FMO DATABASE

FMODB ID: 39NKL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1377802.337865
FMO2-HF: Nuclear repulsion	1317705.656654
FMO2-HF: Total energy	-60096.681211
FMO2-MP2: Total energy	-60270.294768

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.
-114.793	-109.568	0.41	-2.338	-3.296	0.011

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 : -0.859 / q_NPA : -0.924

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	0.018	-0.001	3.436	-12.751	-9.872	0.027	-1.369	-1.537	0.008
4	C	492	SER	0	-0.066	-0.040	2.552	-9.353	-7.478	0.384	-0.795	-1.464	0.003
5	C	493	GLN	0	-0.001	-0.020	4.372	-3.638	-3.167	-0.001	-0.174	-0.295	0.000
6	C	494	ILE	0	0.010	0.010	6.329	-3.442	-3.442	0.000	0.000	0.000	0.000
7	C	495	ARG	1	0.878	0.930	7.757	-24.650	-24.650	0.000	0.000	0.000	0.000
8	C	496	LYS	1	0.917	0.962	7.824	-28.858	-28.858	0.000	0.000	0.000	0.000
9	C	497	GLY	0	0.069	0.027	10.060	-0.419	-0.419	0.000	0.000	0.000	0.000
10	C	498	HIS	0	-0.020	0.008	12.879	-1.058	-1.058	0.000	0.000	0.000	0.000
11	C	499	ASP	-1	-0.809	-0.906	14.078	18.227	18.227	0.000	0.000	0.000	0.000
12	C	500	THR	0	-0.005	-0.003	16.393	-0.622	-0.622	0.000	0.000	0.000	0.000
13	C	501	MET	0	0.013	0.003	17.263	-1.010	-1.010	0.000	0.000	0.000	0.000
14	C	502	PHE	0	0.017	0.016	18.872	-0.765	-0.765	0.000	0.000	0.000	0.000
15	C	503	VAL	0	0.044	0.034	20.752	-0.734	-0.734	0.000	0.000	0.000	0.000
16	C	504	VAL	0	-0.001	0.005	22.095	-0.669	-0.669	0.000	0.000	0.000	0.000
17	C	505	LEU	0	-0.011	-0.006	21.661	-0.567	-0.567	0.000	0.000	0.000	0.000
18	C	506	THR	0	-0.023	-0.018	24.367	-0.585	-0.585	0.000	0.000	0.000	0.000
19	C	507	SER	0	-0.051	-0.038	26.415	-0.531	-0.531	0.000	0.000	0.000	0.000
20	C	508	ARG	1	0.858	0.917	27.058	-10.912	-10.912	0.000	0.000	0.000	0.000
21	C	509	HIS	0	-0.022	-0.004	29.012	-0.134	-0.134	0.000	0.000	0.000	0.000
22	C	510	LYS	1	0.994	0.998	30.860	-9.377	-9.377	0.000	0.000	0.000	0.000
23	C	511	ASN	0	-0.024	-0.019	31.933	-0.472	-0.472	0.000	0.000	0.000	0.000
24	C	512	LEU	0	0.002	-0.004	31.679	-0.340	-0.340	0.000	0.000	0.000	0.000
25	C	513	ASP	-1	-0.879	-0.935	34.664	8.525	8.525	0.000	0.000	0.000	0.000
26	C	514	THR	0	-0.050	-0.030	36.859	-0.317	-0.317	0.000	0.000	0.000	0.000
27	C	515	VAL	0	0.005	-0.002	38.180	-0.247	-0.247	0.000	0.000	0.000	0.000
28	C	516	ARG	1	0.893	0.948	38.929	-7.627	-7.627	0.000	0.000	0.000	0.000
29	C	517	ALA	0	-0.009	-0.005	40.690	-0.194	-0.194	0.000	0.000	0.000	0.000
30	C	518	VAL	0	0.012	0.017	42.998	-0.184	-0.184	0.000	0.000	0.000	0.000
31	C	519	TRP	0	0.020	0.020	42.927	-0.166	-0.166	0.000	0.000	0.000	0.000
32	C	520	THR	0	-0.073	-0.047	44.902	-0.099	-0.099	0.000	0.000	0.000	0.000
33	C	521	THR	0	-0.017	-0.014	46.797	-0.153	-0.153	0.000	0.000	0.000	0.000
34	C	522	GLY	0	-0.007	0.007	48.810	-0.150	-0.150	0.000	0.000	0.000	0.000
35	C	523	ASP	-1	-0.845	-0.890	49.596	6.193	6.193	0.000	0.000	0.000	0.000
36	C	524	ILE	0	-0.010	-0.008	46.205	0.148	0.148	0.000	0.000	0.000	0.000
37	C	525	LYS	1	0.813	0.916	46.162	-6.046	-6.046	0.000	0.000	0.000	0.000
38	C	526	THR	0	0.024	-0.019	46.569	0.139	0.139	0.000	0.000	0.000	0.000
39	C	527	SER	0	-0.032	-0.035	43.276	0.160	0.160	0.000	0.000	0.000	0.000
40	C	528	VAL	0	-0.023	-0.018	42.055	0.207	0.207	0.000	0.000	0.000	0.000
41	C	529	ASP	-1	-0.795	-0.891	42.320	6.766	6.766	0.000	0.000	0.000	0.000
42	C	530	SER	0	-0.030	-0.003	41.837	0.142	0.142	0.000	0.000	0.000	0.000
43	C	531	ALA	0	0.021	0.003	38.202	0.156	0.156	0.000	0.000	0.000	0.000
44	C	532	VAL	0	-0.062	-0.036	38.191	0.201	0.201	0.000	0.000	0.000	0.000
45	C	533	ALA	0	-0.037	-0.015	39.957	0.082	0.082	0.000	0.000	0.000	0.000
46	C	534	ILE	0	-0.015	-0.008	35.164	0.095	0.095	0.000	0.000	0.000	0.000
47	C	535	ASN	0	-0.050	-0.021	35.792	0.143	0.143	0.000	0.000	0.000	0.000
48	C	536	ASP	-1	-0.724	-0.826	31.358	10.079	10.079	0.000	0.000	0.000	0.000
49	C	537	LEU	0	0.013	-0.012	32.469	-0.116	-0.116	0.000	0.000	0.000	0.000
50	C	538	SER	0	-0.092	-0.067	29.451	0.059	0.059	0.000	0.000	0.000	0.000
51	C	539	VAL	0	0.046	0.025	31.400	-0.060	-0.060	0.000	0.000	0.000	0.000
52	C	540	VAL	0	-0.011	-0.004	33.952	-0.227	-0.227	0.000	0.000	0.000	0.000
53	C	541	VAL	0	-0.018	-0.007	32.089	-0.202	-0.202	0.000	0.000	0.000	0.000
54	C	542	ASP	-1	-0.816	-0.892	31.723	9.647	9.647	0.000	0.000	0.000	0.000
55	C	543	LEU	0	-0.012	-0.006	34.660	-0.195	-0.195	0.000	0.000	0.000	0.000
56	C	544	LEU	0	-0.007	-0.012	38.104	-0.252	-0.252	0.000	0.000	0.000	0.000
57	C	545	ASN	0	0.009	0.013	34.134	-0.325	-0.325	0.000	0.000	0.000	0.000
58	C	546	ILE	0	-0.003	0.030	37.495	-0.084	-0.084	0.000	0.000	0.000	0.000
59	C	547	VAL	0	0.002	-0.005	40.075	-0.178	-0.178	0.000	0.000	0.000	0.000
60	C	548	ASN	0	0.022	0.024	39.739	-0.357	-0.357	0.000	0.000	0.000	0.000
61	C	549	GLN	0	-0.044	-0.013	38.734	-0.176	-0.176	0.000	0.000	0.000	0.000
62	C	550	LYS	1	0.928	0.965	43.454	-6.613	-6.613	0.000	0.000	0.000	0.000
63	C	551	ALA	0	0.108	0.046	47.059	-0.063	-0.063	0.000	0.000	0.000	0.000
64	C	552	SER	0	-0.028	-0.022	49.155	-0.043	-0.043	0.000	0.000	0.000	0.000
65	C	553	LEU	0	-0.029	-0.010	46.527	-0.117	-0.117	0.000	0.000	0.000	0.000
66	C	554	TRP	0	0.003	0.001	44.182	-0.084	-0.084	0.000	0.000	0.000	0.000
67	C	555	LYS	1	0.983	0.982	50.561	-5.982	-5.982	0.000	0.000	0.000	0.000
68	C	556	LEU	0	0.086	0.032	52.097	0.097	0.097	0.000	0.000	0.000	0.000
69	C	557	ASP	-1	-0.788	-0.899	52.916	5.963	5.963	0.000	0.000	0.000	0.000
70	C	558	LEU	0	0.013	0.039	46.319	0.051	0.051	0.000	0.000	0.000	0.000
71	C	559	CYS	0	-0.016	-0.002	48.050	0.144	0.144	0.000	0.000	0.000	0.000
72	C	560	THR	0	-0.045	-0.029	48.341	0.107	0.107	0.000	0.000	0.000	0.000
73	C	561	THR	0	0.016	0.002	44.402	-0.004	-0.004	0.000	0.000	0.000	0.000
74	C	562	VAL	0	0.006	-0.005	43.052	0.174	0.174	0.000	0.000	0.000	0.000
75	C	563	LEU	0	-0.001	0.010	43.511	0.171	0.171	0.000	0.000	0.000	0.000
76	C	564	PRO	0	0.016	-0.002	44.040	0.119	0.119	0.000	0.000	0.000	0.000
77	C	565	GLN	0	0.014	0.011	39.453	0.366	0.366	0.000	0.000	0.000	0.000
78	C	566	ILE	0	0.004	0.003	39.397	0.223	0.223	0.000	0.000	0.000	0.000
79	C	567	GLU	-1	-0.860	-0.912	40.320	7.141	7.141	0.000	0.000	0.000	0.000
80	C	568	LYS	1	0.910	0.974	36.739	-8.007	-8.007	0.000	0.000	0.000	0.000
81	C	569	LEU	0	-0.047	-0.019	34.981	0.238	0.238	0.000	0.000	0.000	0.000
82	C	570	LEU	0	-0.044	-0.029	35.673	0.231	0.231	0.000	0.000	0.000	0.000
83	C	571	GLN	0	-0.029	-0.016	36.285	0.002	0.002	0.000	0.000	0.000	0.000
84	C	572	SER	0	-0.034	-0.005	31.377	0.351	0.351	0.000	0.000	0.000	0.000
85	C	573	LYS	1	0.934	0.965	24.766	-11.954	-11.954	0.000	0.000	0.000	0.000
86	C	574	TYR	0	-0.012	-0.006	24.831	0.403	0.403	0.000	0.000	0.000	0.000
87	C	575	GLU	-1	-0.762	-0.878	29.265	8.744	8.744	0.000	0.000	0.000	0.000
88	C	576	SER	0	0.000	-0.001	28.850	-0.282	-0.282	0.000	0.000	0.000	0.000
89	C	577	TYR	0	0.006	-0.001	29.019	-0.138	-0.138	0.000	0.000	0.000	0.000
90	C	578	VAL	0	0.064	0.039	33.244	-0.310	-0.310	0.000	0.000	0.000	0.000
91	C	579	GLN	0	0.014	-0.007	34.853	-0.538	-0.538	0.000	0.000	0.000	0.000
92	C	580	THR	0	-0.016	-0.013	35.488	-0.160	-0.160	0.000	0.000	0.000	0.000
93	C	581	GLY	0	0.027	0.004	37.295	-0.234	-0.234	0.000	0.000	0.000	0.000
94	C	582	CYS	0	-0.034	-0.024	38.842	-0.263	-0.263	0.000	0.000	0.000	0.000
95	C	583	THR	0	-0.037	-0.018	39.465	-0.241	-0.241	0.000	0.000	0.000	0.000
96	C	584	SER	0	-0.010	-0.036	41.568	-0.140	-0.140	0.000	0.000	0.000	0.000
97	C	585	LEU	0	-0.035	-0.008	43.349	-0.196	-0.196	0.000	0.000	0.000	0.000
98	C	586	LYS	1	0.853	0.907	44.284	-7.075	-7.075	0.000	0.000	0.000	0.000
99	C	587	LEU	0	-0.047	0.001	45.671	-0.194	-0.194	0.000	0.000	0.000	0.000
100	C	588	ILE	0	0.014	-0.016	46.640	-0.175	-0.175	0.000	0.000	0.000	0.000
101	C	589	LEU	0	-0.019	-0.014	48.248	-0.159	-0.159	0.000	0.000	0.000	0.000
102	C	590	GLN	0	0.001	-0.018	48.938	-0.042	-0.042	0.000	0.000	0.000	0.000
103	C	591	ARG	1	0.813	0.927	51.658	-6.034	-6.034	0.000	0.000	0.000	0.000
104	C	592	PHE	0	-0.025	-0.030	51.752	-0.095	-0.095	0.000	0.000	0.000	0.000
105	C	593	LEU	0	0.015	0.029	54.027	-0.051	-0.051	0.000	0.000	0.000	0.000
106	C	594	PRO	0	0.038	0.030	55.780	-0.087	-0.087	0.000	0.000	0.000	0.000
107	C	595	LEU	0	-0.025	-0.022	58.330	0.059	0.059	0.000	0.000	0.000	0.000
108	C	596	ILE	0	-0.050	-0.042	54.872	-0.059	-0.059	0.000	0.000	0.000	0.000
109	C	597	THR	0	-0.021	-0.053	58.880	-0.025	-0.025	0.000	0.000	0.000	0.000
110	C	598	ASP	-1	-0.854	-0.886	61.176	5.037	5.037	0.000	0.000	0.000	0.000
111	C	599	ILE	0	-0.081	-0.040	62.075	-0.088	-0.088	0.000	0.000	0.000	0.000
112	C	600	LEU	0	-0.047	-0.010	59.140	-0.067	-0.067	0.000	0.000	0.000	0.000
113	C	610	ILE	0	0.035	0.020	70.355	0.019	0.019	0.000	0.000	0.000	0.000
114	C	611	SER	0	0.037	0.008	66.497	0.015	0.015	0.000	0.000	0.000	0.000
115	C	612	ARG	1	0.900	0.932	65.273	-4.456	-4.456	0.000	0.000	0.000	0.000
116	C	613	GLU	-1	-0.843	-0.919	65.009	4.757	4.757	0.000	0.000	0.000	0.000
117	C	614	GLU	-1	-0.817	-0.887	58.687	5.464	5.464	0.000	0.000	0.000	0.000
118	C	615	ARG	1	0.940	0.970	60.440	-4.886	-4.886	0.000	0.000	0.000	0.000
119	C	616	LEU	0	0.042	0.028	60.469	0.075	0.075	0.000	0.000	0.000	0.000
120	C	617	HIS	0	0.053	0.026	58.675	0.003	0.003	0.000	0.000	0.000	0.000
121	C	618	LYS	1	0.845	0.893	55.812	-5.498	-5.498	0.000	0.000	0.000	0.000
122	C	619	CYS	0	-0.001	0.010	56.004	0.108	0.108	0.000	0.000	0.000	0.000
123	C	620	ARG	1	0.916	0.960	57.214	-4.994	-4.994	0.000	0.000	0.000	0.000
124	C	621	LEU	0	-0.034	-0.003	51.812	0.059	0.059	0.000	0.000	0.000	0.000
125	C	622	CYS	0	0.026	0.009	52.267	0.131	0.131	0.000	0.000	0.000	0.000
126	C	623	PHE	0	0.037	0.016	52.638	0.089	0.089	0.000	0.000	0.000	0.000
127	C	624	LYS	1	0.934	0.962	52.729	-5.850	-5.850	0.000	0.000	0.000	0.000
128	C	625	GLN	0	0.001	-0.019	48.818	0.013	0.013	0.000	0.000	0.000	0.000
129	C	626	LEU	0	0.030	0.014	49.068	0.113	0.113	0.000	0.000	0.000	0.000
130	C	627	LYS	1	0.911	0.960	50.421	-5.587	-5.587	0.000	0.000	0.000	0.000
131	C	628	SER	0	-0.047	-0.039	47.287	-0.039	-0.039	0.000	0.000	0.000	0.000
132	C	629	ILE	0	0.050	0.022	44.674	0.092	0.092	0.000	0.000	0.000	0.000
133	C	630	SER	0	-0.013	-0.008	46.267	0.079	0.079	0.000	0.000	0.000	0.000
134	C	631	GLY	0	-0.038	-0.015	48.377	-0.003	-0.003	0.000	0.000	0.000	0.000
135	C	632	LEU	0	0.011	0.005	40.511	0.048	0.048	0.000	0.000	0.000	0.000
136	C	633	VAL	0	-0.033	-0.024	43.381	0.142	0.142	0.000	0.000	0.000	0.000
137	C	634	LYS	1	0.831	0.930	44.674	-6.116	-6.116	0.000	0.000	0.000	0.000
138	C	635	SER	0	-0.041	-0.006	41.239	0.009	0.009	0.000	0.000	0.000	0.000
139	C	644	GLY	0	0.072	0.026	38.276	0.037	0.037	0.000	0.000	0.000	0.000
140	C	645	SER	0	0.016	-0.002	39.225	-0.208	-0.208	0.000	0.000	0.000	0.000
141	C	646	ALA	0	0.023	0.021	39.337	-0.167	-0.167	0.000	0.000	0.000	0.000
142	C	647	PHE	0	0.065	0.029	37.286	-0.173	-0.173	0.000	0.000	0.000	0.000
143	C	648	ARG	1	0.964	0.985	42.492	-6.706	-6.706	0.000	0.000	0.000	0.000
144	C	649	GLU	-1	-0.804	-0.886	44.639	6.690	6.690	0.000	0.000	0.000	0.000
145	C	650	LEU	0	0.028	0.003	42.523	-0.170	-0.170	0.000	0.000	0.000	0.000
146	C	651	HIS	0	-0.013	-0.015	46.484	-0.261	-0.261	0.000	0.000	0.000	0.000
147	C	652	LEU	0	-0.038	-0.018	48.374	-0.148	-0.148	0.000	0.000	0.000	0.000
148	C	653	LEU	0	-0.020	-0.011	47.706	-0.130	-0.130	0.000	0.000	0.000	0.000
149	C	654	MET	0	-0.061	-0.006	48.134	-0.022	-0.022	0.000	0.000	0.000	0.000
150	C	655	ALA	0	0.008	0.009	51.573	-0.019	-0.019	0.000	0.000	0.000	0.000
151	C	656	SER	0	-0.042	-0.006	54.127	-0.131	-0.131	0.000	0.000	0.000	0.000

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