FMO DATABASE

FMODB ID: 3J42L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-312184.303723
FMO2-HF: Nuclear repulsion	287835.221062
FMO2-HF: Total energy	-24349.082661
FMO2-MP2: Total energy	-24417.47985

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.
-15.403	-10.618	4.596	-3.909	-5.471	-0.025

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 : 0.036 / q_NPA : 0.020

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	-0.003	0.005	3.862	-2.076	-0.453	-0.003	-0.825	-0.796	0.004
4	A	28	TYR	0	-0.065	-0.059	4.542	1.259	1.358	-0.001	-0.010	-0.087	0.000
5	A	29	ILE	0	0.011	-0.002	8.800	-0.006	-0.006	0.000	0.000	0.000	0.000
6	A	30	MET	0	-0.038	-0.007	12.516	0.115	0.115	0.000	0.000	0.000	0.000
7	A	31	SER	0	0.002	-0.004	15.611	-0.038	-0.038	0.000	0.000	0.000	0.000
8	A	32	THR	0	0.037	0.026	19.197	0.033	0.033	0.000	0.000	0.000	0.000
9	A	33	LYS	1	0.934	0.962	21.865	0.161	0.161	0.000	0.000	0.000	0.000
10	A	34	ASP	-1	-0.837	-0.910	24.911	-0.251	-0.251	0.000	0.000	0.000	0.000
11	A	35	GLY	0	-0.022	-0.013	24.963	0.004	0.004	0.000	0.000	0.000	0.000
12	A	36	LYS	1	0.790	0.889	21.609	0.257	0.257	0.000	0.000	0.000	0.000
13	A	37	MET	0	-0.012	-0.006	15.576	-0.015	-0.015	0.000	0.000	0.000	0.000
14	A	38	ILE	0	0.000	0.011	14.323	0.013	0.013	0.000	0.000	0.000	0.000
15	A	39	THR	0	0.001	-0.033	10.760	0.049	0.049	0.000	0.000	0.000	0.000
16	A	40	SER	0	0.003	-0.017	9.032	0.189	0.189	0.000	0.000	0.000	0.000
17	A	41	ASP	-1	-0.826	-0.893	4.230	-3.545	-3.478	-0.001	-0.008	-0.058	0.000
18	A	42	SER	0	-0.040	-0.041	3.888	-0.780	-0.546	0.000	-0.081	-0.153	0.000
19	A	43	LYS	1	0.797	0.894	6.136	0.029	0.029	0.000	0.000	0.000	0.000
20	A	44	PRO	0	0.023	0.027	8.366	0.133	0.133	0.000	0.000	0.000	0.000
21	A	45	LYS	1	0.920	0.952	11.903	0.143	0.143	0.000	0.000	0.000	0.000
22	A	46	LEU	0	-0.034	-0.010	14.283	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	47	ASP	-1	-0.786	-0.855	17.911	-0.021	-0.021	0.000	0.000	0.000	0.000
24	A	48	LYS	1	0.926	0.935	20.795	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	49	THR	0	-0.069	-0.043	23.855	0.008	0.008	0.000	0.000	0.000	0.000
26	A	50	THR	0	-0.047	-0.046	23.982	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	51	GLY	0	-0.017	0.011	23.972	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	52	MET	0	0.012	0.011	21.074	-0.025	-0.025	0.000	0.000	0.000	0.000
29	A	53	TYR	0	-0.016	-0.030	16.005	0.027	0.027	0.000	0.000	0.000	0.000
30	A	54	LEU	0	-0.005	-0.003	15.494	-0.023	-0.023	0.000	0.000	0.000	0.000
31	A	55	TYR	0	0.001	-0.014	12.023	0.021	0.021	0.000	0.000	0.000	0.000
32	A	56	TYR	0	-0.021	-0.023	9.903	0.143	0.143	0.000	0.000	0.000	0.000
33	A	57	ASP	-1	-0.829	-0.900	11.216	-0.731	-0.731	0.000	0.000	0.000	0.000
34	A	58	GLU	-1	-0.854	-0.916	11.599	-1.053	-1.053	0.000	0.000	0.000	0.000
35	A	59	ASP	-1	-0.983	-0.982	12.137	-0.637	-0.637	0.000	0.000	0.000	0.000
36	A	60	GLY	0	-0.015	0.008	13.443	0.111	0.111	0.000	0.000	0.000	0.000
37	A	61	ARG	1	0.745	0.866	14.327	0.303	0.303	0.000	0.000	0.000	0.000
38	A	62	GLU	-1	-0.815	-0.891	14.611	-0.314	-0.314	0.000	0.000	0.000	0.000
39	A	63	VAL	0	-0.013	0.000	15.218	0.061	0.061	0.000	0.000	0.000	0.000
40	A	64	MET	0	-0.031	-0.025	16.839	0.004	0.004	0.000	0.000	0.000	0.000
41	A	65	ILE	0	0.019	0.023	17.783	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	66	LYS	1	0.855	0.911	20.449	0.165	0.165	0.000	0.000	0.000	0.000
43	A	67	GLN	0	-0.005	-0.003	21.422	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	68	GLU	-1	-0.837	-0.912	22.606	-0.141	-0.141	0.000	0.000	0.000	0.000
45	A	69	ASP	-1	-0.856	-0.931	23.060	-0.200	-0.200	0.000	0.000	0.000	0.000
46	A	70	VAL	0	-0.032	-0.008	17.938	-0.028	-0.028	0.000	0.000	0.000	0.000
47	A	71	THR	0	-0.057	-0.035	21.186	0.029	0.029	0.000	0.000	0.000	0.000
48	A	72	GLN	0	-0.010	-0.003	18.343	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	73	ILE	0	0.018	0.009	12.566	-0.048	-0.048	0.000	0.000	0.000	0.000
50	A	74	ILE	0	-0.051	-0.018	12.656	0.095	0.095	0.000	0.000	0.000	0.000
51	A	75	GLU	-1	-0.736	-0.829	6.607	0.511	0.511	0.000	0.000	0.000	0.000
52	A	76	ARG	1	0.893	0.944	8.183	1.171	1.171	0.000	0.000	0.000	0.000
53	A	77	LEU	0	0.033	0.020	5.481	-0.896	-0.896	0.000	0.000	0.000	0.000
54	A	78	GLU	-1	-0.838	-0.922	2.473	-9.705	-7.188	4.599	-2.935	-4.181	-0.029
55	A	79	HIS	0	-0.034	-0.025	4.543	1.241	1.286	-0.001	-0.004	-0.039	0.000
56	A	80	HIS	0	0.018	0.009	7.475	0.252	0.252	0.000	0.000	0.000	0.000
57	A	81	HIS	1	0.877	0.958	3.492	-1.327	-1.127	0.003	-0.046	-0.157	0.000

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