FMO DATABASE

FMODB ID: 2N2GR

Calculation Name: 1NXV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1NXV

Chain ID: A

ChEMBL ID:

UniProt ID: Q9S1K0

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	118
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1015644.610973
FMO2-HF: Nuclear repulsion	969245.10789
FMO2-HF: Total energy	-46399.503083
FMO2-MP2: Total energy	-46535.758684

3D Structure Molmil

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
-264.312	-258.948	23.781	-14.117	-15.026	-0.141

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / q_NPA : 0.914

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

Sort

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	4	ILE	0	-0.049	-0.025	3.812	-3.367	-1.013	-0.016	-1.140	-1.197	0.003
4	A	5	LEU	0	0.007	0.011	6.112	2.219	2.219	0.000	0.000	0.000	0.000
5	A	6	ILE	0	-0.046	-0.034	9.649	0.219	0.219	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.008	-0.015	12.104	0.735	0.735	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.787	-0.896	15.456	-14.657	-14.657	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.875	-0.941	18.337	-12.410	-12.410	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.856	-0.901	21.456	-12.001	-12.001	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.811	0.873	19.669	13.200	13.200	0.000	0.000	0.000	0.000
11	A	12	PRO	0	0.009	-0.017	20.600	-0.420	-0.420	0.000	0.000	0.000	0.000
12	A	13	ILE	0	0.008	0.015	18.130	-0.250	-0.250	0.000	0.000	0.000	0.000
13	A	14	SER	0	0.060	0.031	16.489	-0.999	-0.999	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.841	-0.902	15.763	-15.140	-15.140	0.000	0.000	0.000	0.000
15	A	16	ILE	0	-0.015	0.003	16.461	-0.430	-0.430	0.000	0.000	0.000	0.000
16	A	17	ILE	0	0.030	0.015	11.817	-0.567	-0.567	0.000	0.000	0.000	0.000
17	A	18	LYS	1	1.007	1.018	11.838	16.781	16.781	0.000	0.000	0.000	0.000
18	A	19	PHE	0	-0.017	0.001	11.543	-0.924	-0.924	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.067	-0.054	12.710	0.024	0.024	0.000	0.000	0.000	0.000
20	A	21	MET	0	0.012	0.013	7.730	-1.216	-1.216	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.021	-0.020	7.663	-1.692	-1.692	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.869	0.934	8.823	16.074	16.074	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.824	-0.876	7.212	-23.631	-23.631	0.000	0.000	0.000	0.000
24	A	25	GLY	0	-0.029	0.000	5.977	-0.839	-0.839	0.000	0.000	0.000	0.000
25	A	26	TYR	0	-0.081	-0.051	2.250	-4.166	-2.874	0.969	-0.540	-1.721	-0.002
26	A	27	GLU	-1	-0.913	-0.953	3.582	-28.659	-28.134	0.000	-0.117	-0.408	0.000
27	A	28	VAL	0	-0.045	-0.033	5.656	-1.566	-1.566	0.000	0.000	0.000	0.000
28	A	29	VAL	0	0.005	0.025	8.743	1.942	1.942	0.000	0.000	0.000	0.000
29	A	30	THR	0	-0.010	-0.013	11.119	-0.642	-0.642	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.009	0.001	14.136	0.271	0.271	0.000	0.000	0.000	0.000
31	A	32	PHE	0	-0.027	-0.029	16.752	-0.228	-0.228	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.006	-0.017	19.814	0.621	0.621	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.108	0.054	19.684	-0.788	-0.788	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.804	0.890	20.305	11.634	11.634	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.783	-0.885	18.763	-14.848	-14.848	0.000	0.000	0.000	0.000
36	A	37	ALA	0	-0.053	-0.027	16.009	-0.994	-0.994	0.000	0.000	0.000	0.000
37	A	38	LEU	0	0.007	-0.007	15.666	-1.339	-1.339	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.906	-0.949	17.378	-14.748	-14.748	0.000	0.000	0.000	0.000
39	A	40	GLN	0	-0.008	-0.017	13.413	-0.992	-0.992	0.000	0.000	0.000	0.000
40	A	41	PHE	0	-0.043	-0.025	11.733	-2.092	-2.092	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.969	-0.985	12.630	-18.973	-18.973	0.000	0.000	0.000	0.000
42	A	43	ALA	0	-0.049	-0.023	14.290	-0.599	-0.599	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.873	-0.931	9.505	-25.448	-25.448	0.000	0.000	0.000	0.000
44	A	45	GLN	0	-0.090	-0.026	8.649	-3.330	-3.330	0.000	0.000	0.000	0.000
45	A	46	PRO	0	-0.016	0.001	6.528	-4.495	-4.495	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.795	-0.888	1.700	-131.950	-132.369	22.287	-11.992	-9.876	-0.140
47	A	48	ILE	0	-0.047	-0.031	4.252	1.099	1.319	-0.001	-0.020	-0.199	0.000
48	A	49	ILE	0	0.008	0.016	6.627	0.865	0.865	0.000	0.000	0.000	0.000
49	A	50	ILE	0	-0.055	-0.011	9.652	0.693	0.693	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.013	0.004	11.962	0.394	0.394	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.785	-0.894	15.250	-14.529	-14.529	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.000	-0.016	18.469	0.091	0.091	0.000	0.000	0.000	0.000
53	A	54	MET	0	-0.092	-0.048	21.498	0.626	0.626	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.067	0.052	18.831	-0.195	-0.195	0.000	0.000	0.000	0.000
55	A	56	PRO	0	-0.014	-0.011	23.407	0.403	0.403	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.880	-0.913	24.506	-11.574	-11.574	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.051	-0.035	22.431	0.323	0.323	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.820	-0.898	23.084	-13.073	-13.073	0.000	0.000	0.000	0.000
59	A	60	GLY	0	0.088	0.030	20.076	-0.454	-0.454	0.000	0.000	0.000	0.000
60	A	61	LEU	0	0.000	0.002	20.150	-0.716	-0.716	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.840	-0.909	21.860	-13.501	-13.501	0.000	0.000	0.000	0.000
62	A	63	VAL	0	0.009	0.020	17.132	-0.454	-0.454	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.021	0.007	17.231	-0.759	-0.759	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.839	0.907	17.933	12.657	12.657	0.000	0.000	0.000	0.000
65	A	66	THR	0	-0.095	-0.083	20.182	-0.158	-0.158	0.000	0.000	0.000	0.000
66	A	67	ILE	0	0.023	0.020	13.657	-0.185	-0.185	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.801	0.888	12.014	22.532	22.532	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.820	0.934	16.728	14.461	14.461	0.000	0.000	0.000	0.000
69	A	70	THR	0	-0.019	-0.014	16.329	0.114	0.114	0.000	0.000	0.000	0.000
70	A	71	SER	0	0.024	0.028	10.889	-1.610	-1.610	0.000	0.000	0.000	0.000
71	A	72	SER	0	0.004	-0.004	9.812	1.529	1.529	0.000	0.000	0.000	0.000
72	A	73	VAL	0	-0.035	0.010	7.201	-1.536	-1.536	0.000	0.000	0.000	0.000
73	A	74	PRO	0	0.028	0.017	6.340	3.805	3.805	0.000	0.000	0.000	0.000
74	A	75	ILE	0	0.006	-0.007	9.304	-1.004	-1.004	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.032	-0.003	11.755	1.011	1.011	0.000	0.000	0.000	0.000
76	A	77	MET	0	-0.010	0.005	13.297	0.558	0.558	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.010	-0.005	15.599	0.242	0.242	0.000	0.000	0.000	0.000
78	A	79	SER	0	0.017	0.002	17.948	0.516	0.516	0.000	0.000	0.000	0.000
79	A	80	ALA	0	0.045	0.028	21.663	0.013	0.013	0.000	0.000	0.000	0.000
80	A	81	LYS	1	0.791	0.895	24.842	11.234	11.234	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.848	-0.930	24.877	-11.301	-11.301	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.015	-0.017	26.800	0.216	0.216	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.929	-0.976	27.618	-10.422	-10.422	0.000	0.000	0.000	0.000
84	A	85	PHE	0	0.035	0.017	28.059	-0.314	-0.314	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.791	-0.859	25.599	-11.314	-11.314	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.871	0.937	23.147	11.602	11.602	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.004	0.002	23.211	-0.599	-0.599	0.000	0.000	0.000	0.000
88	A	89	ILE	0	0.035	0.031	24.297	-0.313	-0.313	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.028	-0.001	21.670	-0.380	-0.380	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.046	-0.030	18.404	-0.652	-0.652	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.963	-0.968	19.965	-12.282	-12.282	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.107	-0.076	21.622	-0.041	-0.041	0.000	0.000	0.000	0.000
93	A	94	GLY	0	-0.011	0.012	17.737	-0.377	-0.377	0.000	0.000	0.000	0.000
94	A	95	ALA	0	-0.018	-0.010	15.736	-1.360	-1.360	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.825	-0.916	12.247	-24.433	-24.433	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.860	-0.935	14.552	-18.209	-18.209	0.000	0.000	0.000	0.000
97	A	98	TYR	0	-0.016	-0.027	16.224	-0.068	-0.068	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.053	-0.019	15.804	0.416	0.416	0.000	0.000	0.000	0.000
99	A	100	THR	0	0.015	0.002	18.781	0.046	0.046	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.675	0.847	19.376	13.986	13.986	0.000	0.000	0.000	0.000
101	A	102	PRO	0	0.003	-0.018	22.442	0.395	0.395	0.000	0.000	0.000	0.000
102	A	103	PHE	0	0.076	0.032	17.099	0.011	0.011	0.000	0.000	0.000	0.000
103	A	104	SER	0	-0.005	0.000	19.601	0.183	0.183	0.000	0.000	0.000	0.000
104	A	105	ASN	0	0.047	0.001	15.904	-0.984	-0.984	0.000	0.000	0.000	0.000
105	A	106	ARG	1	0.981	0.981	14.663	13.266	13.266	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.836	-0.898	14.809	-15.815	-15.815	0.000	0.000	0.000	0.000
107	A	108	LEU	0	0.028	0.005	11.955	-0.970	-0.970	0.000	0.000	0.000	0.000
108	A	109	GLN	0	-0.036	-0.024	10.360	-0.414	-0.414	0.000	0.000	0.000	0.000
109	A	110	ALA	0	-0.039	-0.007	10.143	-1.754	-1.754	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.799	0.870	11.548	15.828	15.828	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.050	0.026	6.475	-1.328	-1.328	0.000	0.000	0.000	0.000
112	A	113	LYS	1	0.838	0.905	6.880	21.639	21.639	0.000	0.000	0.000	0.000
113	A	114	ALA	0	-0.071	-0.043	7.849	-2.071	-2.071	0.000	0.000	0.000	0.000
114	A	115	LEU	0	0.051	0.019	8.870	-0.716	-0.716	0.000	0.000	0.000	0.000
115	A	116	LEU	0	0.016	0.017	2.505	-4.321	-2.994	0.543	-0.308	-1.562	-0.002
116	A	117	ARG	1	0.878	0.949	5.030	21.084	21.149	-0.001	0.000	-0.063	0.000
117	A	118	ARG	1	0.894	0.956	7.145	25.027	25.027	0.000	0.000	0.000	0.000
118	A	119	SER	0	0.013	0.014	5.024	-0.311	-0.311	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)