FMO DATABASE

FMODB ID: 2JN2R

Calculation Name: 5VJI-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5VJI

Chain ID: C

ChEMBL ID:

UniProt ID: Q8R0W1

Base Structure: X-ray

Registration Date: 2023-06-21

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	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	62
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-272003.080494
FMO2-HF: Nuclear repulsion	247751.3559
FMO2-HF: Total energy	-24251.724594
FMO2-MP2: Total energy	-24323.459966

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(C:2:ASN)

Summations of interaction energy for fragment #1(C:2:ASN)

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.
-0.376	3.433	1.382	-1.556	-3.633	0.004

Interaction energy analysis for fragmet #1(C:2:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / q_NPA : 0.015

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	C	4	LEU	0	0.043	0.028	3.688	-3.547	-1.961	0.003	-0.634	-0.955	0.002
4	C	5	VAL	0	0.003	-0.001	2.223	-1.583	-0.626	1.096	-0.517	-1.535	-0.001
5	C	6	VAL	0	0.010	0.003	3.165	-1.111	0.049	0.284	-0.400	-1.043	0.003
6	C	7	LEU	0	0.024	0.009	5.690	0.186	0.186	0.000	0.000	0.000	0.000
7	C	8	HIS	0	-0.001	-0.005	7.627	0.084	0.084	0.000	0.000	0.000	0.000
8	C	9	LYS	1	0.928	0.959	4.292	5.511	5.617	-0.001	-0.005	-0.100	0.000
9	C	10	SER	0	-0.038	-0.008	9.365	0.156	0.156	0.000	0.000	0.000	0.000
10	C	11	GLY	0	0.072	0.044	11.055	0.112	0.112	0.000	0.000	0.000	0.000
11	C	12	LEU	0	0.032	0.004	12.295	0.106	0.106	0.000	0.000	0.000	0.000
12	C	13	LEU	0	-0.023	0.016	9.951	0.149	0.149	0.000	0.000	0.000	0.000
13	C	14	GLU	-1	-0.832	-0.909	12.827	-0.163	-0.163	0.000	0.000	0.000	0.000
14	C	15	ILE	0	0.035	0.008	15.974	0.053	0.053	0.000	0.000	0.000	0.000
15	C	16	THR	0	-0.024	-0.026	14.933	0.064	0.064	0.000	0.000	0.000	0.000
16	C	17	LEU	0	-0.046	-0.026	14.759	0.036	0.036	0.000	0.000	0.000	0.000
17	C	18	LYS	1	0.884	0.938	17.992	0.099	0.099	0.000	0.000	0.000	0.000
18	C	19	THR	0	0.007	0.001	20.496	-0.003	-0.003	0.000	0.000	0.000	0.000
19	C	20	LYS	1	0.934	0.964	17.159	-0.488	-0.488	0.000	0.000	0.000	0.000
20	C	21	GLU	-1	-0.758	-0.829	21.780	0.116	0.116	0.000	0.000	0.000	0.000
21	C	22	LEU	0	0.010	0.015	23.998	-0.007	-0.007	0.000	0.000	0.000	0.000
22	C	23	ILE	0	-0.007	-0.010	23.177	-0.001	-0.001	0.000	0.000	0.000	0.000
23	C	24	ARG	1	0.834	0.894	25.648	-0.134	-0.134	0.000	0.000	0.000	0.000
24	C	25	GLN	0	-0.057	-0.050	27.428	-0.012	-0.012	0.000	0.000	0.000	0.000
25	C	26	ASN	0	0.028	0.015	29.700	-0.020	-0.020	0.000	0.000	0.000	0.000
26	C	27	GLN	0	-0.045	-0.034	27.890	0.000	0.000	0.000	0.000	0.000	0.000
27	C	28	ALA	0	-0.020	-0.005	31.698	-0.002	-0.002	0.000	0.000	0.000	0.000
28	C	29	THR	0	0.047	0.025	33.582	-0.006	-0.006	0.000	0.000	0.000	0.000
29	C	30	GLN	0	-0.079	-0.039	35.094	-0.006	-0.006	0.000	0.000	0.000	0.000
30	C	31	ALA	0	0.006	0.009	36.061	-0.003	-0.003	0.000	0.000	0.000	0.000
31	C	32	GLU	-1	-0.936	-0.968	37.748	0.071	0.071	0.000	0.000	0.000	0.000
32	C	33	LEU	0	-0.014	-0.019	39.537	-0.006	-0.006	0.000	0.000	0.000	0.000
33	C	34	ASP	-1	-0.879	-0.929	39.574	0.115	0.115	0.000	0.000	0.000	0.000
34	C	35	GLN	0	0.049	0.021	42.038	-0.006	-0.006	0.000	0.000	0.000	0.000
35	C	36	LEU	0	0.006	0.009	43.866	-0.005	-0.005	0.000	0.000	0.000	0.000
36	C	37	LYS	1	0.907	0.950	42.255	-0.104	-0.104	0.000	0.000	0.000	0.000
37	C	38	GLU	-1	-0.940	-0.964	44.745	0.095	0.095	0.000	0.000	0.000	0.000
38	C	39	GLN	0	-0.021	-0.015	46.652	-0.005	-0.005	0.000	0.000	0.000	0.000
39	C	40	THR	0	-0.012	-0.010	49.463	-0.006	-0.006	0.000	0.000	0.000	0.000
40	C	41	GLN	0	-0.018	-0.009	50.027	-0.002	-0.002	0.000	0.000	0.000	0.000
41	C	42	MET	0	0.006	0.017	51.840	-0.002	-0.002	0.000	0.000	0.000	0.000
42	C	43	PHE	0	-0.006	0.000	54.266	-0.003	-0.003	0.000	0.000	0.000	0.000
43	C	44	ILE	0	0.003	-0.015	55.060	-0.003	-0.003	0.000	0.000	0.000	0.000
44	C	45	GLU	-1	-0.906	-0.960	55.530	0.065	0.065	0.000	0.000	0.000	0.000
45	C	46	ALA	0	-0.017	0.005	58.631	-0.002	-0.002	0.000	0.000	0.000	0.000
46	C	47	THR	0	-0.094	-0.049	59.936	-0.002	-0.002	0.000	0.000	0.000	0.000
47	C	48	LYS	1	0.942	0.980	59.860	-0.051	-0.051	0.000	0.000	0.000	0.000
48	C	49	SER	0	-0.027	-0.005	62.392	0.002	0.002	0.000	0.000	0.000	0.000
49	C	50	ARG	1	0.858	0.904	64.959	-0.046	-0.046	0.000	0.000	0.000	0.000
50	C	51	ALA	0	0.028	0.041	66.830	0.000	0.000	0.000	0.000	0.000	0.000
51	C	52	PRO	0	0.000	-0.010	68.783	-0.001	-0.001	0.000	0.000	0.000	0.000
52	C	53	GLN	0	0.028	-0.010	65.215	0.000	0.000	0.000	0.000	0.000	0.000
53	C	54	ALA	0	-0.046	-0.002	65.613	0.001	0.001	0.000	0.000	0.000	0.000
54	C	55	TRP	0	0.098	0.029	59.763	0.000	0.000	0.000	0.000	0.000	0.000
55	C	56	ALA	0	0.031	0.016	62.140	0.000	0.000	0.000	0.000	0.000	0.000
56	C	57	LYS	1	0.929	0.977	54.183	-0.068	-0.068	0.000	0.000	0.000	0.000
57	C	58	LEU	0	0.070	0.028	56.550	0.002	0.002	0.000	0.000	0.000	0.000
58	C	59	GLN	0	0.010	0.034	57.169	0.000	0.000	0.000	0.000	0.000	0.000
59	C	60	ALA	0	-0.021	-0.012	55.769	0.000	0.000	0.000	0.000	0.000	0.000
60	C	61	SER	0	-0.070	-0.048	52.741	0.001	0.001	0.000	0.000	0.000	0.000
61	C	62	LEU	0	-0.010	-0.016	53.339	0.000	0.000	0.000	0.000	0.000	0.000
62	C	63	THR	0	-0.058	-0.008	54.051	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:2:ASN)