FMO DATABASE

FMODB ID: VQRN1

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	OptH
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	-246552.62225
FMO2-HF: Nuclear repulsion	221773.387266
FMO2-HF: Total energy	-24779.234984
FMO2-MP2: Total energy	-24849.012518

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.
-10.305	-3.361	4.017	-5.007	-5.953	-0.024

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 : 0.031 / q_NPA : 0.014

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	-0.871	-0.924	3.832	-0.155	1.370	0.002	-0.504	-1.024	0.002
4	G	12	LYS	1	0.922	0.960	2.944	-4.399	-2.398	0.561	-0.948	-1.613	0.011
5	G	13	ASP	-1	-0.821	-0.932	2.340	-0.859	2.308	3.454	-3.525	-3.096	-0.037
6	G	14	LYS	1	0.911	0.986	4.218	-0.737	-0.601	0.001	-0.025	-0.112	0.000
7	G	15	LEU	0	-0.001	-0.010	7.278	-0.001	-0.001	0.000	0.000	0.000	0.000
8	G	16	LYS	1	0.887	0.935	4.515	-3.883	-3.768	-0.001	-0.005	-0.108	0.000
9	G	17	MET	0	0.016	0.009	6.929	-0.199	-0.199	0.000	0.000	0.000	0.000
10	G	18	GLU	-1	-0.912	-0.943	10.148	0.290	0.290	0.000	0.000	0.000	0.000
11	G	19	VAL	0	-0.026	-0.033	12.046	-0.072	-0.072	0.000	0.000	0.000	0.000
12	G	20	ASP	-1	-0.939	-0.977	11.891	0.358	0.358	0.000	0.000	0.000	0.000
13	G	21	GLN	0	-0.041	-0.006	13.913	-0.051	-0.051	0.000	0.000	0.000	0.000
14	G	22	LEU	0	0.005	-0.002	16.254	-0.029	-0.029	0.000	0.000	0.000	0.000
15	G	23	LYS	1	0.926	0.966	14.744	-0.488	-0.488	0.000	0.000	0.000	0.000
16	G	24	LYS	1	1.005	1.016	18.747	-0.148	-0.148	0.000	0.000	0.000	0.000
17	G	25	GLU	-1	-0.861	-0.927	20.406	0.131	0.131	0.000	0.000	0.000	0.000
18	G	26	VAL	0	-0.062	-0.033	21.840	-0.017	-0.017	0.000	0.000	0.000	0.000
19	G	27	THR	0	-0.090	-0.054	23.535	-0.010	-0.010	0.000	0.000	0.000	0.000
20	G	28	LEU	0	-0.026	-0.013	25.273	-0.012	-0.012	0.000	0.000	0.000	0.000
21	G	29	GLU	-1	-0.932	-0.961	27.425	0.085	0.085	0.000	0.000	0.000	0.000
22	G	30	ARG	1	0.845	0.928	25.610	-0.122	-0.122	0.000	0.000	0.000	0.000
23	G	31	MET	0	0.043	0.027	32.662	-0.001	-0.001	0.000	0.000	0.000	0.000
24	G	32	LEU	0	-0.026	-0.023	36.091	0.001	0.001	0.000	0.000	0.000	0.000
25	G	33	VAL	0	0.084	0.033	36.773	-0.002	-0.002	0.000	0.000	0.000	0.000
26	G	34	SER	0	0.049	0.026	39.004	-0.002	-0.002	0.000	0.000	0.000	0.000
27	G	35	LYS	1	1.011	1.020	41.133	-0.051	-0.051	0.000	0.000	0.000	0.000
28	G	36	CYS	0	0.038	0.019	37.743	-0.001	-0.001	0.000	0.000	0.000	0.000
29	G	37	CYS	0	-0.073	-0.043	40.249	-0.002	-0.002	0.000	0.000	0.000	0.000
30	G	38	GLU	-1	-0.988	-0.993	42.309	0.032	0.032	0.000	0.000	0.000	0.000
31	G	39	GLU	-1	-0.878	-0.934	42.447	0.036	0.036	0.000	0.000	0.000	0.000
32	G	40	PHE	0	-0.070	-0.027	39.926	-0.002	-0.002	0.000	0.000	0.000	0.000
33	G	41	ARG	1	0.857	0.888	43.154	-0.029	-0.029	0.000	0.000	0.000	0.000
34	G	42	ASP	-1	-0.819	-0.899	46.564	0.025	0.025	0.000	0.000	0.000	0.000
35	G	43	TYR	0	-0.010	0.006	44.836	-0.002	-0.002	0.000	0.000	0.000	0.000
36	G	44	VAL	0	0.018	0.008	45.257	-0.002	-0.002	0.000	0.000	0.000	0.000
37	G	45	GLU	-1	-0.941	-0.975	47.768	0.017	0.017	0.000	0.000	0.000	0.000
38	G	46	GLU	-1	-1.010	-0.988	50.422	0.019	0.019	0.000	0.000	0.000	0.000
39	G	47	ARG	1	0.868	0.922	47.715	-0.018	-0.018	0.000	0.000	0.000	0.000
40	G	48	SER	0	-0.005	0.009	50.593	-0.001	-0.001	0.000	0.000	0.000	0.000
41	G	49	GLY	0	-0.035	-0.021	51.972	-0.001	-0.001	0.000	0.000	0.000	0.000
42	G	50	GLU	-1	-0.979	-1.001	53.297	0.010	0.010	0.000	0.000	0.000	0.000
43	G	51	ASP	-1	-0.850	-0.923	49.232	0.009	0.009	0.000	0.000	0.000	0.000
44	G	52	PRO	0	-0.020	-0.029	51.874	0.000	0.000	0.000	0.000	0.000	0.000
45	G	53	LEU	0	-0.025	-0.012	48.151	-0.001	-0.001	0.000	0.000	0.000	0.000
46	G	54	VAL	0	-0.049	-0.003	50.733	0.000	0.000	0.000	0.000	0.000	0.000
47	G	55	LYS	1	0.851	0.925	53.150	-0.011	-0.011	0.000	0.000	0.000	0.000
48	G	56	GLY	0	0.023	0.039	55.891	0.000	0.000	0.000	0.000	0.000	0.000
49	G	57	ILE	0	-0.033	-0.035	54.811	0.000	0.000	0.000	0.000	0.000	0.000
50	G	58	PRO	0	-0.030	-0.012	59.075	0.000	0.000	0.000	0.000	0.000	0.000
51	G	59	GLU	-1	-0.815	-0.930	61.852	0.000	0.000	0.000	0.000	0.000	0.000
52	G	60	ASP	-1	-0.911	-0.951	63.119	0.001	0.001	0.000	0.000	0.000	0.000
53	G	61	LYS	1	0.850	0.921	60.323	-0.005	-0.005	0.000	0.000	0.000	0.000
54	G	62	ASN	0	0.042	0.017	57.351	0.000	0.000	0.000	0.000	0.000	0.000
55	G	63	PRO	0	-0.059	-0.024	55.625	0.000	0.000	0.000	0.000	0.000	0.000
56	G	64	PHE	0	-0.034	-0.020	52.086	-0.001	-0.001	0.000	0.000	0.000	0.000
57	G	65	LYS	1	0.911	0.991	57.410	0.000	0.000	0.000	0.000	0.000	0.000
58	G	66	GLU	-1	-0.979	-0.994	60.399	-0.005	-0.005	0.000	0.000	0.000	0.000

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