FMO DATABASE

FMODB ID: M3Y9Z

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	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	46
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-210830.802683
FMO2-HF: Nuclear repulsion	192412.224207
FMO2-HF: Total energy	-18418.578476
FMO2-MP2: Total energy	-18473.471786

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.
0.906	2.757	-0.029	-0.918	-0.905	0.001

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 : -0.011 / q_NPA : -0.017

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	4	ALA	0	0.043	0.038	3.804	-0.132	1.719	-0.029	-0.918	-0.905	0.001
4	B	5	GLU	-1	-0.898	-0.943	6.651	0.093	0.093	0.000	0.000	0.000	0.000
5	B	6	ALA	0	0.022	0.016	5.996	0.219	0.219	0.000	0.000	0.000	0.000
6	B	7	SER	0	-0.025	-0.018	7.278	0.112	0.112	0.000	0.000	0.000	0.000
7	B	8	ARG	1	0.856	0.895	8.903	0.044	0.044	0.000	0.000	0.000	0.000
8	B	9	VAL	0	0.028	0.007	11.374	0.040	0.040	0.000	0.000	0.000	0.000
9	B	10	TYR	0	-0.023	-0.028	8.869	-0.002	-0.002	0.000	0.000	0.000	0.000
10	B	11	GLU	-1	-0.811	-0.864	12.814	0.081	0.081	0.000	0.000	0.000	0.000
11	B	12	ILE	0	-0.029	-0.020	14.882	-0.019	-0.019	0.000	0.000	0.000	0.000
12	B	13	ILE	0	-0.016	-0.006	14.642	-0.003	-0.003	0.000	0.000	0.000	0.000
13	B	14	VAL	0	-0.020	-0.006	16.188	-0.007	-0.007	0.000	0.000	0.000	0.000
14	B	15	GLU	-1	-0.823	-0.912	18.675	0.173	0.173	0.000	0.000	0.000	0.000
15	B	16	SER	0	-0.079	-0.049	20.538	-0.019	-0.019	0.000	0.000	0.000	0.000
16	B	17	VAL	0	0.013	0.008	21.256	-0.005	-0.005	0.000	0.000	0.000	0.000
17	B	18	VAL	0	-0.005	-0.006	22.460	-0.009	-0.009	0.000	0.000	0.000	0.000
18	B	19	ASN	0	-0.032	-0.030	24.504	-0.011	-0.011	0.000	0.000	0.000	0.000
19	B	20	GLU	-1	-0.907	-0.924	25.066	0.100	0.100	0.000	0.000	0.000	0.000
20	B	21	VAL	0	-0.014	-0.017	26.268	-0.004	-0.004	0.000	0.000	0.000	0.000
21	B	22	ARG	1	0.784	0.870	28.030	-0.111	-0.111	0.000	0.000	0.000	0.000
22	B	23	GLU	-1	-0.897	-0.929	30.884	0.067	0.067	0.000	0.000	0.000	0.000
23	B	24	ASP	-1	-0.864	-0.940	32.196	0.096	0.096	0.000	0.000	0.000	0.000
24	B	25	PHE	0	-0.076	-0.054	29.293	0.003	0.003	0.000	0.000	0.000	0.000
25	B	26	GLU	-1	-0.931	-0.979	33.414	0.081	0.081	0.000	0.000	0.000	0.000
26	B	27	ASN	0	-0.065	-0.023	36.342	-0.008	-0.008	0.000	0.000	0.000	0.000
27	B	28	ALA	0	-0.112	-0.057	35.948	-0.003	-0.003	0.000	0.000	0.000	0.000
28	B	29	GLY	0	-0.016	-0.003	38.040	0.001	0.001	0.000	0.000	0.000	0.000
29	B	30	ILE	0	-0.057	-0.014	33.390	0.001	0.001	0.000	0.000	0.000	0.000
30	B	31	ASP	-1	-0.772	-0.912	33.939	0.118	0.118	0.000	0.000	0.000	0.000
31	B	32	GLU	-1	-0.769	-0.821	30.154	0.127	0.127	0.000	0.000	0.000	0.000
32	B	33	GLN	0	-0.036	-0.046	30.548	0.014	0.014	0.000	0.000	0.000	0.000
33	B	34	THR	0	0.019	0.015	29.911	0.012	0.012	0.000	0.000	0.000	0.000
34	B	35	LEU	0	-0.051	-0.004	27.113	0.018	0.018	0.000	0.000	0.000	0.000
35	B	36	GLN	0	-0.055	-0.049	26.140	0.030	0.030	0.000	0.000	0.000	0.000
36	B	37	ASP	-1	-0.900	-0.938	25.093	0.208	0.208	0.000	0.000	0.000	0.000
37	B	38	LEU	0	-0.069	-0.031	23.933	0.031	0.031	0.000	0.000	0.000	0.000
38	B	39	LYS	1	0.838	0.904	20.234	-0.185	-0.185	0.000	0.000	0.000	0.000
39	B	40	ASN	0	0.034	0.009	20.351	0.046	0.046	0.000	0.000	0.000	0.000
40	B	41	ILE	0	-0.060	-0.041	20.245	0.048	0.048	0.000	0.000	0.000	0.000
41	B	42	TRP	0	-0.022	0.008	16.768	0.044	0.044	0.000	0.000	0.000	0.000
42	B	43	GLN	0	0.071	0.020	16.017	0.042	0.042	0.000	0.000	0.000	0.000
43	B	44	LYS	1	0.944	0.991	15.463	-0.307	-0.307	0.000	0.000	0.000	0.000
44	B	45	LYS	1	0.847	0.918	16.113	-0.334	-0.334	0.000	0.000	0.000	0.000
45	B	46	LEU	0	-0.015	0.008	11.351	0.070	0.070	0.000	0.000	0.000	0.000
46	B	47	THR	0	-0.062	-0.020	10.195	0.146	0.146	0.000	0.000	0.000	0.000

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