FMO DATABASE

FMODB ID: 43Z6N

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	OptAll
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	-483205.592109
FMO2-HF: Nuclear repulsion	442676.836841
FMO2-HF: Total energy	-40528.755268
FMO2-MP2: Total energy	-40647.924862

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.
-1.936	1.23	0.572	-1.638	-2.101	-0.007

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 : 0.055 / q_NPA : 0.024

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	0.049	0.030	3.854	-0.542	0.439	-0.003	-0.459	-0.520	0.001
4	A	483	ALA	0	0.054	0.025	2.519	-0.384	0.231	0.227	-0.272	-0.570	0.000
5	A	484	ASP	-1	-0.854	-0.924	2.962	-6.290	-4.720	0.348	-0.907	-1.011	-0.008
6	A	485	LEU	0	-0.030	-0.022	5.524	0.784	0.784	0.000	0.000	0.000	0.000
7	A	486	LEU	0	0.001	0.007	7.405	0.241	0.241	0.000	0.000	0.000	0.000
8	A	487	ARG	1	0.854	0.917	4.923	2.702	2.702	0.000	0.000	0.000	0.000
9	A	488	LYS	1	0.962	0.984	9.200	1.206	1.206	0.000	0.000	0.000	0.000
10	A	489	ASN	0	0.030	0.017	11.377	0.148	0.148	0.000	0.000	0.000	0.000
11	A	490	ALA	0	-0.014	0.006	12.797	0.093	0.093	0.000	0.000	0.000	0.000
12	A	491	GLU	-1	-0.846	-0.909	13.925	-0.340	-0.340	0.000	0.000	0.000	0.000
13	A	492	VAL	0	0.011	0.003	15.525	0.057	0.057	0.000	0.000	0.000	0.000
14	A	493	THR	0	-0.030	-0.026	17.193	0.061	0.061	0.000	0.000	0.000	0.000
15	A	494	LYS	1	0.912	0.958	18.377	0.289	0.289	0.000	0.000	0.000	0.000
16	A	495	GLN	0	-0.004	-0.023	17.936	0.044	0.044	0.000	0.000	0.000	0.000
17	A	496	VAL	0	0.009	0.008	21.545	0.026	0.026	0.000	0.000	0.000	0.000
18	A	497	SER	0	-0.021	-0.016	23.232	0.025	0.025	0.000	0.000	0.000	0.000
19	A	498	MET	0	-0.043	-0.016	23.143	0.006	0.006	0.000	0.000	0.000	0.000
20	A	499	ALA	0	0.027	0.020	25.656	0.013	0.013	0.000	0.000	0.000	0.000
21	A	500	ARG	1	0.938	0.963	25.341	0.154	0.154	0.000	0.000	0.000	0.000
22	A	501	GLN	0	-0.047	-0.024	28.996	0.008	0.008	0.000	0.000	0.000	0.000
23	A	502	ALA	0	0.014	-0.003	30.089	0.008	0.008	0.000	0.000	0.000	0.000
24	A	503	GLN	0	-0.076	-0.041	31.699	0.000	0.000	0.000	0.000	0.000	0.000
25	A	504	VAL	0	0.035	0.017	33.672	0.007	0.007	0.000	0.000	0.000	0.000
26	A	505	ASP	-1	-0.825	-0.894	34.542	-0.092	-0.092	0.000	0.000	0.000	0.000
27	A	506	LEU	0	0.037	0.013	34.274	0.004	0.004	0.000	0.000	0.000	0.000
28	A	507	GLU	-1	-0.907	-0.934	37.454	-0.079	-0.079	0.000	0.000	0.000	0.000
29	A	508	ARG	1	0.782	0.887	38.214	0.085	0.085	0.000	0.000	0.000	0.000
30	A	509	GLU	-1	-0.933	-0.970	38.979	-0.082	-0.082	0.000	0.000	0.000	0.000
31	A	510	LYS	1	0.827	0.887	41.428	0.066	0.066	0.000	0.000	0.000	0.000
32	A	511	LYS	1	0.814	0.901	43.311	0.054	0.054	0.000	0.000	0.000	0.000
33	A	512	GLU	-1	-0.914	-0.967	43.820	-0.062	-0.062	0.000	0.000	0.000	0.000
34	A	513	LEU	0	0.001	0.011	43.562	0.003	0.003	0.000	0.000	0.000	0.000
35	A	514	GLU	-1	-0.798	-0.890	46.895	-0.056	-0.056	0.000	0.000	0.000	0.000
36	A	515	ASP	-1	-0.799	-0.880	49.223	-0.047	-0.047	0.000	0.000	0.000	0.000
37	A	516	SER	0	-0.089	-0.066	49.959	0.003	0.003	0.000	0.000	0.000	0.000
38	A	517	LEU	0	-0.009	-0.010	49.729	0.002	0.002	0.000	0.000	0.000	0.000
39	A	518	GLU	-1	-0.946	-0.960	52.976	-0.039	-0.039	0.000	0.000	0.000	0.000
40	A	519	ARG	1	0.920	0.960	51.488	0.048	0.048	0.000	0.000	0.000	0.000
41	A	520	ILE	0	-0.024	-0.013	54.731	0.002	0.002	0.000	0.000	0.000	0.000
42	A	521	SER	0	0.029	0.020	57.075	0.001	0.001	0.000	0.000	0.000	0.000
43	A	522	ASP	-1	-0.856	-0.905	58.813	-0.031	-0.031	0.000	0.000	0.000	0.000
44	A	523	GLN	0	-0.020	-0.020	60.496	0.001	0.001	0.000	0.000	0.000	0.000
45	A	524	GLY	0	0.014	0.011	61.433	0.001	0.001	0.000	0.000	0.000	0.000
46	A	525	GLN	0	-0.009	-0.001	62.936	0.001	0.001	0.000	0.000	0.000	0.000
47	A	526	ARG	1	0.829	0.897	62.804	0.033	0.033	0.000	0.000	0.000	0.000
48	A	527	LYS	1	0.974	0.990	65.054	0.032	0.032	0.000	0.000	0.000	0.000
49	A	528	THR	0	-0.064	-0.030	66.242	0.001	0.001	0.000	0.000	0.000	0.000
50	A	529	GLN	0	-0.031	-0.008	68.798	0.001	0.001	0.000	0.000	0.000	0.000
51	A	530	GLU	-1	-0.834	-0.924	68.720	-0.028	-0.028	0.000	0.000	0.000	0.000
52	A	531	GLN	0	-0.046	-0.025	71.375	0.000	0.000	0.000	0.000	0.000	0.000
53	A	532	LEU	0	-0.020	-0.008	72.366	0.001	0.001	0.000	0.000	0.000	0.000
54	A	533	GLU	-1	-0.914	-0.960	74.375	-0.023	-0.023	0.000	0.000	0.000	0.000
55	A	534	VAL	0	-0.005	-0.003	75.808	0.001	0.001	0.000	0.000	0.000	0.000
56	A	535	LEU	0	-0.038	-0.016	76.668	0.001	0.001	0.000	0.000	0.000	0.000
57	A	536	GLU	-1	-0.824	-0.907	78.907	-0.019	-0.019	0.000	0.000	0.000	0.000
58	A	537	SER	0	-0.041	-0.040	80.889	0.001	0.001	0.000	0.000	0.000	0.000
59	A	538	LEU	0	0.049	0.025	81.051	0.001	0.001	0.000	0.000	0.000	0.000
60	A	539	LYS	1	0.810	0.894	81.380	0.021	0.021	0.000	0.000	0.000	0.000
61	A	540	GLN	0	-0.046	-0.027	84.700	0.001	0.001	0.000	0.000	0.000	0.000
62	A	541	GLU	-1	-0.876	-0.895	83.983	-0.019	-0.019	0.000	0.000	0.000	0.000
63	A	542	LEU	0	0.008	0.011	87.507	0.001	0.001	0.000	0.000	0.000	0.000
64	A	543	ALA	0	-0.009	-0.018	89.350	0.000	0.000	0.000	0.000	0.000	0.000
65	A	544	THR	0	-0.084	-0.053	91.012	0.001	0.001	0.000	0.000	0.000	0.000
66	A	545	SER	0	0.065	0.039	91.877	0.000	0.000	0.000	0.000	0.000	0.000
67	A	546	GLN	0	-0.027	-0.026	92.892	0.000	0.000	0.000	0.000	0.000	0.000
68	A	547	ARG	1	0.900	0.960	92.894	0.016	0.016	0.000	0.000	0.000	0.000
69	A	548	GLU	-1	-0.898	-0.954	94.586	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	549	LEU	0	0.005	-0.001	95.528	0.000	0.000	0.000	0.000	0.000	0.000
71	A	550	GLN	0	-0.002	0.007	99.330	0.000	0.000	0.000	0.000	0.000	0.000
72	A	551	VAL	0	-0.007	-0.009	101.420	0.000	0.000	0.000	0.000	0.000	0.000
73	A	552	LEU	0	-0.002	0.009	100.125	0.000	0.000	0.000	0.000	0.000	0.000
74	A	553	GLN	0	-0.018	-0.011	102.123	0.000	0.000	0.000	0.000	0.000	0.000
75	A	554	GLY	0	0.033	0.025	105.285	0.000	0.000	0.000	0.000	0.000	0.000
76	A	555	SER	0	-0.043	-0.029	106.366	0.000	0.000	0.000	0.000	0.000	0.000
77	A	556	LEU	0	-0.023	-0.006	107.172	0.000	0.000	0.000	0.000	0.000	0.000
78	A	557	GLU	-1	-0.928	-0.963	109.204	-0.011	-0.011	0.000	0.000	0.000	0.000
79	A	558	THR	0	-0.055	-0.041	111.414	0.000	0.000	0.000	0.000	0.000	0.000
80	A	559	SER	0	-0.078	-0.047	111.989	0.000	0.000	0.000	0.000	0.000	0.000
81	A	560	ALA	0	0.052	0.027	113.262	0.000	0.000	0.000	0.000	0.000	0.000
82	A	561	GLN	0	-0.028	-0.016	115.032	0.000	0.000	0.000	0.000	0.000	0.000
83	A	562	SER	0	-0.007	-0.010	116.953	0.000	0.000	0.000	0.000	0.000	0.000
84	A	563	GLU	-1	-0.920	-0.946	114.541	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	564	ALA	0	-0.009	-0.004	119.025	0.000	0.000	0.000	0.000	0.000	0.000
86	A	565	ASN	0	-0.008	-0.006	121.116	0.000	0.000	0.000	0.000	0.000	0.000
87	A	566	TRP	0	0.002	-0.001	119.824	0.000	0.000	0.000	0.000	0.000	0.000
88	A	567	ALA	0	-0.004	0.004	123.128	0.000	0.000	0.000	0.000	0.000	0.000
89	A	568	ALA	0	-0.023	-0.007	124.873	0.000	0.000	0.000	0.000	0.000	0.000
90	A	569	GLU	-1	-0.943	-0.979	126.589	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	570	PHE	0	-0.054	-0.022	127.124	0.000	0.000	0.000	0.000	0.000	0.000
92	A	571	ALA	0	0.006	0.005	129.031	0.000	0.000	0.000	0.000	0.000	0.000
93	A	572	GLU	-1	-0.792	-0.880	130.867	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	573	LEU	0	0.026	0.019	132.172	0.000	0.000	0.000	0.000	0.000	0.000
95	A	574	GLU	-1	-0.880	-0.921	131.312	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	575	LYS	1	0.824	0.889	134.151	0.008	0.008	0.000	0.000	0.000	0.000
97	A	576	GLU	-1	-0.966	-0.971	136.862	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	577	ARG	1	0.711	0.811	133.740	0.008	0.008	0.000	0.000	0.000	0.000
99	A	578	ASP	-1	-0.833	-0.908	137.143	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	579	SER	0	-0.090	-0.048	139.964	0.000	0.000	0.000	0.000	0.000	0.000
101	A	580	LEU	0	-0.072	-0.029	141.924	0.000	0.000	0.000	0.000	0.000	0.000
102	A	581	VAL	0	-0.094	-0.028	140.813	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)