FMO DATABASE

FMODB ID: 94L22

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

Total energy (hartree)

FMO2-HF: Electronic energy	-575635.600477
FMO2-HF: Nuclear repulsion	538828.652973
FMO2-HF: Total energy	-36806.947504
FMO2-MP2: Total energy	-36915.482642

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.
-22.475	-21.875	13.221	-7.336	-6.483	-0.076

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 : 0.962 / q_NPA : 0.970

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	0.012	0.007	3.574	3.221	5.141	-0.001	-0.773	-1.145	0.002
4	B	7	ASP	-1	-0.786	-0.873	5.391	-19.907	-19.795	-0.001	-0.004	-0.107	0.000
5	B	8	GLY	0	0.028	-0.006	8.928	-0.783	-0.783	0.000	0.000	0.000	0.000
6	B	9	ARG	1	0.892	0.921	11.718	17.796	17.796	0.000	0.000	0.000	0.000
7	B	10	ARG	1	0.828	0.870	6.668	24.776	24.776	0.000	0.000	0.000	0.000
8	B	11	LYS	1	0.756	0.853	8.176	29.230	29.230	0.000	0.000	0.000	0.000
9	B	12	ALA	0	0.041	0.029	10.549	0.309	0.309	0.000	0.000	0.000	0.000
10	B	13	ALA	0	0.067	0.039	12.842	0.697	0.697	0.000	0.000	0.000	0.000
11	B	14	VAL	0	-0.018	-0.022	8.910	0.450	0.450	0.000	0.000	0.000	0.000
12	B	15	LEU	0	-0.040	-0.014	12.352	0.421	0.421	0.000	0.000	0.000	0.000
13	B	16	LEU	0	0.039	0.010	14.875	0.779	0.779	0.000	0.000	0.000	0.000
14	B	17	VAL	0	0.016	0.010	14.997	0.741	0.741	0.000	0.000	0.000	0.000
15	B	18	ALA	0	-0.107	-0.059	14.896	0.499	0.499	0.000	0.000	0.000	0.000
16	B	19	LEU	0	-0.008	0.010	16.912	0.538	0.538	0.000	0.000	0.000	0.000
17	B	20	GLY	0	0.003	0.013	19.948	0.768	0.768	0.000	0.000	0.000	0.000
18	B	21	PRO	0	0.057	0.004	21.920	0.041	0.041	0.000	0.000	0.000	0.000
19	B	22	GLU	-1	-0.914	-0.951	24.277	-10.435	-10.435	0.000	0.000	0.000	0.000
20	B	23	LYS	1	0.875	0.931	23.657	13.153	13.153	0.000	0.000	0.000	0.000
21	B	24	ALA	0	-0.001	0.009	21.323	-0.010	-0.010	0.000	0.000	0.000	0.000
22	B	25	ALA	0	0.058	0.025	23.018	0.087	0.087	0.000	0.000	0.000	0.000
23	B	26	GLN	0	0.002	0.004	26.216	0.408	0.408	0.000	0.000	0.000	0.000
24	B	27	VAL	0	-0.021	-0.019	21.805	0.131	0.131	0.000	0.000	0.000	0.000
25	B	28	MET	0	-0.004	-0.013	21.397	0.025	0.025	0.000	0.000	0.000	0.000
26	B	29	LYS	1	0.909	0.967	25.206	10.160	10.160	0.000	0.000	0.000	0.000
27	B	30	HIS	0	-0.085	-0.032	26.576	0.389	0.389	0.000	0.000	0.000	0.000
28	B	31	LEU	0	-0.082	-0.030	22.276	-0.261	-0.261	0.000	0.000	0.000	0.000
29	B	32	ASP	-1	-0.788	-0.860	26.735	-10.751	-10.751	0.000	0.000	0.000	0.000
30	B	33	GLU	-1	-0.873	-0.961	27.269	-9.743	-9.743	0.000	0.000	0.000	0.000
31	B	34	GLU	-1	-0.857	-0.911	26.264	-10.789	-10.789	0.000	0.000	0.000	0.000
32	B	35	THR	0	-0.060	-0.063	22.223	-0.575	-0.575	0.000	0.000	0.000	0.000
33	B	36	VAL	0	-0.044	-0.027	22.728	-0.639	-0.639	0.000	0.000	0.000	0.000
34	B	37	GLU	-1	-0.905	-0.953	23.460	-10.708	-10.708	0.000	0.000	0.000	0.000
35	B	38	GLN	0	-0.078	-0.048	20.687	-0.800	-0.800	0.000	0.000	0.000	0.000
36	B	39	LEU	0	-0.029	-0.017	17.776	-0.784	-0.784	0.000	0.000	0.000	0.000
37	B	40	VAL	0	-0.004	0.003	18.869	-0.644	-0.644	0.000	0.000	0.000	0.000
38	B	41	VAL	0	0.023	0.024	19.388	-0.147	-0.147	0.000	0.000	0.000	0.000
39	B	42	GLU	-1	-0.888	-0.939	14.024	-17.264	-17.264	0.000	0.000	0.000	0.000
40	B	43	ILE	0	-0.070	-0.051	15.468	-0.785	-0.785	0.000	0.000	0.000	0.000
41	B	44	ALA	0	-0.037	-0.004	17.013	-0.286	-0.286	0.000	0.000	0.000	0.000
42	B	45	ASN	0	-0.080	-0.041	16.369	0.386	0.386	0.000	0.000	0.000	0.000
43	B	46	ILE	0	-0.008	0.017	11.794	-0.938	-0.938	0.000	0.000	0.000	0.000
44	B	47	GLY	0	0.022	0.021	11.943	-1.219	-1.219	0.000	0.000	0.000	0.000
45	B	48	ARG	1	0.937	0.964	11.183	18.889	18.889	0.000	0.000	0.000	0.000
46	B	49	VAL	0	0.023	0.013	9.438	-1.115	-1.115	0.000	0.000	0.000	0.000
47	B	50	THR	0	-0.058	-0.047	6.871	0.504	0.504	0.000	0.000	0.000	0.000
48	B	51	PRO	0	0.052	0.006	9.055	-0.583	-0.583	0.000	0.000	0.000	0.000
49	B	52	GLU	-1	-0.844	-0.910	5.511	-34.495	-34.495	0.000	0.000	0.000	0.000
50	B	53	GLU	-1	-0.787	-0.864	4.373	-35.087	-35.009	-0.001	-0.006	-0.070	0.000
51	B	54	LYS	1	0.984	0.999	6.361	20.117	20.117	0.000	0.000	0.000	0.000
52	B	55	LYS	1	0.842	0.913	6.726	40.576	40.576	0.000	0.000	0.000	0.000
53	B	56	GLN	0	-0.002	0.000	1.725	-41.483	-42.993	13.224	-6.553	-5.161	-0.078
54	B	57	VAL	0	0.007	0.008	6.213	1.917	1.917	0.000	0.000	0.000	0.000
55	B	58	LEU	0	-0.011	-0.003	9.376	2.228	2.228	0.000	0.000	0.000	0.000
56	B	59	GLU	-1	-0.855	-0.927	7.468	-35.691	-35.691	0.000	0.000	0.000	0.000
57	B	60	GLU	-1	-0.809	-0.877	8.674	-29.395	-29.395	0.000	0.000	0.000	0.000
58	B	61	PHE	0	0.034	0.010	10.470	2.322	2.322	0.000	0.000	0.000	0.000
59	B	62	LEU	0	-0.023	-0.017	13.430	1.805	1.805	0.000	0.000	0.000	0.000
60	B	63	SER	0	-0.036	-0.014	12.874	1.914	1.914	0.000	0.000	0.000	0.000
61	B	64	LEU	0	0.024	0.008	13.567	1.227	1.227	0.000	0.000	0.000	0.000
62	B	65	ALA	0	-0.026	-0.006	16.399	1.220	1.220	0.000	0.000	0.000	0.000
63	B	66	LYS	1	0.950	0.977	17.247	18.295	18.295	0.000	0.000	0.000	0.000
64	B	67	ALA	0	0.008	0.029	18.564	0.593	0.593	0.000	0.000	0.000	0.000
65	B	68	LYS	1	0.831	0.903	20.309	14.207	14.207	0.000	0.000	0.000	0.000
66	B	69	GLU	-1	-0.924	-0.958	23.111	-13.230	-13.230	0.000	0.000	0.000	0.000
67	B	70	MET	0	0.006	0.001	24.487	-0.165	-0.165	0.000	0.000	0.000	0.000
68	B	71	ILE	0	-0.018	-0.009	21.470	0.083	0.083	0.000	0.000	0.000	0.000
69	B	72	SER	0	0.021	0.004	25.974	0.481	0.481	0.000	0.000	0.000	0.000
70	B	73	GLU	-1	-0.924	-0.956	27.697	-10.864	-10.864	0.000	0.000	0.000	0.000
71	B	74	GLY	0	0.012	0.007	25.509	-0.410	-0.410	0.000	0.000	0.000	0.000
72	B	75	GLY	0	0.022	0.002	23.321	-0.600	-0.600	0.000	0.000	0.000	0.000
73	B	76	ILE	0	0.033	0.018	23.015	-0.595	-0.595	0.000	0.000	0.000	0.000
74	B	77	GLU	-1	-0.781	-0.891	21.854	-15.081	-15.081	0.000	0.000	0.000	0.000
75	B	78	TYR	0	-0.034	-0.012	15.390	-0.993	-0.993	0.000	0.000	0.000	0.000
76	B	79	ALA	0	0.040	0.003	18.650	-1.027	-1.027	0.000	0.000	0.000	0.000
77	B	80	LYS	1	0.825	0.908	19.336	14.668	14.668	0.000	0.000	0.000	0.000
78	B	81	LYS	1	0.852	0.916	16.127	15.566	15.566	0.000	0.000	0.000	0.000
79	B	82	VAL	0	-0.017	-0.004	14.313	-1.356	-1.356	0.000	0.000	0.000	0.000
80	B	83	LEU	0	0.020	0.007	14.726	-1.018	-1.018	0.000	0.000	0.000	0.000
81	B	84	GLU	-1	-0.845	-0.909	16.478	-16.871	-16.871	0.000	0.000	0.000	0.000
82	B	85	LYS	1	0.886	0.938	10.805	26.036	26.036	0.000	0.000	0.000	0.000
83	B	86	ALA	0	-0.047	-0.001	11.765	-1.637	-1.637	0.000	0.000	0.000	0.000
84	B	87	PHE	0	-0.010	-0.018	12.940	-0.216	-0.216	0.000	0.000	0.000	0.000
85	B	88	GLY	0	0.033	0.036	15.741	0.811	0.811	0.000	0.000	0.000	0.000
86	B	89	PRO	0	0.046	-0.003	17.336	0.467	0.467	0.000	0.000	0.000	0.000
87	B	90	GLU	-1	-0.810	-0.896	20.697	-11.483	-11.483	0.000	0.000	0.000	0.000
88	B	91	ARG	1	0.971	0.990	19.446	14.744	14.744	0.000	0.000	0.000	0.000
89	B	92	ALA	0	0.021	0.011	19.523	0.413	0.413	0.000	0.000	0.000	0.000
90	B	93	ARG	1	0.898	0.924	21.276	11.801	11.801	0.000	0.000	0.000	0.000
91	B	94	LYS	1	0.859	0.926	24.410	12.069	12.069	0.000	0.000	0.000	0.000
92	B	95	ILE	0	-0.051	-0.009	19.728	0.259	0.259	0.000	0.000	0.000	0.000
93	B	96	ILE	0	-0.013	-0.007	23.515	0.176	0.176	0.000	0.000	0.000	0.000
94	B	97	GLU	-1	-0.840	-0.876	26.006	-10.400	-10.400	0.000	0.000	0.000	0.000
95	B	98	ARG	1	0.798	0.883	28.935	10.395	10.395	0.000	0.000	0.000	0.000

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