FMO DATABASE

FMODB ID: ZY87N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1087143.754587
FMO2-HF: Nuclear repulsion	1035717.979618
FMO2-HF: Total energy	-51425.774969
FMO2-MP2: Total energy	-51575.677386

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.
-95.911	-84.274	8.182	-8.97	-10.849	0.033

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 : -0.983 / q_NPA : -1.018

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	-0.003	0.003	3.111	-2.583	0.652	0.060	-1.542	-1.753	0.009
4	B	490	VAL	0	0.036	0.025	6.590	-3.232	-3.232	0.000	0.000	0.000	0.000
5	B	491	SER	0	-0.052	-0.044	9.118	-3.345	-3.345	0.000	0.000	0.000	0.000
6	B	492	PRO	0	0.018	-0.007	9.954	2.016	2.016	0.000	0.000	0.000	0.000
7	B	493	ARG	1	0.825	0.908	11.100	-17.803	-17.803	0.000	0.000	0.000	0.000
8	B	494	PHE	0	-0.036	-0.013	9.703	0.236	0.236	0.000	0.000	0.000	0.000
9	B	495	LEU	0	0.064	0.028	2.012	-0.713	-0.886	2.306	-0.537	-1.596	-0.004
10	B	496	VAL	0	-0.009	0.003	4.579	-3.871	-3.523	-0.001	-0.073	-0.274	0.000
11	B	497	ALA	0	0.065	0.018	2.366	6.565	7.577	4.204	-2.504	-2.712	-0.015
12	B	498	ASP	-1	-0.873	-0.941	3.561	37.438	37.682	0.019	-0.003	-0.261	0.000
13	B	499	GLY	0	0.028	0.017	6.330	-3.788	-3.788	0.000	0.000	0.000	0.000
14	B	500	PHE	0	-0.004	-0.014	7.171	-4.014	-4.014	0.000	0.000	0.000	0.000
15	B	501	LEU	0	0.025	0.023	6.935	3.136	3.136	0.000	0.000	0.000	0.000
16	B	502	ILE	0	0.011	-0.009	5.531	-2.443	-2.443	0.000	0.000	0.000	0.000
17	B	503	ASP	-1	-0.773	-0.864	9.030	20.997	20.997	0.000	0.000	0.000	0.000
18	B	504	LEU	0	-0.010	-0.026	7.117	-0.605	-0.605	0.000	0.000	0.000	0.000
19	B	505	ALA	0	-0.038	-0.005	11.177	-0.616	-0.616	0.000	0.000	0.000	0.000
20	B	506	GLU	-1	-0.992	-0.996	14.697	15.282	15.282	0.000	0.000	0.000	0.000
21	B	507	GLU	-1	-0.952	-0.958	12.235	21.133	21.133	0.000	0.000	0.000	0.000
22	B	508	LYS	1	0.959	0.972	12.759	-17.670	-17.670	0.000	0.000	0.000	0.000
23	B	509	PRO	0	0.049	0.016	11.592	0.636	0.636	0.000	0.000	0.000	0.000
24	B	510	ILE	0	-0.054	-0.026	12.392	-1.707	-1.707	0.000	0.000	0.000	0.000
25	B	511	ASN	0	0.081	0.032	13.413	1.260	1.260	0.000	0.000	0.000	0.000
26	B	512	PRO	0	0.050	0.023	12.413	-0.351	-0.351	0.000	0.000	0.000	0.000
27	B	513	LYS	1	0.895	0.938	14.560	-14.417	-14.417	0.000	0.000	0.000	0.000
28	B	514	ASP	-1	-0.861	-0.929	17.503	14.039	14.039	0.000	0.000	0.000	0.000
29	B	515	PRO	0	0.038	0.015	19.262	0.203	0.203	0.000	0.000	0.000	0.000
30	B	516	ARG	1	0.960	0.980	19.617	-13.897	-13.897	0.000	0.000	0.000	0.000
31	B	517	LEU	0	0.001	-0.002	14.696	0.115	0.115	0.000	0.000	0.000	0.000
32	B	518	LEU	0	-0.050	-0.022	18.364	0.084	0.084	0.000	0.000	0.000	0.000
33	B	519	THR	0	-0.059	-0.017	21.309	-0.536	-0.536	0.000	0.000	0.000	0.000
34	B	520	LEU	0	-0.062	-0.034	17.439	-0.015	-0.015	0.000	0.000	0.000	0.000
35	B	521	LEU	0	-0.014	0.012	13.658	0.497	0.497	0.000	0.000	0.000	0.000
36	B	522	LYS	1	0.923	0.957	16.851	-16.353	-16.353	0.000	0.000	0.000	0.000
37	B	523	ASP	-1	-0.839	-0.927	17.394	13.476	13.476	0.000	0.000	0.000	0.000
38	B	524	HIS	0	-0.010	-0.016	15.667	0.858	0.858	0.000	0.000	0.000	0.000
39	B	525	GLN	0	0.045	0.017	13.107	0.001	0.001	0.000	0.000	0.000	0.000
40	B	526	ARG	1	0.977	0.994	12.890	-13.287	-13.287	0.000	0.000	0.000	0.000
41	B	527	ALA	0	0.001	0.003	14.679	0.301	0.301	0.000	0.000	0.000	0.000
42	B	528	MET	0	0.000	0.003	10.308	0.647	0.647	0.000	0.000	0.000	0.000
43	B	529	ILE	0	-0.004	-0.001	9.917	1.144	1.144	0.000	0.000	0.000	0.000
44	B	530	ASP	-1	-0.928	-0.964	11.416	16.445	16.445	0.000	0.000	0.000	0.000
45	B	531	GLN	0	-0.098	-0.047	12.473	-0.194	-0.194	0.000	0.000	0.000	0.000
46	B	532	MET	0	-0.020	0.002	7.311	0.927	0.927	0.000	0.000	0.000	0.000
47	B	533	ASN	0	-0.100	-0.040	9.109	0.862	0.862	0.000	0.000	0.000	0.000
48	B	534	LEU	0	0.015	0.009	8.506	1.438	1.438	0.000	0.000	0.000	0.000
49	B	535	VAL	0	0.015	0.007	11.447	-1.767	-1.767	0.000	0.000	0.000	0.000
50	B	536	LYS	1	0.932	0.959	13.514	-14.740	-14.740	0.000	0.000	0.000	0.000
51	B	537	TRP	0	0.056	0.012	13.478	-0.959	-0.959	0.000	0.000	0.000	0.000
52	B	538	ASN	0	0.020	-0.004	18.132	-0.423	-0.423	0.000	0.000	0.000	0.000
53	B	539	ASP	-1	-0.961	-0.956	19.465	13.530	13.530	0.000	0.000	0.000	0.000
54	B	540	PHE	0	0.011	-0.004	15.528	-0.161	-0.161	0.000	0.000	0.000	0.000
55	B	541	LYS	1	0.953	0.984	21.666	-10.813	-10.813	0.000	0.000	0.000	0.000
56	B	542	LYS	1	0.955	0.965	24.947	-9.994	-9.994	0.000	0.000	0.000	0.000
57	B	543	TYR	0	0.008	0.028	21.019	-0.567	-0.567	0.000	0.000	0.000	0.000
58	B	544	GLN	0	-0.059	-0.045	25.972	-0.118	-0.118	0.000	0.000	0.000	0.000
59	B	545	ASP	-1	-0.830	-0.903	25.814	10.851	10.851	0.000	0.000	0.000	0.000
60	B	546	PRO	0	-0.032	-0.007	22.091	0.253	0.253	0.000	0.000	0.000	0.000
61	B	547	ILE	0	-0.030	-0.017	17.039	-0.267	-0.267	0.000	0.000	0.000	0.000
62	B	548	PRO	0	-0.029	0.007	17.802	0.696	0.696	0.000	0.000	0.000	0.000
63	B	549	LEU	0	-0.007	-0.021	12.336	0.276	0.276	0.000	0.000	0.000	0.000
64	B	550	LYS	1	0.936	0.964	11.586	-18.478	-18.478	0.000	0.000	0.000	0.000
65	B	551	ALA	0	0.008	0.003	8.315	0.648	0.648	0.000	0.000	0.000	0.000
66	B	552	LYS	1	0.986	0.985	6.820	-30.717	-30.717	0.000	0.000	0.000	0.000
67	B	553	THR	0	0.011	0.019	2.479	-17.740	-12.047	1.564	-3.609	-3.648	0.037
68	B	554	LEU	0	0.012	0.012	5.279	-2.554	-2.568	-0.001	-0.002	0.018	0.000
69	B	555	PHE	0	0.003	-0.010	8.106	-1.873	-1.873	0.000	0.000	0.000	0.000
70	B	556	LYS	1	0.898	0.966	5.532	-43.543	-43.543	0.000	0.000	0.000	0.000
71	B	557	PHE	0	0.000	-0.011	3.351	-4.303	-3.011	0.031	-0.700	-0.623	0.006
72	B	558	CYS	0	-0.050	0.004	8.738	-2.817	-2.817	0.000	0.000	0.000	0.000
73	B	559	LYS	1	0.959	0.982	12.057	-18.573	-18.573	0.000	0.000	0.000	0.000
74	B	560	GLN	0	-0.044	-0.020	13.441	-1.400	-1.400	0.000	0.000	0.000	0.000
75	B	561	ILE	0	-0.024	-0.001	17.488	-0.809	-0.809	0.000	0.000	0.000	0.000
76	B	562	LYS	1	0.936	0.958	21.046	-13.853	-13.853	0.000	0.000	0.000	0.000
77	B	563	LYS	1	0.927	0.974	23.527	-12.127	-12.127	0.000	0.000	0.000	0.000
78	B	564	LYS	1	0.916	0.952	25.778	-9.790	-9.790	0.000	0.000	0.000	0.000
79	B	565	PHE	0	0.014	-0.002	23.448	0.044	0.044	0.000	0.000	0.000	0.000
80	B	566	LEU	0	0.030	0.012	28.363	-0.243	-0.243	0.000	0.000	0.000	0.000
81	B	567	ARG	1	0.921	0.978	26.430	-10.641	-10.641	0.000	0.000	0.000	0.000
82	B	568	GLY	0	0.067	0.027	28.356	-0.465	-0.465	0.000	0.000	0.000	0.000
83	B	569	ALA	0	0.027	0.004	29.573	0.228	0.228	0.000	0.000	0.000	0.000
84	B	570	ASP	-1	-0.899	-0.962	27.098	11.541	11.541	0.000	0.000	0.000	0.000
85	B	571	PHE	0	-0.049	-0.040	24.333	0.464	0.464	0.000	0.000	0.000	0.000
86	B	572	LYS	1	0.967	1.012	23.409	-11.633	-11.633	0.000	0.000	0.000	0.000
87	B	573	LEU	0	-0.040	-0.019	22.002	-0.562	-0.562	0.000	0.000	0.000	0.000
88	B	574	HIS	0	-0.056	-0.032	25.423	0.025	0.025	0.000	0.000	0.000	0.000
89	B	575	THR	0	-0.003	-0.010	28.062	0.156	0.156	0.000	0.000	0.000	0.000
90	B	576	LEU	0	-0.038	-0.021	29.289	-0.280	-0.280	0.000	0.000	0.000	0.000
91	B	577	PRO	0	0.013	0.014	32.401	0.059	0.059	0.000	0.000	0.000	0.000
92	B	578	THR	0	-0.074	-0.026	34.780	-0.024	-0.024	0.000	0.000	0.000	0.000
93	B	579	GLU	-1	-0.889	-0.972	37.002	7.263	7.263	0.000	0.000	0.000	0.000
94	B	580	ALA	0	-0.029	0.006	39.579	0.157	0.157	0.000	0.000	0.000	0.000
95	B	581	ASN	0	0.030	-0.003	37.555	-0.127	-0.127	0.000	0.000	0.000	0.000
96	B	582	LEU	0	-0.033	-0.003	40.788	-0.050	-0.050	0.000	0.000	0.000	0.000
97	B	583	LYS	1	0.908	0.964	36.977	-8.551	-8.551	0.000	0.000	0.000	0.000
98	B	584	TYR	0	0.024	0.001	40.638	0.170	0.170	0.000	0.000	0.000	0.000
99	B	585	GLU	-1	-0.883	-0.957	36.275	8.884	8.884	0.000	0.000	0.000	0.000
100	B	586	PRO	0	-0.016	0.001	37.812	0.171	0.171	0.000	0.000	0.000	0.000
101	B	587	GLU	-1	-0.905	-0.963	34.894	8.870	8.870	0.000	0.000	0.000	0.000
102	B	588	ARG	1	0.875	0.957	31.840	-9.336	-9.336	0.000	0.000	0.000	0.000
103	B	589	MET	0	-0.001	0.002	32.402	-0.237	-0.237	0.000	0.000	0.000	0.000
104	B	590	THR	0	-0.023	-0.011	31.444	0.356	0.356	0.000	0.000	0.000	0.000
105	B	591	VAL	0	0.019	0.014	26.359	-0.037	-0.037	0.000	0.000	0.000	0.000
106	B	592	LEU	0	-0.029	-0.010	26.954	0.030	0.030	0.000	0.000	0.000	0.000
107	B	593	ALA	0	0.012	0.003	22.632	0.226	0.226	0.000	0.000	0.000	0.000
108	B	594	SER	0	-0.030	-0.009	18.359	-0.679	-0.679	0.000	0.000	0.000	0.000
109	B	595	CYS	0	-0.028	0.004	18.045	-0.013	-0.013	0.000	0.000	0.000	0.000
110	B	596	VAL	0	0.074	0.022	13.722	-0.062	-0.062	0.000	0.000	0.000	0.000
111	B	597	PRO	0	-0.037	-0.004	17.097	-0.311	-0.311	0.000	0.000	0.000	0.000
112	B	598	ILE	0	-0.012	-0.006	16.065	0.726	0.726	0.000	0.000	0.000	0.000
113	B	599	LEU	0	-0.024	-0.007	19.056	-0.598	-0.598	0.000	0.000	0.000	0.000
114	B	600	LEU	0	-0.014	-0.017	20.255	0.495	0.495	0.000	0.000	0.000	0.000
115	B	601	ASP	-1	-0.939	-0.983	22.338	12.075	12.075	0.000	0.000	0.000	0.000
116	B	602	ASP	-1	-0.928	-0.967	24.063	10.783	10.783	0.000	0.000	0.000	0.000
117	B	603	GLN	0	-0.035	-0.022	26.169	-0.203	-0.203	0.000	0.000	0.000	0.000
118	B	604	THR	0	0.011	0.033	25.272	-0.194	-0.194	0.000	0.000	0.000	0.000
119	B	605	VAL	0	-0.035	-0.021	22.921	0.533	0.533	0.000	0.000	0.000	0.000
120	B	606	GLN	0	0.018	0.009	20.720	0.093	0.093	0.000	0.000	0.000	0.000
121	B	607	TYR	0	-0.007	-0.036	19.803	0.044	0.044	0.000	0.000	0.000	0.000
122	B	608	LEU	0	0.024	0.030	13.880	-0.252	-0.252	0.000	0.000	0.000	0.000
123	B	609	TYR	0	0.037	-0.005	16.497	-0.091	-0.091	0.000	0.000	0.000	0.000
124	B	610	ASP	-1	-0.889	-0.933	13.517	21.777	21.777	0.000	0.000	0.000	0.000
125	B	611	ASP	-1	-0.928	-0.961	15.640	17.344	17.344	0.000	0.000	0.000	0.000

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