FMO DATABASE

FMODB ID: 5343Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-539139.134422
FMO2-HF: Nuclear repulsion	505760.701793
FMO2-HF: Total energy	-33378.432629
FMO2-MP2: Total energy	-33474.54979

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.
-4.877	-2.1	2.073	-2.065	-2.785	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 : 0.031 / q_NPA : 0.001

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	0.024	0.002	3.527	-3.085	-1.145	0.021	-0.917	-1.044	0.005
4	A	8	LYS	1	0.898	0.950	2.161	-2.098	-1.459	2.051	-1.117	-1.573	-0.003
5	A	9	ASN	0	0.026	0.026	4.137	-0.104	0.094	0.001	-0.031	-0.168	0.000
6	A	10	ALA	0	0.017	0.004	6.576	0.081	0.081	0.000	0.000	0.000	0.000
7	A	11	ALA	0	0.011	0.015	7.527	-0.062	-0.062	0.000	0.000	0.000	0.000
8	A	12	LEU	0	0.024	0.004	8.278	-0.081	-0.081	0.000	0.000	0.000	0.000
9	A	13	LYS	1	0.876	0.938	10.041	0.247	0.247	0.000	0.000	0.000	0.000
10	A	14	GLN	0	-0.019	0.001	12.146	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	15	LEU	0	0.021	0.012	12.707	-0.023	-0.023	0.000	0.000	0.000	0.000
12	A	16	THR	0	-0.008	-0.027	14.005	-0.027	-0.027	0.000	0.000	0.000	0.000
13	A	17	LYS	1	0.832	0.924	16.260	-0.122	-0.122	0.000	0.000	0.000	0.000
14	A	18	ASP	-1	-0.788	-0.871	17.722	0.174	0.174	0.000	0.000	0.000	0.000
15	A	19	ALA	0	-0.001	-0.007	18.794	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	20	ASP	-1	-0.831	-0.905	20.386	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	21	GLU	-1	-0.878	-0.925	22.334	0.087	0.087	0.000	0.000	0.000	0.000
18	A	22	ILE	0	0.010	0.007	22.726	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	23	LEU	0	-0.018	-0.024	24.145	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	24	HIS	0	-0.018	-0.001	26.204	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	25	LEU	0	0.001	0.009	28.377	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	26	ILE	0	-0.012	-0.011	27.490	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	27	LYS	1	0.946	0.957	27.399	0.009	0.009	0.000	0.000	0.000	0.000
24	A	28	VAL	0	0.025	0.027	31.747	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	29	GLN	0	-0.028	-0.008	33.994	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	30	LEU	0	-0.055	-0.016	32.535	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	31	ASP	-1	-0.989	-0.986	34.372	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	32	ASN	0	-0.119	-0.077	37.437	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	33	LEU	0	-0.036	-0.076	40.324	0.001	0.001	0.000	0.000	0.000	0.000
30	A	34	THR	0	0.062	0.084	42.522	0.000	0.000	0.000	0.000	0.000	0.000
31	A	35	LEU	0	-0.018	-0.021	44.016	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	36	PRO	0	0.032	0.014	38.807	0.002	0.002	0.000	0.000	0.000	0.000
33	A	37	SER	0	0.018	0.029	38.452	0.001	0.001	0.000	0.000	0.000	0.000
34	A	38	CYS	0	-0.082	0.023	39.260	0.002	0.002	0.000	0.000	0.000	0.000
35	A	39	PRO	0	-0.012	-0.030	41.230	0.001	0.001	0.000	0.000	0.000	0.000
36	A	40	LEU	0	0.065	0.000	39.812	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	41	TYR	0	0.022	0.008	34.000	0.005	0.005	0.000	0.000	0.000	0.000
38	A	42	GLU	-1	-0.838	-0.925	34.920	0.029	0.029	0.000	0.000	0.000	0.000
39	A	43	GLU	-1	-0.922	-0.952	33.918	0.049	0.049	0.000	0.000	0.000	0.000
40	A	44	VAL	0	-0.005	-0.006	32.151	0.006	0.006	0.000	0.000	0.000	0.000
41	A	45	LEU	0	0.005	-0.014	29.653	0.006	0.006	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.844	-0.909	28.965	0.048	0.048	0.000	0.000	0.000	0.000
43	A	47	THR	0	-0.061	-0.026	28.758	0.008	0.008	0.000	0.000	0.000	0.000
44	A	48	GLN	0	-0.052	-0.027	26.544	0.012	0.012	0.000	0.000	0.000	0.000
45	A	49	MET	0	0.013	0.014	24.500	0.010	0.010	0.000	0.000	0.000	0.000
46	A	50	PHE	0	-0.007	-0.003	23.845	0.011	0.011	0.000	0.000	0.000	0.000
47	A	51	GLY	0	0.008	-0.007	23.489	0.013	0.013	0.000	0.000	0.000	0.000
48	A	52	LEU	0	0.027	0.020	18.512	0.023	0.023	0.000	0.000	0.000	0.000
49	A	53	GLN	0	0.032	-0.005	18.980	0.007	0.007	0.000	0.000	0.000	0.000
50	A	54	LYS	1	0.806	0.910	19.232	-0.118	-0.118	0.000	0.000	0.000	0.000
51	A	55	GLH	0	-0.053	-0.045	16.353	0.027	0.027	0.000	0.000	0.000	0.000
52	A	56	VAL	0	0.004	0.009	14.933	0.051	0.051	0.000	0.000	0.000	0.000
53	A	57	ASP	-1	-0.843	-0.912	14.548	0.162	0.162	0.000	0.000	0.000	0.000
54	A	58	PHE	0	-0.057	-0.027	13.696	0.024	0.024	0.000	0.000	0.000	0.000
55	A	59	ALA	0	0.029	0.010	10.701	0.074	0.074	0.000	0.000	0.000	0.000
56	A	60	VAL	0	-0.026	-0.019	10.428	0.066	0.066	0.000	0.000	0.000	0.000
57	A	61	LYS	1	0.918	0.948	11.991	-0.213	-0.213	0.000	0.000	0.000	0.000
58	A	62	LEU	0	-0.052	-0.010	10.251	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.010	0.017	8.552	0.173	0.173	0.000	0.000	0.000	0.000
60	A	64	LEU	0	-0.056	-0.028	5.838	0.182	0.182	0.000	0.000	0.000	0.000
61	A	65	VAL	0	-0.012	-0.019	6.173	-0.141	-0.141	0.000	0.000	0.000	0.000
62	A	66	ASP	-1	-0.830	-0.896	8.415	-0.182	-0.182	0.000	0.000	0.000	0.000
63	A	67	ARG	1	0.907	0.928	10.435	0.046	0.046	0.000	0.000	0.000	0.000
64	A	68	GLU	-1	-0.850	-0.933	13.954	-0.032	-0.032	0.000	0.000	0.000	0.000
65	A	69	ASP	-1	-0.845	-0.917	10.324	-0.198	-0.198	0.000	0.000	0.000	0.000
66	A	70	GLY	0	0.006	-0.009	13.606	0.015	0.015	0.000	0.000	0.000	0.000
67	A	71	LYS	1	0.924	0.958	15.108	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	72	GLN	0	-0.011	0.000	16.735	0.001	0.001	0.000	0.000	0.000	0.000
69	A	73	ILE	0	-0.032	-0.014	13.907	0.000	0.000	0.000	0.000	0.000	0.000
70	A	74	MET	0	-0.028	0.007	18.235	0.007	0.007	0.000	0.000	0.000	0.000
71	A	75	LEU	0	0.049	0.025	21.040	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	76	ARG	1	0.801	0.878	19.800	0.009	0.009	0.000	0.000	0.000	0.000
73	A	77	LEU	0	0.001	-0.001	21.870	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	78	GLU	-1	-0.861	-0.935	24.685	0.028	0.028	0.000	0.000	0.000	0.000
75	A	79	LYS	1	0.916	0.972	26.596	0.018	0.018	0.000	0.000	0.000	0.000
76	A	80	GLU	-1	-0.844	-0.928	27.746	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	81	LEU	0	0.020	-0.004	28.468	0.000	0.000	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.054	-0.029	30.807	0.001	0.001	0.000	0.000	0.000	0.000
79	A	83	LYS	1	0.783	0.884	30.537	0.011	0.011	0.000	0.000	0.000	0.000
80	A	84	LEU	0	-0.006	0.006	33.646	0.000	0.000	0.000	0.000	0.000	0.000
81	A	85	HIS	1	0.769	0.895	34.152	-0.019	-0.019	0.000	0.000	0.000	0.000
82	A	86	GLU	-1	-0.876	-0.945	37.501	0.002	0.002	0.000	0.000	0.000	0.000
83	A	87	ALA	0	-0.022	0.001	40.372	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)