FMO DATABASE

FMODB ID: 4353N

Calculation Name: 2ODM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ODM

Chain ID: A

ChEMBL ID:

UniProt ID: Q7A161

Base Structure: X-ray

Registration Date: 2023-06-19

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	OptH
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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-537525.211546
FMO2-HF: Nuclear repulsion	504147.549575
FMO2-HF: Total energy	-33377.661971
FMO2-MP2: Total energy	-33473.712864

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:ALA)

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

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.
-5.023	-2.124	2.055	-2.053	-2.901	0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.003

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	MET	0	0.020	0.001	3.517	-3.191	-1.255	0.021	-0.924	-1.033	0.005
4	A	8	LYS	1	0.929	0.977	2.206	-2.015	-1.251	2.033	-1.097	-1.699	-0.003
5	A	9	ASN	0	0.020	0.017	4.123	-0.168	0.031	0.001	-0.032	-0.169	0.000
6	A	10	ALA	0	0.015	0.002	6.555	0.086	0.086	0.000	0.000	0.000	0.000
7	A	11	ALA	0	0.012	0.015	7.515	-0.060	-0.060	0.000	0.000	0.000	0.000
8	A	12	LEU	0	0.035	0.006	8.262	-0.072	-0.072	0.000	0.000	0.000	0.000
9	A	13	LYS	1	0.886	0.946	10.120	0.263	0.263	0.000	0.000	0.000	0.000
10	A	14	GLN	0	-0.033	0.000	12.131	0.001	0.001	0.000	0.000	0.000	0.000
11	A	15	LEU	0	0.033	0.014	12.345	-0.021	-0.021	0.000	0.000	0.000	0.000
12	A	16	THR	0	-0.033	-0.024	14.161	-0.025	-0.025	0.000	0.000	0.000	0.000
13	A	17	LYS	1	0.977	1.000	16.243	-0.096	-0.096	0.000	0.000	0.000	0.000
14	A	18	ASP	-1	-0.767	-0.869	17.716	0.165	0.165	0.000	0.000	0.000	0.000
15	A	19	ALA	0	-0.014	-0.019	18.781	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	20	ASP	-1	-0.921	-0.969	20.376	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	21	GLU	-1	-0.968	-0.976	22.317	0.081	0.081	0.000	0.000	0.000	0.000
18	A	22	ILE	0	0.015	0.009	22.577	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	23	LEU	0	-0.025	-0.030	23.934	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	24	HIS	0	-0.023	-0.001	26.188	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	25	LEU	0	-0.010	0.008	28.360	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	26	ILE	0	-0.012	-0.008	27.375	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	27	LYS	1	0.953	0.955	27.137	0.012	0.012	0.000	0.000	0.000	0.000
24	A	28	VAL	0	0.025	0.027	31.730	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	29	GLN	0	-0.033	-0.001	33.978	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	30	LEU	0	-0.040	-0.017	32.715	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	31	ASP	-1	-0.983	-0.978	34.524	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	32	ASN	0	-0.118	-0.059	37.419	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	33	LEU	0	0.009	-0.032	40.307	0.001	0.001	0.000	0.000	0.000	0.000
30	A	34	THR	0	0.118	0.093	42.507	0.000	0.000	0.000	0.000	0.000	0.000
31	A	35	LEU	0	-0.132	-0.091	43.850	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	36	PRO	0	0.024	0.016	39.178	0.001	0.001	0.000	0.000	0.000	0.000
33	A	37	SER	0	-0.005	-0.010	38.634	0.000	0.000	0.000	0.000	0.000	0.000
34	A	38	CYS	0	-0.076	0.033	39.435	0.002	0.002	0.000	0.000	0.000	0.000
35	A	39	PRO	0	0.028	-0.015	41.217	0.001	0.001	0.000	0.000	0.000	0.000
36	A	40	LEU	0	0.059	-0.001	39.800	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	41	TYR	0	0.029	0.009	33.998	0.003	0.003	0.000	0.000	0.000	0.000
38	A	42	GLU	-1	-0.958	-0.987	34.912	0.027	0.027	0.000	0.000	0.000	0.000
39	A	43	GLU	-1	-0.904	-0.942	33.908	0.047	0.047	0.000	0.000	0.000	0.000
40	A	44	VAL	0	-0.003	-0.004	32.124	0.005	0.005	0.000	0.000	0.000	0.000
41	A	45	LEU	0	-0.010	-0.022	29.768	0.006	0.006	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.845	-0.908	28.955	0.042	0.042	0.000	0.000	0.000	0.000
43	A	47	THR	0	-0.053	-0.025	28.750	0.008	0.008	0.000	0.000	0.000	0.000
44	A	48	GLN	0	-0.052	-0.026	26.554	0.010	0.010	0.000	0.000	0.000	0.000
45	A	49	MET	0	0.009	0.014	24.600	0.009	0.009	0.000	0.000	0.000	0.000
46	A	50	PHE	0	-0.011	-0.005	23.848	0.010	0.010	0.000	0.000	0.000	0.000
47	A	51	GLY	0	0.005	-0.010	23.484	0.012	0.012	0.000	0.000	0.000	0.000
48	A	52	LEU	0	0.038	0.024	18.292	0.021	0.021	0.000	0.000	0.000	0.000
49	A	53	GLN	0	0.028	0.003	18.973	0.005	0.005	0.000	0.000	0.000	0.000
50	A	54	LYS	1	0.879	0.949	19.228	-0.103	-0.103	0.000	0.000	0.000	0.000
51	A	55	GLH	0	-0.078	-0.055	16.387	0.023	0.023	0.000	0.000	0.000	0.000
52	A	56	VAL	0	0.000	0.005	14.924	0.047	0.047	0.000	0.000	0.000	0.000
53	A	57	ASP	-1	-0.880	-0.946	14.545	0.144	0.144	0.000	0.000	0.000	0.000
54	A	58	PHE	0	-0.074	-0.033	13.997	0.024	0.024	0.000	0.000	0.000	0.000
55	A	59	ALA	0	0.030	0.008	10.630	0.070	0.070	0.000	0.000	0.000	0.000
56	A	60	VAL	0	-0.024	-0.016	10.429	0.058	0.058	0.000	0.000	0.000	0.000
57	A	61	LYS	1	0.910	0.947	11.996	-0.204	-0.204	0.000	0.000	0.000	0.000
58	A	62	LEU	0	-0.055	-0.013	10.141	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.006	0.016	8.562	0.156	0.156	0.000	0.000	0.000	0.000
60	A	64	LEU	0	-0.063	-0.033	5.837	0.161	0.161	0.000	0.000	0.000	0.000
61	A	65	VAL	0	-0.005	-0.011	6.167	-0.142	-0.142	0.000	0.000	0.000	0.000
62	A	66	ASP	-1	-0.837	-0.912	8.574	-0.199	-0.199	0.000	0.000	0.000	0.000
63	A	67	ARG	1	0.943	0.951	10.433	0.049	0.049	0.000	0.000	0.000	0.000
64	A	68	GLU	-1	-0.930	-0.972	13.929	-0.050	-0.050	0.000	0.000	0.000	0.000
65	A	69	ASP	-1	-0.832	-0.912	10.460	-0.219	-0.219	0.000	0.000	0.000	0.000
66	A	70	GLY	0	0.001	-0.008	13.594	0.016	0.016	0.000	0.000	0.000	0.000
67	A	71	LYS	1	0.929	0.954	15.100	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	72	GLN	0	0.003	0.010	16.702	0.003	0.003	0.000	0.000	0.000	0.000
69	A	73	ILE	0	-0.035	-0.012	13.841	0.001	0.001	0.000	0.000	0.000	0.000
70	A	74	MET	0	-0.031	0.002	18.222	0.008	0.008	0.000	0.000	0.000	0.000
71	A	75	LEU	0	0.056	0.020	21.032	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	76	ARG	1	0.889	0.957	20.149	0.015	0.015	0.000	0.000	0.000	0.000
73	A	77	LEU	0	-0.017	-0.010	22.206	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	78	GLU	-1	-0.850	-0.931	24.667	0.023	0.023	0.000	0.000	0.000	0.000
75	A	79	LYS	1	0.921	0.971	26.585	0.022	0.022	0.000	0.000	0.000	0.000
76	A	80	GLU	-1	-0.885	-0.949	27.697	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	81	LEU	0	0.018	-0.006	28.614	0.001	0.001	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.057	-0.025	30.795	0.001	0.001	0.000	0.000	0.000	0.000
79	A	83	LYS	1	0.819	0.899	31.142	0.015	0.015	0.000	0.000	0.000	0.000
80	A	84	LEU	0	0.002	0.010	33.625	0.000	0.000	0.000	0.000	0.000	0.000
81	A	85	HIS	1	0.877	0.956	33.737	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	86	GLU	-1	-0.895	-0.954	37.490	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	87	ALA	0	-0.034	-0.006	40.360	0.002	0.002	0.000	0.000	0.000	0.000

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