FMO DATABASE

FMODB ID: 9G9M2

Calculation Name: 1YTF-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YTF

Chain ID: B

ChEMBL ID:

UniProt ID: P32774

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	46
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-211002.713098
FMO2-HF: Nuclear repulsion	192584.511603
FMO2-HF: Total energy	-18418.201495
FMO2-MP2: Total energy	-18473.137556

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:2:SER)

Summations of interaction energy for fragment #1(B:2: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.
1.035	2.819	-0.029	-0.872	-0.882	0

Interaction energy analysis for fragmet #1(B:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.018

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].
3	B	4	ALA	0	0.044	0.037	3.804	-0.051	1.733	-0.029	-0.872	-0.882
4	B	5	GLU	-1	-0.908	-0.950	6.800	0.050	0.050	0.000	0.000	0.000
5	B	6	ALA	0	0.021	0.011	5.988	0.235	0.235	0.000	0.000	0.000
6	B	7	SER	0	-0.026	-0.014	7.275	0.126	0.126	0.000	0.000	0.000
7	B	8	ARG	1	0.947	0.980	8.892	0.106	0.106	0.000	0.000	0.000
8	B	9	VAL	0	0.031	0.010	11.372	0.050	0.050	0.000	0.000	0.000
9	B	10	TYR	0	-0.023	-0.031	9.351	0.021	0.021	0.000	0.000	0.000
10	B	11	GLU	-1	-0.895	-0.944	12.811	0.050	0.050	0.000	0.000	0.000
11	B	12	ILE	0	-0.035	-0.020	14.871	-0.013	-0.013	0.000	0.000	0.000
12	B	13	ILE	0	-0.018	-0.006	14.520	0.002	0.002	0.000	0.000	0.000
13	B	14	VAL	0	-0.038	-0.015	16.185	-0.003	-0.003	0.000	0.000	0.000
14	B	15	GLU	-1	-0.915	-0.971	18.671	0.138	0.138	0.000	0.000	0.000
15	B	16	SER	0	-0.062	-0.027	20.534	-0.017	-0.017	0.000	0.000	0.000
16	B	17	VAL	0	0.002	0.006	21.000	-0.003	-0.003	0.000	0.000	0.000
17	B	18	VAL	0	-0.004	-0.005	22.447	-0.007	-0.007	0.000	0.000	0.000
18	B	19	ASN	0	-0.035	-0.040	24.745	0.001	0.001	0.000	0.000	0.000
19	B	20	GLU	-1	-0.922	-0.947	25.274	0.091	0.091	0.000	0.000	0.000
20	B	21	VAL	0	-0.007	-0.009	26.023	-0.003	-0.003	0.000	0.000	0.000
21	B	22	ARG	1	0.845	0.929	27.765	-0.099	-0.099	0.000	0.000	0.000
22	B	23	GLU	-1	-0.910	-0.933	30.880	0.064	0.064	0.000	0.000	0.000
23	B	24	ASP	-1	-0.884	-0.947	32.160	0.097	0.097	0.000	0.000	0.000
24	B	25	PHE	0	-0.069	-0.051	29.120	0.004	0.004	0.000	0.000	0.000
25	B	26	GLU	-1	-0.945	-0.985	33.411	0.075	0.075	0.000	0.000	0.000
26	B	27	ASN	0	-0.034	-0.010	36.338	-0.007	-0.007	0.000	0.000	0.000
27	B	28	ALA	0	-0.116	-0.060	35.993	-0.003	-0.003	0.000	0.000	0.000
28	B	29	GLY	0	-0.017	-0.004	38.040	0.001	0.001	0.000	0.000	0.000
29	B	30	ILE	0	-0.049	-0.008	33.229	0.001	0.001	0.000	0.000	0.000
30	B	31	ASP	-1	-0.876	-0.964	34.001	0.110	0.110	0.000	0.000	0.000
31	B	32	GLU	-1	-0.785	-0.876	30.322	0.116	0.116	0.000	0.000	0.000
32	B	33	GLN	0	0.015	-0.016	30.539	0.015	0.015	0.000	0.000	0.000
33	B	34	THR	0	0.052	0.047	29.903	0.011	0.011	0.000	0.000	0.000
34	B	35	LEU	0	-0.054	-0.008	26.975	0.018	0.018	0.000	0.000	0.000
35	B	36	GLN	0	-0.060	-0.044	26.189	0.028	0.028	0.000	0.000	0.000
36	B	37	ASP	-1	-0.893	-0.941	25.084	0.197	0.197	0.000	0.000	0.000
37	B	38	LEU	0	-0.052	-0.024	23.853	0.031	0.031	0.000	0.000	0.000
38	B	39	LYS	1	0.910	0.959	20.429	-0.165	-0.165	0.000	0.000	0.000
39	B	40	ASN	0	0.046	0.013	20.343	0.043	0.043	0.000	0.000	0.000
40	B	41	ILE	0	-0.059	-0.042	20.237	0.049	0.049	0.000	0.000	0.000
41	B	42	TRP	0	-0.006	0.006	16.771	0.044	0.044	0.000	0.000	0.000
42	B	43	GLN	0	0.077	0.016	16.013	0.056	0.056	0.000	0.000	0.000
43	B	44	LYS	1	0.929	0.992	15.456	-0.325	-0.325	0.000	0.000	0.000
44	B	45	LYS	1	0.817	0.903	16.109	-0.345	-0.345	0.000	0.000	0.000
45	B	46	LEU	0	-0.001	0.010	11.545	0.077	0.077	0.000	0.000	0.000
46	B	47	THR	0	-0.062	-0.015	10.156	0.169	0.169	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:SER)