FMO DATABASE

FMODB ID: G54G1

Calculation Name: 2DBS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DBS

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SGN2

Base Structure: X-ray

Registration Date: 2023-09-23

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	80
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-496523.608794
FMO2-HF: Nuclear repulsion	465543.502345
FMO2-HF: Total energy	-30980.106449
FMO2-MP2: Total energy	-31071.51576

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:7:ARG)

Summations of interaction energy for fragment #1(A:7:ARG)

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.
-310	-316.634	56.784	-24.617	-25.532	-0.258

Interaction energy analysis for fragmet #1(A:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.781 / q_NPA : 0.828

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	9	ALA	0	0.059	0.030	3.875	-1.529	-0.048	-0.009	-0.637	-0.835	0.000
4	A	10	GLU	-1	-0.839	-0.874	1.694	-134.054	-142.461	33.478	-14.094	-10.976	-0.159
5	A	11	LEU	0	-0.027	-0.010	2.441	0.991	3.124	1.941	-0.749	-3.324	0.000
6	A	12	ASP	-1	-0.846	-0.934	5.003	-22.821	-22.670	-0.001	-0.008	-0.142	0.000
7	A	13	GLY	0	-0.015	0.006	7.404	3.096	3.096	0.000	0.000	0.000	0.000
8	A	14	VAL	0	-0.009	-0.013	5.069	3.315	3.315	0.000	0.000	0.000	0.000
9	A	15	LEU	0	-0.013	-0.013	8.296	2.931	2.931	0.000	0.000	0.000	0.000
10	A	16	MET	0	0.005	-0.008	10.922	2.893	2.893	0.000	0.000	0.000	0.000
11	A	17	GLN	0	-0.065	-0.032	10.339	-0.535	-0.535	0.000	0.000	0.000	0.000
12	A	18	TYR	0	-0.014	-0.019	10.294	1.524	1.524	0.000	0.000	0.000	0.000
13	A	19	LEU	0	-0.024	-0.019	14.186	1.400	1.400	0.000	0.000	0.000	0.000
14	A	20	LEU	0	-0.031	-0.005	16.401	1.386	1.386	0.000	0.000	0.000	0.000
15	A	21	GLU	-1	-0.916	-0.961	14.813	-18.870	-18.870	0.000	0.000	0.000	0.000
16	A	22	ALA	0	-0.051	-0.028	17.467	0.292	0.292	0.000	0.000	0.000	0.000
17	A	23	ASP	-1	-0.874	-0.921	19.098	-12.614	-12.614	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.027	0.019	16.727	0.267	0.267	0.000	0.000	0.000	0.000
19	A	25	LEU	0	-0.035	-0.022	18.804	0.020	0.020	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.768	0.891	21.083	12.471	12.471	0.000	0.000	0.000	0.000
21	A	27	GLU	-1	-0.896	-0.954	21.647	-14.091	-14.091	0.000	0.000	0.000	0.000
22	A	28	LEU	0	-0.037	-0.005	17.348	-0.087	-0.087	0.000	0.000	0.000	0.000
23	A	29	PRO	0	-0.015	-0.005	21.291	0.578	0.578	0.000	0.000	0.000	0.000
24	A	30	PRO	0	-0.020	-0.011	22.555	-0.410	-0.410	0.000	0.000	0.000	0.000
25	A	31	THR	0	-0.031	-0.024	22.452	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	32	TYR	0	-0.006	-0.003	16.135	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	33	ARG	1	0.897	0.936	16.613	13.626	13.626	0.000	0.000	0.000	0.000
28	A	34	LEU	0	0.000	0.008	10.846	0.206	0.206	0.000	0.000	0.000	0.000
29	A	35	VAL	0	0.010	0.009	11.713	-0.238	-0.238	0.000	0.000	0.000	0.000
30	A	36	LEU	0	0.015	0.013	6.375	0.148	0.148	0.000	0.000	0.000	0.000
31	A	37	LEU	0	0.019	0.006	7.982	-0.652	-0.652	0.000	0.000	0.000	0.000
32	A	38	PRO	0	0.018	-0.003	4.626	1.163	1.276	-0.001	-0.006	-0.106	0.000
33	A	39	LEU	0	-0.033	-0.021	7.254	1.553	1.553	0.000	0.000	0.000	0.000
34	A	40	ASP	-1	-0.819	-0.892	6.384	-38.476	-38.476	0.000	0.000	0.000	0.000
35	A	41	GLU	-1	-0.849	-0.923	1.752	-112.446	-117.058	19.507	-7.890	-7.005	-0.099
36	A	42	PRO	0	0.015	-0.001	5.910	0.950	0.950	0.000	0.000	0.000	0.000
37	A	43	GLU	-1	-0.884	-0.926	6.433	-21.993	-21.993	0.000	0.000	0.000	0.000
38	A	44	VAL	0	0.003	-0.007	2.431	0.240	1.459	1.383	-0.674	-1.927	-0.001
39	A	45	ALA	0	0.011	0.003	5.053	2.058	2.056	-0.001	-0.003	0.007	0.000
40	A	46	ALA	0	0.002	0.007	8.012	2.043	2.043	0.000	0.000	0.000	0.000
41	A	47	GLN	0	-0.034	-0.027	6.552	2.245	2.245	0.000	0.000	0.000	0.000
42	A	48	ALA	0	-0.012	-0.001	7.192	1.009	1.009	0.000	0.000	0.000	0.000
43	A	49	LEU	0	-0.005	-0.005	8.975	1.163	1.163	0.000	0.000	0.000	0.000
44	A	50	ALA	0	-0.006	-0.006	11.480	1.161	1.161	0.000	0.000	0.000	0.000
45	A	51	TRP	0	-0.013	-0.014	8.255	0.840	0.840	0.000	0.000	0.000	0.000
46	A	52	ALA	0	-0.048	-0.021	12.443	0.732	0.732	0.000	0.000	0.000	0.000
47	A	53	MET	0	-0.065	-0.017	14.921	0.708	0.708	0.000	0.000	0.000	0.000
48	A	54	GLU	-1	-0.954	-0.957	14.088	-14.266	-14.266	0.000	0.000	0.000	0.000
49	A	55	ALA	0	0.007	-0.008	17.542	0.228	0.228	0.000	0.000	0.000	0.000
50	A	56	PRO	0	-0.002	0.024	19.841	-0.218	-0.218	0.000	0.000	0.000	0.000
51	A	57	ASN	0	-0.086	-0.079	21.739	0.742	0.742	0.000	0.000	0.000	0.000
52	A	58	PRO	0	-0.005	-0.012	25.534	-0.187	-0.187	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.898	-0.913	26.309	-9.922	-9.922	0.000	0.000	0.000	0.000
54	A	60	GLY	0	-0.004	-0.015	24.641	-0.448	-0.448	0.000	0.000	0.000	0.000
55	A	61	TRP	0	-0.048	-0.035	20.017	0.038	0.038	0.000	0.000	0.000	0.000
56	A	62	PRO	0	-0.002	0.020	21.484	-0.356	-0.356	0.000	0.000	0.000	0.000
57	A	63	SER	0	0.020	-0.022	18.002	-0.557	-0.557	0.000	0.000	0.000	0.000
58	A	64	VAL	0	-0.029	-0.013	16.354	0.493	0.493	0.000	0.000	0.000	0.000
59	A	65	TYR	0	-0.004	-0.014	14.256	-1.466	-1.466	0.000	0.000	0.000	0.000
60	A	66	ALA	0	-0.004	-0.012	11.609	0.646	0.646	0.000	0.000	0.000	0.000
61	A	67	LEU	0	-0.002	0.009	10.751	-2.112	-2.112	0.000	0.000	0.000	0.000
62	A	68	PHE	0	0.049	0.012	5.604	0.374	0.374	0.000	0.000	0.000	0.000
63	A	69	LEU	0	-0.018	-0.005	7.126	2.244	2.244	0.000	0.000	0.000	0.000
64	A	70	GLN	0	-0.065	-0.049	4.344	-0.254	-0.150	-0.001	-0.008	-0.096	0.000
65	A	71	GLY	0	0.038	0.029	2.657	-2.403	-1.316	0.455	-0.710	-0.833	0.001
66	A	72	ARG	1	0.817	0.907	3.373	39.893	39.992	0.033	0.162	-0.295	0.000
67	A	73	PRO	0	0.028	0.026	7.162	0.717	0.717	0.000	0.000	0.000	0.000
68	A	74	ILE	0	-0.066	-0.041	10.198	1.324	1.324	0.000	0.000	0.000	0.000
69	A	75	ARG	1	0.907	0.944	12.689	19.144	19.144	0.000	0.000	0.000	0.000
70	A	76	LEU	0	0.069	0.048	14.641	-1.013	-1.013	0.000	0.000	0.000	0.000
71	A	77	LEU	0	-0.062	-0.035	16.835	0.943	0.943	0.000	0.000	0.000	0.000
72	A	78	LEU	0	0.039	0.020	19.095	-0.276	-0.276	0.000	0.000	0.000	0.000
73	A	79	LEU	0	-0.023	-0.005	19.465	0.424	0.424	0.000	0.000	0.000	0.000
74	A	80	GLY	0	-0.029	-0.006	22.801	0.290	0.290	0.000	0.000	0.000	0.000
75	A	81	LYN	0	-0.013	-0.018	25.420	0.298	0.298	0.000	0.000	0.000	0.000
76	A	82	GLU	-1	-0.819	-0.863	19.524	-14.763	-14.763	0.000	0.000	0.000	0.000
77	A	83	VAL	0	-0.038	-0.036	23.619	0.546	0.546	0.000	0.000	0.000	0.000
78	A	84	GLU	-1	-0.828	-0.900	22.664	-12.701	-12.701	0.000	0.000	0.000	0.000
79	A	85	VAL	0	-0.088	-0.055	23.783	0.518	0.518	0.000	0.000	0.000	0.000
80	A	86	ALA	0	-0.014	0.006	24.128	-0.099	-0.099	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ARG)