FMO DATABASE

FMODB ID: 22QNR

Calculation Name: 1Y9B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y9B

Chain ID: A

ChEMBL ID:

UniProt ID: Q9K2J6

Base Structure: X-ray

Registration Date: 2023-06-20

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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-359636.756118
FMO2-HF: Nuclear repulsion	329657.142082
FMO2-HF: Total energy	-29979.614036
FMO2-MP2: Total energy	-30067.129881

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:3:THR)

Summations of interaction energy for fragment #1(A:3: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.
-2.587	-0.143	0.014	-0.953	-1.505	0

Interaction energy analysis for fragmet #1(A:3:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.023

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	5	LEU	0	0.016	0.018	3.294	-2.545	-0.682	0.007	-0.801	-1.069	0.001
4	A	6	PRO	0	0.001	-0.010	3.755	-1.280	-0.946	0.007	-0.108	-0.233	-0.001
5	A	7	ARG	1	0.946	0.977	4.081	1.337	1.584	0.000	-0.044	-0.203	0.000
6	A	8	ILE	0	0.052	0.029	5.930	-0.044	-0.044	0.000	0.000	0.000	0.000
7	A	9	THR	0	-0.034	-0.025	9.089	-0.181	-0.181	0.000	0.000	0.000	0.000
8	A	10	ALA	0	-0.004	0.005	11.170	0.046	0.046	0.000	0.000	0.000	0.000
9	A	11	ARG	1	0.934	0.964	14.887	0.172	0.172	0.000	0.000	0.000	0.000
10	A	12	VAL	0	0.002	0.002	17.722	0.027	0.027	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.792	-0.861	20.567	-0.086	-0.086	0.000	0.000	0.000	0.000
12	A	14	VAL	0	0.050	0.007	23.284	0.000	0.000	0.000	0.000	0.000	0.000
13	A	15	ASP	-1	-0.870	-0.924	25.128	-0.055	-0.055	0.000	0.000	0.000	0.000
14	A	16	THR	0	-0.048	-0.055	21.650	0.015	0.015	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.111	-0.066	20.129	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.810	-0.909	22.035	-0.078	-0.078	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.052	-0.013	24.927	0.011	0.011	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.008	-0.016	18.977	0.015	0.015	0.000	0.000	0.000	0.000
19	A	21	ALA	0	-0.007	0.000	21.739	0.010	0.010	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.957	0.984	22.643	0.013	0.013	0.000	0.000	0.000	0.000
21	A	23	ALA	0	-0.020	-0.009	23.482	0.008	0.008	0.000	0.000	0.000	0.000
22	A	24	ALA	0	0.002	-0.004	20.342	0.013	0.013	0.000	0.000	0.000	0.000
23	A	25	ALA	0	0.003	0.002	22.142	0.009	0.009	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.050	-0.029	24.842	0.005	0.005	0.000	0.000	0.000	0.000
25	A	27	ALA	0	-0.030	-0.002	23.061	0.007	0.007	0.000	0.000	0.000	0.000
26	A	28	GLY	0	0.002	0.007	23.975	0.014	0.014	0.000	0.000	0.000	0.000
27	A	29	MET	0	-0.080	-0.027	19.033	0.006	0.006	0.000	0.000	0.000	0.000
28	A	30	SER	0	0.014	-0.001	17.442	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	31	SER	0	0.008	0.001	15.168	-0.026	-0.026	0.000	0.000	0.000	0.000
30	A	32	ILE	0	0.080	0.045	16.328	0.033	0.033	0.000	0.000	0.000	0.000
31	A	33	ASN	0	-0.016	-0.013	10.454	0.049	0.049	0.000	0.000	0.000	0.000
32	A	34	SER	0	-0.002	0.001	13.516	0.072	0.072	0.000	0.000	0.000	0.000
33	A	35	PHE	0	0.067	0.023	14.911	0.053	0.053	0.000	0.000	0.000	0.000
34	A	36	VAL	0	-0.007	-0.004	14.733	0.027	0.027	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.009	0.003	10.373	0.040	0.040	0.000	0.000	0.000	0.000
36	A	38	ASN	0	-0.012	-0.014	14.207	0.033	0.033	0.000	0.000	0.000	0.000
37	A	39	ALA	0	0.069	0.032	16.945	0.017	0.017	0.000	0.000	0.000	0.000
38	A	40	ALA	0	-0.017	-0.013	15.194	0.002	0.002	0.000	0.000	0.000	0.000
39	A	41	ILE	0	-0.014	-0.013	12.564	0.023	0.023	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.850	-0.907	16.951	0.195	0.195	0.000	0.000	0.000	0.000
41	A	43	LYS	1	0.986	0.998	20.497	-0.151	-0.151	0.000	0.000	0.000	0.000
42	A	44	ALA	0	-0.008	-0.017	18.174	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	45	LYS	1	0.875	0.945	17.806	-0.424	-0.424	0.000	0.000	0.000	0.000
44	A	46	GLN	0	0.073	0.039	22.502	-0.026	-0.026	0.000	0.000	0.000	0.000
45	A	47	VAL	0	-0.075	-0.033	23.175	-0.022	-0.022	0.000	0.000	0.000	0.000
46	A	48	ILE	0	0.013	0.009	20.568	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.896	-0.948	25.071	0.198	0.198	0.000	0.000	0.000	0.000
48	A	50	ARG	1	0.841	0.907	27.581	-0.159	-0.159	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.825	-0.889	27.211	0.153	0.153	0.000	0.000	0.000	0.000
50	A	52	GLN	0	-0.029	-0.023	27.314	0.006	0.006	0.000	0.000	0.000	0.000
51	A	53	ALA	0	0.008	0.010	30.919	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.018	0.000	32.590	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	55	LYS	1	0.835	0.880	30.606	-0.160	-0.160	0.000	0.000	0.000	0.000
54	A	56	LEU	0	-0.002	0.014	34.921	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	57	SER	0	0.036	0.013	37.052	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	58	GLN	0	-0.042	-0.020	38.080	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	59	ALA	0	-0.007	-0.005	38.830	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	60	ASP	-1	-0.863	-0.941	40.631	0.098	0.098	0.000	0.000	0.000	0.000
59	A	61	ALA	0	-0.037	-0.017	42.685	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	62	VAL	0	-0.027	-0.012	42.649	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.003	-0.001	43.776	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.017	-0.010	46.875	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	65	MET	0	-0.011	0.002	48.092	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.906	-0.951	49.250	0.068	0.068	0.000	0.000	0.000	0.000
65	A	67	ALA	0	-0.008	-0.024	51.068	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.050	-0.036	51.651	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	69	ASP	-1	-0.878	-0.931	52.843	0.053	0.053	0.000	0.000	0.000	0.000
68	A	70	ASN	0	-0.111	-0.054	54.138	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	71	PRO	0	0.056	0.025	57.085	0.001	0.001	0.000	0.000	0.000	0.000
70	A	72	ALA	0	-0.014	-0.013	58.763	0.000	0.000	0.000	0.000	0.000	0.000
71	A	73	VAL	0	0.023	0.005	56.823	0.000	0.000	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.017	0.014	54.615	0.002	0.002	0.000	0.000	0.000	0.000
73	A	75	ASN	0	0.020	0.000	57.101	0.002	0.002	0.000	0.000	0.000	0.000
74	A	76	ALA	0	-0.016	0.001	60.270	0.000	0.000	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.896	0.950	52.222	-0.067	-0.067	0.000	0.000	0.000	0.000
76	A	78	LEU	0	0.006	-0.001	54.824	0.001	0.001	0.000	0.000	0.000	0.000
77	A	79	LYS	1	0.787	0.869	58.067	-0.045	-0.045	0.000	0.000	0.000	0.000
78	A	80	LEU	0	-0.011	-0.014	59.102	0.000	0.000	0.000	0.000	0.000	0.000
79	A	81	ALA	0	-0.027	-0.005	56.130	0.001	0.001	0.000	0.000	0.000	0.000
80	A	82	SER	0	-0.050	-0.016	57.993	0.000	0.000	0.000	0.000	0.000	0.000
81	A	83	GLU	-1	-0.867	-0.890	60.754	0.044	0.044	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:THR)