FMO DATABASE

FMODB ID: GNM11

Calculation Name: 2X9A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2X9A

Chain ID: A

ChEMBL ID:

UniProt ID: O80297

Base Structure: X-ray

Registration Date: 2023-06-21

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	60
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-329921.388945
FMO2-HF: Nuclear repulsion	305882.023397
FMO2-HF: Total energy	-24039.365548
FMO2-MP2: Total energy	-24108.932967

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:2:THR)

Summations of interaction energy for fragment #1(A:2:THR)

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.
-27.644	-17.996	10.001	-8.346	-11.3	-0.021

Interaction energy analysis for fragmet #1(A:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.071 / q_NPA : -0.037

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	4	ASP	-1	-0.772	-0.902	3.157	-5.407	-3.018	0.074	-1.224	-1.239	-0.002
4	A	5	ALA	0	-0.029	-0.006	5.725	0.497	0.497	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.822	-0.880	2.491	-9.673	-5.384	2.546	-3.341	-3.494	-0.037
6	A	7	CYS	0	-0.038	0.018	3.094	-3.418	-2.067	1.656	-0.999	-2.007	-0.006
7	A	8	LEU	0	-0.021	-0.013	4.327	0.602	0.661	0.000	-0.021	-0.038	0.000
8	A	9	SER	0	-0.113	-0.057	6.483	0.332	0.332	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.817	0.906	3.334	-1.382	-1.091	0.028	-0.063	-0.257	0.000
10	A	11	PRO	0	-0.024	-0.023	8.506	-0.047	-0.047	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.056	0.036	11.365	0.021	0.021	0.000	0.000	0.000	0.000
12	A	13	PHE	0	-0.087	-0.038	11.140	0.041	0.041	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.860	-0.906	15.770	-0.018	-0.018	0.000	0.000	0.000	0.000
14	A	15	GLY	0	-0.012	-0.019	18.060	0.027	0.027	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.039	-0.030	18.720	-0.029	-0.029	0.000	0.000	0.000	0.000
16	A	17	LEU	0	0.009	0.035	12.349	0.043	0.043	0.000	0.000	0.000	0.000
17	A	18	SER	0	0.020	-0.005	16.046	-0.026	-0.026	0.000	0.000	0.000	0.000
18	A	19	ASN	0	-0.068	-0.035	16.120	0.008	0.008	0.000	0.000	0.000	0.000
19	A	20	VAL	0	-0.036	-0.007	17.004	-0.018	-0.018	0.000	0.000	0.000	0.000
20	A	21	TRP	0	-0.065	-0.037	12.034	0.030	0.030	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.784	0.868	19.228	0.083	0.083	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.776	-0.830	15.809	-0.312	-0.312	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.001	0.001	20.648	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.877	-0.942	23.622	-0.082	-0.082	0.000	0.000	0.000	0.000
25	A	26	SER	0	0.004	0.005	18.798	0.027	0.027	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.798	0.876	19.294	0.041	0.041	0.000	0.000	0.000	0.000
27	A	28	TYR	0	-0.023	-0.023	13.884	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	29	ALA	0	0.039	0.013	13.434	0.045	0.045	0.000	0.000	0.000	0.000
29	A	30	ASN	0	0.005	0.007	9.755	-0.163	-0.163	0.000	0.000	0.000	0.000
30	A	31	PHE	0	-0.003	-0.010	8.270	0.145	0.145	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.809	-0.874	4.883	0.754	0.754	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.033	-0.027	2.035	-10.412	-9.340	5.699	-2.679	-4.091	0.024
33	A	35	ILE	0	-0.002	0.010	5.437	0.492	0.492	0.000	0.000	0.000	0.000
34	A	36	TYR	0	-0.030	-0.048	6.977	-0.234	-0.234	0.000	0.000	0.000	0.000
35	A	37	GLU	-1	-0.780	-0.880	11.133	-0.275	-0.275	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.050	-0.010	14.796	0.018	0.018	0.000	0.000	0.000	0.000
37	A	39	SER	0	-0.046	-0.031	17.866	-0.023	-0.023	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.014	0.001	20.322	0.018	0.018	0.000	0.000	0.000	0.000
39	A	41	ILE	0	-0.044	-0.028	23.675	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	42	GLY	0	0.055	0.025	23.480	0.003	0.003	0.000	0.000	0.000	0.000
41	A	43	ILE	0	-0.078	-0.037	24.175	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	44	GLY	0	0.065	0.033	24.115	0.006	0.006	0.000	0.000	0.000	0.000
43	A	45	TYR	0	-0.031	-0.027	23.348	0.006	0.006	0.000	0.000	0.000	0.000
44	A	46	ASP	-1	-0.801	-0.882	23.724	0.095	0.095	0.000	0.000	0.000	0.000
45	A	47	ASN	0	-0.055	-0.025	25.301	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.781	-0.861	25.558	-0.022	-0.022	0.000	0.000	0.000	0.000
47	A	49	THR	0	-0.038	-0.015	21.419	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	50	SER	0	-0.020	-0.039	20.310	0.023	0.023	0.000	0.000	0.000	0.000
49	A	51	TRP	0	-0.062	-0.024	19.934	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	52	ASN	0	-0.083	-0.050	19.514	0.005	0.005	0.000	0.000	0.000	0.000
51	A	53	GLY	0	0.073	0.023	20.117	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	54	HIS	0	-0.025	-0.010	18.110	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	55	TRP	0	-0.018	-0.001	13.710	-0.033	-0.033	0.000	0.000	0.000	0.000
54	A	56	THR	0	0.027	0.000	12.879	0.030	0.030	0.000	0.000	0.000	0.000
55	A	57	PRO	0	-0.022	0.010	7.738	0.004	0.004	0.000	0.000	0.000	0.000
56	A	58	VAL	0	-0.033	-0.032	9.291	-0.037	-0.037	0.000	0.000	0.000	0.000
57	A	59	ARG	1	0.807	0.883	8.047	0.548	0.548	0.000	0.000	0.000	0.000
58	A	60	ALA	0	0.044	0.003	4.433	-0.230	-0.135	-0.001	-0.017	-0.076	0.000
59	A	61	ALA	0	-0.007	-0.003	4.529	0.766	0.868	-0.001	-0.002	-0.098	0.000
60	A	62	ASP	-1	-1.013	-1.002	6.565	-0.446	-0.446	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)