FMO DATABASE

FMODB ID: R9GM8

Calculation Name: 2GBJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GBJ

Chain ID: A

ChEMBL ID:

UniProt ID: P0CG48

Base Structure: X-ray

Registration Date: 2023-09-19

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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-500360.372048
FMO2-HF: Nuclear repulsion	470017.40062
FMO2-HF: Total energy	-30342.971429
FMO2-MP2: Total energy	-30432.714008

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(A:1:MET)

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

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.
-29.64	-22.469	20.991	-8.367	-19.794	-0.066

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.006

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	3	ILE	0	-0.023	-0.003	2.646	-0.995	2.065	0.567	-1.271	-2.355	0.001
4	A	4	PHE	0	0.009	0.003	4.926	0.093	0.136	-0.001	-0.008	-0.033	0.000
5	A	5	VAL	0	-0.002	0.005	8.693	-0.082	-0.082	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.969	0.998	11.291	0.327	0.327	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.017	0.013	14.788	-0.045	-0.045	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.022	-0.019	17.828	0.042	0.042	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.011	0.015	20.354	0.000	0.000	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.037	0.029	23.169	0.000	0.000	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.029	-0.030	25.618	0.015	0.015	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.009	-0.003	28.346	0.009	0.009	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.026	0.001	28.641	0.010	0.010	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.006	-0.012	28.647	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.025	0.010	27.227	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.016	0.012	24.239	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.056	0.017	21.829	0.013	0.013	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.072	-0.049	18.574	-0.028	-0.028	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.979	0.998	17.169	0.255	0.255	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.024	-0.011	12.454	-0.020	-0.020	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.006	0.021	11.877	0.068	0.068	0.000	0.000	0.000	0.000
22	A	22	THR	0	0.006	-0.008	8.536	-0.097	-0.097	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.048	-0.027	6.792	0.207	0.207	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.889	-0.936	3.352	-1.149	-0.527	0.024	-0.202	-0.444	0.000
25	A	25	VAL	0	-0.069	-0.042	2.192	0.931	2.509	2.184	-1.080	-2.682	-0.001
26	A	26	GLU	-1	-0.823	-0.918	1.946	-17.969	-18.900	10.635	-5.132	-4.573	-0.060
27	A	27	PRO	0	-0.017	-0.019	2.648	-2.219	-0.402	1.996	-0.834	-2.979	-0.001
28	A	28	SER	0	0.023	0.003	3.550	0.547	0.468	0.026	0.216	-0.162	0.000
29	A	29	ASP	-1	-0.837	-0.906	5.336	-4.150	-4.150	0.000	0.000	0.000	0.000
30	A	30	THR	0	0.006	-0.007	7.006	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.025	-0.016	8.640	-0.267	-0.267	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.936	-0.973	10.579	-0.879	-0.879	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.006	-0.012	9.343	-0.071	-0.071	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.014	0.003	6.752	-0.066	-0.066	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.828	0.912	9.620	0.993	0.993	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.032	0.025	13.274	0.128	0.128	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.901	0.953	6.524	3.634	3.634	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.060	-0.029	11.346	0.143	0.143	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.003	0.001	13.884	0.104	0.104	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.909	-0.942	13.749	-0.988	-0.988	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.821	0.904	10.680	1.268	1.268	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.928	-0.971	15.957	-0.437	-0.437	0.000	0.000	0.000	0.000
43	A	43	GLY	0	-0.025	0.003	18.827	0.066	0.066	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.059	-0.030	18.998	0.039	0.039	0.000	0.000	0.000	0.000
45	A	45	PRO	0	0.044	0.019	19.221	-0.083	-0.083	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.063	0.021	17.094	0.012	0.012	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.871	-0.923	18.622	-0.504	-0.504	0.000	0.000	0.000	0.000
48	A	48	GLN	0	-0.084	-0.050	21.328	0.026	0.026	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.009	-0.004	15.116	-0.053	-0.053	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.875	0.936	17.188	0.397	0.397	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.067	0.034	10.587	0.025	0.025	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.041	-0.014	13.692	0.055	0.055	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.051	0.018	8.656	-0.118	-0.118	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.010	0.010	12.055	0.041	0.041	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.001	0.004	14.207	0.025	0.025	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.932	0.970	13.814	0.358	0.358	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.001	-0.015	14.908	-0.068	-0.068	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.069	-0.026	9.931	0.040	0.040	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.921	-0.974	13.902	-0.440	-0.440	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.787	-0.906	13.375	-0.890	-0.890	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.006	0.000	13.474	-0.134	-0.134	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.892	0.967	11.472	0.525	0.525	0.000	0.000	0.000	0.000
63	A	63	THR	0	0.045	0.021	7.346	-0.169	-0.169	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.014	-0.013	2.961	-0.230	0.390	0.210	-0.151	-0.679	-0.001
65	A	65	SER	0	-0.038	-0.021	5.260	0.581	0.664	-0.001	-0.007	-0.075	0.000
66	A	66	ASP	-1	-0.836	-0.905	5.810	-0.300	-0.300	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.067	-0.040	7.811	0.255	0.255	0.000	0.000	0.000	0.000
68	A	68	ASN	0	-0.027	-0.015	7.052	0.137	0.137	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.043	-0.001	3.344	0.195	0.482	0.013	-0.057	-0.243	0.000
70	A	70	GLN	0	-0.006	-0.019	2.834	-4.700	-3.053	1.355	-1.091	-1.911	-0.005
71	A	71	LYS	1	1.007	0.989	2.315	-5.490	-5.314	3.829	-0.749	-3.257	0.001
72	A	72	GLU	-1	-0.951	-0.991	2.941	1.563	-0.189	0.154	1.999	-0.401	0.000
73	A	73	SER	0	-0.018	0.005	4.985	-0.357	-0.357	0.000	0.000	0.000	0.000
74	A	74	THR	0	0.001	-0.004	6.732	-0.462	-0.462	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.021	-0.004	7.057	0.157	0.157	0.000	0.000	0.000	0.000
76	A	76	HIS	0	-0.034	-0.023	10.200	0.116	0.116	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.037	0.022	13.923	-0.037	-0.037	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.047	-0.040	15.571	0.088	0.088	0.000	0.000	0.000	0.000
79	A	79	LEU	0	0.035	0.024	19.052	-0.041	-0.041	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.881	0.942	21.169	0.461	0.461	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.045	0.025	23.172	-0.010	-0.010	0.000	0.000	0.000	0.000

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