FMO DATABASE

FMODB ID: 82QYY

Calculation Name: 3U4Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U4Z

Chain ID: A

ChEMBL ID:

UniProt ID: D2CVN6

Base Structure: X-ray

Registration Date: 2023-03-14

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	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-903756.406482
FMO2-HF: Nuclear repulsion	858336.165945
FMO2-HF: Total energy	-45420.240537
FMO2-MP2: Total energy	-45553.36107

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:375:THR)

Summations of interaction energy for fragment #1(A:375:THR)

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.
-8.043	-2.159	6.414	-4.402	-7.896	-0.022

Interaction energy analysis for fragmet #1(A:375:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.040 / 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	377	LEU	0	0.050	0.023	3.193	-1.916	0.140	0.102	-0.948	-1.210	-0.001
4	A	378	ILE	0	0.052	0.012	5.295	0.595	0.632	-0.001	-0.001	-0.035	0.000
5	A	379	SER	0	-0.009	-0.012	8.340	0.222	0.222	0.000	0.000	0.000	0.000
6	A	380	GLU	-1	-0.808	-0.896	7.411	0.184	0.184	0.000	0.000	0.000	0.000
7	A	381	VAL	0	0.008	0.020	7.157	0.315	0.315	0.000	0.000	0.000	0.000
8	A	382	LEU	0	0.075	0.029	9.698	0.172	0.172	0.000	0.000	0.000	0.000
9	A	383	LYS	1	0.885	0.939	12.676	0.203	0.203	0.000	0.000	0.000	0.000
10	A	384	THR	0	-0.033	-0.019	9.504	0.083	0.083	0.000	0.000	0.000	0.000
11	A	385	SER	0	-0.004	-0.005	12.720	0.032	0.032	0.000	0.000	0.000	0.000
12	A	386	LYS	1	0.808	0.900	6.853	-1.256	-1.256	0.000	0.000	0.000	0.000
13	A	387	GLN	0	0.054	0.024	11.910	0.006	0.006	0.000	0.000	0.000	0.000
14	A	388	TYR	0	0.018	0.013	9.817	-0.154	-0.154	0.000	0.000	0.000	0.000
15	A	389	LEU	0	-0.029	-0.022	6.046	0.170	0.170	0.000	0.000	0.000	0.000
16	A	390	SER	0	0.038	0.025	2.821	-2.081	-1.161	0.193	-0.363	-0.750	0.001
17	A	391	VAL	0	-0.018	-0.002	2.518	-2.461	-0.985	2.469	-1.924	-2.021	-0.018
18	A	392	LEU	0	-0.004	0.012	2.358	0.257	0.018	3.261	-0.601	-2.421	-0.006
19	A	393	ALA	0	-0.010	-0.010	3.617	-0.263	-0.309	0.015	0.131	-0.100	0.000
20	A	394	GLN	0	-0.030	-0.014	7.296	0.119	0.119	0.000	0.000	0.000	0.000
21	A	395	VAL	0	0.007	0.009	10.942	0.063	0.063	0.000	0.000	0.000	0.000
22	A	396	VAL	0	-0.024	-0.029	13.242	-0.027	-0.027	0.000	0.000	0.000	0.000
23	A	397	ASP	-1	-0.823	-0.896	16.271	-0.012	-0.012	0.000	0.000	0.000	0.000
24	A	398	ILE	0	-0.022	-0.024	17.211	0.023	0.023	0.000	0.000	0.000	0.000
25	A	399	GLN	0	-0.038	-0.017	19.561	0.010	0.010	0.000	0.000	0.000	0.000
26	A	400	SER	0	0.006	-0.005	21.854	0.029	0.029	0.000	0.000	0.000	0.000
27	A	401	SER	0	-0.014	-0.019	23.334	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	402	ASP	-1	-0.772	-0.856	24.872	0.131	0.131	0.000	0.000	0.000	0.000
29	A	403	LYS	1	0.889	0.930	26.091	-0.130	-0.130	0.000	0.000	0.000	0.000
30	A	404	ASN	0	-0.043	-0.016	21.585	0.050	0.050	0.000	0.000	0.000	0.000
31	A	405	ILE	0	0.026	0.026	18.294	-0.023	-0.023	0.000	0.000	0.000	0.000
32	A	406	ARG	1	0.868	0.927	18.211	-0.110	-0.110	0.000	0.000	0.000	0.000
33	A	407	LEU	0	0.023	0.016	13.474	-0.022	-0.022	0.000	0.000	0.000	0.000
34	A	408	LYS	1	0.882	0.947	15.130	0.081	0.081	0.000	0.000	0.000	0.000
35	A	409	ILE	0	-0.009	-0.003	8.217	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	410	CYS	0	0.048	0.011	11.226	0.027	0.027	0.000	0.000	0.000	0.000
37	A	411	ASP	-1	-0.726	-0.842	7.261	-1.782	-1.782	0.000	0.000	0.000	0.000
38	A	412	ASN	0	0.022	0.008	9.269	0.241	0.241	0.000	0.000	0.000	0.000
39	A	413	SER	0	-0.112	-0.061	8.192	0.171	0.171	0.000	0.000	0.000	0.000
40	A	414	CYS	0	-0.058	-0.026	10.348	0.139	0.139	0.000	0.000	0.000	0.000
41	A	415	ASN	0	0.000	0.012	12.896	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	416	GLN	0	0.003	-0.011	14.529	0.037	0.037	0.000	0.000	0.000	0.000
43	A	417	GLU	-1	-0.843	-0.905	13.540	-0.197	-0.197	0.000	0.000	0.000	0.000
44	A	418	LEU	0	-0.018	-0.004	9.939	0.032	0.032	0.000	0.000	0.000	0.000
45	A	419	LYN	0	0.060	0.053	13.430	0.004	0.004	0.000	0.000	0.000	0.000
46	A	420	VAL	0	-0.010	-0.005	10.949	0.069	0.069	0.000	0.000	0.000	0.000
47	A	421	VAL	0	-0.003	-0.009	14.214	-0.057	-0.057	0.000	0.000	0.000	0.000
48	A	422	ILE	0	0.000	0.001	14.015	0.090	0.090	0.000	0.000	0.000	0.000
49	A	423	PHE	0	0.063	0.010	17.047	-0.045	-0.045	0.000	0.000	0.000	0.000
50	A	424	PRO	0	0.040	-0.015	19.792	0.018	0.018	0.000	0.000	0.000	0.000
51	A	425	ASP	-1	-0.827	-0.908	20.621	0.384	0.384	0.000	0.000	0.000	0.000
52	A	426	LEU	0	-0.012	0.001	13.890	-0.022	-0.022	0.000	0.000	0.000	0.000
53	A	427	CYS	0	-0.058	-0.020	18.176	-0.030	-0.030	0.000	0.000	0.000	0.000
54	A	428	TYR	0	-0.050	-0.026	19.775	-0.043	-0.043	0.000	0.000	0.000	0.000
55	A	429	GLU	-1	-0.910	-0.946	17.440	0.329	0.329	0.000	0.000	0.000	0.000
56	A	430	TRP	0	0.002	-0.026	13.582	-0.041	-0.041	0.000	0.000	0.000	0.000
57	A	431	ARG	1	0.799	0.883	18.877	-0.140	-0.140	0.000	0.000	0.000	0.000
58	A	432	ASP	-1	-0.911	-0.964	22.007	0.067	0.067	0.000	0.000	0.000	0.000
59	A	433	LYS	1	0.863	0.957	16.307	-0.241	-0.241	0.000	0.000	0.000	0.000
60	A	434	PHE	0	0.023	0.019	12.550	-0.018	-0.018	0.000	0.000	0.000	0.000
61	A	435	SER	0	-0.037	-0.027	16.082	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	436	ILE	0	0.038	0.019	15.829	-0.026	-0.026	0.000	0.000	0.000	0.000
63	A	437	ASN	0	-0.038	-0.024	15.200	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	438	LYS	1	0.806	0.918	13.408	0.092	0.092	0.000	0.000	0.000	0.000
65	A	439	TRP	0	-0.020	-0.008	7.050	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	440	TYR	0	-0.012	-0.033	8.483	0.031	0.031	0.000	0.000	0.000	0.000
67	A	441	TYR	0	0.010	0.012	2.471	-2.502	-0.822	0.375	-0.696	-1.359	0.002
68	A	442	PHE	0	0.011	0.009	5.451	0.050	0.050	0.000	0.000	0.000	0.000
69	A	443	ASN	0	-0.027	-0.037	5.560	1.946	1.946	0.000	0.000	0.000	0.000
70	A	444	GLU	-1	-0.853	-0.939	6.610	1.614	1.614	0.000	0.000	0.000	0.000
71	A	445	PHE	0	-0.002	0.024	8.127	-0.603	-0.603	0.000	0.000	0.000	0.000
72	A	446	VAL	0	-0.036	-0.020	9.732	0.164	0.164	0.000	0.000	0.000	0.000
73	A	447	ARG	1	0.857	0.928	11.272	-0.489	-0.489	0.000	0.000	0.000	0.000
74	A	448	GLN	0	-0.013	-0.007	12.868	-0.036	-0.036	0.000	0.000	0.000	0.000
75	A	449	ILE	0	0.015	0.002	16.283	-0.020	-0.020	0.000	0.000	0.000	0.000
76	A	450	TYR	0	-0.090	-0.044	18.835	0.005	0.005	0.000	0.000	0.000	0.000
77	A	451	ASN	0	-0.017	-0.020	22.210	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	452	ASP	-1	-0.893	-0.920	22.579	0.052	0.052	0.000	0.000	0.000	0.000
79	A	453	GLU	-1	-0.944	-0.977	19.472	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	454	VAL	0	-0.055	-0.034	13.615	0.047	0.047	0.000	0.000	0.000	0.000
81	A	455	GLN	0	-0.008	-0.014	14.694	-0.077	-0.077	0.000	0.000	0.000	0.000
82	A	456	LEU	0	-0.022	-0.008	8.943	0.085	0.085	0.000	0.000	0.000	0.000
83	A	457	LYS	1	0.815	0.907	13.107	-0.596	-0.596	0.000	0.000	0.000	0.000
84	A	458	ASN	0	0.026	0.022	13.413	0.205	0.205	0.000	0.000	0.000	0.000
85	A	459	ASN	0	-0.017	-0.016	14.078	-0.046	-0.046	0.000	0.000	0.000	0.000
86	A	460	ILE	0	0.038	0.020	15.637	0.034	0.034	0.000	0.000	0.000	0.000
87	A	461	HIS	0	0.027	0.014	13.420	-0.036	-0.036	0.000	0.000	0.000	0.000
88	A	462	SER	0	-0.073	-0.033	11.357	0.097	0.097	0.000	0.000	0.000	0.000
89	A	463	SER	0	-0.001	-0.006	10.588	-0.184	-0.184	0.000	0.000	0.000	0.000
90	A	464	ILE	0	0.006	0.001	9.735	0.211	0.211	0.000	0.000	0.000	0.000
91	A	465	LYS	1	0.950	0.981	8.460	-0.610	-0.610	0.000	0.000	0.000	0.000
92	A	466	GLU	-1	-0.750	-0.859	9.297	-0.202	-0.202	0.000	0.000	0.000	0.000
93	A	467	SER	0	-0.057	-0.027	7.765	-0.113	-0.113	0.000	0.000	0.000	0.000
94	A	468	ASP	-1	-0.894	-0.945	9.343	-0.314	-0.314	0.000	0.000	0.000	0.000
95	A	469	ASP	-1	-0.889	-0.908	10.442	-0.671	-0.671	0.000	0.000	0.000	0.000
96	A	470	GLN	0	0.024	-0.001	10.625	-0.133	-0.133	0.000	0.000	0.000	0.000
97	A	471	ARG	1	0.833	0.892	13.173	0.650	0.650	0.000	0.000	0.000	0.000
98	A	472	LYS	1	0.971	0.990	16.488	0.192	0.192	0.000	0.000	0.000	0.000
99	A	473	VAL	0	0.040	0.026	18.618	0.033	0.033	0.000	0.000	0.000	0.000
100	A	474	ILE	0	-0.021	-0.012	20.740	0.013	0.013	0.000	0.000	0.000	0.000
101	A	475	THR	0	-0.034	-0.027	23.930	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	476	TYR	0	0.011	0.008	26.332	0.006	0.006	0.000	0.000	0.000	0.000
103	A	477	ASN	0	-0.007	-0.001	26.647	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	478	GLN	0	-0.020	-0.010	30.567	0.008	0.008	0.000	0.000	0.000	0.000
105	A	479	GLU	-1	-0.823	-0.910	34.347	-0.099	-0.099	0.000	0.000	0.000	0.000
106	A	480	GLN	0	0.007	0.000	32.315	0.002	0.002	0.000	0.000	0.000	0.000
107	A	481	GLY	0	0.025	0.014	37.548	0.001	0.001	0.000	0.000	0.000	0.000
108	A	482	VAL	0	-0.067	-0.029	40.360	0.004	0.004	0.000	0.000	0.000	0.000
109	A	483	PHE	0	-0.088	-0.034	36.437	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:375:THR)