FMO DATABASE

FMODB ID: 1NK6Z

Calculation Name: 3JXO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JXO

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0F6

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	84
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-523784.317211
FMO2-HF: Nuclear repulsion	492293.478265
FMO2-HF: Total energy	-31490.838946
FMO2-MP2: Total energy	-31584.307307

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(A:-7:ASN)

Summations of interaction energy for fragment #1(A:-7: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.
-3.158	-0.135	0.192	-1.199	-2.016	0.009

Interaction energy analysis for fragmet #1(A:-7:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.033

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	A	-5	TYR	0	-0.053	-0.026	2.905	-2.483	0.536	0.193	-1.195	-2.017	0.009
4	A	-4	PHE	0	0.037	0.034	5.445	-0.575	-0.571	-0.001	-0.004	0.001	0.000
5	A	-3	GLN	0	0.035	0.004	8.673	0.636	0.636	0.000	0.000	0.000	0.000
6	A	-2	GLY	0	0.011	0.021	10.831	-0.125	-0.125	0.000	0.000	0.000	0.000
7	A	-1	MET	0	0.048	0.043	14.568	-0.013	-0.013	0.000	0.000	0.000	0.000
8	A	140	ILE	0	-0.041	-0.018	16.143	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	141	PRO	0	0.063	0.034	18.889	-0.008	-0.008	0.000	0.000	0.000	0.000
10	A	142	LEU	0	-0.098	-0.044	19.356	0.007	0.007	0.000	0.000	0.000	0.000
11	A	143	GLU	-1	-0.897	-0.951	23.070	0.116	0.116	0.000	0.000	0.000	0.000
12	A	144	GLN	0	-0.048	-0.031	26.856	0.007	0.007	0.000	0.000	0.000	0.000
13	A	145	GLY	0	0.014	0.012	28.761	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	146	ILE	0	-0.023	-0.008	23.929	0.000	0.000	0.000	0.000	0.000	0.000
15	A	147	GLU	-1	-0.853	-0.927	20.477	0.305	0.305	0.000	0.000	0.000	0.000
16	A	148	PHE	0	-0.027	-0.011	13.880	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	149	LEU	0	0.042	0.006	16.310	0.029	0.029	0.000	0.000	0.000	0.000
18	A	150	SER	0	-0.039	-0.020	12.053	0.071	0.071	0.000	0.000	0.000	0.000
19	A	151	VAL	0	0.027	0.017	14.089	-0.027	-0.027	0.000	0.000	0.000	0.000
20	A	152	ASN	0	-0.017	-0.016	9.544	0.115	0.115	0.000	0.000	0.000	0.000
21	A	153	VAL	0	-0.004	0.006	13.654	-0.091	-0.091	0.000	0.000	0.000	0.000
22	A	154	GLU	-1	-0.875	-0.926	15.273	0.663	0.663	0.000	0.000	0.000	0.000
23	A	155	GLU	-1	-0.973	-1.019	17.534	0.204	0.204	0.000	0.000	0.000	0.000
24	A	156	ASP	-1	-0.971	-0.975	20.341	0.272	0.272	0.000	0.000	0.000	0.000
25	A	157	SER	0	-0.018	0.012	20.061	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	158	PRO	0	0.009	0.002	22.053	-0.021	-0.021	0.000	0.000	0.000	0.000
27	A	159	VAL	0	-0.081	-0.045	21.272	-0.024	-0.024	0.000	0.000	0.000	0.000
28	A	160	VAL	0	0.013	0.008	20.212	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	161	GLY	0	-0.022	-0.015	22.285	-0.025	-0.025	0.000	0.000	0.000	0.000
30	A	162	LYS	1	0.866	0.958	24.219	-0.182	-0.182	0.000	0.000	0.000	0.000
31	A	163	LYS	1	0.948	0.973	24.014	-0.070	-0.070	0.000	0.000	0.000	0.000
32	A	164	LEU	0	0.029	0.013	20.714	0.003	0.003	0.000	0.000	0.000	0.000
33	A	165	LYS	1	0.774	0.879	24.974	-0.078	-0.078	0.000	0.000	0.000	0.000
34	A	166	ASP	-1	-0.898	-0.946	28.193	0.098	0.098	0.000	0.000	0.000	0.000
35	A	167	LEU	0	-0.094	-0.041	23.160	0.000	0.000	0.000	0.000	0.000	0.000
36	A	168	PRO	0	-0.020	0.001	27.767	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	169	LEU	0	0.033	0.006	24.747	0.014	0.014	0.000	0.000	0.000	0.000
38	A	170	PRO	0	0.021	0.025	27.626	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	171	ARG	1	0.847	0.895	29.434	-0.104	-0.104	0.000	0.000	0.000	0.000
40	A	172	ASP	-1	-0.843	-0.893	29.155	0.125	0.125	0.000	0.000	0.000	0.000
41	A	173	SER	0	0.005	-0.014	24.889	0.019	0.019	0.000	0.000	0.000	0.000
42	A	174	ILE	0	0.009	0.011	21.611	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	175	ILE	0	0.024	0.010	18.816	0.031	0.031	0.000	0.000	0.000	0.000
44	A	176	ALA	0	-0.013	-0.004	17.448	-0.031	-0.031	0.000	0.000	0.000	0.000
45	A	177	ALA	0	-0.036	-0.035	13.847	-0.044	-0.044	0.000	0.000	0.000	0.000
46	A	178	ILE	0	0.033	0.024	14.073	0.058	0.058	0.000	0.000	0.000	0.000
47	A	179	VAL	0	-0.039	-0.011	7.358	-0.082	-0.082	0.000	0.000	0.000	0.000
48	A	180	ARG	1	0.836	0.879	10.806	-0.105	-0.105	0.000	0.000	0.000	0.000
49	A	181	GLY	0	0.028	0.011	9.887	-0.136	-0.136	0.000	0.000	0.000	0.000
50	A	182	GLY	0	-0.025	-0.017	6.328	-0.183	-0.183	0.000	0.000	0.000	0.000
51	A	183	VAL	0	-0.014	0.005	7.005	-0.455	-0.455	0.000	0.000	0.000	0.000
52	A	184	LEU	0	-0.020	-0.006	9.935	0.182	0.182	0.000	0.000	0.000	0.000
53	A	185	VAL	0	-0.007	-0.008	11.847	-0.070	-0.070	0.000	0.000	0.000	0.000
54	A	186	VAL	0	-0.013	-0.019	15.277	0.036	0.036	0.000	0.000	0.000	0.000
55	A	187	PRO	0	0.016	0.017	17.396	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	188	ARG	1	0.933	0.962	20.177	-0.062	-0.062	0.000	0.000	0.000	0.000
57	A	189	GLY	0	0.062	0.028	23.734	0.013	0.013	0.000	0.000	0.000	0.000
58	A	190	ASP	-1	-0.837	-0.921	26.478	0.074	0.074	0.000	0.000	0.000	0.000
59	A	191	THR	0	-0.044	-0.021	19.491	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	192	GLU	-1	-0.904	-0.948	22.490	0.112	0.112	0.000	0.000	0.000	0.000
61	A	193	ILE	0	0.014	0.008	18.287	0.011	0.011	0.000	0.000	0.000	0.000
62	A	194	LEU	0	-0.032	-0.018	17.300	-0.039	-0.039	0.000	0.000	0.000	0.000
63	A	195	SER	0	0.067	0.034	16.999	0.041	0.041	0.000	0.000	0.000	0.000
64	A	196	GLY	0	-0.033	-0.019	13.479	-0.034	-0.034	0.000	0.000	0.000	0.000
65	A	197	ASP	-1	-0.785	-0.851	11.929	0.562	0.562	0.000	0.000	0.000	0.000
66	A	198	LYS	1	0.854	0.927	7.265	-2.412	-2.412	0.000	0.000	0.000	0.000
67	A	199	LEU	0	0.008	-0.005	11.914	-0.114	-0.114	0.000	0.000	0.000	0.000
68	A	200	TYR	0	-0.019	-0.010	8.493	0.186	0.186	0.000	0.000	0.000	0.000
69	A	201	VAL	0	0.015	0.002	15.125	-0.076	-0.076	0.000	0.000	0.000	0.000
70	A	202	ILE	0	-0.007	0.004	18.749	0.017	0.017	0.000	0.000	0.000	0.000
71	A	203	VAL	0	-0.015	-0.007	21.371	-0.017	-0.017	0.000	0.000	0.000	0.000
72	A	204	SER	0	0.064	0.035	24.356	0.007	0.007	0.000	0.000	0.000	0.000
73	A	205	ALA	0	-0.017	-0.032	26.850	0.011	0.011	0.000	0.000	0.000	0.000
74	A	206	GLU	-1	-0.971	-0.987	27.943	0.130	0.130	0.000	0.000	0.000	0.000
75	A	207	ALA	0	-0.012	-0.001	27.955	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	208	LYS	1	0.848	0.910	21.997	-0.284	-0.284	0.000	0.000	0.000	0.000
77	A	209	GLU	-1	-0.886	-0.941	24.800	0.208	0.208	0.000	0.000	0.000	0.000
78	A	210	THR	0	0.001	0.000	26.740	0.000	0.000	0.000	0.000	0.000	0.000
79	A	211	VAL	0	-0.016	-0.016	22.357	0.000	0.000	0.000	0.000	0.000	0.000
80	A	212	GLU	-1	-0.936	-0.981	21.082	0.342	0.342	0.000	0.000	0.000	0.000
81	A	213	GLU	-1	-0.930	-0.960	23.155	0.195	0.195	0.000	0.000	0.000	0.000
82	A	214	THR	0	-0.076	-0.029	25.418	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	215	LEU	0	-0.061	-0.039	19.595	0.002	0.002	0.000	0.000	0.000	0.000
84	A	216	LEU	0	0.015	0.006	18.300	0.015	0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-7:ASN)