FMO DATABASE

FMODB ID: 3J9YL

Calculation Name: 3I3U-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3I3U

Chain ID: D

ChEMBL ID:

UniProt ID: F9UPN6

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	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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-720062.198872
FMO2-HF: Nuclear repulsion	681112.946088
FMO2-HF: Total energy	-38949.252784
FMO2-MP2: Total energy	-39064.357615

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(D:2:ASN)

Summations of interaction energy for fragment #1(D: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.
-22.993	-19.048	6.136	-3.595	-6.487	0.027

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / 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	D	4	LYS	1	0.976	0.980	3.756	-1.888	-0.809	0.006	-0.382	-0.702	0.000
4	D	5	LYS	1	0.942	0.976	2.114	-20.624	-19.026	5.549	-2.774	-4.373	0.031
5	D	6	ILE	0	0.061	0.026	2.707	-0.588	0.557	0.582	-0.431	-1.297	-0.004
6	D	7	GLU	-1	-0.901	-0.924	4.969	-0.677	-0.554	-0.001	-0.008	-0.115	0.000
7	D	8	LEU	0	-0.035	-0.023	7.162	0.447	0.447	0.000	0.000	0.000	0.000
8	D	9	LEU	0	-0.037	-0.036	5.485	0.210	0.210	0.000	0.000	0.000	0.000
9	D	10	THR	0	0.016	0.000	8.570	0.108	0.108	0.000	0.000	0.000	0.000
10	D	11	THR	0	0.043	0.019	10.723	0.192	0.192	0.000	0.000	0.000	0.000
11	D	12	TYR	0	-0.047	-0.004	12.076	0.130	0.130	0.000	0.000	0.000	0.000
12	D	13	LEU	0	0.007	-0.018	11.467	0.084	0.084	0.000	0.000	0.000	0.000
13	D	14	SER	0	-0.080	-0.024	14.707	0.046	0.046	0.000	0.000	0.000	0.000
14	D	15	LEU	0	0.008	0.006	16.747	0.057	0.057	0.000	0.000	0.000	0.000
15	D	16	TYR	0	-0.055	-0.024	17.085	0.076	0.076	0.000	0.000	0.000	0.000
16	D	17	ILE	0	0.012	0.019	20.176	-0.055	-0.055	0.000	0.000	0.000	0.000
17	D	18	ASP	-1	-0.911	-0.972	22.746	-0.313	-0.313	0.000	0.000	0.000	0.000
18	D	19	HIS	0	0.045	0.008	23.838	0.026	0.026	0.000	0.000	0.000	0.000
19	D	20	HIS	0	0.028	0.019	26.601	0.021	0.021	0.000	0.000	0.000	0.000
20	D	21	THR	0	0.014	-0.004	25.177	0.008	0.008	0.000	0.000	0.000	0.000
21	D	22	VAL	0	0.017	0.020	27.572	0.012	0.012	0.000	0.000	0.000	0.000
22	D	23	LEU	0	-0.020	-0.026	30.130	0.013	0.013	0.000	0.000	0.000	0.000
23	D	24	ALA	0	-0.041	-0.008	31.180	0.009	0.009	0.000	0.000	0.000	0.000
24	D	25	ASP	-1	-0.804	-0.925	32.268	-0.183	-0.183	0.000	0.000	0.000	0.000
25	D	26	MET	0	-0.003	0.026	33.506	0.014	0.014	0.000	0.000	0.000	0.000
26	D	27	GLN	0	-0.035	-0.006	36.474	0.020	0.020	0.000	0.000	0.000	0.000
27	D	28	ASN	0	-0.090	-0.070	38.829	0.006	0.006	0.000	0.000	0.000	0.000
28	D	29	ALA	0	-0.008	0.009	39.029	0.003	0.003	0.000	0.000	0.000	0.000
29	D	30	THR	0	-0.087	-0.058	35.950	-0.007	-0.007	0.000	0.000	0.000	0.000
30	D	31	GLY	0	0.030	0.013	37.477	0.010	0.010	0.000	0.000	0.000	0.000
31	D	32	LYS	1	0.851	0.948	32.438	0.231	0.231	0.000	0.000	0.000	0.000
32	D	33	TYR	0	0.042	0.017	27.478	-0.004	-0.004	0.000	0.000	0.000	0.000
33	D	34	VAL	0	-0.032	-0.007	32.691	0.012	0.012	0.000	0.000	0.000	0.000
34	D	35	VAL	0	-0.008	-0.011	31.594	0.004	0.004	0.000	0.000	0.000	0.000
35	D	36	LEU	0	0.002	-0.005	31.921	0.010	0.010	0.000	0.000	0.000	0.000
36	D	37	ASP	-1	-0.816	-0.878	32.084	-0.016	-0.016	0.000	0.000	0.000	0.000
37	D	38	VAL	0	0.035	0.019	29.505	0.006	0.006	0.000	0.000	0.000	0.000
38	D	39	ARG	1	0.863	0.935	32.269	0.021	0.021	0.000	0.000	0.000	0.000
39	D	40	ASN	0	0.002	-0.028	33.615	-0.011	-0.011	0.000	0.000	0.000	0.000
40	D	41	ALA	0	-0.020	-0.004	35.843	0.001	0.001	0.000	0.000	0.000	0.000
41	D	42	PRO	0	0.027	0.004	37.719	-0.007	-0.007	0.000	0.000	0.000	0.000
42	D	43	ALA	0	0.022	0.019	40.825	-0.001	-0.001	0.000	0.000	0.000	0.000
43	D	44	GLN	0	0.045	0.040	40.020	0.005	0.005	0.000	0.000	0.000	0.000
44	D	45	VAL	0	-0.014	-0.006	42.624	-0.005	-0.005	0.000	0.000	0.000	0.000
45	D	46	LYS	1	0.869	0.922	43.726	0.035	0.035	0.000	0.000	0.000	0.000
46	D	47	LYS	1	0.852	0.937	37.210	0.031	0.031	0.000	0.000	0.000	0.000
47	D	48	ASP	-1	-0.846	-0.940	40.649	-0.055	-0.055	0.000	0.000	0.000	0.000
48	D	49	GLN	0	-0.015	-0.019	36.780	0.004	0.004	0.000	0.000	0.000	0.000
49	D	50	ILE	0	0.096	0.062	31.467	-0.003	-0.003	0.000	0.000	0.000	0.000
50	D	51	LYS	1	0.863	0.929	35.951	0.065	0.065	0.000	0.000	0.000	0.000
51	D	52	GLY	0	0.001	-0.005	37.189	-0.006	-0.006	0.000	0.000	0.000	0.000
52	D	53	ALA	0	-0.017	0.008	35.332	-0.003	-0.003	0.000	0.000	0.000	0.000
53	D	54	ILE	0	0.031	0.013	36.685	0.011	0.011	0.000	0.000	0.000	0.000
54	D	55	ALA	0	-0.047	-0.031	36.645	0.001	0.001	0.000	0.000	0.000	0.000
55	D	56	MET	0	-0.005	-0.001	34.927	0.003	0.003	0.000	0.000	0.000	0.000
56	D	57	PRO	0	-0.004	0.005	34.713	0.002	0.002	0.000	0.000	0.000	0.000
57	D	58	ALA	0	0.075	0.042	31.346	-0.002	-0.002	0.000	0.000	0.000	0.000
58	D	59	LYS	1	0.815	0.918	33.278	-0.032	-0.032	0.000	0.000	0.000	0.000
59	D	60	ASP	-1	-0.889	-0.956	35.720	0.019	0.019	0.000	0.000	0.000	0.000
60	D	61	LEU	0	0.008	0.014	31.295	-0.005	-0.005	0.000	0.000	0.000	0.000
61	D	62	ALA	0	-0.016	-0.013	34.416	-0.007	-0.007	0.000	0.000	0.000	0.000
62	D	63	THR	0	-0.050	-0.024	35.879	-0.001	-0.001	0.000	0.000	0.000	0.000
63	D	64	ARG	1	0.881	0.952	38.415	0.019	0.019	0.000	0.000	0.000	0.000
64	D	65	ILE	0	0.035	0.026	34.374	-0.007	-0.007	0.000	0.000	0.000	0.000
65	D	66	GLY	0	-0.030	-0.016	37.385	-0.008	-0.008	0.000	0.000	0.000	0.000
66	D	67	GLU	-1	-0.908	-0.958	39.886	-0.042	-0.042	0.000	0.000	0.000	0.000
67	D	68	LEU	0	-0.074	-0.029	33.862	-0.005	-0.005	0.000	0.000	0.000	0.000
68	D	69	ASP	-1	-0.864	-0.935	37.419	-0.116	-0.116	0.000	0.000	0.000	0.000
69	D	70	PRO	0	0.019	-0.019	34.675	-0.009	-0.009	0.000	0.000	0.000	0.000
70	D	71	ALA	0	-0.035	-0.002	33.837	-0.012	-0.012	0.000	0.000	0.000	0.000
71	D	72	LYS	1	0.856	0.947	34.350	0.099	0.099	0.000	0.000	0.000	0.000
72	D	73	THR	0	0.023	0.015	28.006	0.003	0.003	0.000	0.000	0.000	0.000
73	D	74	TYR	0	-0.013	-0.012	29.896	0.009	0.009	0.000	0.000	0.000	0.000
74	D	75	VAL	0	0.021	0.015	26.867	-0.014	-0.014	0.000	0.000	0.000	0.000
75	D	76	VAL	0	-0.010	0.000	26.233	0.018	0.018	0.000	0.000	0.000	0.000
76	D	77	TYR	0	0.021	0.005	26.783	-0.007	-0.007	0.000	0.000	0.000	0.000
77	D	78	ASP	-1	-0.811	-0.917	27.809	0.046	0.046	0.000	0.000	0.000	0.000
78	D	79	TRP	0	-0.047	-0.034	28.983	-0.018	-0.018	0.000	0.000	0.000	0.000
79	D	80	THR	0	0.045	0.022	23.311	0.031	0.031	0.000	0.000	0.000	0.000
80	D	81	GLY	0	0.006	0.006	22.882	-0.010	-0.010	0.000	0.000	0.000	0.000
81	D	82	GLY	0	-0.021	-0.022	20.656	0.039	0.039	0.000	0.000	0.000	0.000
82	D	83	THR	0	-0.029	-0.010	21.307	0.015	0.015	0.000	0.000	0.000	0.000
83	D	84	THR	0	0.064	0.013	23.974	-0.023	-0.023	0.000	0.000	0.000	0.000
84	D	85	LEU	0	-0.001	0.017	25.218	-0.014	-0.014	0.000	0.000	0.000	0.000
85	D	86	GLY	0	0.038	0.038	25.921	-0.013	-0.013	0.000	0.000	0.000	0.000
86	D	87	LYS	1	0.930	0.961	19.274	-0.041	-0.041	0.000	0.000	0.000	0.000
87	D	88	THR	0	-0.050	-0.028	23.904	-0.006	-0.006	0.000	0.000	0.000	0.000
88	D	89	ALA	0	0.028	0.002	26.785	-0.010	-0.010	0.000	0.000	0.000	0.000
89	D	90	LEU	0	0.009	0.016	21.742	-0.008	-0.008	0.000	0.000	0.000	0.000
90	D	91	LEU	0	0.000	-0.006	23.528	-0.014	-0.014	0.000	0.000	0.000	0.000
91	D	92	VAL	0	-0.040	-0.017	25.491	-0.008	-0.008	0.000	0.000	0.000	0.000
92	D	93	LEU	0	-0.008	-0.015	28.061	-0.008	-0.008	0.000	0.000	0.000	0.000
93	D	94	LEU	0	0.017	0.000	22.331	-0.006	-0.006	0.000	0.000	0.000	0.000
94	D	95	SER	0	-0.072	-0.030	26.541	-0.004	-0.004	0.000	0.000	0.000	0.000
95	D	96	ALA	0	-0.052	-0.027	28.035	0.001	0.001	0.000	0.000	0.000	0.000
96	D	97	GLY	0	-0.007	0.008	29.443	0.001	0.001	0.000	0.000	0.000	0.000
97	D	98	PHE	0	-0.043	-0.015	30.045	-0.012	-0.012	0.000	0.000	0.000	0.000
98	D	99	GLU	-1	-0.828	-0.892	25.880	-0.297	-0.297	0.000	0.000	0.000	0.000
99	D	100	ALA	0	-0.042	-0.039	26.091	0.007	0.007	0.000	0.000	0.000	0.000
100	D	101	TYR	0	-0.006	0.000	21.430	-0.028	-0.028	0.000	0.000	0.000	0.000
101	D	102	GLU	-1	-0.870	-0.952	21.995	-0.005	-0.005	0.000	0.000	0.000	0.000
102	D	103	LEU	0	-0.037	-0.033	23.186	-0.033	-0.033	0.000	0.000	0.000	0.000
103	D	104	ALA	0	-0.032	-0.011	21.223	0.037	0.037	0.000	0.000	0.000	0.000

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