60.461	-0.002	-0.002	0.000	0.000	0.000	0.000

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