FMO DATABASE

FMODB ID: V5VV1

Calculation Name: 5JK7-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5JK7

Chain ID: F

ChEMBL ID:

UniProt ID: Q9Y4B6

Base Structure: X-ray

Registration Date: 2023-06-22

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	74
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-454724.619856
FMO2-HF: Nuclear repulsion	424014.556445
FMO2-HF: Total energy	-30710.06341
FMO2-MP2: Total energy	-30801.426697

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(F:1:MET)

Summations of interaction energy for fragment #1(F: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.
8.887	0.765	0.812	7.981	-0.671	0.002

Interaction energy analysis for fragmet #1(F:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.048 / q_NPA : -0.023

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	F	3	GLN	0	-0.041	-0.008	2.593	9.209	1.087	0.812	7.981	-0.671	0.002
4	F	4	ALA	0	-0.023	0.003	6.327	0.058	0.058	0.000	0.000	0.000	0.000
5	F	5	PRO	0	-0.022	-0.020	9.858	-0.022	-0.022	0.000	0.000	0.000	0.000
6	F	6	GLU	-1	-0.932	-0.967	12.421	-0.167	-0.167	0.000	0.000	0.000	0.000
7	F	7	ASP	-1	-0.932	-0.958	15.388	-0.155	-0.155	0.000	0.000	0.000	0.000
8	F	8	GLN	0	-0.106	-0.038	18.705	0.032	0.032	0.000	0.000	0.000	0.000
9	F	9	GLY	0	-0.007	-0.031	20.782	0.000	0.000	0.000	0.000	0.000	0.000
10	F	10	PRO	0	-0.018	-0.001	23.108	-0.002	-0.002	0.000	0.000	0.000	0.000
11	F	11	GLN	0	0.020	-0.003	23.701	-0.010	-0.010	0.000	0.000	0.000	0.000
12	F	12	ARG	1	0.902	0.951	24.433	0.110	0.110	0.000	0.000	0.000	0.000
13	F	13	GLU	-1	-0.850	-0.909	28.201	-0.085	-0.085	0.000	0.000	0.000	0.000
14	F	14	PRO	0	0.032	0.016	31.328	0.001	0.001	0.000	0.000	0.000	0.000
15	F	15	TYR	0	-0.076	-0.076	29.820	0.001	0.001	0.000	0.000	0.000	0.000
16	F	16	ASN	0	-0.064	-0.021	34.388	-0.001	-0.001	0.000	0.000	0.000	0.000
17	F	17	GLU	-1	-0.852	-0.964	37.117	-0.036	-0.036	0.000	0.000	0.000	0.000
18	F	18	TRP	0	-0.042	0.040	30.558	0.000	0.000	0.000	0.000	0.000	0.000
19	F	19	THR	0	-0.037	-0.054	34.325	0.001	0.001	0.000	0.000	0.000	0.000
20	F	20	LEU	0	-0.043	-0.016	36.089	0.002	0.002	0.000	0.000	0.000	0.000
21	F	21	GLU	-1	-0.936	-0.967	38.128	-0.033	-0.033	0.000	0.000	0.000	0.000
22	F	22	LEU	0	0.027	0.026	33.128	0.002	0.002	0.000	0.000	0.000	0.000
23	F	23	LEU	0	-0.054	0.002	37.482	0.001	0.001	0.000	0.000	0.000	0.000
24	F	24	GLU	-1	-0.717	-0.910	39.656	-0.027	-0.027	0.000	0.000	0.000	0.000
25	F	25	GLU	-1	-0.941	-0.925	36.220	-0.031	-0.031	0.000	0.000	0.000	0.000
26	F	26	LEU	0	-0.030	-0.019	35.810	0.003	0.003	0.000	0.000	0.000	0.000
27	F	27	LYS	1	0.833	0.898	38.809	0.030	0.030	0.000	0.000	0.000	0.000
28	F	28	SER	0	-0.060	-0.029	42.341	0.002	0.002	0.000	0.000	0.000	0.000
29	F	29	GLU	-1	-0.766	-0.859	38.569	-0.016	-0.016	0.000	0.000	0.000	0.000
30	F	30	ALA	0	0.023	0.010	40.840	0.001	0.001	0.000	0.000	0.000	0.000
31	F	31	VAL	0	-0.086	-0.057	42.222	0.001	0.001	0.000	0.000	0.000	0.000
32	F	32	ARG	1	0.875	0.940	41.758	0.019	0.019	0.000	0.000	0.000	0.000
33	F	33	HIS	1	0.777	0.887	41.113	0.016	0.016	0.000	0.000	0.000	0.000
34	F	34	PHE	0	0.012	0.009	40.296	0.001	0.001	0.000	0.000	0.000	0.000
35	F	35	PRO	0	0.031	0.014	45.994	0.000	0.000	0.000	0.000	0.000	0.000
36	F	36	ARG	1	0.992	0.976	48.854	0.016	0.016	0.000	0.000	0.000	0.000
37	F	37	ILE	0	0.021	0.024	49.872	-0.001	-0.001	0.000	0.000	0.000	0.000
38	F	38	TRP	0	0.026	0.009	42.643	-0.001	-0.001	0.000	0.000	0.000	0.000
39	F	39	LEU	0	-0.011	-0.023	43.457	-0.001	-0.001	0.000	0.000	0.000	0.000
40	F	40	HIS	0	0.002	0.032	46.033	-0.002	-0.002	0.000	0.000	0.000	0.000
41	F	41	ASN	0	-0.006	0.001	48.327	-0.001	-0.001	0.000	0.000	0.000	0.000
42	F	42	LEU	0	0.018	0.004	42.494	0.000	0.000	0.000	0.000	0.000	0.000
43	F	43	GLY	0	-0.085	-0.014	44.683	-0.001	-0.001	0.000	0.000	0.000	0.000
44	F	44	GLN	0	0.086	0.005	45.770	0.000	0.000	0.000	0.000	0.000	0.000
45	F	45	HIS	0	-0.028	0.007	44.920	-0.001	-0.001	0.000	0.000	0.000	0.000
46	F	46	ILE	0	-0.027	0.004	39.864	-0.001	-0.001	0.000	0.000	0.000	0.000
47	F	47	TYR	0	-0.032	-0.056	43.331	-0.001	-0.001	0.000	0.000	0.000	0.000
48	F	48	GLU	-1	-0.926	-0.971	45.864	-0.026	-0.026	0.000	0.000	0.000	0.000
49	F	49	THR	0	-0.104	-0.066	42.994	-0.001	-0.001	0.000	0.000	0.000	0.000
50	F	50	TYR	0	-0.052	-0.011	37.099	-0.003	-0.003	0.000	0.000	0.000	0.000
51	F	51	GLY	0	0.044	0.039	42.477	-0.002	-0.002	0.000	0.000	0.000	0.000
52	F	52	ASP	-1	-0.897	-0.916	43.499	-0.034	-0.034	0.000	0.000	0.000	0.000
53	F	53	THR	0	-0.051	-0.035	40.266	-0.002	-0.002	0.000	0.000	0.000	0.000
54	F	54	TRP	0	0.066	0.011	37.028	0.000	0.000	0.000	0.000	0.000	0.000
55	F	55	ALA	0	0.079	0.035	35.703	0.000	0.000	0.000	0.000	0.000	0.000
56	F	56	GLY	0	-0.016	-0.028	36.517	0.000	0.000	0.000	0.000	0.000	0.000
57	F	57	VAL	0	0.018	0.027	37.467	0.003	0.003	0.000	0.000	0.000	0.000
58	F	58	GLU	-1	-0.874	-0.943	32.617	-0.061	-0.061	0.000	0.000	0.000	0.000
59	F	59	ALA	0	-0.004	0.025	34.097	-0.001	-0.001	0.000	0.000	0.000	0.000
60	F	60	ILE	0	0.021	0.000	36.430	0.002	0.002	0.000	0.000	0.000	0.000
61	F	61	ILE	0	0.003	-0.002	33.513	0.002	0.002	0.000	0.000	0.000	0.000
62	F	62	ARG	1	0.966	0.977	27.581	0.061	0.061	0.000	0.000	0.000	0.000
63	F	63	ILE	0	0.018	0.005	33.888	0.002	0.002	0.000	0.000	0.000	0.000
64	F	64	LEU	0	-0.016	-0.008	36.921	0.003	0.003	0.000	0.000	0.000	0.000
65	F	65	GLN	0	0.022	-0.002	31.585	0.005	0.005	0.000	0.000	0.000	0.000
66	F	66	GLN	0	-0.015	0.006	31.859	-0.001	-0.001	0.000	0.000	0.000	0.000
67	F	67	LEU	0	-0.006	0.012	34.083	0.003	0.003	0.000	0.000	0.000	0.000
68	F	68	LEU	0	0.017	0.009	35.953	0.003	0.003	0.000	0.000	0.000	0.000
69	F	69	PHE	0	0.005	0.014	28.787	0.002	0.002	0.000	0.000	0.000	0.000
70	F	70	ILE	0	0.000	-0.007	33.733	0.003	0.003	0.000	0.000	0.000	0.000
71	F	71	HIS	0	-0.023	-0.028	35.659	0.002	0.002	0.000	0.000	0.000	0.000
72	F	72	PHE	0	-0.019	-0.014	30.835	0.002	0.002	0.000	0.000	0.000	0.000
73	F	73	ARG	1	0.902	0.958	27.322	0.011	0.011	0.000	0.000	0.000	0.000
74	F	74	ILE	0	-0.049	0.002	34.668	0.003	0.003	0.000	0.000	0.000	0.000

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