FMO DATABASE

FMODB ID: LZMG9

Calculation Name: 3TNU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TNU

Chain ID: A

ChEMBL ID:

UniProt ID: P02533

Base Structure: X-ray

Registration Date: 2023-06-21

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	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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-439914.288767
FMO2-HF: Nuclear repulsion	401231.986122
FMO2-HF: Total energy	-38682.302646
FMO2-MP2: Total energy	-38790.113657

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:332:SER)

Summations of interaction energy for fragment #1(A:332:SER)

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.
-12.996	-11.729	8.083	-4.455	-4.893	0.036

Interaction energy analysis for fragmet #1(A:332:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.035

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	334	LEU	0	0.034	0.031	3.460	1.027	2.572	0.002	-0.657	-0.889	0.001
4	A	335	ARG	1	0.988	0.997	3.579	-5.176	-4.396	0.016	-0.211	-0.584	0.000
5	A	336	ARG	1	0.884	0.922	1.875	-10.098	-11.156	8.065	-3.587	-3.420	0.035
6	A	337	THR	0	-0.014	-0.024	5.940	-0.001	-0.001	0.000	0.000	0.000	0.000
7	A	338	MET	0	-0.010	0.005	8.166	0.053	0.053	0.000	0.000	0.000	0.000
8	A	339	GLN	0	0.041	0.010	6.938	0.385	0.385	0.000	0.000	0.000	0.000
9	A	340	ASN	0	-0.023	-0.011	10.118	0.010	0.010	0.000	0.000	0.000	0.000
10	A	341	LEU	0	-0.011	0.004	12.172	-0.085	-0.085	0.000	0.000	0.000	0.000
11	A	342	GLU	-1	-0.908	-0.959	11.591	0.989	0.989	0.000	0.000	0.000	0.000
12	A	343	ILE	0	-0.006	-0.005	12.873	-0.047	-0.047	0.000	0.000	0.000	0.000
13	A	344	GLU	-1	-0.819	-0.886	16.014	0.142	0.142	0.000	0.000	0.000	0.000
14	A	345	LEU	0	-0.026	-0.011	17.757	-0.042	-0.042	0.000	0.000	0.000	0.000
15	A	346	GLN	0	-0.014	-0.022	18.103	-0.053	-0.053	0.000	0.000	0.000	0.000
16	A	347	SER	0	-0.015	-0.003	20.375	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	348	GLN	0	-0.019	-0.026	22.365	-0.030	-0.030	0.000	0.000	0.000	0.000
18	A	349	LEU	0	-0.033	-0.010	22.467	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	350	SER	0	-0.018	-0.019	24.324	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	351	MET	0	-0.030	-0.009	26.429	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	352	LYS	1	0.839	0.921	28.129	-0.152	-0.152	0.000	0.000	0.000	0.000
22	A	353	ALA	0	0.043	0.022	29.417	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	354	SER	0	-0.069	-0.038	30.955	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	355	LEU	0	0.018	0.002	31.713	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	356	GLU	-1	-0.808	-0.895	32.872	0.121	0.121	0.000	0.000	0.000	0.000
26	A	357	ASN	0	-0.039	-0.029	34.579	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	358	SER	0	0.005	0.018	37.070	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	359	LEU	0	0.004	0.009	38.568	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	360	GLU	-1	-0.835	-0.908	40.045	0.077	0.077	0.000	0.000	0.000	0.000
30	A	361	GLU	-1	-0.820	-0.893	41.433	0.065	0.065	0.000	0.000	0.000	0.000
31	A	362	THR	0	-0.022	-0.022	42.447	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	363	LYS	1	0.779	0.877	42.158	-0.081	-0.081	0.000	0.000	0.000	0.000
33	A	364	GLY	0	0.022	0.014	45.976	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	365	ARG	1	0.841	0.903	44.208	-0.062	-0.062	0.000	0.000	0.000	0.000
35	A	366	TYR	0	0.016	-0.009	47.262	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	367	CYS	0	-0.020	-0.002	50.423	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	368	MET	0	-0.022	-0.007	51.335	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	369	GLN	0	0.014	0.002	51.760	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	370	LEU	0	-0.013	-0.001	54.825	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	371	ALA	0	0.003	-0.002	56.376	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	372	GLN	0	0.043	0.015	55.940	0.000	0.000	0.000	0.000	0.000	0.000
42	A	373	ILE	0	-0.027	-0.012	59.066	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	374	GLN	0	-0.010	-0.013	60.073	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	375	GLU	-1	-0.929	-0.952	62.253	0.039	0.039	0.000	0.000	0.000	0.000
45	A	376	MET	0	-0.039	-0.015	62.829	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	377	ILE	0	-0.037	-0.013	64.099	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	378	GLY	0	0.066	0.038	66.849	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	379	SER	0	-0.008	-0.015	67.831	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	380	VAL	0	-0.030	-0.016	70.132	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	381	GLU	-1	-0.960	-0.982	69.719	0.025	0.025	0.000	0.000	0.000	0.000
51	A	382	GLU	-1	-0.939	-0.969	72.370	0.029	0.029	0.000	0.000	0.000	0.000
52	A	383	GLN	0	-0.013	-0.001	74.412	0.000	0.000	0.000	0.000	0.000	0.000
53	A	384	LEU	0	-0.056	-0.033	75.912	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	385	ALA	0	-0.019	-0.018	77.180	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	386	GLN	0	-0.031	-0.024	78.826	0.000	0.000	0.000	0.000	0.000	0.000
56	A	387	LEU	0	0.025	0.017	80.530	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	388	ARG	1	0.915	0.944	79.104	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	389	CYS	0	0.000	0.004	83.228	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	390	GLU	-1	-0.875	-0.920	84.203	0.021	0.021	0.000	0.000	0.000	0.000
60	A	391	MET	0	-0.070	-0.040	85.362	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	392	GLU	-1	-0.830	-0.887	87.736	0.015	0.015	0.000	0.000	0.000	0.000
62	A	393	GLN	0	-0.056	-0.041	89.317	0.000	0.000	0.000	0.000	0.000	0.000
63	A	394	GLN	0	-0.016	-0.006	90.945	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	395	ASN	0	-0.052	-0.037	90.475	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	396	GLN	0	-0.071	-0.049	92.144	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	397	GLU	-1	-0.856	-0.916	93.421	0.016	0.016	0.000	0.000	0.000	0.000
67	A	398	TYR	0	-0.005	-0.001	96.728	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	399	LYS	1	0.797	0.876	98.214	-0.013	-0.013	0.000	0.000	0.000	0.000
69	A	400	ILE	0	0.019	0.008	98.853	0.000	0.000	0.000	0.000	0.000	0.000
70	A	401	LEU	0	-0.008	-0.002	101.399	0.000	0.000	0.000	0.000	0.000	0.000
71	A	402	LEU	0	-0.002	-0.002	102.298	0.000	0.000	0.000	0.000	0.000	0.000
72	A	403	ASP	-1	-0.777	-0.861	104.219	0.012	0.012	0.000	0.000	0.000	0.000
73	A	404	VAL	0	-0.061	-0.029	106.150	0.000	0.000	0.000	0.000	0.000	0.000
74	A	405	LYS	1	0.818	0.896	106.952	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	406	THR	0	-0.018	-0.028	107.806	0.000	0.000	0.000	0.000	0.000	0.000
76	A	407	ARG	1	0.907	0.949	110.026	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	408	LEU	0	0.005	0.005	110.758	0.000	0.000	0.000	0.000	0.000	0.000
78	A	409	GLU	-1	-0.807	-0.891	111.196	0.010	0.010	0.000	0.000	0.000	0.000
79	A	410	GLN	0	-0.019	-0.007	114.279	0.000	0.000	0.000	0.000	0.000	0.000
80	A	411	GLU	-1	-0.844	-0.901	115.518	0.011	0.011	0.000	0.000	0.000	0.000
81	A	412	ILE	0	0.007	0.006	115.872	0.000	0.000	0.000	0.000	0.000	0.000
82	A	413	ALA	0	-0.019	-0.006	118.958	0.000	0.000	0.000	0.000	0.000	0.000
83	A	414	THR	0	-0.090	-0.058	120.789	0.000	0.000	0.000	0.000	0.000	0.000
84	A	415	TYR	0	0.032	0.003	119.995	0.000	0.000	0.000	0.000	0.000	0.000
85	A	416	ARG	1	0.952	0.965	119.112	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	417	ARG	1	0.938	0.976	124.945	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	418	LEU	0	-0.049	-0.024	126.332	0.000	0.000	0.000	0.000	0.000	0.000
88	A	419	LEU	0	-0.039	-0.012	126.783	0.000	0.000	0.000	0.000	0.000	0.000
89	A	420	GLU	-1	-0.950	-0.960	129.681	0.007	0.007	0.000	0.000	0.000	0.000
90	A	421	GLY	0	-0.063	-0.019	132.098	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:332:SER)