FMO DATABASE

FMODB ID: N93ZQ

Calculation Name: 5NBT-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5NBT

Chain ID: C

ChEMBL ID:

UniProt ID: Q9WV86

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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	151
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1373960.723518
FMO2-HF: Nuclear repulsion	1313865.191026
FMO2-HF: Total energy	-60095.532492
FMO2-MP2: Total energy	-60269.325877

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(C:489:ASP)

Summations of interaction energy for fragment #1(C:489:ASP)

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.
-120.009	-114.231	0.935	-2.747	-3.966	0.01

Interaction energy analysis for fragmet #1(C:489:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.852 / q_NPA : -0.920

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	C	491	MET	0	0.050	0.007	3.487	-12.150	-9.065	0.020	-1.387	-1.718	0.008
4	C	492	SER	0	-0.072	-0.036	2.415	-9.314	-7.291	0.915	-1.045	-1.893	0.001
5	C	493	GLN	0	0.000	-0.020	4.112	-4.979	-4.309	0.000	-0.315	-0.355	0.001
6	C	494	ILE	0	-0.005	0.006	6.045	-3.587	-3.587	0.000	0.000	0.000	0.000
7	C	495	ARG	1	0.961	0.970	7.546	-25.966	-25.966	0.000	0.000	0.000	0.000
8	C	496	LYS	1	0.903	0.960	7.338	-29.897	-29.897	0.000	0.000	0.000	0.000
9	C	497	GLY	0	0.060	0.033	9.938	-0.302	-0.302	0.000	0.000	0.000	0.000
10	C	498	HIS	0	0.027	0.017	12.765	-1.037	-1.037	0.000	0.000	0.000	0.000
11	C	499	ASP	-1	-0.880	-0.938	14.595	16.846	16.846	0.000	0.000	0.000	0.000
12	C	500	THR	0	-0.020	-0.013	16.438	-0.651	-0.651	0.000	0.000	0.000	0.000
13	C	501	MET	0	-0.004	0.001	16.641	-0.983	-0.983	0.000	0.000	0.000	0.000
14	C	502	PHE	0	0.025	0.014	18.699	-0.818	-0.818	0.000	0.000	0.000	0.000
15	C	503	VAL	0	0.053	0.045	20.649	-0.770	-0.770	0.000	0.000	0.000	0.000
16	C	504	VAL	0	-0.022	0.007	21.904	-0.710	-0.710	0.000	0.000	0.000	0.000
17	C	505	LEU	0	-0.025	-0.017	21.871	-0.585	-0.585	0.000	0.000	0.000	0.000
18	C	506	THR	0	-0.020	-0.029	24.298	-0.558	-0.558	0.000	0.000	0.000	0.000
19	C	507	SER	0	-0.037	-0.046	26.267	-0.503	-0.503	0.000	0.000	0.000	0.000
20	C	508	ARG	1	0.945	0.979	25.592	-11.403	-11.403	0.000	0.000	0.000	0.000
21	C	509	HIS	0	0.017	0.019	28.976	-0.338	-0.338	0.000	0.000	0.000	0.000
22	C	510	LYS	1	1.002	0.998	30.750	-9.595	-9.595	0.000	0.000	0.000	0.000
23	C	511	ASN	0	-0.018	-0.019	31.858	-0.487	-0.487	0.000	0.000	0.000	0.000
24	C	512	LEU	0	-0.006	-0.009	31.787	-0.324	-0.324	0.000	0.000	0.000	0.000
25	C	513	ASP	-1	-0.906	-0.940	34.898	8.450	8.450	0.000	0.000	0.000	0.000
26	C	514	THR	0	-0.064	-0.026	36.894	-0.311	-0.311	0.000	0.000	0.000	0.000
27	C	515	VAL	0	-0.009	-0.006	37.873	-0.242	-0.242	0.000	0.000	0.000	0.000
28	C	516	ARG	1	0.917	0.973	38.892	-7.603	-7.603	0.000	0.000	0.000	0.000
29	C	517	ALA	0	-0.013	-0.019	40.586	-0.208	-0.208	0.000	0.000	0.000	0.000
30	C	518	VAL	0	0.035	0.022	42.967	-0.186	-0.186	0.000	0.000	0.000	0.000
31	C	519	TRP	0	0.026	0.046	42.940	-0.155	-0.155	0.000	0.000	0.000	0.000
32	C	520	THR	0	-0.092	-0.062	44.778	-0.103	-0.103	0.000	0.000	0.000	0.000
33	C	521	THR	0	-0.048	-0.047	46.469	-0.155	-0.155	0.000	0.000	0.000	0.000
34	C	522	GLY	0	-0.018	0.006	48.698	-0.153	-0.153	0.000	0.000	0.000	0.000
35	C	523	ASP	-1	-0.857	-0.875	49.555	6.150	6.150	0.000	0.000	0.000	0.000
36	C	524	ILE	0	0.021	0.018	46.026	0.145	0.145	0.000	0.000	0.000	0.000
37	C	525	LYS	1	0.851	0.944	46.290	-6.007	-6.007	0.000	0.000	0.000	0.000
38	C	526	THR	0	0.040	-0.024	46.688	0.127	0.127	0.000	0.000	0.000	0.000
39	C	527	SER	0	-0.015	-0.034	43.385	0.155	0.155	0.000	0.000	0.000	0.000
40	C	528	VAL	0	-0.039	-0.027	42.194	0.204	0.204	0.000	0.000	0.000	0.000
41	C	529	ASP	-1	-0.825	-0.911	42.443	6.760	6.760	0.000	0.000	0.000	0.000
42	C	530	SER	0	-0.053	-0.020	41.643	0.153	0.153	0.000	0.000	0.000	0.000
43	C	531	ALA	0	0.027	0.001	38.199	0.155	0.155	0.000	0.000	0.000	0.000
44	C	532	VAL	0	-0.038	-0.028	38.231	0.198	0.198	0.000	0.000	0.000	0.000
45	C	533	ALA	0	-0.029	-0.006	39.609	0.100	0.100	0.000	0.000	0.000	0.000
46	C	534	ILE	0	-0.036	-0.015	34.980	0.113	0.113	0.000	0.000	0.000	0.000
47	C	535	ASN	0	-0.066	-0.024	35.426	0.169	0.169	0.000	0.000	0.000	0.000
48	C	536	ASP	-1	-0.792	-0.879	30.834	10.243	10.243	0.000	0.000	0.000	0.000
49	C	537	LEU	0	0.016	-0.007	31.911	-0.119	-0.119	0.000	0.000	0.000	0.000
50	C	538	SER	0	-0.063	-0.045	28.972	-0.036	-0.036	0.000	0.000	0.000	0.000
51	C	539	VAL	0	0.049	0.030	31.031	-0.065	-0.065	0.000	0.000	0.000	0.000
52	C	540	VAL	0	-0.001	0.001	33.680	-0.246	-0.246	0.000	0.000	0.000	0.000
53	C	541	VAL	0	-0.028	-0.022	32.208	-0.197	-0.197	0.000	0.000	0.000	0.000
54	C	542	ASP	-1	-0.885	-0.941	31.492	9.635	9.635	0.000	0.000	0.000	0.000
55	C	543	LEU	0	-0.018	-0.006	34.446	-0.213	-0.213	0.000	0.000	0.000	0.000
56	C	544	LEU	0	-0.013	-0.019	37.829	-0.241	-0.241	0.000	0.000	0.000	0.000
57	C	545	ASN	0	0.000	-0.004	33.643	-0.302	-0.302	0.000	0.000	0.000	0.000
58	C	546	ILE	0	0.000	0.017	37.306	-0.137	-0.137	0.000	0.000	0.000	0.000
59	C	547	VAL	0	0.011	0.001	39.937	-0.196	-0.196	0.000	0.000	0.000	0.000
60	C	548	ASN	0	0.009	0.009	39.791	-0.366	-0.366	0.000	0.000	0.000	0.000
61	C	549	GLN	0	-0.046	-0.009	38.674	-0.149	-0.149	0.000	0.000	0.000	0.000
62	C	550	LYS	1	0.939	0.977	43.630	-6.515	-6.515	0.000	0.000	0.000	0.000
63	C	551	ALA	0	0.098	0.036	47.138	-0.030	-0.030	0.000	0.000	0.000	0.000
64	C	552	SER	0	-0.060	-0.044	49.354	-0.046	-0.046	0.000	0.000	0.000	0.000
65	C	553	LEU	0	-0.028	-0.007	46.422	-0.113	-0.113	0.000	0.000	0.000	0.000
66	C	554	TRP	0	0.016	0.015	43.993	-0.076	-0.076	0.000	0.000	0.000	0.000
67	C	555	LYS	1	0.982	0.971	50.221	-5.882	-5.882	0.000	0.000	0.000	0.000
68	C	556	LEU	0	0.057	0.008	51.950	0.077	0.077	0.000	0.000	0.000	0.000
69	C	557	ASP	-1	-0.843	-0.947	52.989	5.946	5.946	0.000	0.000	0.000	0.000
70	C	558	LEU	0	0.011	0.017	46.110	0.050	0.050	0.000	0.000	0.000	0.000
71	C	559	CYS	0	-0.019	-0.006	47.994	0.142	0.142	0.000	0.000	0.000	0.000
72	C	560	THR	0	-0.040	-0.014	48.316	0.111	0.111	0.000	0.000	0.000	0.000
73	C	561	THR	0	0.036	0.011	44.461	0.003	0.003	0.000	0.000	0.000	0.000
74	C	562	VAL	0	-0.003	-0.002	42.990	0.167	0.167	0.000	0.000	0.000	0.000
75	C	563	LEU	0	-0.018	0.002	43.480	0.181	0.181	0.000	0.000	0.000	0.000
76	C	564	PRO	0	0.015	-0.003	43.803	0.108	0.108	0.000	0.000	0.000	0.000
77	C	565	GLN	0	0.007	0.001	38.927	0.372	0.372	0.000	0.000	0.000	0.000
78	C	566	ILE	0	-0.013	-0.003	39.398	0.214	0.214	0.000	0.000	0.000	0.000
79	C	567	GLU	-1	-0.883	-0.937	40.040	7.221	7.221	0.000	0.000	0.000	0.000
80	C	568	LYS	1	0.959	0.968	36.354	-8.200	-8.200	0.000	0.000	0.000	0.000
81	C	569	LEU	0	-0.054	-0.027	34.880	0.253	0.253	0.000	0.000	0.000	0.000
82	C	570	LEU	0	-0.053	-0.026	35.518	0.219	0.219	0.000	0.000	0.000	0.000
83	C	571	GLN	0	-0.015	-0.002	36.027	0.065	0.065	0.000	0.000	0.000	0.000
84	C	572	SER	0	-0.049	-0.013	31.116	0.349	0.349	0.000	0.000	0.000	0.000
85	C	573	LYS	1	0.986	0.986	24.665	-11.954	-11.954	0.000	0.000	0.000	0.000
86	C	574	TYR	0	-0.050	-0.020	24.349	0.341	0.341	0.000	0.000	0.000	0.000
87	C	575	GLU	-1	-0.801	-0.903	28.769	8.988	8.988	0.000	0.000	0.000	0.000
88	C	576	SER	0	-0.015	-0.011	29.191	-0.321	-0.321	0.000	0.000	0.000	0.000
89	C	577	TYR	0	0.017	-0.004	29.552	-0.190	-0.190	0.000	0.000	0.000	0.000
90	C	578	VAL	0	0.082	0.056	32.845	-0.312	-0.312	0.000	0.000	0.000	0.000
91	C	579	GLN	0	0.019	0.006	34.443	-0.486	-0.486	0.000	0.000	0.000	0.000
92	C	580	THR	0	0.005	0.014	34.502	-0.282	-0.282	0.000	0.000	0.000	0.000
93	C	581	GLY	0	0.024	0.014	37.093	-0.229	-0.229	0.000	0.000	0.000	0.000
94	C	582	CYS	0	-0.029	-0.020	38.724	-0.273	-0.273	0.000	0.000	0.000	0.000
95	C	583	THR	0	-0.033	-0.026	39.138	-0.237	-0.237	0.000	0.000	0.000	0.000
96	C	584	SER	0	-0.022	-0.025	41.306	-0.131	-0.131	0.000	0.000	0.000	0.000
97	C	585	LEU	0	-0.003	0.002	43.152	-0.199	-0.199	0.000	0.000	0.000	0.000
98	C	586	LYS	1	0.932	0.970	44.661	-6.937	-6.937	0.000	0.000	0.000	0.000
99	C	587	LEU	0	-0.042	0.006	45.675	-0.211	-0.211	0.000	0.000	0.000	0.000
100	C	588	ILE	0	0.016	-0.011	46.570	-0.181	-0.181	0.000	0.000	0.000	0.000
101	C	589	LEU	0	-0.013	-0.009	48.197	-0.165	-0.165	0.000	0.000	0.000	0.000
102	C	590	GLN	0	-0.015	-0.024	49.870	-0.094	-0.094	0.000	0.000	0.000	0.000
103	C	591	ARG	1	0.840	0.950	51.715	-6.051	-6.051	0.000	0.000	0.000	0.000
104	C	592	PHE	0	-0.029	-0.041	50.981	-0.120	-0.120	0.000	0.000	0.000	0.000
105	C	593	LEU	0	0.023	0.043	53.663	-0.069	-0.069	0.000	0.000	0.000	0.000
106	C	594	PRO	0	0.060	0.027	55.494	-0.099	-0.099	0.000	0.000	0.000	0.000
107	C	595	LEU	0	0.041	0.015	58.246	0.046	0.046	0.000	0.000	0.000	0.000
108	C	596	ILE	0	-0.047	-0.044	54.747	-0.059	-0.059	0.000	0.000	0.000	0.000
109	C	597	THR	0	-0.038	-0.039	58.500	-0.075	-0.075	0.000	0.000	0.000	0.000
110	C	598	ASP	-1	-0.905	-0.936	60.846	4.968	4.968	0.000	0.000	0.000	0.000
111	C	599	ILE	0	-0.091	-0.043	61.987	-0.095	-0.095	0.000	0.000	0.000	0.000
112	C	600	LEU	0	-0.058	-0.015	58.951	-0.073	-0.073	0.000	0.000	0.000	0.000
113	C	610	ILE	0	0.072	0.033	70.351	0.027	0.027	0.000	0.000	0.000	0.000
114	C	611	SER	0	0.106	0.059	66.459	0.028	0.028	0.000	0.000	0.000	0.000
115	C	612	ARG	1	0.914	0.935	65.039	-4.512	-4.512	0.000	0.000	0.000	0.000
116	C	613	GLU	-1	-0.928	-0.975	64.638	4.864	4.864	0.000	0.000	0.000	0.000
117	C	614	GLU	-1	-0.845	-0.903	58.860	5.404	5.404	0.000	0.000	0.000	0.000
118	C	615	ARG	1	0.845	0.911	60.319	-4.839	-4.839	0.000	0.000	0.000	0.000
119	C	616	LEU	0	0.020	0.013	60.579	0.067	0.067	0.000	0.000	0.000	0.000
120	C	617	HIS	0	0.033	0.008	58.007	0.004	0.004	0.000	0.000	0.000	0.000
121	C	618	LYS	1	0.962	0.988	55.640	-5.378	-5.378	0.000	0.000	0.000	0.000
122	C	619	CYS	0	-0.012	0.006	55.823	0.108	0.108	0.000	0.000	0.000	0.000
123	C	620	ARG	1	0.977	1.000	57.002	-4.974	-4.974	0.000	0.000	0.000	0.000
124	C	621	LEU	0	-0.021	0.001	51.655	0.057	0.057	0.000	0.000	0.000	0.000
125	C	622	CYS	0	-0.012	-0.007	52.312	0.131	0.131	0.000	0.000	0.000	0.000
126	C	623	PHE	0	0.038	0.029	52.494	0.105	0.105	0.000	0.000	0.000	0.000
127	C	624	LYS	1	0.947	0.964	52.905	-5.839	-5.839	0.000	0.000	0.000	0.000
128	C	625	GLN	0	0.009	-0.015	48.873	0.046	0.046	0.000	0.000	0.000	0.000
129	C	626	LEU	0	0.031	0.015	48.906	0.115	0.115	0.000	0.000	0.000	0.000
130	C	627	LYS	1	0.935	0.967	50.025	-5.687	-5.687	0.000	0.000	0.000	0.000
131	C	628	SER	0	-0.041	-0.012	47.219	-0.037	-0.037	0.000	0.000	0.000	0.000
132	C	629	ILE	0	0.048	0.030	44.531	0.103	0.103	0.000	0.000	0.000	0.000
133	C	630	SER	0	-0.023	-0.013	45.932	0.104	0.104	0.000	0.000	0.000	0.000
134	C	631	GLY	0	-0.029	-0.021	47.804	0.024	0.024	0.000	0.000	0.000	0.000
135	C	632	LEU	0	0.007	0.008	40.275	0.054	0.054	0.000	0.000	0.000	0.000
136	C	633	VAL	0	-0.049	-0.036	43.183	0.132	0.132	0.000	0.000	0.000	0.000
137	C	634	LYS	1	0.874	0.954	44.304	-6.075	-6.075	0.000	0.000	0.000	0.000
138	C	635	SER	0	-0.007	0.013	40.841	0.039	0.039	0.000	0.000	0.000	0.000
139	C	644	GLY	0	0.069	0.022	38.435	0.032	0.032	0.000	0.000	0.000	0.000
140	C	645	SER	0	0.016	-0.012	39.053	-0.232	-0.232	0.000	0.000	0.000	0.000
141	C	646	ALA	0	0.032	0.028	38.925	-0.152	-0.152	0.000	0.000	0.000	0.000
142	C	647	PHE	0	0.066	0.023	37.043	-0.184	-0.184	0.000	0.000	0.000	0.000
143	C	648	ARG	1	0.961	0.993	42.199	-6.804	-6.804	0.000	0.000	0.000	0.000
144	C	649	GLU	-1	-0.878	-0.937	44.239	6.789	6.789	0.000	0.000	0.000	0.000
145	C	650	LEU	0	0.023	0.001	42.274	-0.174	-0.174	0.000	0.000	0.000	0.000
146	C	651	HIS	0	-0.023	-0.019	46.058	-0.243	-0.243	0.000	0.000	0.000	0.000
147	C	652	LEU	0	-0.036	-0.021	47.934	-0.146	-0.146	0.000	0.000	0.000	0.000
148	C	653	LEU	0	-0.014	-0.008	47.352	-0.128	-0.128	0.000	0.000	0.000	0.000
149	C	654	MET	0	-0.071	-0.017	48.102	-0.045	-0.045	0.000	0.000	0.000	0.000
150	C	655	ALA	0	-0.027	-0.002	51.493	-0.038	-0.038	0.000	0.000	0.000	0.000
151	C	656	SER	0	-0.041	-0.009	54.142	-0.127	-0.127	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:489:ASP)