FMO DATABASE

FMODB ID: 59L7Z

Calculation Name: 2NO2-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NO2

Chain ID: A

ChEMBL ID:

UniProt ID: O00291

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	103
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-484344.646777
FMO2-HF: Nuclear repulsion	443798.22634
FMO2-HF: Total energy	-40546.420437
FMO2-MP2: Total energy	-40665.901343

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:480:GLY )

Summations of interaction energy for fragment #1(A:480:GLY )

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.
-3.016	-0.598	1.29	-1.532	-2.173	0.003

Interaction energy analysis for fragmet #1(A:480:GLY )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.056 / q_NPA : 0.012

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	482	HIS	0	0.040	0.021	3.325	0.287	1.342	0.022	-0.469	-0.608	0.001
4	A	483	ALA	0	0.039	0.029	2.249	-0.922	-0.305	1.263	-0.749	-1.130	0.003
5	A	484	ASP	-1	-0.887	-0.955	3.388	-6.616	-5.968	0.005	-0.306	-0.346	-0.001
6	A	485	LEU	0	-0.026	-0.020	5.186	0.711	0.809	0.000	-0.008	-0.089	0.000
7	A	486	LEU	0	0.029	0.022	7.533	0.198	0.198	0.000	0.000	0.000	0.000
8	A	487	ARG	1	0.919	0.968	5.628	1.768	1.768	0.000	0.000	0.000	0.000
9	A	488	LYS	1	0.924	0.948	8.625	1.542	1.542	0.000	0.000	0.000	0.000
10	A	489	ASN	0	0.022	-0.001	10.757	0.082	0.082	0.000	0.000	0.000	0.000
11	A	490	ALA	0	-0.029	-0.011	12.258	0.064	0.064	0.000	0.000	0.000	0.000
12	A	491	GLU	-1	-0.909	-0.950	13.444	-0.246	-0.246	0.000	0.000	0.000	0.000
13	A	492	VAL	0	0.025	0.020	15.192	0.040	0.040	0.000	0.000	0.000	0.000
14	A	493	THR	0	-0.025	-0.008	17.002	0.045	0.045	0.000	0.000	0.000	0.000
15	A	494	LYS	1	0.961	0.975	18.215	0.104	0.104	0.000	0.000	0.000	0.000
16	A	495	GLN	0	0.041	0.008	18.069	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	496	VAL	0	-0.007	0.013	21.214	0.017	0.017	0.000	0.000	0.000	0.000
18	A	497	SER	0	-0.083	-0.044	22.888	0.015	0.015	0.000	0.000	0.000	0.000
19	A	498	MET	0	0.009	-0.005	23.098	0.002	0.002	0.000	0.000	0.000	0.000
20	A	499	ALA	0	0.012	0.017	25.393	0.006	0.006	0.000	0.000	0.000	0.000
21	A	500	ARG	1	0.955	0.974	25.518	0.079	0.079	0.000	0.000	0.000	0.000
22	A	501	GLN	0	-0.050	-0.017	28.626	0.010	0.010	0.000	0.000	0.000	0.000
23	A	502	ALA	0	0.036	0.015	29.755	0.004	0.004	0.000	0.000	0.000	0.000
24	A	503	GLN	0	-0.035	0.001	31.440	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	504	VAL	0	0.009	0.004	33.316	0.005	0.005	0.000	0.000	0.000	0.000
26	A	505	ASP	-1	-0.902	-0.961	33.195	-0.057	-0.057	0.000	0.000	0.000	0.000
27	A	506	LEU	0	0.006	-0.001	33.837	0.002	0.002	0.000	0.000	0.000	0.000
28	A	507	GLU	-1	-0.962	-0.993	36.433	-0.055	-0.055	0.000	0.000	0.000	0.000
29	A	508	ARG	1	0.895	0.960	38.733	0.046	0.046	0.000	0.000	0.000	0.000
30	A	509	GLU	-1	-0.919	-0.969	38.846	-0.060	-0.060	0.000	0.000	0.000	0.000
31	A	510	LYS	1	0.917	0.949	41.298	0.055	0.055	0.000	0.000	0.000	0.000
32	A	511	LYS	1	0.958	0.989	43.126	0.033	0.033	0.000	0.000	0.000	0.000
33	A	512	GLU	-1	-0.917	-0.954	44.157	-0.040	-0.040	0.000	0.000	0.000	0.000
34	A	513	LEU	0	-0.021	0.002	43.554	0.001	0.001	0.000	0.000	0.000	0.000
35	A	514	GLU	-1	-0.868	-0.941	46.871	-0.044	-0.044	0.000	0.000	0.000	0.000
36	A	515	ASP	-1	-0.892	-0.940	49.109	-0.030	-0.030	0.000	0.000	0.000	0.000
37	A	516	SER	0	-0.093	-0.095	49.660	0.002	0.002	0.000	0.000	0.000	0.000
38	A	517	LEU	0	-0.026	-0.019	49.561	0.001	0.001	0.000	0.000	0.000	0.000
39	A	518	GLU	-1	-0.931	-0.960	52.806	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	519	ARG	1	0.925	0.990	51.850	0.032	0.032	0.000	0.000	0.000	0.000
41	A	520	ILE	0	-0.063	-0.028	54.579	0.001	0.001	0.000	0.000	0.000	0.000
42	A	521	SER	0	-0.020	0.005	57.020	0.000	0.000	0.000	0.000	0.000	0.000
43	A	522	ASP	-1	-0.824	-0.897	58.709	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	523	GLN	0	-0.081	-0.070	60.289	0.001	0.001	0.000	0.000	0.000	0.000
45	A	524	GLY	0	0.036	0.014	61.202	0.001	0.001	0.000	0.000	0.000	0.000
46	A	525	GLN	0	0.004	-0.001	62.702	0.000	0.000	0.000	0.000	0.000	0.000
47	A	526	ARG	1	0.868	0.930	63.124	0.023	0.023	0.000	0.000	0.000	0.000
48	A	527	LYS	1	0.970	0.987	64.363	0.025	0.025	0.000	0.000	0.000	0.000
49	A	528	THR	0	-0.033	-0.008	66.085	0.000	0.000	0.000	0.000	0.000	0.000
50	A	529	GLN	0	-0.009	-0.008	68.734	0.001	0.001	0.000	0.000	0.000	0.000
51	A	530	GLU	-1	-0.850	-0.921	69.376	-0.020	-0.020	0.000	0.000	0.000	0.000
52	A	531	GLN	0	0.002	0.010	71.367	0.001	0.001	0.000	0.000	0.000	0.000
53	A	532	LEU	0	-0.061	-0.035	72.077	0.000	0.000	0.000	0.000	0.000	0.000
54	A	533	GLU	-1	-0.909	-0.958	74.919	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	534	VAL	0	-0.026	-0.007	74.975	0.001	0.001	0.000	0.000	0.000	0.000
56	A	535	LEU	0	-0.049	-0.032	77.028	0.000	0.000	0.000	0.000	0.000	0.000
57	A	536	GLU	-1	-0.903	-0.956	78.988	-0.016	-0.016	0.000	0.000	0.000	0.000
58	A	537	SER	0	-0.012	-0.008	80.853	0.001	0.001	0.000	0.000	0.000	0.000
59	A	538	LEU	0	0.003	0.015	80.332	0.000	0.000	0.000	0.000	0.000	0.000
60	A	539	LYS	1	0.897	0.956	81.075	0.018	0.018	0.000	0.000	0.000	0.000
61	A	540	GLN	0	0.007	0.005	85.248	0.001	0.001	0.000	0.000	0.000	0.000
62	A	541	GLU	-1	-0.919	-0.970	83.998	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	542	LEU	0	-0.019	0.000	87.427	0.000	0.000	0.000	0.000	0.000	0.000
64	A	543	ALA	0	0.002	-0.013	89.234	0.000	0.000	0.000	0.000	0.000	0.000
65	A	544	THR	0	-0.066	-0.042	90.767	0.000	0.000	0.000	0.000	0.000	0.000
66	A	545	SER	0	0.072	0.043	91.732	0.000	0.000	0.000	0.000	0.000	0.000
67	A	546	GLN	0	-0.037	-0.014	92.844	0.000	0.000	0.000	0.000	0.000	0.000
68	A	547	ARG	1	0.909	0.968	91.959	0.013	0.013	0.000	0.000	0.000	0.000
69	A	548	GLU	-1	-0.889	-0.961	94.760	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	549	LEU	0	0.002	-0.009	96.014	0.000	0.000	0.000	0.000	0.000	0.000
71	A	550	GLN	0	-0.039	-0.011	99.142	0.000	0.000	0.000	0.000	0.000	0.000
72	A	551	VAL	0	-0.012	-0.003	101.304	0.000	0.000	0.000	0.000	0.000	0.000
73	A	552	LEU	0	0.001	-0.004	101.042	0.000	0.000	0.000	0.000	0.000	0.000
74	A	553	GLN	0	-0.006	-0.005	102.526	0.000	0.000	0.000	0.000	0.000	0.000
75	A	554	GLY	0	0.028	0.029	105.126	0.000	0.000	0.000	0.000	0.000	0.000
76	A	555	SER	0	-0.022	-0.016	106.762	0.000	0.000	0.000	0.000	0.000	0.000
77	A	556	LEU	0	-0.019	-0.014	106.529	0.000	0.000	0.000	0.000	0.000	0.000
78	A	557	GLU	-1	-0.934	-0.948	109.150	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	558	THR	0	-0.017	-0.013	111.258	0.000	0.000	0.000	0.000	0.000	0.000
80	A	559	SER	0	-0.009	-0.012	111.881	0.000	0.000	0.000	0.000	0.000	0.000
81	A	560	ALA	0	0.002	0.002	112.988	0.000	0.000	0.000	0.000	0.000	0.000
82	A	561	GLN	0	0.020	0.012	114.689	0.000	0.000	0.000	0.000	0.000	0.000
83	A	562	SER	0	-0.091	-0.053	116.693	0.000	0.000	0.000	0.000	0.000	0.000
84	A	563	GLU	-1	-0.949	-0.983	114.967	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	564	ALA	0	-0.023	-0.005	118.895	0.000	0.000	0.000	0.000	0.000	0.000
86	A	565	ASN	0	0.005	-0.009	121.051	0.000	0.000	0.000	0.000	0.000	0.000
87	A	566	TRP	0	0.017	0.027	120.034	0.000	0.000	0.000	0.000	0.000	0.000
88	A	567	ALA	0	0.016	0.025	123.190	0.000	0.000	0.000	0.000	0.000	0.000
89	A	568	ALA	0	0.000	-0.006	124.909	0.000	0.000	0.000	0.000	0.000	0.000
90	A	569	GLU	-1	-0.942	-0.982	126.250	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	570	PHE	0	-0.089	-0.051	126.942	0.000	0.000	0.000	0.000	0.000	0.000
92	A	571	ALA	0	-0.027	-0.013	128.878	0.000	0.000	0.000	0.000	0.000	0.000
93	A	572	GLU	-1	-0.922	-0.960	130.841	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	573	LEU	0	0.020	0.009	131.979	0.000	0.000	0.000	0.000	0.000	0.000
95	A	574	GLU	-1	-0.985	-0.978	131.736	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	575	LYS	1	0.984	0.994	134.297	0.006	0.006	0.000	0.000	0.000	0.000
97	A	576	GLU	-1	-0.959	-0.979	136.940	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	577	ARG	1	0.862	0.925	134.039	0.006	0.006	0.000	0.000	0.000	0.000
99	A	578	ASP	-1	-0.889	-0.971	136.966	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	579	SER	0	-0.106	-0.043	139.778	0.000	0.000	0.000	0.000	0.000	0.000
101	A	580	LEU	0	-0.085	-0.037	141.137	0.000	0.000	0.000	0.000	0.000	0.000
102	A	581	VAL	0	-0.077	-0.017	140.538	0.000	0.000	0.000	0.000	0.000	0.000
103	A	1	NME	0	-0.009	-0.004	143.462	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:480:GLY )