FMO DATABASE

FMODB ID: JLM49

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	OptHSide
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	-1373914.728049
FMO2-HF: Nuclear repulsion	1313818.344045
FMO2-HF: Total energy	-60096.384005
FMO2-MP2: Total energy	-60270.126058

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.
-117.53	-111.955	1.209	-2.802	-3.983	0.009

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 : -0.863 / q_NPA : -0.925

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	0.036	0.002	3.501	-12.487	-9.496	0.014	-1.351	-1.654	0.008
4	C	492	SER	0	-0.069	-0.035	2.341	-8.860	-6.989	1.195	-1.115	-1.952	0.000
5	C	493	GLN	0	-0.005	-0.024	4.133	-4.480	-3.767	0.000	-0.336	-0.377	0.001
6	C	494	ILE	0	-0.004	0.007	6.072	-3.594	-3.594	0.000	0.000	0.000	0.000
7	C	495	ARG	1	0.952	0.971	7.562	-25.727	-25.727	0.000	0.000	0.000	0.000
8	C	496	LYS	1	0.928	0.965	7.758	-29.435	-29.435	0.000	0.000	0.000	0.000
9	C	497	GLY	0	0.060	0.034	9.960	-0.270	-0.270	0.000	0.000	0.000	0.000
10	C	498	HIS	0	0.010	0.015	12.799	-0.924	-0.924	0.000	0.000	0.000	0.000
11	C	499	ASP	-1	-0.882	-0.950	14.514	17.442	17.442	0.000	0.000	0.000	0.000
12	C	500	THR	0	-0.014	-0.009	16.456	-0.605	-0.605	0.000	0.000	0.000	0.000
13	C	501	MET	0	0.016	0.011	17.048	-1.021	-1.021	0.000	0.000	0.000	0.000
14	C	502	PHE	0	0.003	0.007	18.722	-0.816	-0.816	0.000	0.000	0.000	0.000
15	C	503	VAL	0	0.047	0.025	20.669	-0.760	-0.760	0.000	0.000	0.000	0.000
16	C	504	VAL	0	-0.018	-0.007	22.011	-0.696	-0.696	0.000	0.000	0.000	0.000
17	C	505	LEU	0	-0.013	-0.011	21.851	-0.581	-0.581	0.000	0.000	0.000	0.000
18	C	506	THR	0	-0.017	-0.011	24.413	-0.582	-0.582	0.000	0.000	0.000	0.000
19	C	507	SER	0	-0.035	-0.027	26.450	-0.536	-0.536	0.000	0.000	0.000	0.000
20	C	508	ARG	1	0.876	0.935	26.482	-11.086	-11.086	0.000	0.000	0.000	0.000
21	C	509	HIS	0	-0.016	0.001	28.999	-0.153	-0.153	0.000	0.000	0.000	0.000
22	C	510	LYS	1	0.985	0.990	30.771	-9.492	-9.492	0.000	0.000	0.000	0.000
23	C	511	ASN	0	-0.030	-0.030	31.883	-0.455	-0.455	0.000	0.000	0.000	0.000
24	C	512	LEU	0	-0.005	-0.012	31.675	-0.328	-0.328	0.000	0.000	0.000	0.000
25	C	513	ASP	-1	-0.869	-0.923	34.930	8.441	8.441	0.000	0.000	0.000	0.000
26	C	514	THR	0	-0.061	-0.024	36.916	-0.306	-0.306	0.000	0.000	0.000	0.000
27	C	515	VAL	0	0.004	-0.001	38.046	-0.242	-0.242	0.000	0.000	0.000	0.000
28	C	516	ARG	1	0.910	0.966	38.844	-7.632	-7.632	0.000	0.000	0.000	0.000
29	C	517	ALA	0	-0.012	-0.017	40.609	-0.206	-0.206	0.000	0.000	0.000	0.000
30	C	518	VAL	0	0.025	0.016	42.990	-0.186	-0.186	0.000	0.000	0.000	0.000
31	C	519	TRP	0	0.022	0.033	42.936	-0.161	-0.161	0.000	0.000	0.000	0.000
32	C	520	THR	0	-0.085	-0.060	44.802	-0.102	-0.102	0.000	0.000	0.000	0.000
33	C	521	THR	0	-0.035	-0.028	46.492	-0.160	-0.160	0.000	0.000	0.000	0.000
34	C	522	GLY	0	-0.015	0.006	48.725	-0.153	-0.153	0.000	0.000	0.000	0.000
35	C	523	ASP	-1	-0.867	-0.896	49.681	6.165	6.165	0.000	0.000	0.000	0.000
36	C	524	ILE	0	0.008	0.001	46.120	0.143	0.143	0.000	0.000	0.000	0.000
37	C	525	LYS	1	0.850	0.925	46.316	-6.028	-6.028	0.000	0.000	0.000	0.000
38	C	526	THR	0	0.037	-0.006	46.713	0.135	0.135	0.000	0.000	0.000	0.000
39	C	527	SER	0	-0.011	-0.015	43.364	0.163	0.163	0.000	0.000	0.000	0.000
40	C	528	VAL	0	-0.041	-0.030	42.081	0.207	0.207	0.000	0.000	0.000	0.000
41	C	529	ASP	-1	-0.806	-0.903	42.468	6.758	6.758	0.000	0.000	0.000	0.000
42	C	530	SER	0	-0.046	-0.015	41.964	0.140	0.140	0.000	0.000	0.000	0.000
43	C	531	ALA	0	0.019	-0.003	38.268	0.160	0.160	0.000	0.000	0.000	0.000
44	C	532	VAL	0	-0.044	-0.031	38.256	0.197	0.197	0.000	0.000	0.000	0.000
45	C	533	ALA	0	-0.027	-0.004	39.634	0.100	0.100	0.000	0.000	0.000	0.000
46	C	534	ILE	0	-0.032	-0.015	34.973	0.112	0.112	0.000	0.000	0.000	0.000
47	C	535	ASN	0	-0.064	-0.023	35.533	0.154	0.154	0.000	0.000	0.000	0.000
48	C	536	ASP	-1	-0.755	-0.845	31.112	10.192	10.192	0.000	0.000	0.000	0.000
49	C	537	LEU	0	0.023	-0.010	31.980	-0.126	-0.126	0.000	0.000	0.000	0.000
50	C	538	SER	0	-0.073	-0.059	29.037	-0.007	-0.007	0.000	0.000	0.000	0.000
51	C	539	VAL	0	0.046	0.028	31.057	-0.063	-0.063	0.000	0.000	0.000	0.000
52	C	540	VAL	0	-0.001	-0.002	33.705	-0.249	-0.249	0.000	0.000	0.000	0.000
53	C	541	VAL	0	-0.016	-0.010	32.113	-0.205	-0.205	0.000	0.000	0.000	0.000
54	C	542	ASP	-1	-0.842	-0.910	31.352	9.731	9.731	0.000	0.000	0.000	0.000
55	C	543	LEU	0	-0.007	0.000	34.473	-0.206	-0.206	0.000	0.000	0.000	0.000
56	C	544	LEU	0	-0.008	-0.014	37.861	-0.232	-0.232	0.000	0.000	0.000	0.000
57	C	545	ASN	0	0.019	0.015	33.834	-0.317	-0.317	0.000	0.000	0.000	0.000
58	C	546	ILE	0	0.002	0.028	37.140	-0.132	-0.132	0.000	0.000	0.000	0.000
59	C	547	VAL	0	0.017	0.006	39.960	-0.190	-0.190	0.000	0.000	0.000	0.000
60	C	548	ASN	0	0.011	0.025	39.767	-0.356	-0.356	0.000	0.000	0.000	0.000
61	C	549	GLN	0	-0.046	-0.016	38.804	-0.179	-0.179	0.000	0.000	0.000	0.000
62	C	550	LYS	1	0.940	0.972	43.630	-6.567	-6.567	0.000	0.000	0.000	0.000
63	C	551	ALA	0	0.103	0.042	47.138	-0.027	-0.027	0.000	0.000	0.000	0.000
64	C	552	SER	0	-0.044	-0.031	49.354	-0.043	-0.043	0.000	0.000	0.000	0.000
65	C	553	LEU	0	-0.033	-0.011	46.413	-0.108	-0.108	0.000	0.000	0.000	0.000
66	C	554	TRP	0	0.012	0.005	43.906	-0.068	-0.068	0.000	0.000	0.000	0.000
67	C	555	LYS	1	0.986	0.983	50.248	-5.935	-5.935	0.000	0.000	0.000	0.000
68	C	556	LEU	0	0.078	0.025	51.976	0.087	0.087	0.000	0.000	0.000	0.000
69	C	557	ASP	-1	-0.831	-0.937	53.016	5.970	5.970	0.000	0.000	0.000	0.000
70	C	558	LEU	0	0.000	0.022	46.401	0.053	0.053	0.000	0.000	0.000	0.000
71	C	559	CYS	0	-0.008	0.001	48.020	0.149	0.149	0.000	0.000	0.000	0.000
72	C	560	THR	0	-0.044	-0.021	48.343	0.103	0.103	0.000	0.000	0.000	0.000
73	C	561	THR	0	0.006	-0.005	44.430	0.002	0.002	0.000	0.000	0.000	0.000
74	C	562	VAL	0	-0.009	-0.010	42.866	0.170	0.170	0.000	0.000	0.000	0.000
75	C	563	LEU	0	-0.010	0.005	43.507	0.176	0.176	0.000	0.000	0.000	0.000
76	C	564	PRO	0	0.011	-0.004	43.833	0.101	0.101	0.000	0.000	0.000	0.000
77	C	565	GLN	0	0.008	0.004	39.411	0.367	0.367	0.000	0.000	0.000	0.000
78	C	566	ILE	0	0.005	0.006	39.426	0.214	0.214	0.000	0.000	0.000	0.000
79	C	567	GLU	-1	-0.854	-0.914	40.073	7.201	7.201	0.000	0.000	0.000	0.000
80	C	568	LYS	1	0.947	0.984	36.716	-8.126	-8.126	0.000	0.000	0.000	0.000
81	C	569	LEU	0	-0.059	-0.030	34.803	0.256	0.256	0.000	0.000	0.000	0.000
82	C	570	LEU	0	-0.048	-0.025	35.552	0.217	0.217	0.000	0.000	0.000	0.000
83	C	571	GLN	0	-0.023	-0.015	36.059	0.034	0.034	0.000	0.000	0.000	0.000
84	C	572	SER	0	-0.045	-0.012	31.199	0.352	0.352	0.000	0.000	0.000	0.000
85	C	573	LYS	1	0.960	0.975	24.637	-11.934	-11.934	0.000	0.000	0.000	0.000
86	C	574	TYR	0	-0.033	-0.014	24.478	0.303	0.303	0.000	0.000	0.000	0.000
87	C	575	GLU	-1	-0.758	-0.881	28.804	8.857	8.857	0.000	0.000	0.000	0.000
88	C	576	SER	0	-0.009	-0.007	28.878	-0.288	-0.288	0.000	0.000	0.000	0.000
89	C	577	TYR	0	0.002	-0.011	29.213	-0.140	-0.140	0.000	0.000	0.000	0.000
90	C	578	VAL	0	0.069	0.047	32.881	-0.312	-0.312	0.000	0.000	0.000	0.000
91	C	579	GLN	0	-0.002	-0.006	34.477	-0.535	-0.535	0.000	0.000	0.000	0.000
92	C	580	THR	0	-0.010	-0.008	35.346	-0.192	-0.192	0.000	0.000	0.000	0.000
93	C	581	GLY	0	0.023	0.010	37.131	-0.232	-0.232	0.000	0.000	0.000	0.000
94	C	582	CYS	0	-0.031	-0.022	38.647	-0.273	-0.273	0.000	0.000	0.000	0.000
95	C	583	THR	0	-0.036	-0.021	39.217	-0.237	-0.237	0.000	0.000	0.000	0.000
96	C	584	SER	0	-0.019	-0.036	41.347	-0.133	-0.133	0.000	0.000	0.000	0.000
97	C	585	LEU	0	-0.015	-0.005	43.189	-0.201	-0.201	0.000	0.000	0.000	0.000
98	C	586	LYS	1	0.862	0.919	44.367	-7.069	-7.069	0.000	0.000	0.000	0.000
99	C	587	LEU	0	-0.038	0.007	45.777	-0.207	-0.207	0.000	0.000	0.000	0.000
100	C	588	ILE	0	0.002	-0.015	46.457	-0.179	-0.179	0.000	0.000	0.000	0.000
101	C	589	LEU	0	-0.007	-0.008	48.124	-0.163	-0.163	0.000	0.000	0.000	0.000
102	C	590	GLN	0	-0.016	-0.022	49.081	-0.039	-0.039	0.000	0.000	0.000	0.000
103	C	591	ARG	1	0.816	0.927	51.635	-6.060	-6.060	0.000	0.000	0.000	0.000
104	C	592	PHE	0	-0.027	-0.044	51.344	-0.112	-0.112	0.000	0.000	0.000	0.000
105	C	593	LEU	0	0.008	0.035	53.770	-0.064	-0.064	0.000	0.000	0.000	0.000
106	C	594	PRO	0	0.057	0.027	55.530	-0.090	-0.090	0.000	0.000	0.000	0.000
107	C	595	LEU	0	0.000	-0.004	58.342	0.047	0.047	0.000	0.000	0.000	0.000
108	C	596	ILE	0	-0.056	-0.048	54.798	-0.058	-0.058	0.000	0.000	0.000	0.000
109	C	597	THR	0	-0.014	-0.026	58.616	-0.020	-0.020	0.000	0.000	0.000	0.000
110	C	598	ASP	-1	-0.893	-0.935	60.882	5.024	5.024	0.000	0.000	0.000	0.000
111	C	599	ILE	0	-0.100	-0.035	61.656	-0.094	-0.094	0.000	0.000	0.000	0.000
112	C	600	LEU	0	-0.050	-0.011	58.993	-0.071	-0.071	0.000	0.000	0.000	0.000
113	C	610	ILE	0	0.046	0.024	70.331	0.020	0.020	0.000	0.000	0.000	0.000
114	C	611	SER	0	0.078	0.050	66.435	-0.007	-0.007	0.000	0.000	0.000	0.000
115	C	612	ARG	1	0.918	0.933	65.065	-4.490	-4.490	0.000	0.000	0.000	0.000
116	C	613	GLU	-1	-0.880	-0.949	64.665	4.797	4.797	0.000	0.000	0.000	0.000
117	C	614	GLU	-1	-0.791	-0.865	58.628	5.474	5.474	0.000	0.000	0.000	0.000
118	C	615	ARG	1	0.921	0.959	60.345	-4.871	-4.871	0.000	0.000	0.000	0.000
119	C	616	LEU	0	0.017	0.014	60.606	0.066	0.066	0.000	0.000	0.000	0.000
120	C	617	HIS	0	0.035	0.000	58.133	-0.003	-0.003	0.000	0.000	0.000	0.000
121	C	618	LYS	1	0.883	0.929	55.566	-5.438	-5.438	0.000	0.000	0.000	0.000
122	C	619	CYS	0	0.002	0.017	55.850	0.113	0.113	0.000	0.000	0.000	0.000
123	C	620	ARG	1	0.960	0.993	57.029	-4.984	-4.984	0.000	0.000	0.000	0.000
124	C	621	LEU	0	-0.042	-0.011	51.860	0.055	0.055	0.000	0.000	0.000	0.000
125	C	622	CYS	0	0.014	0.001	52.339	0.132	0.132	0.000	0.000	0.000	0.000
126	C	623	PHE	0	0.022	0.014	52.527	0.097	0.097	0.000	0.000	0.000	0.000
127	C	624	LYS	1	0.953	0.969	52.702	-5.858	-5.858	0.000	0.000	0.000	0.000
128	C	625	GLN	0	0.005	-0.017	48.898	0.021	0.021	0.000	0.000	0.000	0.000
129	C	626	LEU	0	0.039	0.019	48.938	0.115	0.115	0.000	0.000	0.000	0.000
130	C	627	LYS	1	0.911	0.963	50.058	-5.616	-5.616	0.000	0.000	0.000	0.000
131	C	628	SER	0	-0.049	-0.034	47.119	-0.040	-0.040	0.000	0.000	0.000	0.000
132	C	629	ILE	0	0.042	0.022	44.528	0.108	0.108	0.000	0.000	0.000	0.000
133	C	630	SER	0	-0.029	-0.015	45.965	0.098	0.098	0.000	0.000	0.000	0.000
134	C	631	GLY	0	-0.041	-0.024	47.837	0.022	0.022	0.000	0.000	0.000	0.000
135	C	632	LEU	0	0.011	0.011	40.232	0.057	0.057	0.000	0.000	0.000	0.000
136	C	633	VAL	0	-0.044	-0.034	43.216	0.135	0.135	0.000	0.000	0.000	0.000
137	C	634	LYS	1	0.866	0.954	44.338	-6.083	-6.083	0.000	0.000	0.000	0.000
138	C	635	SER	0	-0.015	0.008	40.879	0.025	0.025	0.000	0.000	0.000	0.000
139	C	644	GLY	0	0.064	0.022	38.476	0.024	0.024	0.000	0.000	0.000	0.000
140	C	645	SER	0	0.022	-0.008	39.089	-0.231	-0.231	0.000	0.000	0.000	0.000
141	C	646	ALA	0	0.024	0.022	38.935	-0.156	-0.156	0.000	0.000	0.000	0.000
142	C	647	PHE	0	0.069	0.027	36.972	-0.180	-0.180	0.000	0.000	0.000	0.000
143	C	648	ARG	1	0.978	0.999	42.236	-6.750	-6.750	0.000	0.000	0.000	0.000
144	C	649	GLU	-1	-0.819	-0.891	44.277	6.723	6.723	0.000	0.000	0.000	0.000
145	C	650	LEU	0	0.034	0.008	42.277	-0.170	-0.170	0.000	0.000	0.000	0.000
146	C	651	HIS	0	-0.012	-0.014	46.097	-0.261	-0.261	0.000	0.000	0.000	0.000
147	C	652	LEU	0	-0.054	-0.029	47.970	-0.150	-0.150	0.000	0.000	0.000	0.000
148	C	653	LEU	0	-0.016	-0.007	47.352	-0.132	-0.132	0.000	0.000	0.000	0.000
149	C	654	MET	0	-0.068	-0.017	48.114	-0.046	-0.046	0.000	0.000	0.000	0.000
150	C	655	ALA	0	-0.029	-0.007	51.530	-0.038	-0.038	0.000	0.000	0.000	0.000
151	C	656	SER	0	-0.031	-0.003	54.177	-0.128	-0.128	0.000	0.000	0.000	0.000

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