FMO DATABASE

FMODB ID: 2NR8R

Calculation Name: 1PAQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PAQ

Chain ID: A

ChEMBL ID:

UniProt ID: P32501

Base Structure: X-ray

Registration Date: 2023-09-23

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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1784063.449941
FMO2-HF: Nuclear repulsion	1717569.188717
FMO2-HF: Total energy	-66494.261224
FMO2-MP2: Total energy	-66689.376311

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:544:ASP)

Summations of interaction energy for fragment #1(A:544: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.
22.93	23.187	15.31	-8.81	-6.756	0.101

Interaction energy analysis for fragmet #1(A:544: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 : -0.934

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	546	GLU	-1	-0.915	-0.956	3.819	28.751	30.596	-0.001	-0.747	-1.097	0.002
4	A	547	LYS	1	0.890	0.929	1.666	-123.588	-125.589	15.283	-7.956	-5.325	0.099
5	A	548	GLU	-1	-0.823	-0.894	5.018	24.672	24.672	0.000	0.000	0.000	0.000
6	A	549	GLY	0	0.026	0.023	6.744	-3.625	-3.625	0.000	0.000	0.000	0.000
7	A	550	ILE	0	-0.031	-0.007	7.979	-2.564	-2.564	0.000	0.000	0.000	0.000
8	A	551	ALA	0	0.020	0.016	9.283	-2.402	-2.402	0.000	0.000	0.000	0.000
9	A	552	THR	0	-0.042	-0.036	10.342	-2.283	-2.283	0.000	0.000	0.000	0.000
10	A	553	VAL	0	0.001	-0.001	12.575	-1.723	-1.723	0.000	0.000	0.000	0.000
11	A	554	GLU	-1	-0.838	-0.917	12.865	21.044	21.044	0.000	0.000	0.000	0.000
12	A	555	ARG	1	0.762	0.833	11.025	-22.581	-22.581	0.000	0.000	0.000	0.000
13	A	556	ALA	0	-0.010	0.005	16.391	-1.012	-1.012	0.000	0.000	0.000	0.000
14	A	557	MET	0	-0.030	-0.015	17.239	-1.203	-1.203	0.000	0.000	0.000	0.000
15	A	558	GLU	-1	-0.901	-0.933	19.046	13.789	13.789	0.000	0.000	0.000	0.000
16	A	559	ASN	0	-0.100	-0.053	20.516	-1.124	-1.124	0.000	0.000	0.000	0.000
17	A	560	ASN	0	-0.051	-0.040	22.456	-0.229	-0.229	0.000	0.000	0.000	0.000
18	A	561	HIS	0	0.005	0.019	18.899	-0.251	-0.251	0.000	0.000	0.000	0.000
19	A	562	ASP	-1	-0.801	-0.865	23.243	11.898	11.898	0.000	0.000	0.000	0.000
20	A	563	LEU	0	0.041	-0.003	22.081	0.515	0.515	0.000	0.000	0.000	0.000
21	A	564	ASP	-1	-0.824	-0.857	21.481	12.167	12.167	0.000	0.000	0.000	0.000
22	A	565	THR	0	-0.041	-0.058	20.603	0.450	0.450	0.000	0.000	0.000	0.000
23	A	566	ALA	0	0.016	0.010	18.233	0.674	0.674	0.000	0.000	0.000	0.000
24	A	567	LEU	0	-0.019	-0.011	17.020	1.080	1.080	0.000	0.000	0.000	0.000
25	A	568	LEU	0	0.008	0.020	17.495	0.626	0.626	0.000	0.000	0.000	0.000
26	A	569	GLU	-1	-0.823	-0.871	13.459	19.812	19.812	0.000	0.000	0.000	0.000
27	A	570	LEU	0	0.033	0.024	11.470	1.196	1.196	0.000	0.000	0.000	0.000
28	A	571	ASN	0	-0.011	-0.019	12.678	1.340	1.340	0.000	0.000	0.000	0.000
29	A	572	THR	0	-0.032	-0.020	13.934	0.104	0.104	0.000	0.000	0.000	0.000
30	A	573	LEU	0	0.008	0.000	8.284	0.780	0.780	0.000	0.000	0.000	0.000
31	A	574	ARG	1	0.866	0.944	9.274	-16.610	-16.610	0.000	0.000	0.000	0.000
32	A	575	MET	0	-0.043	-0.024	10.201	0.240	0.240	0.000	0.000	0.000	0.000
33	A	576	SER	0	-0.036	-0.020	10.272	-0.148	-0.148	0.000	0.000	0.000	0.000
34	A	577	MET	0	-0.064	-0.016	3.403	0.519	0.932	0.028	-0.107	-0.334	0.000
35	A	578	ASN	0	-0.092	-0.034	6.660	0.622	0.622	0.000	0.000	0.000	0.000
36	A	579	VAL	0	-0.022	0.014	6.658	0.729	0.729	0.000	0.000	0.000	0.000
37	A	580	THR	0	-0.031	-0.055	9.059	-2.820	-2.820	0.000	0.000	0.000	0.000
38	A	581	TYR	0	0.042	-0.011	11.755	0.982	0.982	0.000	0.000	0.000	0.000
39	A	582	HIS	1	0.853	0.941	12.349	-19.639	-19.639	0.000	0.000	0.000	0.000
40	A	583	GLU	-1	-0.755	-0.869	7.750	24.930	24.930	0.000	0.000	0.000	0.000
41	A	584	VAL	0	-0.023	-0.010	10.278	0.716	0.716	0.000	0.000	0.000	0.000
42	A	585	ARG	1	0.773	0.868	12.099	-16.418	-16.418	0.000	0.000	0.000	0.000
43	A	586	ILE	0	0.013	0.009	10.101	-0.557	-0.557	0.000	0.000	0.000	0.000
44	A	587	ALA	0	-0.006	0.006	9.001	-0.242	-0.242	0.000	0.000	0.000	0.000
45	A	588	THR	0	0.011	-0.001	10.743	-0.732	-0.732	0.000	0.000	0.000	0.000
46	A	589	ILE	0	0.013	0.009	14.381	-0.733	-0.733	0.000	0.000	0.000	0.000
47	A	590	THR	0	-0.017	-0.033	11.733	-0.292	-0.292	0.000	0.000	0.000	0.000
48	A	591	ALA	0	0.004	0.015	13.243	-0.625	-0.625	0.000	0.000	0.000	0.000
49	A	592	LEU	0	-0.005	-0.016	14.658	-0.939	-0.939	0.000	0.000	0.000	0.000
50	A	593	LEU	0	-0.011	-0.004	17.412	-0.789	-0.789	0.000	0.000	0.000	0.000
51	A	594	ARG	1	0.912	0.951	10.181	-25.064	-25.064	0.000	0.000	0.000	0.000
52	A	595	ARG	1	0.820	0.914	17.735	-14.671	-14.671	0.000	0.000	0.000	0.000
53	A	596	VAL	0	-0.024	-0.015	20.199	-0.716	-0.716	0.000	0.000	0.000	0.000
54	A	597	TYR	0	0.013	-0.004	20.446	-0.473	-0.473	0.000	0.000	0.000	0.000
55	A	598	HIS	0	0.003	0.002	20.805	-0.331	-0.331	0.000	0.000	0.000	0.000
56	A	599	PHE	0	-0.001	-0.012	22.750	-0.509	-0.509	0.000	0.000	0.000	0.000
57	A	600	ILE	0	-0.005	0.009	25.584	-0.554	-0.554	0.000	0.000	0.000	0.000
58	A	601	ALA	0	0.013	0.012	24.605	-0.432	-0.432	0.000	0.000	0.000	0.000
59	A	602	THR	0	-0.083	-0.055	25.518	-0.170	-0.170	0.000	0.000	0.000	0.000
60	A	603	GLN	0	-0.061	-0.036	28.192	-0.519	-0.519	0.000	0.000	0.000	0.000
61	A	604	THR	0	-0.051	-0.006	28.803	-0.218	-0.218	0.000	0.000	0.000	0.000
62	A	605	LEU	0	-0.046	-0.018	28.125	-0.221	-0.221	0.000	0.000	0.000	0.000
63	A	606	GLY	0	0.055	0.042	30.545	0.117	0.117	0.000	0.000	0.000	0.000
64	A	607	PRO	0	0.018	-0.010	29.100	0.221	0.221	0.000	0.000	0.000	0.000
65	A	608	LYS	1	1.017	1.011	28.718	-8.674	-8.674	0.000	0.000	0.000	0.000
66	A	609	ASP	-1	-0.897	-0.952	30.067	9.433	9.433	0.000	0.000	0.000	0.000
67	A	610	ALA	0	0.009	-0.001	26.175	0.135	0.135	0.000	0.000	0.000	0.000
68	A	611	VAL	0	0.015	0.015	25.262	0.357	0.357	0.000	0.000	0.000	0.000
69	A	612	VAL	0	0.007	0.008	26.270	0.207	0.207	0.000	0.000	0.000	0.000
70	A	613	LYS	1	0.878	0.948	26.806	-11.036	-11.036	0.000	0.000	0.000	0.000
71	A	614	VAL	0	-0.037	-0.009	21.495	0.131	0.131	0.000	0.000	0.000	0.000
72	A	615	PHE	0	0.059	0.002	20.837	0.236	0.236	0.000	0.000	0.000	0.000
73	A	616	ASN	0	0.048	0.045	24.883	0.168	0.168	0.000	0.000	0.000	0.000
74	A	617	GLN	0	-0.071	-0.010	25.268	-0.469	-0.469	0.000	0.000	0.000	0.000
75	A	618	TRP	0	0.030	-0.014	20.516	0.288	0.288	0.000	0.000	0.000	0.000
76	A	619	GLY	0	0.041	0.026	21.491	0.549	0.549	0.000	0.000	0.000	0.000
77	A	620	LEU	0	0.008	-0.004	23.035	0.100	0.100	0.000	0.000	0.000	0.000
78	A	621	LEU	0	-0.055	-0.024	17.783	-0.059	-0.059	0.000	0.000	0.000	0.000
79	A	622	PHE	0	0.032	0.002	17.685	0.241	0.241	0.000	0.000	0.000	0.000
80	A	623	LYS	1	0.840	0.929	21.112	-10.265	-10.265	0.000	0.000	0.000	0.000
81	A	624	ARG	1	0.736	0.827	21.847	-12.386	-12.386	0.000	0.000	0.000	0.000
82	A	625	GLN	0	-0.050	-0.043	16.180	0.751	0.751	0.000	0.000	0.000	0.000
83	A	626	ALA	0	0.056	0.035	18.302	0.771	0.771	0.000	0.000	0.000	0.000
84	A	627	PHE	0	-0.078	-0.031	19.108	-0.579	-0.579	0.000	0.000	0.000	0.000
85	A	628	ASP	-1	-0.861	-0.923	23.618	11.906	11.906	0.000	0.000	0.000	0.000
86	A	629	GLU	-1	-0.762	-0.881	24.800	10.157	10.157	0.000	0.000	0.000	0.000
87	A	630	GLU	-1	-0.926	-0.960	22.442	12.861	12.861	0.000	0.000	0.000	0.000
88	A	631	GLU	-1	-0.783	-0.882	18.612	15.760	15.760	0.000	0.000	0.000	0.000
89	A	632	TYR	0	0.003	-0.013	20.980	0.539	0.539	0.000	0.000	0.000	0.000
90	A	633	ILE	0	0.011	0.017	23.559	0.162	0.162	0.000	0.000	0.000	0.000
91	A	634	ASP	-1	-0.773	-0.862	17.425	17.305	17.305	0.000	0.000	0.000	0.000
92	A	635	LEU	0	-0.046	-0.013	18.676	0.605	0.605	0.000	0.000	0.000	0.000
93	A	636	MET	0	-0.002	0.002	20.165	0.249	0.249	0.000	0.000	0.000	0.000
94	A	637	ASN	0	0.032	0.019	20.817	-0.279	-0.279	0.000	0.000	0.000	0.000
95	A	638	ILE	0	-0.001	-0.001	15.087	0.429	0.429	0.000	0.000	0.000	0.000
96	A	639	ILE	0	-0.026	-0.012	17.863	0.451	0.451	0.000	0.000	0.000	0.000
97	A	640	MET	0	-0.022	-0.003	20.061	-0.230	-0.230	0.000	0.000	0.000	0.000
98	A	641	GLU	-1	-0.890	-0.926	17.976	15.884	15.884	0.000	0.000	0.000	0.000
99	A	642	LYS	1	0.812	0.887	11.146	-23.062	-23.062	0.000	0.000	0.000	0.000
100	A	643	ILE	0	-0.030	0.001	17.354	0.083	0.083	0.000	0.000	0.000	0.000
101	A	644	VAL	0	-0.031	-0.015	20.773	-0.307	-0.307	0.000	0.000	0.000	0.000
102	A	645	GLU	-1	-0.894	-0.930	13.403	22.139	22.139	0.000	0.000	0.000	0.000
103	A	646	GLN	0	-0.052	-0.024	17.377	0.984	0.984	0.000	0.000	0.000	0.000
104	A	647	SER	0	-0.022	-0.011	18.780	-0.284	-0.284	0.000	0.000	0.000	0.000
105	A	648	PHE	0	-0.002	0.001	20.882	-0.266	-0.266	0.000	0.000	0.000	0.000
106	A	649	ASP	-1	-0.889	-0.942	24.740	11.147	11.147	0.000	0.000	0.000	0.000
107	A	650	LYN	0	-0.051	-0.030	27.474	-0.311	-0.311	0.000	0.000	0.000	0.000
108	A	651	PRO	0	0.034	0.010	25.489	-0.025	-0.025	0.000	0.000	0.000	0.000
109	A	652	ASP	-1	-0.810	-0.904	26.934	9.952	9.952	0.000	0.000	0.000	0.000
110	A	653	LEU	0	-0.008	0.003	29.578	-0.105	-0.105	0.000	0.000	0.000	0.000
111	A	654	ILE	0	-0.007	0.011	24.057	-0.133	-0.133	0.000	0.000	0.000	0.000
112	A	655	LEU	0	0.031	0.016	24.116	0.118	0.118	0.000	0.000	0.000	0.000
113	A	656	PHE	0	-0.006	-0.012	26.459	-0.080	-0.080	0.000	0.000	0.000	0.000
114	A	657	SER	0	-0.037	-0.042	28.590	-0.232	-0.232	0.000	0.000	0.000	0.000
115	A	658	ALA	0	-0.021	-0.005	24.201	-0.065	-0.065	0.000	0.000	0.000	0.000
116	A	659	LEU	0	0.009	0.001	24.938	0.024	0.024	0.000	0.000	0.000	0.000
117	A	660	VAL	0	0.012	0.015	27.713	-0.177	-0.177	0.000	0.000	0.000	0.000
118	A	661	SER	0	-0.038	-0.021	27.505	0.000	0.000	0.000	0.000	0.000	0.000
119	A	662	LEU	0	-0.042	-0.026	23.354	0.057	0.057	0.000	0.000	0.000	0.000
120	A	663	TYR	0	-0.045	-0.036	27.787	-0.056	-0.056	0.000	0.000	0.000	0.000
121	A	664	ASP	-1	-0.930	-0.974	31.279	8.886	8.886	0.000	0.000	0.000	0.000
122	A	665	ASN	0	-0.114	-0.075	29.352	-0.247	-0.247	0.000	0.000	0.000	0.000
123	A	666	ASP	-1	-0.851	-0.914	30.445	9.164	9.164	0.000	0.000	0.000	0.000
124	A	667	ILE	0	-0.139	-0.075	24.661	0.216	0.216	0.000	0.000	0.000	0.000
125	A	668	ILE	0	-0.031	-0.013	26.228	0.409	0.409	0.000	0.000	0.000	0.000
126	A	669	GLU	-1	-0.794	-0.897	29.004	9.553	9.553	0.000	0.000	0.000	0.000
127	A	670	GLU	-1	-0.775	-0.893	32.051	8.733	8.733	0.000	0.000	0.000	0.000
128	A	671	ASP	-1	-0.930	-0.944	33.926	8.612	8.612	0.000	0.000	0.000	0.000
129	A	672	VAL	0	-0.032	-0.026	27.561	0.201	0.201	0.000	0.000	0.000	0.000
130	A	673	ILE	0	-0.047	-0.022	29.633	0.325	0.325	0.000	0.000	0.000	0.000
131	A	674	TYR	0	-0.053	-0.058	30.891	0.177	0.177	0.000	0.000	0.000	0.000
132	A	675	LYS	1	0.872	0.927	30.086	-9.305	-9.305	0.000	0.000	0.000	0.000
133	A	676	TRP	0	-0.022	-0.025	24.617	0.021	0.021	0.000	0.000	0.000	0.000
134	A	677	TRP	0	0.002	-0.012	28.280	0.287	0.287	0.000	0.000	0.000	0.000
135	A	678	ASP	-1	-0.940	-0.973	30.732	8.996	8.996	0.000	0.000	0.000	0.000
136	A	679	ASN	0	-0.142	-0.078	27.667	-0.048	-0.048	0.000	0.000	0.000	0.000
137	A	680	VAL	0	-0.018	0.018	26.474	0.545	0.545	0.000	0.000	0.000	0.000
138	A	681	SER	0	0.008	0.003	24.531	-0.366	-0.366	0.000	0.000	0.000	0.000
139	A	682	THR	0	0.022	-0.008	26.676	-0.147	-0.147	0.000	0.000	0.000	0.000
140	A	683	ASP	-1	-0.900	-0.941	25.103	11.928	11.928	0.000	0.000	0.000	0.000
141	A	684	PRO	0	0.060	0.010	27.938	0.138	0.138	0.000	0.000	0.000	0.000
142	A	685	ARG	1	0.846	0.939	19.721	-14.741	-14.741	0.000	0.000	0.000	0.000
143	A	686	TYR	0	-0.025	-0.046	20.731	0.342	0.342	0.000	0.000	0.000	0.000
144	A	687	ASP	-1	-0.841	-0.919	26.483	9.816	9.816	0.000	0.000	0.000	0.000
145	A	688	GLU	-1	-0.892	-0.940	28.077	9.832	9.832	0.000	0.000	0.000	0.000
146	A	689	VAL	0	-0.003	-0.014	24.658	-0.146	-0.146	0.000	0.000	0.000	0.000
147	A	690	LYS	1	0.880	0.924	28.053	-10.624	-10.624	0.000	0.000	0.000	0.000
148	A	691	LYS	1	0.743	0.883	30.390	-10.079	-10.079	0.000	0.000	0.000	0.000
149	A	692	LEU	0	-0.023	0.002	32.511	-0.363	-0.363	0.000	0.000	0.000	0.000
150	A	693	THR	0	0.080	0.027	29.232	-0.136	-0.136	0.000	0.000	0.000	0.000
151	A	694	VAL	0	0.008	0.022	32.206	-0.147	-0.147	0.000	0.000	0.000	0.000
152	A	695	LYS	1	0.837	0.914	34.633	-8.523	-8.523	0.000	0.000	0.000	0.000
153	A	696	TRP	0	0.009	0.011	30.147	-0.168	-0.168	0.000	0.000	0.000	0.000
154	A	697	VAL	0	0.058	0.029	32.373	-0.109	-0.109	0.000	0.000	0.000	0.000
155	A	698	GLU	-1	-0.853	-0.917	35.499	7.501	7.501	0.000	0.000	0.000	0.000
156	A	699	TRP	0	-0.068	-0.033	38.736	-0.331	-0.331	0.000	0.000	0.000	0.000
157	A	700	LEU	0	-0.003	-0.001	34.614	-0.159	-0.159	0.000	0.000	0.000	0.000
158	A	701	GLN	0	-0.003	-0.008	37.687	0.051	0.051	0.000	0.000	0.000	0.000
159	A	702	ASN	0	-0.160	-0.096	40.582	-0.346	-0.346	0.000	0.000	0.000	0.000
160	A	703	ALA	0	-0.074	-0.023	41.747	-0.199	-0.199	0.000	0.000	0.000	0.000
161	A	704	ASP	-1	-0.939	-0.923	40.373	7.315	7.315	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:544:ASP)