FMO DATABASE

FMODB ID: Z6LGN

Calculation Name: 2YH9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YH9

Chain ID: A

ChEMBL ID:

UniProt ID: P0A937

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:

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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-309171.700181
FMO2-HF: Nuclear repulsion	283494.752963
FMO2-HF: Total energy	-25676.947218
FMO2-MP2: Total energy	-25751.680082

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(A:5:VAL)

Summations of interaction energy for fragment #1(A:5:VAL)

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.
-18.322	-12.901	5.086	-3.516	-6.99	0.018

Interaction energy analysis for fragmet #1(A:5:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.057 / 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	A	7	LYS	1	0.953	0.980	2.388	-14.542	-11.240	3.453	-2.541	-4.215	0.023
4	A	8	ILE	0	0.037	0.023	2.602	-2.387	-1.341	0.357	-0.348	-1.054	0.000
5	A	9	ARG	1	0.856	0.890	5.165	-1.277	-1.283	-0.001	-0.007	0.015	0.000
6	A	10	VAL	0	0.062	0.013	8.266	0.037	0.037	0.000	0.000	0.000	0.000
7	A	11	GLY	0	0.015	0.013	10.898	0.081	0.081	0.000	0.000	0.000	0.000
8	A	12	MET	0	-0.061	0.021	8.207	0.045	0.045	0.000	0.000	0.000	0.000
9	A	13	THR	0	0.056	0.029	11.884	-0.075	-0.075	0.000	0.000	0.000	0.000
10	A	14	GLN	0	0.061	0.004	11.987	0.067	0.067	0.000	0.000	0.000	0.000
11	A	15	GLN	0	0.022	0.010	12.269	0.036	0.036	0.000	0.000	0.000	0.000
12	A	16	GLN	0	0.031	0.019	11.076	0.016	0.016	0.000	0.000	0.000	0.000
13	A	17	VAL	0	0.034	0.013	6.620	0.253	0.253	0.000	0.000	0.000	0.000
14	A	18	ALA	0	-0.008	0.003	7.960	0.198	0.198	0.000	0.000	0.000	0.000
15	A	19	TYR	0	-0.058	-0.018	10.319	0.028	0.028	0.000	0.000	0.000	0.000
16	A	20	ALA	0	-0.038	-0.014	5.958	0.173	0.173	0.000	0.000	0.000	0.000
17	A	21	LEU	0	-0.075	-0.057	2.434	-0.493	0.586	1.277	-0.620	-1.736	-0.005
18	A	22	GLY	0	0.048	0.051	5.956	-0.335	-0.335	0.000	0.000	0.000	0.000
19	A	23	THR	0	-0.005	-0.019	9.174	-0.063	-0.063	0.000	0.000	0.000	0.000
20	A	24	PRO	0	-0.033	-0.010	9.336	-0.030	-0.030	0.000	0.000	0.000	0.000
21	A	25	LEU	0	0.016	0.013	10.231	0.071	0.071	0.000	0.000	0.000	0.000
22	A	26	MET	0	-0.022	-0.024	12.149	0.051	0.051	0.000	0.000	0.000	0.000
23	A	27	SER	0	0.010	-0.003	12.955	-0.055	-0.055	0.000	0.000	0.000	0.000
24	A	28	ASP	-1	-0.892	-0.945	15.308	-0.212	-0.212	0.000	0.000	0.000	0.000
25	A	29	PRO	0	0.021	0.019	18.377	0.016	0.016	0.000	0.000	0.000	0.000
26	A	30	PHE	0	0.009	0.006	21.467	0.030	0.030	0.000	0.000	0.000	0.000
27	A	31	GLY	0	-0.004	0.003	21.947	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	32	THR	0	-0.072	-0.030	19.931	0.018	0.018	0.000	0.000	0.000	0.000
29	A	33	ASN	0	0.034	0.000	23.084	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	34	THR	0	-0.020	-0.005	24.180	0.010	0.010	0.000	0.000	0.000	0.000
31	A	35	TRP	0	-0.036	-0.006	23.598	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	36	PHE	0	0.026	0.001	24.111	0.011	0.011	0.000	0.000	0.000	0.000
33	A	37	TYR	0	-0.004	0.008	25.044	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	38	VAL	0	0.014	-0.009	25.903	0.011	0.011	0.000	0.000	0.000	0.000
35	A	39	PHE	0	-0.010	0.004	28.260	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	40	ARG	1	0.962	0.986	23.122	0.104	0.104	0.000	0.000	0.000	0.000
37	A	41	GLN	0	-0.037	-0.034	28.440	-0.013	-0.013	0.000	0.000	0.000	0.000
38	A	42	GLN	0	0.029	0.026	31.426	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	43	PRO	0	0.006	-0.010	34.194	0.005	0.005	0.000	0.000	0.000	0.000
40	A	44	GLY	0	0.022	0.008	37.940	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	45	HIS	0	0.012	0.034	34.609	0.001	0.001	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.921	-0.952	38.353	-0.030	-0.030	0.000	0.000	0.000	0.000
43	A	47	GLY	0	-0.017	-0.007	39.532	0.000	0.000	0.000	0.000	0.000	0.000
44	A	48	VAL	0	-0.030	-0.027	40.488	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	49	THR	0	-0.040	-0.031	35.536	0.002	0.002	0.000	0.000	0.000	0.000
46	A	50	GLN	0	-0.050	-0.021	30.334	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	51	GLN	0	0.059	0.031	33.653	0.001	0.001	0.000	0.000	0.000	0.000
48	A	52	THR	0	-0.047	-0.028	29.545	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	53	LEU	0	-0.021	-0.012	30.129	0.003	0.003	0.000	0.000	0.000	0.000
50	A	54	THR	0	0.004	0.007	27.669	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	55	LEU	0	-0.034	-0.007	28.859	0.005	0.005	0.000	0.000	0.000	0.000
52	A	56	THR	0	0.032	0.015	28.466	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	57	PHE	0	0.010	-0.003	27.995	0.000	0.000	0.000	0.000	0.000	0.000
54	A	58	ASN	0	0.018	0.008	29.335	0.000	0.000	0.000	0.000	0.000	0.000
55	A	59	SER	0	0.042	0.008	28.288	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	60	SER	0	-0.046	-0.018	28.791	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.016	0.016	29.213	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	62	VAL	0	-0.037	-0.020	30.003	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	63	LEU	0	0.002	0.005	32.417	0.004	0.004	0.000	0.000	0.000	0.000
60	A	64	THR	0	-0.062	-0.043	33.016	0.005	0.005	0.000	0.000	0.000	0.000
61	A	65	ASN	0	-0.033	-0.019	33.711	0.004	0.004	0.000	0.000	0.000	0.000
62	A	66	ILE	0	0.035	0.015	33.555	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	67	ASP	-1	-0.803	-0.874	32.882	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	68	ASN	0	-0.005	-0.003	33.455	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	69	LYS	1	0.833	0.895	32.572	0.014	0.014	0.000	0.000	0.000	0.000
66	A	70	PRO	0	0.048	0.032	35.045	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:VAL)