FMO DATABASE

FMODB ID: 179MZ

Calculation Name: 5LZ3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LZ3

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H3P7

Base Structure: X-ray

Registration Date: 2023-06-22

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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1139453.61948
FMO2-HF: Nuclear repulsion	1088667.108648
FMO2-HF: Total energy	-50786.510832
FMO2-MP2: Total energy	-50937.351727

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:368:VAL)

Summations of interaction energy for fragment #1(A:368:VAL)

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.
-2.118	0.56	0.068	-1.302	-1.445	-0.004

Interaction energy analysis for fragmet #1(A:368:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.032

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	370	ALA	0	0.014	0.021	3.169	-0.936	1.742	0.068	-1.302	-1.445	-0.004
4	A	371	ALA	0	0.029	0.009	5.467	-0.292	-0.292	0.000	0.000	0.000	0.000
5	A	372	PRO	0	-0.018	0.005	7.893	0.003	0.003	0.000	0.000	0.000	0.000
6	A	373	SER	0	-0.026	-0.006	11.402	0.060	0.060	0.000	0.000	0.000	0.000
7	A	374	MET	0	-0.045	-0.030	14.618	-0.037	-0.037	0.000	0.000	0.000	0.000
8	A	375	TRP	0	-0.042	-0.011	17.618	0.017	0.017	0.000	0.000	0.000	0.000
9	A	376	THR	0	0.027	0.008	21.350	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	377	ARG	1	0.853	0.923	25.029	0.008	0.008	0.000	0.000	0.000	0.000
11	A	378	PRO	0	0.095	0.053	28.396	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	379	GLN	0	-0.005	0.010	31.747	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	380	ILE	0	0.039	-0.008	32.260	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	381	LYS	1	0.934	0.952	33.490	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	382	ASP	-1	-0.870	-0.925	35.086	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	383	PHE	0	-0.042	-0.025	28.371	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	384	LYS	1	0.870	0.947	33.086	0.010	0.010	0.000	0.000	0.000	0.000
18	A	385	GLU	-1	-0.888	-0.928	34.805	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	386	LYS	1	0.899	0.949	31.121	0.014	0.014	0.000	0.000	0.000	0.000
20	A	387	ILE	0	-0.080	-0.036	29.929	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	388	GLN	0	0.002	-0.010	33.816	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	389	GLN	0	-0.081	-0.021	37.001	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	390	ASP	-1	-0.833	-0.860	32.666	-0.059	-0.059	0.000	0.000	0.000	0.000
24	A	391	ALA	0	-0.013	0.001	35.930	0.001	0.001	0.000	0.000	0.000	0.000
25	A	392	ASP	-1	-0.899	-0.946	32.062	-0.065	-0.065	0.000	0.000	0.000	0.000
26	A	393	SER	0	-0.105	-0.114	30.422	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	394	VAL	0	-0.017	-0.023	31.099	0.003	0.003	0.000	0.000	0.000	0.000
28	A	395	ILE	0	-0.013	0.017	27.535	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	396	THR	0	-0.024	-0.025	31.955	0.006	0.006	0.000	0.000	0.000	0.000
30	A	397	VAL	0	-0.006	0.016	28.751	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	398	GLY	0	0.048	0.009	31.949	0.006	0.006	0.000	0.000	0.000	0.000
32	A	399	ARG	1	0.879	0.932	33.052	0.026	0.026	0.000	0.000	0.000	0.000
33	A	400	GLY	0	0.023	0.024	31.879	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	401	GLU	-1	-0.877	-0.906	30.136	-0.062	-0.062	0.000	0.000	0.000	0.000
35	A	402	VAL	0	-0.011	-0.025	24.082	0.001	0.001	0.000	0.000	0.000	0.000
36	A	403	VAL	0	0.020	0.026	26.706	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	404	THR	0	-0.029	-0.018	20.923	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	405	VAL	0	0.033	0.020	22.446	0.001	0.001	0.000	0.000	0.000	0.000
39	A	406	ARG	1	0.835	0.920	19.671	0.210	0.210	0.000	0.000	0.000	0.000
40	A	407	VAL	0	0.018	0.006	19.256	0.015	0.015	0.000	0.000	0.000	0.000
41	A	408	PRO	0	-0.003	-0.009	18.230	-0.034	-0.034	0.000	0.000	0.000	0.000
42	A	409	THR	0	-0.029	0.003	13.110	0.002	0.002	0.000	0.000	0.000	0.000
43	A	410	HIS	0	0.064	0.031	16.444	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	411	GLU	-1	-0.966	-0.989	17.072	-0.241	-0.241	0.000	0.000	0.000	0.000
45	A	412	GLU	-1	-0.944	-0.966	18.009	-0.107	-0.107	0.000	0.000	0.000	0.000
46	A	413	GLY	0	-0.054	-0.030	17.007	0.032	0.032	0.000	0.000	0.000	0.000
47	A	414	SER	0	-0.030	-0.047	12.418	-0.029	-0.029	0.000	0.000	0.000	0.000
48	A	415	TYR	0	-0.020	0.001	11.878	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	416	LEU	0	-0.003	0.004	14.320	0.004	0.004	0.000	0.000	0.000	0.000
50	A	417	PHE	0	-0.001	-0.010	16.302	0.030	0.030	0.000	0.000	0.000	0.000
51	A	418	TRP	0	-0.008	-0.007	14.621	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	419	GLU	-1	-0.813	-0.903	21.142	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	420	PHE	0	-0.022	-0.033	21.637	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	421	ALA	0	0.028	0.011	26.344	0.008	0.008	0.000	0.000	0.000	0.000
55	A	422	THR	0	-0.003	-0.009	29.239	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	423	ASP	-1	-0.799	-0.899	32.022	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	424	ASN	0	-0.033	-0.017	35.684	0.004	0.004	0.000	0.000	0.000	0.000
58	A	425	TYR	0	-0.026	-0.017	34.008	0.001	0.001	0.000	0.000	0.000	0.000
59	A	426	ASP	-1	-0.696	-0.807	28.872	-0.014	-0.014	0.000	0.000	0.000	0.000
60	A	427	ILE	0	-0.018	-0.018	26.173	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	428	GLY	0	-0.002	0.010	24.291	0.004	0.004	0.000	0.000	0.000	0.000
62	A	429	PHE	0	0.023	0.000	18.812	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	430	GLY	0	0.046	0.007	17.638	0.016	0.016	0.000	0.000	0.000	0.000
64	A	431	VAL	0	-0.067	-0.023	14.127	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	432	TYR	0	0.027	0.021	12.848	0.002	0.002	0.000	0.000	0.000	0.000
66	A	433	PHE	0	-0.005	-0.008	9.900	0.016	0.016	0.000	0.000	0.000	0.000
67	A	434	GLU	-1	-0.810	-0.912	11.842	-0.311	-0.311	0.000	0.000	0.000	0.000
68	A	435	TRP	0	-0.053	-0.033	6.231	0.018	0.018	0.000	0.000	0.000	0.000
69	A	436	THR	0	-0.026	-0.013	12.619	0.080	0.080	0.000	0.000	0.000	0.000
70	A	474	PRO	0	0.022	0.009	16.559	0.002	0.002	0.000	0.000	0.000	0.000
71	A	475	LEU	0	-0.029	-0.013	9.027	0.034	0.034	0.000	0.000	0.000	0.000
72	A	476	LEU	0	-0.005	-0.014	12.248	-0.040	-0.040	0.000	0.000	0.000	0.000
73	A	477	ASP	-1	-0.822	-0.892	7.050	-0.909	-0.909	0.000	0.000	0.000	0.000
74	A	478	GLU	-1	-0.940	-0.994	9.349	-0.066	-0.066	0.000	0.000	0.000	0.000
75	A	479	ILE	0	-0.058	-0.009	8.634	0.021	0.021	0.000	0.000	0.000	0.000
76	A	480	VAL	0	-0.042	-0.033	10.636	0.080	0.080	0.000	0.000	0.000	0.000
77	A	481	PRO	0	0.060	0.060	13.296	-0.020	-0.020	0.000	0.000	0.000	0.000
78	A	482	VAL	0	-0.017	-0.030	15.550	0.010	0.010	0.000	0.000	0.000	0.000
79	A	483	TYR	0	0.001	0.013	17.196	0.010	0.010	0.000	0.000	0.000	0.000
80	A	484	ARG	1	0.842	0.910	21.603	0.004	0.004	0.000	0.000	0.000	0.000
81	A	485	ARG	1	0.903	0.966	18.052	0.014	0.014	0.000	0.000	0.000	0.000
82	A	486	ASP	-1	-0.832	-0.906	25.517	0.004	0.004	0.000	0.000	0.000	0.000
83	A	487	CYS	0	-0.054	-0.025	26.723	0.000	0.000	0.000	0.000	0.000	0.000
84	A	488	HIS	0	-0.018	-0.007	28.595	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	489	GLU	-1	-0.951	-0.979	31.337	0.010	0.010	0.000	0.000	0.000	0.000
86	A	490	GLU	-1	-0.955	-0.982	28.625	0.028	0.028	0.000	0.000	0.000	0.000
87	A	491	VAL	0	-0.051	-0.021	26.548	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	492	TYR	0	0.029	0.013	22.422	0.007	0.007	0.000	0.000	0.000	0.000
89	A	493	ALA	0	-0.015	-0.017	21.973	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	494	GLY	0	0.018	0.011	17.773	0.017	0.017	0.000	0.000	0.000	0.000
91	A	495	SER	0	-0.051	-0.010	15.406	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	496	HIS	0	0.051	-0.006	7.902	0.061	0.061	0.000	0.000	0.000	0.000
93	A	497	GLN	0	-0.004	0.012	7.215	0.032	0.032	0.000	0.000	0.000	0.000
94	A	498	TYR	0	-0.009	-0.011	8.956	-0.130	-0.130	0.000	0.000	0.000	0.000
95	A	499	PRO	0	0.007	0.020	5.984	-0.039	-0.039	0.000	0.000	0.000	0.000
96	A	500	GLY	0	0.020	-0.005	6.399	-0.313	-0.313	0.000	0.000	0.000	0.000
97	A	501	ARG	1	0.925	0.972	9.169	0.528	0.528	0.000	0.000	0.000	0.000
98	A	502	GLY	0	0.047	0.011	12.846	-0.039	-0.039	0.000	0.000	0.000	0.000
99	A	503	VAL	0	-0.053	-0.022	14.065	0.059	0.059	0.000	0.000	0.000	0.000
100	A	504	TYR	0	0.020	0.012	11.455	-0.030	-0.030	0.000	0.000	0.000	0.000
101	A	505	LEU	0	-0.032	-0.018	15.741	0.046	0.046	0.000	0.000	0.000	0.000
102	A	506	LEU	0	0.031	0.006	17.485	0.006	0.006	0.000	0.000	0.000	0.000
103	A	507	LYS	1	0.878	0.947	18.600	0.145	0.145	0.000	0.000	0.000	0.000
104	A	508	PHE	0	0.047	0.020	21.157	0.010	0.010	0.000	0.000	0.000	0.000
105	A	509	ASP	-1	-0.850	-0.920	23.430	-0.056	-0.056	0.000	0.000	0.000	0.000
106	A	510	ASN	0	0.017	-0.034	25.371	0.011	0.011	0.000	0.000	0.000	0.000
107	A	511	SER	0	-0.041	-0.009	26.707	0.006	0.006	0.000	0.000	0.000	0.000
108	A	512	TYR	0	-0.067	-0.031	27.770	0.002	0.002	0.000	0.000	0.000	0.000
109	A	513	SER	0	-0.086	-0.041	30.680	0.006	0.006	0.000	0.000	0.000	0.000
110	A	514	LEU	0	0.061	0.014	33.596	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	515	TRP	0	-0.012	-0.022	36.770	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	516	ARG	1	0.889	0.959	35.947	0.015	0.015	0.000	0.000	0.000	0.000
113	A	517	SER	0	0.076	0.036	35.075	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	518	LYS	1	0.786	0.891	31.181	0.030	0.030	0.000	0.000	0.000	0.000
115	A	519	SER	0	0.028	0.016	32.962	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	520	VAL	0	-0.024	-0.010	27.477	0.004	0.004	0.000	0.000	0.000	0.000
117	A	521	TYR	0	-0.041	-0.049	30.526	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	522	TYR	0	-0.023	-0.023	25.058	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	523	ARG	1	0.922	0.964	25.957	0.052	0.052	0.000	0.000	0.000	0.000
120	A	524	VAL	0	-0.003	0.008	21.683	0.002	0.002	0.000	0.000	0.000	0.000
121	A	525	TYR	0	-0.040	-0.019	21.425	0.005	0.005	0.000	0.000	0.000	0.000
122	A	526	TYR	0	0.020	-0.005	18.330	-0.022	-0.022	0.000	0.000	0.000	0.000
123	A	527	THR	0	0.012	0.018	17.066	0.026	0.026	0.000	0.000	0.000	0.000
124	A	528	ARG	1	0.959	1.010	16.617	0.067	0.067	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:368:VAL)