FMO DATABASE

FMODB ID: YY4Q2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-540117.869476
FMO2-HF: Nuclear repulsion	506738.717866
FMO2-HF: Total energy	-33379.15161
FMO2-MP2: Total energy	-33475.176448

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.
-5.139	-1.403	0.652	-1.669	-2.719	0.005

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 : 0.038 / q_NPA : 0.013

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

Sort

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	0.041	0.016	3.337	-2.147	-0.155	0.038	-0.922	-1.108	0.004
4	A	8	LYS	1	0.861	0.943	2.605	-3.437	-1.971	0.615	-0.673	-1.408	0.001
5	A	9	ASN	0	0.006	0.015	4.241	-0.398	-0.120	-0.001	-0.074	-0.203	0.000
6	A	10	ALA	0	0.007	0.001	6.279	0.065	0.065	0.000	0.000	0.000	0.000
7	A	11	ALA	0	0.017	0.014	7.770	-0.118	-0.118	0.000	0.000	0.000	0.000
8	A	12	LEU	0	0.033	0.011	8.390	-0.130	-0.130	0.000	0.000	0.000	0.000
9	A	13	LYS	1	0.873	0.943	9.335	0.087	0.087	0.000	0.000	0.000	0.000
10	A	14	GLN	0	-0.030	-0.010	12.204	-0.028	-0.028	0.000	0.000	0.000	0.000
11	A	15	LEU	0	0.018	0.005	13.081	-0.032	-0.032	0.000	0.000	0.000	0.000
12	A	16	THR	0	-0.030	-0.036	13.923	-0.041	-0.041	0.000	0.000	0.000	0.000
13	A	17	LYS	1	0.825	0.899	16.163	-0.147	-0.147	0.000	0.000	0.000	0.000
14	A	18	ASP	-1	-0.797	-0.848	17.718	0.206	0.206	0.000	0.000	0.000	0.000
15	A	19	ALA	0	0.011	0.000	18.687	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	20	ASP	-1	-0.796	-0.890	19.828	0.033	0.033	0.000	0.000	0.000	0.000
17	A	21	GLU	-1	-0.866	-0.911	22.213	0.094	0.094	0.000	0.000	0.000	0.000
18	A	22	ILE	0	0.006	0.008	22.617	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	23	LEU	0	-0.016	-0.019	23.806	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	24	HIS	0	-0.020	-0.004	25.941	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	25	LEU	0	-0.014	-0.001	28.224	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	26	ILE	0	-0.008	-0.012	27.257	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	27	LYS	1	0.926	0.967	27.275	-0.023	-0.023	0.000	0.000	0.000	0.000
24	A	28	VAL	0	0.027	0.028	31.717	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	29	GLN	0	-0.011	0.010	33.844	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	30	LEU	0	-0.061	-0.025	32.287	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	31	ASP	-1	-0.960	-0.984	33.911	0.017	0.017	0.000	0.000	0.000	0.000
28	A	32	ASN	0	-0.098	-0.066	37.158	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	33	LEU	0	-0.012	-0.014	40.163	0.001	0.001	0.000	0.000	0.000	0.000
30	A	34	THR	0	-0.005	-0.004	42.732	0.000	0.000	0.000	0.000	0.000	0.000
31	A	35	LEU	0	-0.011	-0.009	43.857	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	36	PRO	0	0.028	0.027	38.441	0.001	0.001	0.000	0.000	0.000	0.000
33	A	37	SER	0	0.006	0.021	38.295	0.000	0.000	0.000	0.000	0.000	0.000
34	A	38	CYS	0	-0.044	-0.023	39.176	0.003	0.003	0.000	0.000	0.000	0.000
35	A	39	PRO	0	-0.047	-0.016	41.161	0.001	0.001	0.000	0.000	0.000	0.000
36	A	40	LEU	0	0.074	0.002	40.091	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	41	TYR	0	0.024	0.013	33.770	0.005	0.005	0.000	0.000	0.000	0.000
38	A	42	GLU	-1	-0.809	-0.893	34.634	0.049	0.049	0.000	0.000	0.000	0.000
39	A	43	GLU	-1	-0.916	-0.946	33.694	0.061	0.061	0.000	0.000	0.000	0.000
40	A	44	VAL	0	-0.017	0.000	32.202	0.007	0.007	0.000	0.000	0.000	0.000
41	A	45	LEU	0	0.003	-0.010	29.604	0.007	0.007	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.846	-0.921	28.957	0.074	0.074	0.000	0.000	0.000	0.000
43	A	47	THR	0	-0.070	-0.040	28.682	0.011	0.011	0.000	0.000	0.000	0.000
44	A	48	GLN	0	-0.054	-0.025	26.370	0.016	0.016	0.000	0.000	0.000	0.000
45	A	49	MET	0	0.008	0.014	24.522	0.015	0.015	0.000	0.000	0.000	0.000
46	A	50	PHE	0	0.017	0.003	23.928	0.016	0.016	0.000	0.000	0.000	0.000
47	A	51	GLY	0	0.018	0.002	23.686	0.016	0.016	0.000	0.000	0.000	0.000
48	A	52	LEU	0	0.024	0.013	18.480	0.026	0.026	0.000	0.000	0.000	0.000
49	A	53	GLN	0	0.027	-0.001	19.254	0.017	0.017	0.000	0.000	0.000	0.000
50	A	54	LYS	1	0.794	0.904	19.684	-0.156	-0.156	0.000	0.000	0.000	0.000
51	A	55	GLH	0	-0.054	-0.050	16.504	0.031	0.031	0.000	0.000	0.000	0.000
52	A	56	VAL	0	-0.003	0.005	15.141	0.070	0.070	0.000	0.000	0.000	0.000
53	A	57	ASP	-1	-0.859	-0.934	14.994	0.239	0.239	0.000	0.000	0.000	0.000
54	A	58	PHE	0	-0.013	-0.012	13.741	0.028	0.028	0.000	0.000	0.000	0.000
55	A	59	ALA	0	0.028	0.005	10.997	0.079	0.079	0.000	0.000	0.000	0.000
56	A	60	VAL	0	-0.020	-0.010	10.724	0.126	0.126	0.000	0.000	0.000	0.000
57	A	61	LYS	1	0.867	0.937	12.466	-0.268	-0.268	0.000	0.000	0.000	0.000
58	A	62	LEU	0	-0.026	0.003	10.056	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.007	0.014	8.463	0.242	0.242	0.000	0.000	0.000	0.000
60	A	64	LEU	0	-0.043	-0.027	6.105	0.273	0.273	0.000	0.000	0.000	0.000
61	A	65	VAL	0	0.003	-0.006	6.554	-0.048	-0.048	0.000	0.000	0.000	0.000
62	A	66	ASP	-1	-0.839	-0.907	8.385	0.145	0.145	0.000	0.000	0.000	0.000
63	A	67	ARG	1	0.887	0.919	10.490	-0.080	-0.080	0.000	0.000	0.000	0.000
64	A	68	GLU	-1	-0.860	-0.932	13.773	0.048	0.048	0.000	0.000	0.000	0.000
65	A	69	ASP	-1	-0.832	-0.913	9.800	0.047	0.047	0.000	0.000	0.000	0.000
66	A	70	GLY	0	0.018	-0.005	13.453	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	71	LYS	1	0.933	0.976	15.170	-0.098	-0.098	0.000	0.000	0.000	0.000
68	A	72	GLN	0	-0.003	-0.001	16.684	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	73	ILE	0	-0.031	-0.015	13.686	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	74	MET	0	-0.010	0.017	18.077	0.001	0.001	0.000	0.000	0.000	0.000
71	A	75	LEU	0	0.050	0.030	20.966	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	76	ARG	1	0.761	0.849	19.117	-0.053	-0.053	0.000	0.000	0.000	0.000
73	A	77	LEU	0	-0.008	-0.001	21.816	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	78	GLU	-1	-0.867	-0.939	24.474	0.071	0.071	0.000	0.000	0.000	0.000
75	A	79	LYS	1	0.914	0.971	26.433	-0.021	-0.021	0.000	0.000	0.000	0.000
76	A	80	GLU	-1	-0.828	-0.920	27.449	0.016	0.016	0.000	0.000	0.000	0.000
77	A	81	LEU	0	0.046	0.004	28.705	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.058	-0.042	30.581	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	83	LYS	1	0.784	0.885	30.252	-0.021	-0.021	0.000	0.000	0.000	0.000
80	A	84	LEU	0	-0.016	0.002	33.456	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	85	HIS	1	0.764	0.874	34.445	-0.040	-0.040	0.000	0.000	0.000	0.000
82	A	86	GLU	-1	-0.877	-0.932	37.643	0.021	0.021	0.000	0.000	0.000	0.000
83	A	87	ALA	0	-0.022	-0.003	40.538	0.002	0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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