FMO DATABASE

FMODB ID: 2NJ8R

Calculation Name: 2YZT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YZT

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SHH4

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	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	67
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-376538.959935
FMO2-HF: Nuclear repulsion	349650.264329
FMO2-HF: Total energy	-26888.695606
FMO2-MP2: Total energy	-26967.947544

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.
-72.329	-73.784	39.366	-16.612	-21.297	-0.054

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 : 0.036 / q_NPA : 0.051

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	ARG	1	0.870	0.915	2.311	-20.987	-29.837	25.058	-7.157	-9.051	0.057
4	A	4	ARG	1	0.884	0.923	5.136	-1.510	-1.475	-0.001	-0.009	-0.024	0.000
5	A	5	TYR	0	0.022	0.010	5.406	0.873	0.873	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.844	0.904	10.383	-0.783	-0.783	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.005	-0.004	13.691	-0.022	-0.022	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.005	0.007	15.532	0.028	0.028	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.010	-0.020	18.405	-0.048	-0.048	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.925	-0.949	20.853	0.040	0.040	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.810	0.879	24.417	0.053	0.053	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.824	-0.908	27.171	-0.100	-0.100	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.982	-1.002	30.093	-0.062	-0.062	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.849	-0.896	32.106	-0.126	-0.126	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.023	0.008	30.734	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	16	TYR	0	-0.108	-0.071	27.106	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	17	PHE	0	0.007	-0.011	22.747	0.024	0.024	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.033	0.007	21.892	-0.040	-0.040	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.000	0.004	17.313	0.039	0.039	0.000	0.000	0.000	0.000
20	A	20	HIS	0	-0.017	-0.018	17.140	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.027	0.006	10.626	0.064	0.064	0.000	0.000	0.000	0.000
22	A	22	PRO	0	-0.007	-0.003	13.735	0.027	0.027	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.817	-0.896	10.272	0.910	0.910	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.028	-0.010	7.353	0.167	0.167	0.000	0.000	0.000	0.000
25	A	25	HIS	0	-0.052	-0.021	11.262	-0.259	-0.259	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.039	0.045	12.874	-0.085	-0.085	0.000	0.000	0.000	0.000
27	A	27	HIS	0	0.002	-0.005	14.990	0.080	0.080	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.034	-0.013	15.525	-0.095	-0.095	0.000	0.000	0.000	0.000
29	A	29	GLN	0	0.015	0.005	18.526	0.050	0.050	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.038	-0.014	21.284	-0.053	-0.053	0.000	0.000	0.000	0.000
31	A	31	GLN	0	0.011	0.016	23.317	0.018	0.018	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.019	-0.008	24.249	0.022	0.022	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.057	0.017	19.907	-0.031	-0.031	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.904	-0.941	19.193	-0.294	-0.294	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.831	-0.908	18.947	-0.404	-0.404	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.007	-0.003	18.361	-0.066	-0.066	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.016	0.015	14.392	-0.055	-0.055	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.840	0.911	14.317	0.530	0.530	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.869	0.914	14.272	0.328	0.328	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.006	0.011	12.368	-0.092	-0.092	0.000	0.000	0.000	0.000
41	A	41	GLN	0	0.016	0.006	10.004	0.056	0.056	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.834	-0.909	9.803	-1.325	-1.325	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.016	0.008	10.774	-0.279	-0.279	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.034	-0.010	6.330	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.020	-0.002	6.201	-0.383	-0.383	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.039	0.016	6.019	-0.922	-0.922	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.078	-0.056	7.867	0.007	0.007	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.088	-0.056	2.354	0.347	1.102	3.356	-0.972	-3.139	-0.007
49	A	49	GLU	-1	-0.980	-0.982	2.845	-9.465	-7.955	0.453	-0.943	-1.020	-0.010
50	A	50	GLU	-1	-0.898	-0.937	2.011	-38.904	-33.868	10.501	-7.524	-8.012	-0.094
51	A	51	GLU	-1	-0.958	-0.983	4.790	-0.800	-0.741	-0.001	-0.007	-0.051	0.000
52	A	52	ARG	1	0.793	0.868	6.911	2.132	2.132	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.016	0.011	5.571	-1.479	-1.479	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.833	-0.908	6.464	-0.456	-0.456	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.006	-0.005	8.060	0.150	0.150	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.077	-0.043	8.861	0.147	0.147	0.000	0.000	0.000	0.000
57	A	57	GLY	0	-0.025	-0.012	11.262	0.083	0.083	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.007	0.006	12.949	-0.042	-0.042	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.880	-0.929	14.515	0.575	0.575	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.009	-0.009	17.572	0.020	0.020	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.034	-0.010	20.296	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.016	-0.015	22.538	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.886	-0.930	25.444	0.105	0.105	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.085	-0.051	28.233	-0.014	-0.014	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.875	-0.937	30.995	0.024	0.024	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.063	-0.032	34.286	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.031	-0.002	37.153	0.000	0.000	0.000	0.000	0.000	0.000

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