FMO DATABASE

FMODB ID: JQR89

Calculation Name: 2RB6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RB6

Chain ID: A

ChEMBL ID:

UniProt ID: Q8EI81

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	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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-312258.191746
FMO2-HF: Nuclear repulsion	287909.31522
FMO2-HF: Total energy	-24348.876526
FMO2-MP2: Total energy	-24417.269677

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:25:SER)

Summations of interaction energy for fragment #1(A:25:SER)

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.
-19.021	-14.45	3.175	-3.409	-4.338	-0.024

Interaction energy analysis for fragmet #1(A:25:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.018

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	27	GLN	0	-0.025	-0.010	3.619	-2.496	-1.149	-0.003	-0.772	-0.573	0.002
4	A	28	TYR	0	-0.044	-0.055	4.963	1.434	1.434	0.000	0.000	0.000	0.000
5	A	29	ILE	0	0.044	0.019	8.702	-0.048	-0.048	0.000	0.000	0.000	0.000
6	A	30	MET	0	-0.069	-0.030	12.365	0.151	0.151	0.000	0.000	0.000	0.000
7	A	31	SER	0	0.000	0.007	15.307	-0.044	-0.044	0.000	0.000	0.000	0.000
8	A	32	THR	0	0.040	0.019	18.849	0.036	0.036	0.000	0.000	0.000	0.000
9	A	33	LYS	1	0.957	0.976	21.746	0.171	0.171	0.000	0.000	0.000	0.000
10	A	34	ASP	-1	-0.863	-0.932	24.695	-0.307	-0.307	0.000	0.000	0.000	0.000
11	A	35	GLY	0	-0.029	-0.012	24.722	0.009	0.009	0.000	0.000	0.000	0.000
12	A	36	LYS	1	0.817	0.906	21.628	0.308	0.308	0.000	0.000	0.000	0.000
13	A	37	MET	0	-0.016	-0.010	16.037	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	38	ILE	0	-0.006	0.006	14.322	0.000	0.000	0.000	0.000	0.000	0.000
15	A	39	THR	0	0.003	-0.019	11.125	0.070	0.070	0.000	0.000	0.000	0.000
16	A	40	SER	0	-0.007	-0.028	9.266	0.178	0.178	0.000	0.000	0.000	0.000
17	A	41	ASP	-1	-0.814	-0.891	4.644	-4.293	-4.238	-0.001	-0.003	-0.051	0.000
18	A	42	SER	0	-0.067	-0.033	3.765	-1.532	-1.357	0.000	-0.093	-0.083	-0.001
19	A	43	LYS	1	0.848	0.928	6.070	-0.398	-0.398	0.000	0.000	0.000	0.000
20	A	44	PRO	0	0.017	0.020	8.315	0.089	0.089	0.000	0.000	0.000	0.000
21	A	45	LYS	1	0.934	0.960	11.768	0.127	0.127	0.000	0.000	0.000	0.000
22	A	46	LEU	0	-0.035	-0.016	14.120	-0.030	-0.030	0.000	0.000	0.000	0.000
23	A	47	ASP	-1	-0.801	-0.863	17.672	-0.021	-0.021	0.000	0.000	0.000	0.000
24	A	48	LYS	1	0.937	0.942	20.595	-0.080	-0.080	0.000	0.000	0.000	0.000
25	A	49	THR	0	-0.070	-0.030	23.623	0.009	0.009	0.000	0.000	0.000	0.000
26	A	50	THR	0	-0.033	-0.051	23.488	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	51	GLY	0	-0.005	0.019	23.531	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	52	MET	0	-0.008	0.010	20.896	-0.032	-0.032	0.000	0.000	0.000	0.000
29	A	53	TYR	0	0.006	-0.019	15.801	0.043	0.043	0.000	0.000	0.000	0.000
30	A	54	LEU	0	-0.021	-0.010	15.379	-0.035	-0.035	0.000	0.000	0.000	0.000
31	A	55	TYR	0	0.008	-0.012	11.656	0.067	0.067	0.000	0.000	0.000	0.000
32	A	56	TYR	0	-0.029	-0.024	9.740	0.146	0.146	0.000	0.000	0.000	0.000
33	A	57	ASP	-1	-0.872	-0.917	11.006	-1.032	-1.032	0.000	0.000	0.000	0.000
34	A	58	GLU	-1	-0.860	-0.917	11.902	-1.343	-1.343	0.000	0.000	0.000	0.000
35	A	59	ASP	-1	-0.982	-0.979	12.608	-0.949	-0.949	0.000	0.000	0.000	0.000
36	A	60	GLY	0	0.003	0.002	13.669	0.154	0.154	0.000	0.000	0.000	0.000
37	A	61	ARG	1	0.801	0.908	13.962	0.377	0.377	0.000	0.000	0.000	0.000
38	A	62	GLU	-1	-0.820	-0.901	14.568	-0.492	-0.492	0.000	0.000	0.000	0.000
39	A	63	VAL	0	0.006	0.003	15.510	0.077	0.077	0.000	0.000	0.000	0.000
40	A	64	MET	0	-0.038	-0.027	16.819	0.014	0.014	0.000	0.000	0.000	0.000
41	A	65	ILE	0	0.026	0.022	17.414	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	66	LYS	1	0.866	0.925	20.287	0.195	0.195	0.000	0.000	0.000	0.000
43	A	67	GLN	0	0.020	-0.003	20.783	-0.017	-0.017	0.000	0.000	0.000	0.000
44	A	68	GLU	-1	-0.887	-0.934	22.016	-0.148	-0.148	0.000	0.000	0.000	0.000
45	A	69	ASP	-1	-0.870	-0.937	22.778	-0.230	-0.230	0.000	0.000	0.000	0.000
46	A	70	VAL	0	-0.044	-0.014	17.558	-0.032	-0.032	0.000	0.000	0.000	0.000
47	A	71	THR	0	-0.048	-0.027	20.822	0.036	0.036	0.000	0.000	0.000	0.000
48	A	72	GLN	0	-0.021	-0.013	18.094	0.005	0.005	0.000	0.000	0.000	0.000
49	A	73	ILE	0	0.012	0.004	12.415	-0.067	-0.067	0.000	0.000	0.000	0.000
50	A	74	ILE	0	-0.051	-0.025	12.939	0.116	0.116	0.000	0.000	0.000	0.000
51	A	75	GLU	-1	-0.780	-0.863	7.330	0.903	0.903	0.000	0.000	0.000	0.000
52	A	76	ARG	1	0.902	0.956	8.577	1.262	1.262	0.000	0.000	0.000	0.000
53	A	77	LEU	0	0.042	0.013	5.622	-0.843	-0.843	0.000	0.000	0.000	0.000
54	A	78	GLU	-1	-0.854	-0.917	2.707	-9.944	-7.111	3.180	-2.516	-3.498	-0.025
55	A	79	HIS	0	-0.029	-0.043	4.679	1.403	1.436	-0.001	-0.002	-0.029	0.000
56	A	80	HIS	0	-0.017	0.006	7.296	0.287	0.287	0.000	0.000	0.000	0.000
57	A	81	HIS	1	0.924	0.975	3.960	-2.239	-2.111	0.000	-0.023	-0.104	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:25:SER)