FMO DATABASE

FMODB ID: YVZ22

Calculation Name: 3MZY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MZY

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RIQ2

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1130927.202693
FMO2-HF: Nuclear repulsion	1080086.516136
FMO2-HF: Total energy	-50840.686556
FMO2-MP2: Total energy	-50991.535833

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:45:GLU)

Summations of interaction energy for fragment #1(A:45: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.
-129.781	-124.771	3.04	-3.206	-4.845	0.03

Interaction energy analysis for fragmet #1(A:45: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 : -0.993

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	47	LEU	0	-0.030	-0.030	3.832	-1.862	-0.439	-0.012	-0.557	-0.854	0.002
4	A	48	VAL	0	-0.025	-0.001	2.434	-6.172	-5.849	2.863	-0.997	-2.190	0.009
5	A	49	GLN	0	0.066	0.042	2.738	-13.197	-10.728	0.181	-1.319	-1.331	0.016
6	A	50	GLU	-1	-0.863	-0.942	7.030	27.477	27.477	0.000	0.000	0.000	0.000
7	A	51	GLY	0	0.005	0.006	8.399	-3.245	-3.245	0.000	0.000	0.000	0.000
8	A	52	ILE	0	-0.006	-0.003	7.085	-3.353	-3.353	0.000	0.000	0.000	0.000
9	A	53	LEU	0	0.042	0.031	10.600	-2.919	-2.919	0.000	0.000	0.000	0.000
10	A	54	GLY	0	-0.003	-0.031	12.699	-2.135	-2.135	0.000	0.000	0.000	0.000
11	A	55	LEU	0	-0.017	-0.016	13.426	-1.882	-1.882	0.000	0.000	0.000	0.000
12	A	56	LEU	0	0.045	0.015	13.615	-1.452	-1.452	0.000	0.000	0.000	0.000
13	A	57	LYS	1	0.822	0.911	16.700	-19.296	-19.296	0.000	0.000	0.000	0.000
14	A	58	ALA	0	-0.026	-0.024	17.962	-1.062	-1.062	0.000	0.000	0.000	0.000
15	A	59	ILE	0	-0.040	-0.038	17.521	-0.975	-0.975	0.000	0.000	0.000	0.000
16	A	60	LYS	1	0.814	0.912	19.357	-16.678	-16.678	0.000	0.000	0.000	0.000
17	A	61	PHE	0	-0.034	-0.015	22.100	-0.664	-0.664	0.000	0.000	0.000	0.000
18	A	62	TYR	0	-0.106	-0.054	23.775	-0.330	-0.330	0.000	0.000	0.000	0.000
19	A	63	ASP	-1	-0.749	-0.846	25.421	9.757	9.757	0.000	0.000	0.000	0.000
20	A	64	GLU	-1	-0.751	-0.866	28.867	11.394	11.394	0.000	0.000	0.000	0.000
21	A	65	THR	0	-0.073	-0.052	30.254	-0.173	-0.173	0.000	0.000	0.000	0.000
22	A	66	LYS	1	0.806	0.908	29.057	-10.111	-10.111	0.000	0.000	0.000	0.000
23	A	67	SER	0	0.009	0.000	26.117	0.044	0.044	0.000	0.000	0.000	0.000
24	A	68	SER	0	0.013	0.040	25.613	0.180	0.180	0.000	0.000	0.000	0.000
25	A	69	PHE	0	0.067	0.029	19.425	0.278	0.278	0.000	0.000	0.000	0.000
26	A	70	SER	0	-0.003	-0.035	20.884	0.854	0.854	0.000	0.000	0.000	0.000
27	A	71	SER	0	-0.013	-0.005	20.245	0.560	0.560	0.000	0.000	0.000	0.000
28	A	72	PHE	0	0.003	0.016	21.400	0.290	0.290	0.000	0.000	0.000	0.000
29	A	73	ALA	0	0.050	0.012	17.432	0.468	0.468	0.000	0.000	0.000	0.000
30	A	74	PHE	0	-0.027	-0.005	16.495	0.798	0.798	0.000	0.000	0.000	0.000
31	A	75	LEU	0	0.010	-0.006	16.803	0.590	0.590	0.000	0.000	0.000	0.000
32	A	76	CYS	0	-0.031	0.007	17.757	0.156	0.156	0.000	0.000	0.000	0.000
33	A	77	ILE	0	-0.030	-0.002	11.776	0.482	0.482	0.000	0.000	0.000	0.000
34	A	78	ARG	1	0.932	0.949	12.992	-17.330	-17.330	0.000	0.000	0.000	0.000
35	A	79	ARG	1	0.802	0.899	14.474	-16.521	-16.521	0.000	0.000	0.000	0.000
36	A	80	GLU	-1	-0.764	-0.847	13.150	18.283	18.283	0.000	0.000	0.000	0.000
37	A	81	MET	0	0.019	0.017	7.603	0.131	0.131	0.000	0.000	0.000	0.000
38	A	82	ILE	0	0.000	-0.004	11.296	-0.200	-0.200	0.000	0.000	0.000	0.000
39	A	83	SER	0	-0.027	-0.017	14.183	-0.942	-0.942	0.000	0.000	0.000	0.000
40	A	84	ALA	0	0.030	0.030	10.908	-0.883	-0.883	0.000	0.000	0.000	0.000
41	A	85	ILE	0	0.000	0.005	10.178	-0.075	-0.075	0.000	0.000	0.000	0.000
42	A	86	ARG	1	0.943	0.959	12.879	-14.301	-14.301	0.000	0.000	0.000	0.000
43	A	87	LYS	1	0.934	0.975	12.997	-21.138	-21.138	0.000	0.000	0.000	0.000
44	A	88	ALA	0	0.010	0.002	12.848	-0.644	-0.644	0.000	0.000	0.000	0.000
45	A	89	ASN	0	-0.015	-0.013	14.871	0.221	0.221	0.000	0.000	0.000	0.000
46	A	90	THR	0	-0.009	0.000	17.312	-0.503	-0.503	0.000	0.000	0.000	0.000
47	A	91	GLN	0	-0.024	-0.005	15.975	0.402	0.402	0.000	0.000	0.000	0.000
48	A	92	LYS	1	0.895	0.966	13.841	-17.832	-17.832	0.000	0.000	0.000	0.000
49	A	130	GLU	-1	-0.903	-0.969	20.342	14.639	14.639	0.000	0.000	0.000	0.000
50	A	131	GLU	-1	-0.911	-0.959	19.810	14.809	14.809	0.000	0.000	0.000	0.000
51	A	132	ALA	0	-0.034	-0.025	15.440	0.702	0.702	0.000	0.000	0.000	0.000
52	A	133	TYR	0	0.022	0.001	14.897	2.358	2.358	0.000	0.000	0.000	0.000
53	A	134	LEU	0	0.092	0.055	15.811	0.819	0.819	0.000	0.000	0.000	0.000
54	A	135	LEU	0	0.023	0.012	14.437	0.809	0.809	0.000	0.000	0.000	0.000
55	A	136	LYS	1	0.848	0.927	10.145	-21.336	-21.336	0.000	0.000	0.000	0.000
56	A	137	GLU	-1	-0.930	-0.963	11.238	20.198	20.198	0.000	0.000	0.000	0.000
57	A	138	GLU	-1	-0.817	-0.891	13.513	18.411	18.411	0.000	0.000	0.000	0.000
58	A	139	ILE	0	-0.040	-0.033	8.298	0.823	0.823	0.000	0.000	0.000	0.000
59	A	140	GLU	-1	-0.869	-0.940	7.583	43.387	43.387	0.000	0.000	0.000	0.000
60	A	141	GLU	-1	-0.821	-0.902	10.264	21.213	21.213	0.000	0.000	0.000	0.000
61	A	142	PHE	0	0.008	0.015	11.074	-0.265	-0.265	0.000	0.000	0.000	0.000
62	A	143	LYS	1	0.789	0.896	4.803	-52.712	-52.636	-0.001	-0.001	-0.074	0.000
63	A	144	LYS	1	0.860	0.931	10.152	-24.536	-24.536	0.000	0.000	0.000	0.000
64	A	145	PHE	0	0.034	0.034	12.638	-1.279	-1.279	0.000	0.000	0.000	0.000
65	A	146	SER	0	-0.002	-0.019	12.325	-0.312	-0.312	0.000	0.000	0.000	0.000
66	A	147	GLU	-1	-0.865	-0.936	11.118	24.869	24.869	0.000	0.000	0.000	0.000
67	A	148	ASN	0	-0.077	-0.059	13.135	-1.969	-1.969	0.000	0.000	0.000	0.000
68	A	149	ASN	0	-0.038	-0.012	16.657	-2.104	-2.104	0.000	0.000	0.000	0.000
69	A	150	PHE	0	-0.082	-0.027	15.089	-0.732	-0.732	0.000	0.000	0.000	0.000
70	A	151	SER	0	0.020	-0.021	17.843	-0.028	-0.028	0.000	0.000	0.000	0.000
71	A	152	LYS	1	0.955	0.951	16.754	-16.442	-16.442	0.000	0.000	0.000	0.000
72	A	153	PHE	0	-0.018	-0.012	16.672	0.810	0.810	0.000	0.000	0.000	0.000
73	A	154	GLU	-1	-0.745	-0.838	17.608	16.079	16.079	0.000	0.000	0.000	0.000
74	A	155	LYS	1	0.871	0.940	12.919	-21.956	-21.956	0.000	0.000	0.000	0.000
75	A	156	GLU	-1	-0.854	-0.909	12.750	19.460	19.460	0.000	0.000	0.000	0.000
76	A	157	VAL	0	-0.023	-0.023	13.409	0.728	0.728	0.000	0.000	0.000	0.000
77	A	158	LEU	0	0.029	0.023	11.056	0.150	0.150	0.000	0.000	0.000	0.000
78	A	159	THR	0	-0.012	-0.008	8.057	2.668	2.668	0.000	0.000	0.000	0.000
79	A	160	TYR	0	-0.002	-0.008	9.019	2.498	2.498	0.000	0.000	0.000	0.000
80	A	161	LEU	0	0.009	0.011	11.330	-0.379	-0.379	0.000	0.000	0.000	0.000
81	A	162	ILE	0	-0.010	-0.009	7.222	-0.780	-0.780	0.000	0.000	0.000	0.000
82	A	163	ARG	1	0.931	0.967	3.335	-50.729	-50.010	0.009	-0.332	-0.396	0.003
83	A	164	GLY	0	0.035	0.017	8.662	-1.455	-1.455	0.000	0.000	0.000	0.000
84	A	165	TYR	0	-0.021	0.012	9.838	-1.280	-1.280	0.000	0.000	0.000	0.000
85	A	166	SER	0	-0.039	-0.059	14.158	-0.346	-0.346	0.000	0.000	0.000	0.000
86	A	167	TYR	0	0.076	0.008	17.794	0.167	0.167	0.000	0.000	0.000	0.000
87	A	168	ARG	1	0.945	0.971	19.703	-12.227	-12.227	0.000	0.000	0.000	0.000
88	A	169	GLU	-1	-0.788	-0.856	16.897	16.163	16.163	0.000	0.000	0.000	0.000
89	A	170	ILE	0	0.013	0.007	14.915	0.098	0.098	0.000	0.000	0.000	0.000
90	A	171	ALA	0	-0.061	-0.028	17.389	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	172	THR	0	0.006	-0.004	19.753	-0.435	-0.435	0.000	0.000	0.000	0.000
92	A	173	ILE	0	-0.017	0.002	13.650	-0.199	-0.199	0.000	0.000	0.000	0.000
93	A	174	LEU	0	-0.047	-0.024	15.278	-0.054	-0.054	0.000	0.000	0.000	0.000
94	A	175	SER	0	0.002	0.015	18.829	-0.689	-0.689	0.000	0.000	0.000	0.000
95	A	176	LYS	1	0.848	0.949	20.128	-15.618	-15.618	0.000	0.000	0.000	0.000
96	A	177	ASN	0	0.038	0.009	23.556	0.112	0.112	0.000	0.000	0.000	0.000
97	A	178	LEU	0	0.089	0.013	24.332	0.342	0.342	0.000	0.000	0.000	0.000
98	A	179	LYS	1	0.983	1.008	24.839	-9.777	-9.777	0.000	0.000	0.000	0.000
99	A	180	SER	0	0.048	0.024	24.250	0.062	0.062	0.000	0.000	0.000	0.000
100	A	181	ILE	0	-0.027	0.006	19.450	0.361	0.361	0.000	0.000	0.000	0.000
101	A	182	ASP	-1	-0.871	-0.913	21.598	13.234	13.234	0.000	0.000	0.000	0.000
102	A	183	ASN	0	-0.020	-0.035	23.657	-0.076	-0.076	0.000	0.000	0.000	0.000
103	A	184	THR	0	-0.038	-0.016	19.108	-0.099	-0.099	0.000	0.000	0.000	0.000
104	A	185	ILE	0	0.025	0.010	18.071	0.492	0.492	0.000	0.000	0.000	0.000
105	A	186	GLN	0	0.018	0.021	20.088	0.285	0.285	0.000	0.000	0.000	0.000
106	A	187	ARG	1	0.864	0.920	22.139	-14.292	-14.292	0.000	0.000	0.000	0.000
107	A	188	ILE	0	-0.008	0.004	15.998	0.002	0.002	0.000	0.000	0.000	0.000
108	A	189	ARG	1	0.755	0.860	19.502	-12.223	-12.223	0.000	0.000	0.000	0.000
109	A	190	LYS	1	0.834	0.904	21.228	-12.048	-12.048	0.000	0.000	0.000	0.000
110	A	191	LYS	1	0.954	0.963	21.105	-14.978	-14.978	0.000	0.000	0.000	0.000
111	A	192	SER	0	0.012	-0.021	18.178	0.590	0.590	0.000	0.000	0.000	0.000
112	A	193	GLU	-1	-0.809	-0.883	20.041	12.371	12.371	0.000	0.000	0.000	0.000
113	A	194	GLU	-1	-0.965	-0.986	23.136	12.307	12.307	0.000	0.000	0.000	0.000
114	A	195	TRP	0	0.069	0.037	15.763	0.195	0.195	0.000	0.000	0.000	0.000
115	A	196	ILE	0	0.002	0.000	18.926	-0.101	-0.101	0.000	0.000	0.000	0.000
116	A	197	LYS	1	0.871	0.924	21.726	-12.510	-12.510	0.000	0.000	0.000	0.000
117	A	198	GLU	-1	-0.944	-0.968	24.359	12.026	12.026	0.000	0.000	0.000	0.000
118	A	199	GLU	-1	-0.930	-0.979	19.619	14.923	14.923	0.000	0.000	0.000	0.000
119	A	200	GLU	-1	-0.920	-0.949	22.575	13.666	13.666	0.000	0.000	0.000	0.000
120	A	201	ASN	0	-0.075	-0.045	25.160	-0.947	-0.947	0.000	0.000	0.000	0.000
121	A	202	ILE	0	-0.047	0.003	23.652	-0.729	-0.729	0.000	0.000	0.000	0.000
122	A	203	LYS	1	0.897	0.936	27.667	-10.180	-10.180	0.000	0.000	0.000	0.000
123	A	204	ARG	1	0.966	1.000	23.206	-13.274	-13.274	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:45:GLU)