FMO DATABASE

FMODB ID: LZQ69

Calculation Name: 5TDY-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5TDY

Chain ID: B

ChEMBL ID:

UniProt ID: Q9WY63

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:

Apendix: None

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	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-575241.106446
FMO2-HF: Nuclear repulsion	538434.795677
FMO2-HF: Total energy	-36806.310769
FMO2-MP2: Total energy	-36914.840027

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:4:LYS)

Summations of interaction energy for fragment #1(B:4:LYS)

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.
1.719	9.349	1.617	-3.943	-5.304	-0.034

Interaction energy analysis for fragmet #1(B:4:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.015 / q_NPA : 1.011

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	6	ILE	0	0.000	0.011	3.689	4.030	6.130	-0.001	-0.838	-1.261	0.002
4	B	7	ASP	-1	-0.788	-0.904	5.419	-21.106	-21.106	0.000	0.000	0.000	0.000
5	B	8	GLY	0	0.006	-0.011	8.959	-0.787	-0.787	0.000	0.000	0.000	0.000
6	B	9	ARG	1	0.973	0.990	11.744	18.228	18.228	0.000	0.000	0.000	0.000
7	B	10	ARG	1	0.842	0.894	6.670	25.253	25.253	0.000	0.000	0.000	0.000
8	B	11	LYS	1	0.800	0.889	7.495	34.200	34.200	0.000	0.000	0.000	0.000
9	B	12	ALA	0	0.039	0.028	10.559	0.422	0.422	0.000	0.000	0.000	0.000
10	B	13	ALA	0	0.064	0.038	12.848	0.783	0.783	0.000	0.000	0.000	0.000
11	B	14	VAL	0	-0.021	-0.024	8.907	0.542	0.542	0.000	0.000	0.000	0.000
12	B	15	LEU	0	-0.038	-0.014	12.347	0.509	0.509	0.000	0.000	0.000	0.000
13	B	16	LEU	0	0.035	0.010	14.871	0.880	0.880	0.000	0.000	0.000	0.000
14	B	17	VAL	0	0.012	0.009	14.992	0.794	0.794	0.000	0.000	0.000	0.000
15	B	18	ALA	0	-0.111	-0.059	14.916	0.560	0.560	0.000	0.000	0.000	0.000
16	B	19	LEU	0	-0.024	-0.006	16.897	0.572	0.572	0.000	0.000	0.000	0.000
17	B	20	GLY	0	-0.012	0.010	19.940	0.758	0.758	0.000	0.000	0.000	0.000
18	B	21	PRO	0	0.045	-0.004	21.907	0.053	0.053	0.000	0.000	0.000	0.000
19	B	22	GLU	-1	-0.907	-0.947	24.268	-10.367	-10.367	0.000	0.000	0.000	0.000
20	B	23	LYS	1	0.922	0.956	23.699	12.888	12.888	0.000	0.000	0.000	0.000
21	B	24	ALA	0	0.004	0.013	21.292	-0.029	-0.029	0.000	0.000	0.000	0.000
22	B	25	ALA	0	0.050	0.021	23.014	0.076	0.076	0.000	0.000	0.000	0.000
23	B	26	GLN	0	-0.034	-0.018	26.215	0.421	0.421	0.000	0.000	0.000	0.000
24	B	27	VAL	0	-0.024	-0.021	21.664	0.118	0.118	0.000	0.000	0.000	0.000
25	B	28	MET	0	-0.012	-0.017	21.174	0.067	0.067	0.000	0.000	0.000	0.000
26	B	29	LYS	1	0.959	0.994	25.220	10.187	10.187	0.000	0.000	0.000	0.000
27	B	30	HIS	0	-0.081	-0.028	26.229	0.369	0.369	0.000	0.000	0.000	0.000
28	B	31	LEU	0	-0.082	-0.031	22.370	-0.299	-0.299	0.000	0.000	0.000	0.000
29	B	32	ASP	-1	-0.812	-0.866	26.749	-10.950	-10.950	0.000	0.000	0.000	0.000
30	B	33	GLU	-1	-0.873	-0.967	27.285	-10.051	-10.051	0.000	0.000	0.000	0.000
31	B	34	GLU	-1	-0.912	-0.954	26.101	-11.032	-11.032	0.000	0.000	0.000	0.000
32	B	35	THR	0	-0.049	-0.050	22.318	-0.608	-0.608	0.000	0.000	0.000	0.000
33	B	36	VAL	0	-0.062	-0.035	22.745	-0.665	-0.665	0.000	0.000	0.000	0.000
34	B	37	GLU	-1	-0.900	-0.952	23.473	-10.832	-10.832	0.000	0.000	0.000	0.000
35	B	38	GLN	0	-0.007	-0.006	20.662	-0.079	-0.079	0.000	0.000	0.000	0.000
36	B	39	LEU	0	-0.028	-0.018	17.686	-0.799	-0.799	0.000	0.000	0.000	0.000
37	B	40	VAL	0	-0.007	0.005	18.880	-0.651	-0.651	0.000	0.000	0.000	0.000
38	B	41	VAL	0	0.025	0.023	19.282	-0.122	-0.122	0.000	0.000	0.000	0.000
39	B	42	GLU	-1	-0.968	-0.992	13.898	-17.819	-17.819	0.000	0.000	0.000	0.000
40	B	43	ILE	0	-0.078	-0.053	15.476	-0.781	-0.781	0.000	0.000	0.000	0.000
41	B	44	ALA	0	-0.036	-0.004	17.014	-0.262	-0.262	0.000	0.000	0.000	0.000
42	B	45	ASN	0	-0.069	-0.028	16.314	0.446	0.446	0.000	0.000	0.000	0.000
43	B	46	ILE	0	-0.011	0.012	11.769	-0.967	-0.967	0.000	0.000	0.000	0.000
44	B	47	GLY	0	0.031	0.018	11.940	-1.202	-1.202	0.000	0.000	0.000	0.000
45	B	48	ARG	1	0.953	0.970	10.704	18.696	18.696	0.000	0.000	0.000	0.000
46	B	49	VAL	0	0.013	0.008	9.421	-1.163	-1.163	0.000	0.000	0.000	0.000
47	B	50	THR	0	-0.023	-0.006	6.352	-0.056	-0.056	0.000	0.000	0.000	0.000
48	B	51	PRO	0	0.046	0.004	9.023	-0.763	-0.763	0.000	0.000	0.000	0.000
49	B	52	GLU	-1	-0.876	-0.947	5.429	-33.050	-33.050	0.000	0.000	0.000	0.000
50	B	53	GLU	-1	-0.778	-0.870	4.293	-36.172	-36.078	-0.001	-0.007	-0.086	0.000
51	B	54	LYS	1	0.974	0.998	6.352	19.909	19.909	0.000	0.000	0.000	0.000
52	B	55	LYS	1	0.850	0.908	6.439	39.975	39.975	0.000	0.000	0.000	0.000
53	B	56	GLN	0	-0.033	-0.026	2.631	-14.585	-9.149	1.619	-3.098	-3.957	-0.036
54	B	57	VAL	0	0.004	0.007	6.054	1.536	1.536	0.000	0.000	0.000	0.000
55	B	58	LEU	0	-0.014	-0.004	8.795	2.318	2.318	0.000	0.000	0.000	0.000
56	B	59	GLU	-1	-0.878	-0.927	6.816	-37.576	-37.576	0.000	0.000	0.000	0.000
57	B	60	GLU	-1	-0.867	-0.922	7.651	-32.345	-32.345	0.000	0.000	0.000	0.000
58	B	61	PHE	0	0.026	0.009	9.535	2.557	2.557	0.000	0.000	0.000	0.000
59	B	62	LEU	0	-0.025	-0.019	12.786	1.951	1.951	0.000	0.000	0.000	0.000
60	B	63	SER	0	-0.053	-0.019	11.900	2.081	2.081	0.000	0.000	0.000	0.000
61	B	64	LEU	0	0.035	0.011	12.519	1.381	1.381	0.000	0.000	0.000	0.000
62	B	65	ALA	0	-0.057	-0.023	15.297	1.344	1.344	0.000	0.000	0.000	0.000
63	B	66	LYS	1	0.967	0.970	16.761	18.823	18.823	0.000	0.000	0.000	0.000
64	B	67	ALA	0	0.006	0.028	17.660	0.642	0.642	0.000	0.000	0.000	0.000
65	B	68	LYS	1	0.899	0.950	19.427	14.767	14.767	0.000	0.000	0.000	0.000
66	B	69	GLU	-1	-0.976	-0.982	22.257	-13.461	-13.461	0.000	0.000	0.000	0.000
67	B	70	MET	0	-0.010	-0.005	23.832	-0.155	-0.155	0.000	0.000	0.000	0.000
68	B	71	ILE	0	-0.012	-0.007	21.230	0.116	0.116	0.000	0.000	0.000	0.000
69	B	72	SER	0	0.003	-0.003	25.599	0.398	0.398	0.000	0.000	0.000	0.000
70	B	73	GLU	-1	-0.901	-0.946	27.538	-10.776	-10.776	0.000	0.000	0.000	0.000
71	B	74	GLY	0	0.015	0.009	25.161	-0.429	-0.429	0.000	0.000	0.000	0.000
72	B	75	GLY	0	0.014	-0.002	23.136	-0.594	-0.594	0.000	0.000	0.000	0.000
73	B	76	ILE	0	0.034	0.018	22.836	-0.581	-0.581	0.000	0.000	0.000	0.000
74	B	77	GLU	-1	-0.837	-0.927	21.357	-14.640	-14.640	0.000	0.000	0.000	0.000
75	B	78	TYR	0	-0.048	-0.021	15.077	-1.004	-1.004	0.000	0.000	0.000	0.000
76	B	79	ALA	0	0.042	0.002	18.415	-1.022	-1.022	0.000	0.000	0.000	0.000
77	B	80	LYS	1	0.899	0.961	19.344	14.216	14.216	0.000	0.000	0.000	0.000
78	B	81	LYS	1	0.906	0.955	16.004	16.543	16.543	0.000	0.000	0.000	0.000
79	B	82	VAL	0	-0.008	-0.001	14.341	-1.264	-1.264	0.000	0.000	0.000	0.000
80	B	83	LEU	0	0.022	0.009	14.919	-0.920	-0.920	0.000	0.000	0.000	0.000
81	B	84	GLU	-1	-0.907	-0.957	16.563	-16.740	-16.740	0.000	0.000	0.000	0.000
82	B	85	LYS	1	0.902	0.940	11.297	23.127	23.127	0.000	0.000	0.000	0.000
83	B	86	ALA	0	-0.039	0.004	12.334	-1.398	-1.398	0.000	0.000	0.000	0.000
84	B	87	PHE	0	-0.012	-0.019	13.454	-0.131	-0.131	0.000	0.000	0.000	0.000
85	B	88	GLY	0	0.032	0.035	16.386	0.789	0.789	0.000	0.000	0.000	0.000
86	B	89	PRO	0	0.043	-0.005	18.041	0.419	0.419	0.000	0.000	0.000	0.000
87	B	90	GLU	-1	-0.871	-0.938	21.277	-11.405	-11.405	0.000	0.000	0.000	0.000
88	B	91	ARG	1	0.959	0.985	20.203	14.364	14.364	0.000	0.000	0.000	0.000
89	B	92	ALA	0	0.025	0.013	20.044	0.376	0.376	0.000	0.000	0.000	0.000
90	B	93	ARG	1	0.899	0.939	21.822	11.596	11.596	0.000	0.000	0.000	0.000
91	B	94	LYS	1	0.897	0.938	25.041	11.520	11.520	0.000	0.000	0.000	0.000
92	B	95	ILE	0	-0.040	0.004	20.318	0.197	0.197	0.000	0.000	0.000	0.000
93	B	96	ILE	0	-0.002	0.005	23.897	0.134	0.134	0.000	0.000	0.000	0.000
94	B	97	GLU	-1	-0.913	-0.942	26.381	-10.667	-10.667	0.000	0.000	0.000	0.000
95	B	98	ARG	1	0.885	0.948	29.479	10.093	10.093	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:4:LYS)