FMO DATABASE

FMODB ID: 7G7MK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-210516.407464
FMO2-HF: Nuclear repulsion	192097.668146
FMO2-HF: Total energy	-18418.739318
FMO2-MP2: Total energy	-18473.578439

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.
1.569	3.041	-0.019	-0.729	-0.724	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 : -0.018 / q_NPA : -0.024

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	0.052	0.034	3.866	0.434	1.906	-0.019	-0.729	-0.724
4	B	5	GLU	-1	-0.868	-0.905	6.679	0.558	0.558	0.000	0.000	0.000
5	B	6	ALA	0	0.057	0.020	6.263	0.144	0.144	0.000	0.000	0.000
6	B	7	SER	0	-0.058	-0.033	6.914	-0.007	-0.007	0.000	0.000	0.000
7	B	8	ARG	1	0.850	0.883	8.632	-0.196	-0.196	0.000	0.000	0.000
8	B	9	VAL	0	0.017	0.003	11.324	-0.030	-0.030	0.000	0.000	0.000
9	B	10	TYR	0	-0.017	-0.022	8.527	-0.068	-0.068	0.000	0.000	0.000
10	B	11	GLU	-1	-0.800	-0.854	12.695	0.171	0.171	0.000	0.000	0.000
11	B	12	ILE	0	-0.020	-0.014	14.620	-0.049	-0.049	0.000	0.000	0.000
12	B	13	ILE	0	-0.013	-0.002	14.862	-0.026	-0.026	0.000	0.000	0.000
13	B	14	VAL	0	-0.024	-0.009	16.224	-0.027	-0.027	0.000	0.000	0.000
14	B	15	GLU	-1	-0.796	-0.895	18.373	0.270	0.270	0.000	0.000	0.000
15	B	16	SER	0	-0.088	-0.046	20.521	-0.040	-0.040	0.000	0.000	0.000
16	B	17	VAL	0	0.044	0.019	21.512	-0.013	-0.013	0.000	0.000	0.000
17	B	18	VAL	0	-0.017	-0.017	22.163	-0.014	-0.014	0.000	0.000	0.000
18	B	19	ASN	0	-0.047	-0.033	24.252	-0.031	-0.031	0.000	0.000	0.000
19	B	20	GLU	-1	-0.905	-0.919	24.727	0.214	0.214	0.000	0.000	0.000
20	B	21	VAL	0	-0.025	-0.021	26.372	-0.010	-0.010	0.000	0.000	0.000
21	B	22	ARG	1	0.787	0.864	28.053	-0.166	-0.166	0.000	0.000	0.000
22	B	23	GLU	-1	-0.870	-0.913	30.861	0.116	0.116	0.000	0.000	0.000
23	B	24	ASP	-1	-0.840	-0.929	32.401	0.152	0.152	0.000	0.000	0.000
24	B	25	PHE	0	-0.081	-0.050	29.241	0.003	0.003	0.000	0.000	0.000
25	B	26	GLU	-1	-0.938	-0.976	33.661	0.118	0.118	0.000	0.000	0.000
26	B	27	ASN	0	-0.102	-0.058	36.599	-0.013	-0.013	0.000	0.000	0.000
27	B	28	ALA	0	-0.089	-0.047	36.043	-0.005	-0.005	0.000	0.000	0.000
28	B	29	GLY	0	-0.030	-0.004	38.114	-0.001	-0.001	0.000	0.000	0.000
29	B	30	ILE	0	-0.062	-0.014	33.639	-0.002	-0.002	0.000	0.000	0.000
30	B	31	ASP	-1	-0.758	-0.890	33.882	0.148	0.148	0.000	0.000	0.000
31	B	32	GLU	-1	-0.759	-0.821	29.846	0.178	0.178	0.000	0.000	0.000
32	B	33	GLN	0	-0.049	-0.041	30.316	0.016	0.016	0.000	0.000	0.000
33	B	34	THR	0	-0.011	-0.022	29.445	0.017	0.017	0.000	0.000	0.000
34	B	35	LEU	0	-0.027	0.011	27.272	0.021	0.021	0.000	0.000	0.000
35	B	36	GLN	0	-0.051	-0.045	25.722	0.040	0.040	0.000	0.000	0.000
36	B	37	ASP	-1	-0.862	-0.932	24.836	0.259	0.259	0.000	0.000	0.000
37	B	38	LEU	0	-0.062	-0.020	24.194	0.034	0.034	0.000	0.000	0.000
38	B	39	LYS	1	0.842	0.900	20.103	-0.257	-0.257	0.000	0.000	0.000
39	B	40	ASN	0	-0.035	-0.022	20.355	0.059	0.059	0.000	0.000	0.000
40	B	41	ILE	0	-0.073	-0.045	20.262	0.052	0.052	0.000	0.000	0.000
41	B	42	TRP	0	-0.001	0.008	17.034	0.046	0.046	0.000	0.000	0.000
42	B	43	GLN	0	0.040	0.013	15.921	0.060	0.060	0.000	0.000	0.000
43	B	44	LYS	1	0.937	0.969	15.309	-0.344	-0.344	0.000	0.000	0.000
44	B	45	LYS	1	0.872	0.939	16.767	-0.490	-0.490	0.000	0.000	0.000
45	B	46	LEU	0	-0.015	0.004	11.239	0.081	0.081	0.000	0.000	0.000
46	B	47	THR	0	-0.068	-0.021	9.724	0.167	0.167	0.000	0.000	0.000

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