FMO DATABASE

FMODB ID: MVR2Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-577948.277277
FMO2-HF: Nuclear repulsion	541141.044929
FMO2-HF: Total energy	-36807.232348
FMO2-MP2: Total energy	-36915.729056

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.
-23.016	-24.171	13.537	-6.707	-5.675	-0.073

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 : 0.945 / q_NPA : 0.959

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	0.040	0.031	3.716	3.449	5.118	-0.001	-0.670	-0.998	0.001
4	B	7	ASP	-1	-0.801	-0.873	5.829	-19.707	-19.707	0.000	0.000	0.000	0.000
5	B	8	GLY	0	0.012	-0.008	9.368	-0.726	-0.726	0.000	0.000	0.000	0.000
6	B	9	ARG	1	0.884	0.911	12.368	17.569	17.569	0.000	0.000	0.000	0.000
7	B	10	ARG	1	0.818	0.860	7.124	24.722	24.722	0.000	0.000	0.000	0.000
8	B	11	LYS	1	0.771	0.855	8.363	27.640	27.640	0.000	0.000	0.000	0.000
9	B	12	ALA	0	0.043	0.031	11.161	0.258	0.258	0.000	0.000	0.000	0.000
10	B	13	ALA	0	0.073	0.039	13.435	0.641	0.641	0.000	0.000	0.000	0.000
11	B	14	VAL	0	-0.024	-0.022	9.433	0.461	0.461	0.000	0.000	0.000	0.000
12	B	15	LEU	0	-0.025	-0.009	12.896	0.287	0.287	0.000	0.000	0.000	0.000
13	B	16	LEU	0	0.021	0.007	15.483	0.765	0.765	0.000	0.000	0.000	0.000
14	B	17	VAL	0	0.007	-0.006	15.325	0.715	0.715	0.000	0.000	0.000	0.000
15	B	18	ALA	0	-0.120	-0.073	15.269	0.282	0.282	0.000	0.000	0.000	0.000
16	B	19	LEU	0	-0.008	0.018	17.245	0.479	0.479	0.000	0.000	0.000	0.000
17	B	20	GLY	0	0.038	0.030	20.492	0.709	0.709	0.000	0.000	0.000	0.000
18	B	21	PRO	0	0.032	-0.001	22.291	0.142	0.142	0.000	0.000	0.000	0.000
19	B	22	GLU	-1	-0.799	-0.887	24.851	-11.502	-11.502	0.000	0.000	0.000	0.000
20	B	23	LYS	1	0.803	0.888	24.116	12.767	12.767	0.000	0.000	0.000	0.000
21	B	24	ALA	0	0.001	0.008	21.801	-0.055	-0.055	0.000	0.000	0.000	0.000
22	B	25	ALA	0	0.058	0.022	23.361	0.069	0.069	0.000	0.000	0.000	0.000
23	B	26	GLN	0	-0.021	-0.008	26.500	0.416	0.416	0.000	0.000	0.000	0.000
24	B	27	VAL	0	-0.019	-0.016	22.308	0.170	0.170	0.000	0.000	0.000	0.000
25	B	28	MET	0	-0.013	-0.017	22.589	-0.044	-0.044	0.000	0.000	0.000	0.000
26	B	29	LYS	1	0.886	0.950	25.502	10.220	10.220	0.000	0.000	0.000	0.000
27	B	30	HIS	0	-0.081	-0.023	26.961	0.411	0.411	0.000	0.000	0.000	0.000
28	B	31	LEU	0	-0.059	-0.024	22.922	-0.346	-0.346	0.000	0.000	0.000	0.000
29	B	32	ASP	-1	-0.781	-0.853	27.341	-10.779	-10.779	0.000	0.000	0.000	0.000
30	B	33	GLU	-1	-0.866	-0.954	27.569	-9.721	-9.721	0.000	0.000	0.000	0.000
31	B	34	GLU	-1	-0.865	-0.898	26.268	-10.819	-10.819	0.000	0.000	0.000	0.000
32	B	35	THR	0	-0.054	-0.068	22.477	-0.585	-0.585	0.000	0.000	0.000	0.000
33	B	36	VAL	0	-0.053	-0.029	22.953	-0.639	-0.639	0.000	0.000	0.000	0.000
34	B	37	GLU	-1	-0.902	-0.956	23.805	-10.815	-10.815	0.000	0.000	0.000	0.000
35	B	38	GLN	0	-0.083	-0.061	20.924	-0.887	-0.887	0.000	0.000	0.000	0.000
36	B	39	LEU	0	-0.025	-0.014	18.065	-0.813	-0.813	0.000	0.000	0.000	0.000
37	B	40	VAL	0	-0.007	-0.005	19.295	-0.642	-0.642	0.000	0.000	0.000	0.000
38	B	41	VAL	0	0.019	0.024	19.738	-0.152	-0.152	0.000	0.000	0.000	0.000
39	B	42	GLU	-1	-0.870	-0.925	14.436	-17.190	-17.190	0.000	0.000	0.000	0.000
40	B	43	ILE	0	-0.063	-0.043	15.837	-0.767	-0.767	0.000	0.000	0.000	0.000
41	B	44	ALA	0	-0.036	-0.009	17.343	-0.298	-0.298	0.000	0.000	0.000	0.000
42	B	45	ASN	0	-0.063	-0.035	16.199	0.370	0.370	0.000	0.000	0.000	0.000
43	B	46	ILE	0	-0.041	-0.002	12.169	-0.954	-0.954	0.000	0.000	0.000	0.000
44	B	47	GLY	0	0.033	0.027	12.241	-1.164	-1.164	0.000	0.000	0.000	0.000
45	B	48	ARG	1	0.918	0.960	10.693	19.522	19.522	0.000	0.000	0.000	0.000
46	B	49	VAL	0	0.044	0.033	9.400	-1.030	-1.030	0.000	0.000	0.000	0.000
47	B	50	THR	0	-0.061	-0.056	6.846	0.652	0.652	0.000	0.000	0.000	0.000
48	B	51	PRO	0	0.042	0.006	9.095	-0.420	-0.420	0.000	0.000	0.000	0.000
49	B	52	GLU	-1	-0.834	-0.899	5.212	-35.331	-35.331	0.000	0.000	0.000	0.000
50	B	53	GLU	-1	-0.790	-0.870	4.749	-34.957	-34.887	-0.001	-0.004	-0.065	0.000
51	B	54	LYS	1	0.993	1.001	6.733	20.253	20.253	0.000	0.000	0.000	0.000
52	B	55	LYS	1	0.853	0.915	6.759	40.512	40.512	0.000	0.000	0.000	0.000
53	B	56	GLN	0	-0.011	-0.005	1.703	-41.423	-44.317	13.539	-6.033	-4.612	-0.074
54	B	57	VAL	0	0.024	0.019	6.402	2.172	2.172	0.000	0.000	0.000	0.000
55	B	58	LEU	0	0.009	0.009	9.753	2.295	2.295	0.000	0.000	0.000	0.000
56	B	59	GLU	-1	-0.836	-0.905	7.933	-33.805	-33.805	0.000	0.000	0.000	0.000
57	B	60	GLU	-1	-0.814	-0.877	8.887	-28.169	-28.169	0.000	0.000	0.000	0.000
58	B	61	PHE	0	0.038	0.014	10.676	2.236	2.236	0.000	0.000	0.000	0.000
59	B	62	LEU	0	-0.022	-0.020	13.682	1.772	1.772	0.000	0.000	0.000	0.000
60	B	63	SER	0	-0.019	0.010	13.200	1.879	1.879	0.000	0.000	0.000	0.000
61	B	64	LEU	0	0.032	0.002	13.354	1.353	1.353	0.000	0.000	0.000	0.000
62	B	65	ALA	0	-0.015	-0.003	16.543	1.156	1.156	0.000	0.000	0.000	0.000
63	B	66	LYS	1	0.885	0.936	17.783	18.135	18.135	0.000	0.000	0.000	0.000
64	B	67	ALA	0	-0.002	0.011	18.883	0.534	0.534	0.000	0.000	0.000	0.000
65	B	68	LYS	1	0.803	0.890	20.732	13.987	13.987	0.000	0.000	0.000	0.000
66	B	69	GLU	-1	-0.876	-0.923	23.407	-13.081	-13.081	0.000	0.000	0.000	0.000
67	B	70	MET	0	0.006	0.001	25.124	-0.155	-0.155	0.000	0.000	0.000	0.000
68	B	71	ILE	0	-0.018	-0.012	21.580	0.177	0.177	0.000	0.000	0.000	0.000
69	B	72	SER	0	-0.003	-0.002	26.109	0.430	0.430	0.000	0.000	0.000	0.000
70	B	73	GLU	-1	-0.857	-0.932	28.099	-11.012	-11.012	0.000	0.000	0.000	0.000
71	B	74	GLY	0	0.005	0.010	25.883	-0.343	-0.343	0.000	0.000	0.000	0.000
72	B	75	GLY	0	-0.010	-0.007	23.724	-0.573	-0.573	0.000	0.000	0.000	0.000
73	B	76	ILE	0	0.029	0.010	23.141	-0.643	-0.643	0.000	0.000	0.000	0.000
74	B	77	GLU	-1	-0.764	-0.883	22.412	-14.825	-14.825	0.000	0.000	0.000	0.000
75	B	78	TYR	0	-0.025	0.003	15.945	-1.000	-1.000	0.000	0.000	0.000	0.000
76	B	79	ALA	0	0.043	0.006	18.748	-1.015	-1.015	0.000	0.000	0.000	0.000
77	B	80	LYS	1	0.827	0.912	19.228	14.571	14.571	0.000	0.000	0.000	0.000
78	B	81	LYS	1	0.823	0.889	15.966	15.292	15.292	0.000	0.000	0.000	0.000
79	B	82	VAL	0	-0.025	-0.004	14.457	-1.433	-1.433	0.000	0.000	0.000	0.000
80	B	83	LEU	0	0.016	0.000	14.868	-1.001	-1.001	0.000	0.000	0.000	0.000
81	B	84	GLU	-1	-0.858	-0.917	16.568	-16.954	-16.954	0.000	0.000	0.000	0.000
82	B	85	LYS	1	0.857	0.916	11.110	25.737	25.737	0.000	0.000	0.000	0.000
83	B	86	ALA	0	-0.029	0.007	11.700	-1.800	-1.800	0.000	0.000	0.000	0.000
84	B	87	PHE	0	-0.024	-0.020	13.171	-0.027	-0.027	0.000	0.000	0.000	0.000
85	B	88	GLY	0	0.047	0.044	15.858	0.731	0.731	0.000	0.000	0.000	0.000
86	B	89	PRO	0	0.025	-0.008	17.437	0.553	0.553	0.000	0.000	0.000	0.000
87	B	90	GLU	-1	-0.796	-0.901	20.910	-11.455	-11.455	0.000	0.000	0.000	0.000
88	B	91	ARG	1	0.907	0.956	19.353	14.659	14.659	0.000	0.000	0.000	0.000
89	B	92	ALA	0	0.059	0.029	19.873	0.443	0.443	0.000	0.000	0.000	0.000
90	B	93	ARG	1	0.922	0.947	21.700	11.761	11.761	0.000	0.000	0.000	0.000
91	B	94	LYS	1	0.850	0.934	24.549	12.254	12.254	0.000	0.000	0.000	0.000
92	B	95	ILE	0	-0.040	-0.005	19.992	-0.066	-0.066	0.000	0.000	0.000	0.000
93	B	96	ILE	0	-0.035	-0.022	24.007	0.195	0.195	0.000	0.000	0.000	0.000
94	B	97	GLU	-1	-0.822	-0.893	26.397	-10.259	-10.259	0.000	0.000	0.000	0.000
95	B	98	ARG	1	0.795	0.902	28.795	10.563	10.563	0.000	0.000	0.000	0.000

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