FMO DATABASE

FMODB ID: 6NY6Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-272055.718777
FMO2-HF: Nuclear repulsion	247803.636345
FMO2-HF: Total energy	-24252.082432
FMO2-MP2: Total energy	-24323.771774

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.
-2.999	0.802	0.929	-1.457	-3.273	0.003

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 : 0.049 / q_NPA : 0.009

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	0.035	0.024	3.682	-3.269	-1.724	0.003	-0.624	-0.924	0.002
4	C	5	VAL	0	0.011	-0.001	2.403	-1.513	-0.369	0.807	-0.460	-1.491	-0.001
5	C	6	VAL	0	0.016	0.007	3.312	-1.006	0.106	0.119	-0.373	-0.858	0.002
6	C	7	LEU	0	0.013	0.018	5.724	-0.140	-0.140	0.000	0.000	0.000	0.000
7	C	8	HIS	0	0.020	0.003	7.652	-0.013	-0.013	0.000	0.000	0.000	0.000
8	C	9	LYS	1	0.930	0.959	5.174	3.358	3.358	0.000	0.000	0.000	0.000
9	C	10	SER	0	-0.043	-0.023	9.389	0.038	0.038	0.000	0.000	0.000	0.000
10	C	11	GLY	0	0.052	0.034	11.333	0.034	0.034	0.000	0.000	0.000	0.000
11	C	12	LEU	0	0.030	0.006	11.868	0.037	0.037	0.000	0.000	0.000	0.000
12	C	13	LEU	0	-0.017	0.015	9.982	0.086	0.086	0.000	0.000	0.000	0.000
13	C	14	GLU	-1	-0.816	-0.899	12.839	0.024	0.024	0.000	0.000	0.000	0.000
14	C	15	ILE	0	0.068	0.026	16.000	0.020	0.020	0.000	0.000	0.000	0.000
15	C	16	THR	0	-0.026	-0.016	15.000	0.030	0.030	0.000	0.000	0.000	0.000
16	C	17	LEU	0	-0.050	-0.029	14.595	0.006	0.006	0.000	0.000	0.000	0.000
17	C	18	LYS	1	0.853	0.916	17.998	-0.060	-0.060	0.000	0.000	0.000	0.000
18	C	19	THR	0	0.008	-0.001	20.500	-0.017	-0.017	0.000	0.000	0.000	0.000
19	C	20	LYS	1	0.923	0.957	17.253	-0.554	-0.554	0.000	0.000	0.000	0.000
20	C	21	GLU	-1	-0.752	-0.816	21.780	0.167	0.167	0.000	0.000	0.000	0.000
21	C	22	LEU	0	0.014	0.017	24.001	-0.014	-0.014	0.000	0.000	0.000	0.000
22	C	23	ILE	0	-0.002	-0.009	23.346	-0.008	-0.008	0.000	0.000	0.000	0.000
23	C	24	ARG	1	0.824	0.880	25.592	-0.189	-0.189	0.000	0.000	0.000	0.000
24	C	25	GLN	0	-0.054	-0.047	27.426	-0.017	-0.017	0.000	0.000	0.000	0.000
25	C	26	ASN	0	0.012	0.009	29.696	-0.020	-0.020	0.000	0.000	0.000	0.000
26	C	27	GLN	0	-0.033	-0.029	27.872	-0.004	-0.004	0.000	0.000	0.000	0.000
27	C	28	ALA	0	-0.021	-0.008	31.694	-0.006	-0.006	0.000	0.000	0.000	0.000
28	C	29	THR	0	0.049	0.029	33.580	-0.007	-0.007	0.000	0.000	0.000	0.000
29	C	30	GLN	0	-0.093	-0.051	35.091	-0.008	-0.008	0.000	0.000	0.000	0.000
30	C	31	ALA	0	0.003	0.002	36.058	-0.005	-0.005	0.000	0.000	0.000	0.000
31	C	32	GLU	-1	-0.915	-0.958	37.479	0.102	0.102	0.000	0.000	0.000	0.000
32	C	33	LEU	0	-0.015	-0.018	39.142	-0.008	-0.008	0.000	0.000	0.000	0.000
33	C	34	ASP	-1	-0.830	-0.887	39.614	0.138	0.138	0.000	0.000	0.000	0.000
34	C	35	GLN	0	0.044	0.024	42.034	-0.008	-0.008	0.000	0.000	0.000	0.000
35	C	36	LEU	0	0.020	0.011	43.863	-0.006	-0.006	0.000	0.000	0.000	0.000
36	C	37	LYS	1	0.857	0.918	42.106	-0.132	-0.132	0.000	0.000	0.000	0.000
37	C	38	GLU	-1	-0.931	-0.957	45.183	0.109	0.109	0.000	0.000	0.000	0.000
38	C	39	GLN	0	-0.025	-0.019	46.912	-0.006	-0.006	0.000	0.000	0.000	0.000
39	C	40	THR	0	-0.019	-0.020	49.360	-0.006	-0.006	0.000	0.000	0.000	0.000
40	C	41	GLN	0	-0.029	-0.011	49.874	-0.001	-0.001	0.000	0.000	0.000	0.000
41	C	42	MET	0	-0.002	0.017	52.009	-0.003	-0.003	0.000	0.000	0.000	0.000
42	C	43	PHE	0	0.010	0.006	54.259	-0.004	-0.004	0.000	0.000	0.000	0.000
43	C	44	ILE	0	0.011	-0.013	55.363	-0.003	-0.003	0.000	0.000	0.000	0.000
44	C	45	GLU	-1	-0.834	-0.917	55.119	0.077	0.077	0.000	0.000	0.000	0.000
45	C	46	ALA	0	0.002	0.013	58.627	-0.002	-0.002	0.000	0.000	0.000	0.000
46	C	47	THR	0	-0.084	-0.039	60.233	-0.003	-0.003	0.000	0.000	0.000	0.000
47	C	48	LYS	1	0.922	0.970	59.785	-0.064	-0.064	0.000	0.000	0.000	0.000
48	C	49	SER	0	-0.030	-0.008	62.402	0.001	0.001	0.000	0.000	0.000	0.000
49	C	50	ARG	1	0.865	0.908	64.952	-0.055	-0.055	0.000	0.000	0.000	0.000
50	C	51	ALA	0	0.023	0.040	66.816	0.000	0.000	0.000	0.000	0.000	0.000
51	C	52	PRO	0	0.014	-0.003	68.771	-0.001	-0.001	0.000	0.000	0.000	0.000
52	C	53	GLN	0	0.023	-0.013	64.938	0.000	0.000	0.000	0.000	0.000	0.000
53	C	54	ALA	0	-0.049	-0.003	65.616	0.001	0.001	0.000	0.000	0.000	0.000
54	C	55	TRP	0	0.102	0.029	59.902	0.000	0.000	0.000	0.000	0.000	0.000
55	C	56	ALA	0	0.018	0.008	62.133	0.000	0.000	0.000	0.000	0.000	0.000
56	C	57	LYS	1	0.834	0.913	54.975	-0.077	-0.077	0.000	0.000	0.000	0.000
57	C	58	LEU	0	0.064	0.031	56.679	0.002	0.002	0.000	0.000	0.000	0.000
58	C	59	GLN	0	0.010	0.014	57.162	0.000	0.000	0.000	0.000	0.000	0.000
59	C	60	ALA	0	-0.012	0.008	55.800	0.000	0.000	0.000	0.000	0.000	0.000
60	C	61	SER	0	-0.037	-0.020	52.919	0.002	0.002	0.000	0.000	0.000	0.000
61	C	62	LEU	0	-0.036	-0.025	53.333	0.000	0.000	0.000	0.000	0.000	0.000
62	C	63	THR	0	-0.058	-0.021	54.045	-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)