FMO DATABASE

FMODB ID: 7G76K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-358961.008686
FMO2-HF: Nuclear repulsion	328981.62195
FMO2-HF: Total energy	-29979.386735
FMO2-MP2: Total energy	-30066.906046

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.
-2.676	-0.358	0.027	-0.849	-1.496	0.001

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 : -0.018 / q_NPA : -0.028

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	0.013	0.015	3.735	-2.544	-1.048	-0.002	-0.592	-0.902	0.002
4	A	6	PRO	0	0.013	0.004	3.575	-1.614	-1.199	0.017	-0.167	-0.266	-0.001
5	A	7	ARG	1	0.959	0.980	3.569	1.547	1.954	0.012	-0.090	-0.328	0.000
6	A	8	ILE	0	0.048	0.023	5.892	-0.003	-0.003	0.000	0.000	0.000	0.000
7	A	9	THR	0	-0.049	-0.038	8.853	-0.126	-0.126	0.000	0.000	0.000	0.000
8	A	10	ALA	0	0.001	0.011	11.147	0.029	0.029	0.000	0.000	0.000	0.000
9	A	11	ARG	1	0.950	0.983	14.898	0.244	0.244	0.000	0.000	0.000	0.000
10	A	12	VAL	0	0.010	0.003	17.355	0.026	0.026	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.821	-0.883	19.921	-0.106	-0.106	0.000	0.000	0.000	0.000
12	A	14	VAL	0	0.038	-0.003	23.005	0.002	0.002	0.000	0.000	0.000	0.000
13	A	15	ASP	-1	-0.861	-0.926	24.804	-0.064	-0.064	0.000	0.000	0.000	0.000
14	A	16	THR	0	-0.066	-0.052	21.226	0.016	0.016	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.088	-0.056	19.859	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.815	-0.909	21.791	-0.075	-0.075	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.047	-0.008	24.827	0.013	0.013	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.015	-0.023	18.643	0.015	0.015	0.000	0.000	0.000	0.000
19	A	21	ALA	0	0.002	0.009	21.832	0.013	0.013	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.959	0.975	22.675	0.016	0.016	0.000	0.000	0.000	0.000
21	A	23	ALA	0	-0.041	-0.023	23.616	0.009	0.009	0.000	0.000	0.000	0.000
22	A	24	ALA	0	0.012	0.002	20.506	0.014	0.014	0.000	0.000	0.000	0.000
23	A	25	ALA	0	0.007	0.010	22.353	0.011	0.011	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.048	-0.026	25.144	0.007	0.007	0.000	0.000	0.000	0.000
25	A	27	ALA	0	-0.035	-0.004	23.275	0.007	0.007	0.000	0.000	0.000	0.000
26	A	28	GLY	0	0.004	0.008	24.453	0.015	0.015	0.000	0.000	0.000	0.000
27	A	29	MET	0	-0.084	-0.033	19.207	0.012	0.012	0.000	0.000	0.000	0.000
28	A	30	SER	0	0.006	0.005	17.682	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	31	SER	0	-0.002	-0.010	14.799	-0.038	-0.038	0.000	0.000	0.000	0.000
30	A	32	ILE	0	0.111	0.047	16.298	0.032	0.032	0.000	0.000	0.000	0.000
31	A	33	ASN	0	-0.006	-0.009	10.984	0.036	0.036	0.000	0.000	0.000	0.000
32	A	34	SER	0	-0.021	-0.009	13.179	0.039	0.039	0.000	0.000	0.000	0.000
33	A	35	PHE	0	0.080	0.035	14.731	0.048	0.048	0.000	0.000	0.000	0.000
34	A	36	VAL	0	-0.001	0.004	14.200	0.025	0.025	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.016	0.001	10.335	0.029	0.029	0.000	0.000	0.000	0.000
36	A	38	ASN	0	-0.016	-0.017	14.187	0.024	0.024	0.000	0.000	0.000	0.000
37	A	39	ALA	0	0.057	0.029	16.986	0.007	0.007	0.000	0.000	0.000	0.000
38	A	40	ALA	0	-0.023	-0.019	15.243	0.000	0.000	0.000	0.000	0.000	0.000
39	A	41	ILE	0	-0.015	-0.019	12.997	0.017	0.017	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.912	-0.944	17.200	0.170	0.170	0.000	0.000	0.000	0.000
41	A	43	LYS	1	1.001	1.004	20.508	-0.132	-0.132	0.000	0.000	0.000	0.000
42	A	44	ALA	0	-0.012	-0.008	18.122	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	45	LYS	1	0.946	0.973	18.211	-0.413	-0.413	0.000	0.000	0.000	0.000
44	A	46	GLN	0	0.066	0.045	22.301	-0.028	-0.028	0.000	0.000	0.000	0.000
45	A	47	VAL	0	-0.089	-0.046	22.908	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	48	ILE	0	0.006	-0.001	20.135	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.894	-0.946	24.648	0.179	0.179	0.000	0.000	0.000	0.000
48	A	50	ARG	1	0.856	0.919	27.235	-0.136	-0.136	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.840	-0.908	27.413	0.117	0.117	0.000	0.000	0.000	0.000
50	A	52	GLN	0	-0.036	-0.024	27.627	0.006	0.006	0.000	0.000	0.000	0.000
51	A	53	ALA	0	-0.005	-0.006	30.527	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.008	0.003	32.331	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	55	LYS	1	0.859	0.920	30.605	-0.135	-0.135	0.000	0.000	0.000	0.000
54	A	56	LEU	0	0.001	0.012	34.791	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	57	SER	0	0.029	0.023	36.909	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	58	GLN	0	-0.017	-0.016	37.912	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	59	ALA	0	-0.023	-0.026	38.517	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	60	ASP	-1	-0.872	-0.939	40.367	0.086	0.086	0.000	0.000	0.000	0.000
59	A	61	ALA	0	-0.043	-0.018	42.770	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	62	VAL	0	-0.026	-0.009	42.376	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	63	LEU	0	0.013	0.012	43.750	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.018	-0.005	46.774	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	65	MET	0	-0.019	-0.007	48.127	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.932	-0.960	49.188	0.060	0.060	0.000	0.000	0.000	0.000
65	A	67	ALA	0	-0.026	-0.034	50.962	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.049	-0.043	51.853	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	69	ASP	-1	-0.877	-0.924	52.990	0.043	0.043	0.000	0.000	0.000	0.000
68	A	70	ASN	0	-0.142	-0.067	54.268	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	71	PRO	0	0.097	0.044	57.207	0.001	0.001	0.000	0.000	0.000	0.000
70	A	72	ALA	0	-0.023	-0.018	58.815	0.000	0.000	0.000	0.000	0.000	0.000
71	A	73	VAL	0	0.047	0.017	56.737	0.000	0.000	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.040	0.010	54.455	0.002	0.002	0.000	0.000	0.000	0.000
73	A	75	ASN	0	0.030	-0.011	57.116	0.002	0.002	0.000	0.000	0.000	0.000
74	A	76	ALA	0	-0.033	-0.007	60.284	0.000	0.000	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.956	0.967	52.759	-0.058	-0.058	0.000	0.000	0.000	0.000
76	A	78	LEU	0	0.003	0.005	55.005	0.001	0.001	0.000	0.000	0.000	0.000
77	A	79	LYS	1	0.785	0.880	58.294	-0.041	-0.041	0.000	0.000	0.000	0.000
78	A	80	LEU	0	-0.018	-0.009	59.341	0.000	0.000	0.000	0.000	0.000	0.000
79	A	81	ALA	0	-0.022	-0.007	56.507	0.000	0.000	0.000	0.000	0.000	0.000
80	A	82	SER	0	-0.039	-0.011	58.440	0.000	0.000	0.000	0.000	0.000	0.000
81	A	83	GLU	-1	-0.874	-0.899	61.033	0.041	0.041	0.000	0.000	0.000	0.000

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