FMO DATABASE

FMODB ID: Z2Q5N

Calculation Name: 2DB7-A-Xray310

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DB7

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y5J3

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	59
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-266375.257624
FMO2-HF: Nuclear repulsion	243684.69306
FMO2-HF: Total energy	-22690.564564
FMO2-MP2: Total energy	-22756.480666

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:0:ACE )

Summations of interaction energy for fragment #1(A:0:ACE )

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.
-0.293	1.642	3.233	-3.065	-2.102	-0.02

Interaction energy analysis for fragmet #1(A:0:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : -0.002

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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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	2	GLY	0	0.045	0.019	3.842	1.047	1.825	-0.006	-0.356	-0.416	0.000
4	A	3	GLY	0	-0.006	-0.004	6.423	0.032	0.032	0.000	0.000	0.000	0.000
5	A	4	TYR	0	-0.023	0.003	2.516	0.046	0.210	1.143	-0.663	-0.644	-0.002
6	A	5	PHE	0	0.029	0.007	2.795	-2.084	-0.971	0.633	-1.160	-0.585	-0.011
7	A	6	ASP	-1	-0.808	-0.920	2.524	3.097	3.046	1.452	-0.879	-0.522	-0.007
8	A	7	ALA	0	-0.005	-0.014	3.927	-1.040	-1.109	0.011	-0.007	0.065	0.000
9	A	8	HIS	0	-0.008	0.003	7.175	-0.380	-0.380	0.000	0.000	0.000	0.000
10	A	9	ALA	0	0.002	-0.012	6.156	-0.308	-0.308	0.000	0.000	0.000	0.000
11	A	10	LEU	0	0.015	0.017	7.930	-0.233	-0.233	0.000	0.000	0.000	0.000
12	A	11	ALA	0	0.006	-0.001	9.698	-0.163	-0.163	0.000	0.000	0.000	0.000
13	A	12	MET	0	-0.045	-0.023	11.350	-0.092	-0.092	0.000	0.000	0.000	0.000
14	A	13	ASP	-1	-0.889	-0.933	10.809	0.323	0.323	0.000	0.000	0.000	0.000
15	A	14	TYR	0	0.004	-0.012	13.746	-0.079	-0.079	0.000	0.000	0.000	0.000
16	A	15	ARG	1	0.930	0.980	16.452	-0.256	-0.256	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.033	-0.026	16.800	-0.036	-0.036	0.000	0.000	0.000	0.000
18	A	17	LEU	0	0.006	0.007	17.330	-0.026	-0.026	0.000	0.000	0.000	0.000
19	A	18	GLY	0	0.085	0.048	20.463	-0.016	-0.016	0.000	0.000	0.000	0.000
20	A	19	PHE	0	-0.076	-0.042	22.088	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	20	ARG	1	0.934	0.936	18.853	-0.128	-0.128	0.000	0.000	0.000	0.000
22	A	21	GLU	-1	-0.914	-0.921	24.706	0.100	0.100	0.000	0.000	0.000	0.000
23	A	22	CYS	0	-0.006	-0.006	26.534	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	23	LEU	0	-0.038	-0.008	27.294	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	24	ALA	0	0.001	-0.012	28.765	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	25	GLU	-1	-0.832	-0.920	30.516	0.054	0.054	0.000	0.000	0.000	0.000
27	A	26	VAL	0	-0.032	-0.011	32.331	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	27	ALA	0	-0.027	-0.020	33.470	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	28	ARG	1	0.920	0.964	34.784	-0.054	-0.054	0.000	0.000	0.000	0.000
30	A	29	TYR	0	-0.057	-0.036	36.549	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	30	LEU	0	0.018	-0.003	37.531	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	31	SER	0	-0.017	0.004	39.314	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	32	ILE	0	-0.098	-0.057	39.299	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	33	ILE	0	-0.055	-0.019	41.222	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	34	GLU	-1	-0.899	-0.937	42.553	0.035	0.035	0.000	0.000	0.000	0.000
36	A	35	GLY	0	-0.018	0.018	44.306	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	36	LEU	0	-0.032	-0.009	41.764	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	37	ASP	-1	-0.785	-0.898	42.417	0.025	0.025	0.000	0.000	0.000	0.000
39	A	38	ALA	0	-0.056	-0.061	40.547	0.001	0.001	0.000	0.000	0.000	0.000
40	A	39	SER	0	-0.046	-0.025	40.990	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	40	ASP	-1	-0.802	-0.892	42.781	0.028	0.028	0.000	0.000	0.000	0.000
42	A	41	PRO	0	0.009	-0.012	41.929	0.002	0.002	0.000	0.000	0.000	0.000
43	A	42	LEU	0	-0.019	-0.004	40.100	0.001	0.001	0.000	0.000	0.000	0.000
44	A	43	ARG	1	0.913	0.958	37.343	-0.031	-0.031	0.000	0.000	0.000	0.000
45	A	44	VAL	0	0.015	0.015	37.202	0.003	0.003	0.000	0.000	0.000	0.000
46	A	45	ARG	1	0.943	0.974	36.287	-0.028	-0.028	0.000	0.000	0.000	0.000
47	A	46	LEU	0	0.003	0.014	34.175	0.002	0.002	0.000	0.000	0.000	0.000
48	A	47	VAL	0	0.038	0.010	31.946	0.004	0.004	0.000	0.000	0.000	0.000
49	A	48	SER	0	-0.049	-0.037	31.399	0.003	0.003	0.000	0.000	0.000	0.000
50	A	49	HIS	0	0.017	0.017	30.962	0.000	0.000	0.000	0.000	0.000	0.000
51	A	50	LEU	0	0.000	-0.007	28.945	0.005	0.005	0.000	0.000	0.000	0.000
52	A	51	ASN	0	0.022	0.001	27.058	0.012	0.012	0.000	0.000	0.000	0.000
53	A	52	ASN	0	0.015	-0.001	26.086	0.002	0.002	0.000	0.000	0.000	0.000
54	A	53	TYR	0	-0.001	0.021	24.740	0.007	0.007	0.000	0.000	0.000	0.000
55	A	54	ALA	0	-0.032	-0.029	22.745	0.008	0.008	0.000	0.000	0.000	0.000
56	A	55	SER	0	-0.068	-0.028	21.537	0.006	0.006	0.000	0.000	0.000	0.000
57	A	56	GLN	0	-0.024	-0.014	21.569	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	57	ARG	1	0.854	0.949	19.854	-0.127	-0.127	0.000	0.000	0.000	0.000
59	A	58	NME	0	0.008	0.010	17.217	0.011	0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ACE )