FMO DATABASE

FMODB ID: 4JK4N

Calculation Name: 2II7-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2II7

Chain ID: F

ChEMBL ID:

UniProt ID: Q8YSC3

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	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	91
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-622882.036726
FMO2-HF: Nuclear repulsion	587497.208896
FMO2-HF: Total energy	-35384.82783
FMO2-MP2: Total energy	-35488.970816

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:2:LEU)

Summations of interaction energy for fragment #1(F:2:LEU)

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.
-6.218	-4.012	4.324	-2.444	-4.085	-0.02

Interaction energy analysis for fragmet #1(F:2:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.010

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	4	ILE	0	0.012	0.000	3.827	1.168	2.859	-0.025	-0.825	-0.841	0.002
4	F	5	GLY	0	0.002	0.006	6.916	-0.465	-0.465	0.000	0.000	0.000	0.000
5	F	6	ARG	1	0.900	0.952	10.193	-0.078	-0.078	0.000	0.000	0.000	0.000
6	F	7	THR	0	0.025	0.014	11.625	-0.069	-0.069	0.000	0.000	0.000	0.000
7	F	8	CYS	0	0.006	0.017	13.798	-0.061	-0.061	0.000	0.000	0.000	0.000
8	F	9	TRP	0	-0.042	-0.020	13.589	0.091	0.091	0.000	0.000	0.000	0.000
9	F	10	ALA	0	0.030	0.016	19.366	-0.025	-0.025	0.000	0.000	0.000	0.000
10	F	11	ILE	0	-0.063	-0.023	22.447	0.016	0.016	0.000	0.000	0.000	0.000
11	F	12	ALA	0	-0.008	-0.020	25.353	-0.008	-0.008	0.000	0.000	0.000	0.000
12	F	13	GLU	-1	-0.890	-0.923	28.459	0.009	0.009	0.000	0.000	0.000	0.000
13	F	14	GLY	0	0.015	-0.022	28.951	-0.005	-0.005	0.000	0.000	0.000	0.000
14	F	15	TYR	0	0.043	-0.001	31.216	0.000	0.000	0.000	0.000	0.000	0.000
15	F	16	ILE	0	-0.036	-0.001	32.083	-0.005	-0.005	0.000	0.000	0.000	0.000
16	F	17	PRO	0	0.006	0.004	35.086	0.001	0.001	0.000	0.000	0.000	0.000
17	F	18	PRO	0	-0.036	-0.005	38.460	-0.006	-0.006	0.000	0.000	0.000	0.000
18	F	31	GLU	-1	-0.869	-0.916	28.712	-0.024	-0.024	0.000	0.000	0.000	0.000
19	F	32	THR	0	-0.079	-0.057	23.006	-0.016	-0.016	0.000	0.000	0.000	0.000
20	F	33	VAL	0	0.031	0.031	20.101	0.017	0.017	0.000	0.000	0.000	0.000
21	F	34	CYS	0	-0.045	-0.023	18.883	-0.035	-0.035	0.000	0.000	0.000	0.000
22	F	35	ILE	0	0.043	0.021	14.063	0.026	0.026	0.000	0.000	0.000	0.000
23	F	36	LEU	0	-0.015	-0.006	9.967	-0.039	-0.039	0.000	0.000	0.000	0.000
24	F	37	ASN	0	0.010	0.011	7.858	-0.256	-0.256	0.000	0.000	0.000	0.000
25	F	38	ALA	0	-0.038	-0.033	5.925	-0.058	-0.058	0.000	0.000	0.000	0.000
26	F	39	GLY	0	0.046	0.032	3.657	-1.233	-1.001	0.003	-0.059	-0.176	0.000
27	F	40	ASP	-1	-0.894	-0.974	2.391	-7.521	-7.415	4.348	-1.550	-2.904	-0.022
28	F	41	GLU	-1	-0.944	-0.976	4.702	-0.479	-0.405	-0.001	-0.006	-0.066	0.000
29	F	42	ASP	-1	-0.894	-0.944	8.160	-0.955	-0.955	0.000	0.000	0.000	0.000
30	F	43	ALA	0	-0.013	-0.013	11.079	0.040	0.040	0.000	0.000	0.000	0.000
31	F	44	HIS	0	-0.003	-0.017	12.735	0.056	0.056	0.000	0.000	0.000	0.000
32	F	45	VAL	0	-0.032	-0.021	15.859	0.036	0.036	0.000	0.000	0.000	0.000
33	F	46	GLU	-1	-0.934	-0.971	17.907	-0.153	-0.153	0.000	0.000	0.000	0.000
34	F	47	ILE	0	-0.014	-0.014	21.325	0.022	0.022	0.000	0.000	0.000	0.000
35	F	48	THR	0	-0.016	0.007	23.576	-0.001	-0.001	0.000	0.000	0.000	0.000
36	F	49	ILE	0	-0.010	0.003	26.738	0.009	0.009	0.000	0.000	0.000	0.000
37	F	50	TYR	0	-0.011	-0.027	27.087	0.001	0.001	0.000	0.000	0.000	0.000
38	F	51	TYR	0	0.042	0.004	31.827	-0.002	-0.002	0.000	0.000	0.000	0.000
39	F	52	SER	0	0.030	0.012	35.401	0.003	0.003	0.000	0.000	0.000	0.000
40	F	53	ASP	-1	-0.918	-0.960	38.065	-0.008	-0.008	0.000	0.000	0.000	0.000
41	F	54	LYS	1	0.892	0.965	37.818	0.024	0.024	0.000	0.000	0.000	0.000
42	F	55	GLU	-1	-0.942	-0.984	35.844	-0.006	-0.006	0.000	0.000	0.000	0.000
43	F	56	PRO	0	-0.016	-0.013	30.872	-0.004	-0.004	0.000	0.000	0.000	0.000
44	F	57	VAL	0	-0.043	-0.013	31.704	-0.003	-0.003	0.000	0.000	0.000	0.000
45	F	58	GLY	0	-0.002	-0.017	30.030	-0.004	-0.004	0.000	0.000	0.000	0.000
46	F	59	PRO	0	0.008	0.003	25.151	0.000	0.000	0.000	0.000	0.000	0.000
47	F	60	TYR	0	0.018	0.017	25.504	-0.006	-0.006	0.000	0.000	0.000	0.000
48	F	61	ARG	1	0.917	0.953	22.500	0.155	0.155	0.000	0.000	0.000	0.000
49	F	62	LEU	0	0.012	0.016	18.068	0.001	0.001	0.000	0.000	0.000	0.000
50	F	63	THR	0	0.019	0.007	15.226	0.010	0.010	0.000	0.000	0.000	0.000
51	F	64	VAL	0	-0.064	-0.038	12.416	0.034	0.034	0.000	0.000	0.000	0.000
52	F	65	PRO	0	-0.008	-0.007	12.208	-0.101	-0.101	0.000	0.000	0.000	0.000
53	F	66	ALA	0	0.062	0.033	6.869	-0.002	-0.002	0.000	0.000	0.000	0.000
54	F	67	ARG	1	0.826	0.925	4.638	2.459	2.562	-0.001	-0.004	-0.098	0.000
55	F	68	ARG	1	0.892	0.955	7.615	1.081	1.081	0.000	0.000	0.000	0.000
56	F	69	THR	0	0.004	-0.006	11.286	0.000	0.000	0.000	0.000	0.000	0.000
57	F	70	LYS	1	0.914	0.947	13.956	0.328	0.328	0.000	0.000	0.000	0.000
58	F	71	HIS	0	0.023	0.029	17.243	0.004	0.004	0.000	0.000	0.000	0.000
59	F	72	VAL	0	0.015	0.001	20.394	-0.016	-0.016	0.000	0.000	0.000	0.000
60	F	73	ARG	1	0.946	0.986	22.835	0.126	0.126	0.000	0.000	0.000	0.000
61	F	74	PHE	0	0.093	0.025	25.571	-0.009	-0.009	0.000	0.000	0.000	0.000
62	F	75	ASN	0	-0.067	-0.029	28.214	-0.005	-0.005	0.000	0.000	0.000	0.000
63	F	76	ASP	-1	-0.876	-0.945	27.413	-0.126	-0.126	0.000	0.000	0.000	0.000
64	F	77	LEU	0	-0.086	-0.023	25.106	-0.012	-0.012	0.000	0.000	0.000	0.000
65	F	78	ASN	0	-0.033	-0.043	28.859	0.006	0.006	0.000	0.000	0.000	0.000
66	F	79	ASP	-1	-0.907	-0.895	29.270	-0.125	-0.125	0.000	0.000	0.000	0.000
67	F	80	PRO	0	-0.006	-0.027	28.781	-0.007	-0.007	0.000	0.000	0.000	0.000
68	F	81	ALA	0	-0.002	-0.025	32.056	0.004	0.004	0.000	0.000	0.000	0.000
69	F	82	PRO	0	-0.007	0.005	32.534	-0.003	-0.003	0.000	0.000	0.000	0.000
70	F	83	ILE	0	-0.010	0.013	30.148	0.004	0.004	0.000	0.000	0.000	0.000
71	F	84	PRO	0	-0.049	-0.022	34.168	0.000	0.000	0.000	0.000	0.000	0.000
72	F	85	HIS	0	-0.013	-0.018	35.363	0.000	0.000	0.000	0.000	0.000	0.000
73	F	86	ASP	-1	-0.964	-0.989	38.227	-0.015	-0.015	0.000	0.000	0.000	0.000
74	F	87	THR	0	-0.034	-0.018	37.505	0.002	0.002	0.000	0.000	0.000	0.000
75	F	88	ASP	-1	-0.903	-0.936	35.789	-0.003	-0.003	0.000	0.000	0.000	0.000
76	F	89	PHE	0	-0.126	-0.056	29.206	-0.002	-0.002	0.000	0.000	0.000	0.000
77	F	90	ALA	0	0.047	0.043	29.221	0.006	0.006	0.000	0.000	0.000	0.000
78	F	91	SER	0	-0.003	-0.012	25.687	-0.014	-0.014	0.000	0.000	0.000	0.000
79	F	92	VAL	0	0.000	0.005	22.309	0.019	0.019	0.000	0.000	0.000	0.000
80	F	93	ILE	0	-0.018	-0.011	18.007	-0.022	-0.022	0.000	0.000	0.000	0.000
81	F	94	GLN	0	0.005	-0.011	17.846	0.024	0.024	0.000	0.000	0.000	0.000
82	F	95	SER	0	-0.051	-0.071	12.437	-0.075	-0.075	0.000	0.000	0.000	0.000
83	F	96	ASN	0	0.055	0.047	12.481	0.117	0.117	0.000	0.000	0.000	0.000
84	F	97	VAL	0	0.029	0.023	8.499	0.052	0.052	0.000	0.000	0.000	0.000
85	F	98	PRO	0	-0.030	0.017	7.010	0.028	0.028	0.000	0.000	0.000	0.000
86	F	99	ILE	0	0.025	0.030	9.146	-0.303	-0.303	0.000	0.000	0.000	0.000
87	F	100	VAL	0	-0.012	-0.030	10.428	0.213	0.213	0.000	0.000	0.000	0.000
88	F	101	VAL	0	0.000	0.002	13.070	-0.086	-0.086	0.000	0.000	0.000	0.000
89	F	102	GLN	0	0.000	0.004	16.818	0.061	0.061	0.000	0.000	0.000	0.000
90	F	103	HIS	0	0.030	0.025	19.671	-0.022	-0.022	0.000	0.000	0.000	0.000
91	F	104	THR	0	0.006	0.001	23.372	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:2:LEU)