FMO DATABASE

FMODB ID: R52Q8

Calculation Name: 1ZHI-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZHI

Chain ID: B

ChEMBL ID:

UniProt ID: P54784

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	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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1088212.366676
FMO2-HF: Nuclear repulsion	1036785.285198
FMO2-HF: Total energy	-51427.081478
FMO2-MP2: Total energy	-51576.995608

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(B:487:GLU)

Summations of interaction energy for fragment #1(B:487:GLU)

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.
-133.332	-129.952	25.871	-14.837	-14.415	0.089

Interaction energy analysis for fragmet #1(B:487:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.938 / q_NPA : -0.970

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

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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	B	489	TYR	0	-0.002	0.008	2.624	-13.538	-9.054	0.637	-2.291	-2.829	0.020
4	B	490	VAL	0	0.039	0.024	6.514	-3.337	-3.337	0.000	0.000	0.000	0.000
5	B	491	SER	0	-0.045	-0.035	9.109	-3.271	-3.271	0.000	0.000	0.000	0.000
6	B	492	PRO	0	0.022	-0.009	10.165	1.999	1.999	0.000	0.000	0.000	0.000
7	B	493	ARG	1	0.813	0.892	11.126	-17.950	-17.950	0.000	0.000	0.000	0.000
8	B	494	PHE	0	-0.024	-0.012	9.762	0.379	0.379	0.000	0.000	0.000	0.000
9	B	495	LEU	0	0.047	0.023	2.325	-2.185	-0.821	1.074	-0.810	-1.629	0.000
10	B	496	VAL	0	-0.024	-0.004	4.594	-3.576	-3.230	-0.001	-0.082	-0.263	0.000
11	B	497	ALA	0	0.065	0.020	2.243	6.344	7.004	5.145	-2.725	-3.081	-0.018
12	B	498	ASP	-1	-0.874	-0.941	3.540	40.486	40.744	0.021	0.004	-0.284	0.000
13	B	499	GLY	0	0.027	0.017	6.154	-3.815	-3.815	0.000	0.000	0.000	0.000
14	B	500	PHE	0	0.005	-0.012	7.135	-4.053	-4.053	0.000	0.000	0.000	0.000
15	B	501	LEU	0	0.018	0.022	6.912	3.198	3.198	0.000	0.000	0.000	0.000
16	B	502	ILE	0	0.013	-0.010	5.252	-2.437	-2.437	0.000	0.000	0.000	0.000
17	B	503	ASP	-1	-0.766	-0.850	8.883	21.294	21.294	0.000	0.000	0.000	0.000
18	B	504	LEU	0	0.012	-0.014	7.224	-0.653	-0.653	0.000	0.000	0.000	0.000
19	B	505	ALA	0	-0.042	-0.008	11.225	-0.723	-0.723	0.000	0.000	0.000	0.000
20	B	506	GLU	-1	-0.882	-0.926	14.674	15.506	15.506	0.000	0.000	0.000	0.000
21	B	507	GLU	-1	-0.868	-0.890	12.181	20.969	20.969	0.000	0.000	0.000	0.000
22	B	508	LYS	1	0.870	0.913	12.629	-18.274	-18.274	0.000	0.000	0.000	0.000
23	B	509	PRO	0	0.035	0.015	11.392	0.560	0.560	0.000	0.000	0.000	0.000
24	B	510	ILE	0	-0.048	-0.024	12.324	-1.836	-1.836	0.000	0.000	0.000	0.000
25	B	511	ASN	0	0.044	0.020	13.394	1.150	1.150	0.000	0.000	0.000	0.000
26	B	512	PRO	0	0.040	0.016	12.207	-0.444	-0.444	0.000	0.000	0.000	0.000
27	B	513	LYS	1	0.918	0.955	14.526	-14.355	-14.355	0.000	0.000	0.000	0.000
28	B	514	ASP	-1	-0.833	-0.913	17.480	14.214	14.214	0.000	0.000	0.000	0.000
29	B	515	PRO	0	0.032	0.006	19.239	0.188	0.188	0.000	0.000	0.000	0.000
30	B	516	ARG	1	0.925	0.968	19.376	-14.329	-14.329	0.000	0.000	0.000	0.000
31	B	517	LEU	0	-0.005	-0.009	14.868	0.144	0.144	0.000	0.000	0.000	0.000
32	B	518	LEU	0	-0.043	-0.019	18.346	0.070	0.070	0.000	0.000	0.000	0.000
33	B	519	THR	0	-0.044	-0.012	21.353	-0.411	-0.411	0.000	0.000	0.000	0.000
34	B	520	LEU	0	-0.061	-0.031	17.522	-0.017	-0.017	0.000	0.000	0.000	0.000
35	B	521	LEU	0	-0.016	0.010	13.491	0.515	0.515	0.000	0.000	0.000	0.000
36	B	522	LYS	1	0.925	0.961	16.858	-15.850	-15.850	0.000	0.000	0.000	0.000
37	B	523	ASP	-1	-0.830	-0.920	17.370	13.614	13.614	0.000	0.000	0.000	0.000
38	B	524	HIS	0	-0.002	-0.015	15.522	0.820	0.820	0.000	0.000	0.000	0.000
39	B	525	GLN	0	0.035	0.011	13.107	0.022	0.022	0.000	0.000	0.000	0.000
40	B	526	ARG	1	0.857	0.929	12.857	-13.826	-13.826	0.000	0.000	0.000	0.000
41	B	527	ALA	0	0.012	0.006	14.636	0.338	0.338	0.000	0.000	0.000	0.000
42	B	528	MET	0	-0.004	0.001	10.275	0.543	0.543	0.000	0.000	0.000	0.000
43	B	529	ILE	0	0.012	0.006	9.920	1.077	1.077	0.000	0.000	0.000	0.000
44	B	530	ASP	-1	-0.872	-0.929	11.369	16.032	16.032	0.000	0.000	0.000	0.000
45	B	531	GLN	0	-0.095	-0.043	12.551	-0.115	-0.115	0.000	0.000	0.000	0.000
46	B	532	MET	0	-0.008	0.003	6.872	0.555	0.555	0.000	0.000	0.000	0.000
47	B	533	ASN	0	-0.094	-0.036	9.109	0.984	0.984	0.000	0.000	0.000	0.000
48	B	534	LEU	0	0.018	0.013	8.330	1.571	1.571	0.000	0.000	0.000	0.000
49	B	535	VAL	0	0.010	0.003	11.323	-1.780	-1.780	0.000	0.000	0.000	0.000
50	B	536	LYS	1	0.834	0.904	13.469	-14.890	-14.890	0.000	0.000	0.000	0.000
51	B	537	TRP	0	0.057	0.011	13.497	-0.874	-0.874	0.000	0.000	0.000	0.000
52	B	538	ASN	0	-0.053	-0.040	18.099	-0.798	-0.798	0.000	0.000	0.000	0.000
53	B	539	ASP	-1	-0.862	-0.904	19.082	13.987	13.987	0.000	0.000	0.000	0.000
54	B	540	PHE	0	0.034	0.002	15.344	-0.163	-0.163	0.000	0.000	0.000	0.000
55	B	541	LYS	1	0.864	0.934	21.637	-11.044	-11.044	0.000	0.000	0.000	0.000
56	B	542	LYS	1	0.965	0.973	24.918	-10.102	-10.102	0.000	0.000	0.000	0.000
57	B	543	TYR	0	0.012	0.033	21.496	-0.520	-0.520	0.000	0.000	0.000	0.000
58	B	544	GLN	0	-0.066	-0.049	25.858	-0.195	-0.195	0.000	0.000	0.000	0.000
59	B	545	ASP	-1	-0.808	-0.871	25.608	11.083	11.083	0.000	0.000	0.000	0.000
60	B	546	PRO	0	-0.026	-0.008	21.812	0.273	0.273	0.000	0.000	0.000	0.000
61	B	547	ILE	0	-0.022	-0.015	17.015	-0.275	-0.275	0.000	0.000	0.000	0.000
62	B	548	PRO	0	-0.010	0.016	17.597	0.789	0.789	0.000	0.000	0.000	0.000
63	B	549	LEU	0	-0.010	-0.020	12.120	0.278	0.278	0.000	0.000	0.000	0.000
64	B	550	LYS	1	0.840	0.900	11.425	-18.606	-18.606	0.000	0.000	0.000	0.000
65	B	551	ALA	0	0.005	-0.001	8.070	0.642	0.642	0.000	0.000	0.000	0.000
66	B	552	LYS	1	0.987	0.987	6.257	-33.165	-33.165	0.000	0.000	0.000	0.000
67	B	553	THR	0	-0.021	-0.027	1.657	-29.396	-34.282	18.978	-8.384	-5.707	0.083
68	B	554	LEU	0	0.005	0.012	4.637	-3.641	-3.604	-0.001	-0.037	0.001	0.000
69	B	555	PHE	0	0.019	-0.004	7.883	-2.282	-2.282	0.000	0.000	0.000	0.000
70	B	556	LYS	1	0.912	0.972	4.938	-54.423	-54.360	-0.001	-0.001	-0.061	0.000
71	B	557	PHE	0	-0.002	-0.008	3.501	-3.786	-2.732	0.019	-0.511	-0.562	0.004
72	B	558	CYS	0	-0.066	-0.009	8.492	-3.110	-3.110	0.000	0.000	0.000	0.000
73	B	559	LYS	1	0.820	0.887	11.692	-20.125	-20.125	0.000	0.000	0.000	0.000
74	B	560	GLN	0	-0.052	-0.023	12.779	-1.689	-1.689	0.000	0.000	0.000	0.000
75	B	561	ILE	0	-0.008	0.002	17.055	-0.880	-0.880	0.000	0.000	0.000	0.000
76	B	562	LYS	1	0.898	0.933	20.541	-14.139	-14.139	0.000	0.000	0.000	0.000
77	B	563	LYS	1	0.897	0.957	23.035	-12.635	-12.635	0.000	0.000	0.000	0.000
78	B	564	LYS	1	0.919	0.963	25.227	-9.872	-9.872	0.000	0.000	0.000	0.000
79	B	565	PHE	0	0.011	-0.010	22.988	0.051	0.051	0.000	0.000	0.000	0.000
80	B	566	LEU	0	0.030	0.018	28.010	-0.251	-0.251	0.000	0.000	0.000	0.000
81	B	567	ARG	1	0.904	0.969	26.236	-10.704	-10.704	0.000	0.000	0.000	0.000
82	B	568	GLY	0	0.067	0.024	28.166	-0.483	-0.483	0.000	0.000	0.000	0.000
83	B	569	ALA	0	0.040	0.007	29.310	0.236	0.236	0.000	0.000	0.000	0.000
84	B	570	ASP	-1	-0.831	-0.911	26.932	11.810	11.810	0.000	0.000	0.000	0.000
85	B	571	PHE	0	-0.046	-0.034	24.118	0.474	0.474	0.000	0.000	0.000	0.000
86	B	572	LYS	1	0.893	0.954	23.082	-11.587	-11.587	0.000	0.000	0.000	0.000
87	B	573	LEU	0	-0.038	-0.020	21.862	-0.600	-0.600	0.000	0.000	0.000	0.000
88	B	574	HIS	0	-0.063	-0.057	25.245	0.009	0.009	0.000	0.000	0.000	0.000
89	B	575	THR	0	-0.001	-0.020	27.874	0.171	0.171	0.000	0.000	0.000	0.000
90	B	576	LEU	0	-0.030	-0.014	29.123	-0.289	-0.289	0.000	0.000	0.000	0.000
91	B	577	PRO	0	0.001	0.007	32.257	0.051	0.051	0.000	0.000	0.000	0.000
92	B	578	THR	0	-0.067	-0.022	34.630	-0.039	-0.039	0.000	0.000	0.000	0.000
93	B	579	GLU	-1	-0.887	-0.969	36.873	7.331	7.331	0.000	0.000	0.000	0.000
94	B	580	ALA	0	-0.038	0.001	39.424	0.164	0.164	0.000	0.000	0.000	0.000
95	B	581	ASN	0	0.050	0.005	37.264	-0.139	-0.139	0.000	0.000	0.000	0.000
96	B	582	LEU	0	-0.020	0.002	40.604	-0.051	-0.051	0.000	0.000	0.000	0.000
97	B	583	LYS	1	0.857	0.928	35.690	-8.889	-8.889	0.000	0.000	0.000	0.000
98	B	584	TYR	0	0.028	0.000	40.439	0.198	0.198	0.000	0.000	0.000	0.000
99	B	585	GLU	-1	-0.769	-0.864	35.671	9.194	9.194	0.000	0.000	0.000	0.000
100	B	586	PRO	0	-0.005	0.005	37.625	0.184	0.184	0.000	0.000	0.000	0.000
101	B	587	GLU	-1	-0.919	-0.962	34.781	9.022	9.022	0.000	0.000	0.000	0.000
102	B	588	ARG	1	0.740	0.869	30.900	-9.517	-9.517	0.000	0.000	0.000	0.000
103	B	589	MET	0	0.004	0.007	32.031	-0.164	-0.164	0.000	0.000	0.000	0.000
104	B	590	THR	0	-0.005	-0.003	30.984	0.377	0.377	0.000	0.000	0.000	0.000
105	B	591	VAL	0	0.003	0.004	25.830	-0.036	-0.036	0.000	0.000	0.000	0.000
106	B	592	LEU	0	-0.024	-0.003	26.058	0.051	0.051	0.000	0.000	0.000	0.000
107	B	593	ALA	0	0.038	0.013	22.074	0.238	0.238	0.000	0.000	0.000	0.000
108	B	594	SER	0	-0.020	-0.003	18.085	-0.751	-0.751	0.000	0.000	0.000	0.000
109	B	595	CYS	0	-0.038	0.004	17.561	-0.013	-0.013	0.000	0.000	0.000	0.000
110	B	596	VAL	0	0.084	0.029	13.311	-0.069	-0.069	0.000	0.000	0.000	0.000
111	B	597	PRO	0	-0.041	-0.007	16.776	-0.361	-0.361	0.000	0.000	0.000	0.000
112	B	598	ILE	0	0.002	0.001	15.678	0.748	0.748	0.000	0.000	0.000	0.000
113	B	599	LEU	0	-0.030	-0.009	18.780	-0.679	-0.679	0.000	0.000	0.000	0.000
114	B	600	LEU	0	0.000	-0.011	20.291	0.505	0.505	0.000	0.000	0.000	0.000
115	B	601	ASP	-1	-0.855	-0.940	21.887	12.877	12.877	0.000	0.000	0.000	0.000
116	B	602	ASP	-1	-0.847	-0.901	24.039	10.929	10.929	0.000	0.000	0.000	0.000
117	B	603	GLN	0	-0.037	-0.022	26.155	-0.263	-0.263	0.000	0.000	0.000	0.000
118	B	604	THR	0	0.002	0.007	25.829	-0.258	-0.258	0.000	0.000	0.000	0.000
119	B	605	VAL	0	-0.042	-0.025	22.704	0.533	0.533	0.000	0.000	0.000	0.000
120	B	606	GLN	0	0.006	0.000	20.608	0.102	0.102	0.000	0.000	0.000	0.000
121	B	607	TYR	0	0.028	-0.015	19.644	-0.015	-0.015	0.000	0.000	0.000	0.000
122	B	608	LEU	0	0.030	0.037	13.682	-0.292	-0.292	0.000	0.000	0.000	0.000
123	B	609	TYR	0	0.047	0.003	16.207	-0.065	-0.065	0.000	0.000	0.000	0.000
124	B	610	ASP	-1	-0.887	-0.933	12.896	23.201	23.201	0.000	0.000	0.000	0.000
125	B	611	ASP	-1	-0.864	-0.910	15.411	17.488	17.488	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:487:GLU)