FMO DATABASE

FMODB ID: Q16MY

Calculation Name: 2NO2-A-Xray372

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: 2023-06-20

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-483643.687642
FMO2-HF: Nuclear repulsion	443116.407726
FMO2-HF: Total energy	-40527.279916
FMO2-MP2: Total energy	-40646.656253

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.
-2.929	-0.501	1.301	-1.531	-2.197	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 : 0.057 / q_NPA : 0.013

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	0.039	0.020	3.326	0.238	1.298	0.019	-0.463	-0.616	0.001
4	A	483	ALA	0	0.039	0.029	2.236	-0.907	-0.293	1.280	-0.752	-1.142	0.003
5	A	484	ASP	-1	-0.888	-0.955	3.378	-6.558	-5.904	0.003	-0.309	-0.348	-0.001
6	A	485	LEU	0	-0.026	-0.020	5.179	0.705	0.805	-0.001	-0.007	-0.091	0.000
7	A	486	LEU	0	0.029	0.022	7.519	0.199	0.199	0.000	0.000	0.000	0.000
8	A	487	ARG	1	0.917	0.968	5.628	1.796	1.796	0.000	0.000	0.000	0.000
9	A	488	LYS	1	0.925	0.949	8.623	1.586	1.586	0.000	0.000	0.000	0.000
10	A	489	ASN	0	0.022	-0.001	10.750	0.082	0.082	0.000	0.000	0.000	0.000
11	A	490	ALA	0	-0.030	-0.012	12.247	0.064	0.064	0.000	0.000	0.000	0.000
12	A	491	GLU	-1	-0.909	-0.950	13.435	-0.251	-0.251	0.000	0.000	0.000	0.000
13	A	492	VAL	0	0.025	0.020	15.184	0.041	0.041	0.000	0.000	0.000	0.000
14	A	493	THR	0	-0.022	-0.007	16.992	0.044	0.044	0.000	0.000	0.000	0.000
15	A	494	LYS	1	0.956	0.974	18.207	0.109	0.109	0.000	0.000	0.000	0.000
16	A	495	GLN	0	0.043	0.009	18.064	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	496	VAL	0	-0.005	0.013	21.206	0.017	0.017	0.000	0.000	0.000	0.000
18	A	497	SER	0	-0.085	-0.046	22.879	0.015	0.015	0.000	0.000	0.000	0.000
19	A	498	MET	0	0.010	-0.004	23.093	0.003	0.003	0.000	0.000	0.000	0.000
20	A	499	ALA	0	0.012	0.018	25.386	0.006	0.006	0.000	0.000	0.000	0.000
21	A	500	ARG	1	0.955	0.973	25.507	0.083	0.083	0.000	0.000	0.000	0.000
22	A	501	GLN	0	-0.051	-0.017	28.618	0.010	0.010	0.000	0.000	0.000	0.000
23	A	502	ALA	0	0.037	0.015	29.748	0.005	0.005	0.000	0.000	0.000	0.000
24	A	503	GLN	0	-0.036	0.001	31.433	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	504	VAL	0	0.008	0.003	33.309	0.005	0.005	0.000	0.000	0.000	0.000
26	A	505	ASP	-1	-0.902	-0.960	33.188	-0.059	-0.059	0.000	0.000	0.000	0.000
27	A	506	LEU	0	0.006	0.000	33.832	0.002	0.002	0.000	0.000	0.000	0.000
28	A	507	GLU	-1	-0.960	-0.993	36.425	-0.058	-0.058	0.000	0.000	0.000	0.000
29	A	508	ARG	1	0.893	0.960	38.725	0.048	0.048	0.000	0.000	0.000	0.000
30	A	509	GLU	-1	-0.918	-0.968	38.842	-0.062	-0.062	0.000	0.000	0.000	0.000
31	A	510	LYS	1	0.918	0.949	41.292	0.057	0.057	0.000	0.000	0.000	0.000
32	A	511	LYS	1	0.957	0.988	43.120	0.034	0.034	0.000	0.000	0.000	0.000
33	A	512	GLU	-1	-0.917	-0.954	44.151	-0.041	-0.041	0.000	0.000	0.000	0.000
34	A	513	LEU	0	-0.021	0.002	43.551	0.002	0.002	0.000	0.000	0.000	0.000
35	A	514	GLU	-1	-0.867	-0.941	46.864	-0.045	-0.045	0.000	0.000	0.000	0.000
36	A	515	ASP	-1	-0.892	-0.940	49.103	-0.032	-0.032	0.000	0.000	0.000	0.000
37	A	516	SER	0	-0.094	-0.094	49.655	0.002	0.002	0.000	0.000	0.000	0.000
38	A	517	LEU	0	-0.025	-0.019	49.557	0.001	0.001	0.000	0.000	0.000	0.000
39	A	518	GLU	-1	-0.930	-0.961	52.801	-0.029	-0.029	0.000	0.000	0.000	0.000
40	A	519	ARG	1	0.924	0.990	51.844	0.033	0.033	0.000	0.000	0.000	0.000
41	A	520	ILE	0	-0.062	-0.028	54.575	0.001	0.001	0.000	0.000	0.000	0.000
42	A	521	SER	0	-0.020	0.005	57.015	0.001	0.001	0.000	0.000	0.000	0.000
43	A	522	ASP	-1	-0.825	-0.898	58.704	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	523	GLN	0	-0.080	-0.069	60.284	0.001	0.001	0.000	0.000	0.000	0.000
45	A	524	GLY	0	0.035	0.013	61.197	0.001	0.001	0.000	0.000	0.000	0.000
46	A	525	GLN	0	0.005	0.000	62.698	0.000	0.000	0.000	0.000	0.000	0.000
47	A	526	ARG	1	0.867	0.930	63.117	0.024	0.024	0.000	0.000	0.000	0.000
48	A	527	LYS	1	0.971	0.987	64.360	0.026	0.026	0.000	0.000	0.000	0.000
49	A	528	THR	0	-0.033	-0.008	66.078	0.000	0.000	0.000	0.000	0.000	0.000
50	A	529	GLN	0	-0.009	-0.008	68.731	0.001	0.001	0.000	0.000	0.000	0.000
51	A	530	GLU	-1	-0.850	-0.921	69.371	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	531	GLN	0	0.003	0.009	71.364	0.001	0.001	0.000	0.000	0.000	0.000
53	A	532	LEU	0	-0.063	-0.036	72.073	0.000	0.000	0.000	0.000	0.000	0.000
54	A	533	GLU	-1	-0.911	-0.959	74.914	-0.018	-0.018	0.000	0.000	0.000	0.000
55	A	534	VAL	0	-0.023	-0.006	74.972	0.001	0.001	0.000	0.000	0.000	0.000
56	A	535	LEU	0	-0.049	-0.031	77.026	0.000	0.000	0.000	0.000	0.000	0.000
57	A	536	GLU	-1	-0.903	-0.956	78.985	-0.017	-0.017	0.000	0.000	0.000	0.000
58	A	537	SER	0	-0.014	-0.008	80.849	0.001	0.001	0.000	0.000	0.000	0.000
59	A	538	LEU	0	0.005	0.015	80.329	0.000	0.000	0.000	0.000	0.000	0.000
60	A	539	LYS	1	0.899	0.957	81.072	0.019	0.019	0.000	0.000	0.000	0.000
61	A	540	GLN	0	0.005	0.004	85.244	0.001	0.001	0.000	0.000	0.000	0.000
62	A	541	GLU	-1	-0.920	-0.971	83.994	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	542	LEU	0	-0.019	0.001	87.424	0.000	0.000	0.000	0.000	0.000	0.000
64	A	543	ALA	0	0.001	-0.014	89.231	0.000	0.000	0.000	0.000	0.000	0.000
65	A	544	THR	0	-0.065	-0.042	90.763	0.000	0.000	0.000	0.000	0.000	0.000
66	A	545	SER	0	0.072	0.043	91.729	0.000	0.000	0.000	0.000	0.000	0.000
67	A	546	GLN	0	-0.037	-0.015	92.841	0.000	0.000	0.000	0.000	0.000	0.000
68	A	547	ARG	1	0.910	0.968	91.955	0.013	0.013	0.000	0.000	0.000	0.000
69	A	548	GLU	-1	-0.889	-0.960	94.756	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	549	LEU	0	0.002	-0.009	96.012	0.000	0.000	0.000	0.000	0.000	0.000
71	A	550	GLN	0	-0.039	-0.011	99.139	0.000	0.000	0.000	0.000	0.000	0.000
72	A	551	VAL	0	-0.013	-0.003	101.301	0.000	0.000	0.000	0.000	0.000	0.000
73	A	552	LEU	0	0.002	-0.004	101.039	0.000	0.000	0.000	0.000	0.000	0.000
74	A	553	GLN	0	-0.006	-0.005	102.524	0.000	0.000	0.000	0.000	0.000	0.000
75	A	554	GLY	0	0.028	0.029	105.124	0.000	0.000	0.000	0.000	0.000	0.000
76	A	555	SER	0	-0.023	-0.016	106.760	0.000	0.000	0.000	0.000	0.000	0.000
77	A	556	LEU	0	-0.017	-0.013	106.526	0.000	0.000	0.000	0.000	0.000	0.000
78	A	557	GLU	-1	-0.935	-0.949	109.147	-0.010	-0.010	0.000	0.000	0.000	0.000
79	A	558	THR	0	-0.018	-0.013	111.256	0.000	0.000	0.000	0.000	0.000	0.000
80	A	559	SER	0	-0.008	-0.011	111.879	0.000	0.000	0.000	0.000	0.000	0.000
81	A	560	ALA	0	0.003	0.002	112.986	0.000	0.000	0.000	0.000	0.000	0.000
82	A	561	GLN	0	0.019	0.011	114.687	0.000	0.000	0.000	0.000	0.000	0.000
83	A	562	SER	0	-0.091	-0.053	116.690	0.000	0.000	0.000	0.000	0.000	0.000
84	A	563	GLU	-1	-0.947	-0.982	114.965	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	564	ALA	0	-0.023	-0.005	118.892	0.000	0.000	0.000	0.000	0.000	0.000
86	A	565	ASN	0	0.006	-0.008	121.048	0.000	0.000	0.000	0.000	0.000	0.000
87	A	566	TRP	0	0.015	0.027	120.030	0.000	0.000	0.000	0.000	0.000	0.000
88	A	567	ALA	0	0.017	0.025	123.187	0.000	0.000	0.000	0.000	0.000	0.000
89	A	568	ALA	0	0.000	-0.006	124.907	0.000	0.000	0.000	0.000	0.000	0.000
90	A	569	GLU	-1	-0.942	-0.982	126.247	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	570	PHE	0	-0.089	-0.051	126.939	0.000	0.000	0.000	0.000	0.000	0.000
92	A	571	ALA	0	-0.028	-0.013	128.875	0.000	0.000	0.000	0.000	0.000	0.000
93	A	572	GLU	-1	-0.922	-0.959	130.839	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	573	LEU	0	0.020	0.009	131.977	0.000	0.000	0.000	0.000	0.000	0.000
95	A	574	GLU	-1	-0.984	-0.978	131.734	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	575	LYS	1	0.984	0.994	134.294	0.006	0.006	0.000	0.000	0.000	0.000
97	A	576	GLU	-1	-0.959	-0.979	136.938	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	577	ARG	1	0.866	0.926	134.037	0.006	0.006	0.000	0.000	0.000	0.000
99	A	578	ASP	-1	-0.888	-0.970	136.964	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	579	SER	0	-0.113	-0.047	139.776	0.000	0.000	0.000	0.000	0.000	0.000
101	A	580	LEU	0	-0.084	-0.037	141.134	0.000	0.000	0.000	0.000	0.000	0.000
102	A	581	VAL	0	-0.081	-0.018	140.534	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)