FMO DATABASE

FMODB ID: JQ6Z9

Calculation Name: 2YY9-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 2YY9

Chain ID: A

ChEMBL ID:
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UniProt ID: Q1H9T6

Base Structure: X-ray

Registration Date: 2023-09-20

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	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-822898.644736
FMO2-HF: Nuclear repulsion	780573.708804
FMO2-HF: Total energy	-42324.935932
FMO2-MP2: Total energy	-42448.26565

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:7:GLY)

Summations of interaction energy for fragment #1(A:7:GLY)

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.
-18.068	-18.375	7.555	-3.349	-3.898	0.033

Interaction energy analysis for fragmet #1(A:7:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.065 / q_NPA : 0.030

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	9	SER	0	0.076	0.034	3.834	-0.957	0.347	-0.008	-0.579	-0.717	0.000
4	A	10	VAL	0	0.069	0.038	3.453	0.413	0.828	0.022	-0.111	-0.325	0.000
5	A	11	ARG	1	0.885	0.947	2.089	-17.563	-19.589	7.541	-2.659	-2.856	0.033
6	A	12	VAL	0	0.005	0.001	6.265	0.299	0.299	0.000	0.000	0.000	0.000
7	A	13	LEU	0	0.041	0.030	8.485	0.139	0.139	0.000	0.000	0.000	0.000
8	A	14	GLN	0	0.013	0.004	7.008	0.333	0.333	0.000	0.000	0.000	0.000
9	A	15	GLU	-1	-0.860	-0.918	10.391	0.199	0.199	0.000	0.000	0.000	0.000
10	A	16	LEU	0	0.009	0.004	12.373	0.031	0.031	0.000	0.000	0.000	0.000
11	A	17	ASN	0	0.033	0.008	13.460	0.012	0.012	0.000	0.000	0.000	0.000
12	A	18	LYS	1	0.882	0.918	12.659	-0.101	-0.101	0.000	0.000	0.000	0.000
13	A	19	GLN	0	-0.081	-0.048	15.082	0.014	0.014	0.000	0.000	0.000	0.000
14	A	20	ARG	1	0.817	0.889	17.604	0.147	0.147	0.000	0.000	0.000	0.000
15	A	21	GLU	-1	-0.825	-0.891	18.440	-0.081	-0.081	0.000	0.000	0.000	0.000
16	A	22	LYS	1	0.750	0.893	17.014	-0.030	-0.030	0.000	0.000	0.000	0.000
17	A	23	GLY	0	0.023	0.008	22.761	0.007	0.007	0.000	0.000	0.000	0.000
18	A	24	GLN	0	-0.017	-0.016	19.858	0.003	0.003	0.000	0.000	0.000	0.000
19	A	25	TYR	0	-0.018	-0.026	19.553	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	26	CYS	0	-0.072	0.000	21.766	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	27	ASP	-1	-0.818	-0.902	23.673	-0.085	-0.085	0.000	0.000	0.000	0.000
22	A	28	ALA	0	0.010	0.024	24.659	0.003	0.003	0.000	0.000	0.000	0.000
23	A	29	THR	0	-0.014	-0.025	25.977	0.003	0.003	0.000	0.000	0.000	0.000
24	A	30	LEU	0	0.010	0.003	25.468	0.000	0.000	0.000	0.000	0.000	0.000
25	A	31	ASP	-1	-0.865	-0.929	29.489	-0.043	-0.043	0.000	0.000	0.000	0.000
26	A	32	VAL	0	0.018	0.004	29.728	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	33	GLY	0	-0.001	-0.001	32.905	0.001	0.001	0.000	0.000	0.000	0.000
28	A	34	GLY	0	-0.028	-0.012	34.892	0.004	0.004	0.000	0.000	0.000	0.000
29	A	35	LEU	0	-0.036	-0.004	30.698	0.003	0.003	0.000	0.000	0.000	0.000
30	A	36	VAL	0	0.005	0.010	29.900	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	37	PHE	0	0.029	0.013	24.874	0.001	0.001	0.000	0.000	0.000	0.000
32	A	38	LYS	1	0.883	0.926	24.102	0.044	0.044	0.000	0.000	0.000	0.000
33	A	39	ALA	0	0.037	0.010	21.358	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	40	HIS	0	0.035	0.034	18.109	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	41	TRP	0	0.028	0.000	21.115	-0.024	-0.024	0.000	0.000	0.000	0.000
36	A	42	SER	0	-0.013	0.002	18.882	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	43	VAL	0	0.025	0.013	15.918	-0.020	-0.020	0.000	0.000	0.000	0.000
38	A	44	LEU	0	-0.019	-0.005	18.347	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	45	ALA	0	0.006	-0.002	21.723	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	46	CYS	0	-0.100	-0.048	16.934	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	47	CYS	0	0.012	0.024	17.798	-0.020	-0.020	0.000	0.000	0.000	0.000
42	A	48	SER	0	-0.036	-0.026	20.261	0.017	0.017	0.000	0.000	0.000	0.000
43	A	49	HIS	0	0.082	0.030	23.676	0.005	0.005	0.000	0.000	0.000	0.000
44	A	50	PHE	0	-0.038	-0.003	26.769	0.011	0.011	0.000	0.000	0.000	0.000
45	A	51	PHE	0	0.055	0.001	25.094	0.007	0.007	0.000	0.000	0.000	0.000
46	A	52	GLN	0	-0.057	-0.039	23.231	0.016	0.016	0.000	0.000	0.000	0.000
47	A	53	ARG	1	0.816	0.889	27.122	0.105	0.105	0.000	0.000	0.000	0.000
48	A	54	ILE	0	-0.039	-0.007	30.163	0.007	0.007	0.000	0.000	0.000	0.000
49	A	55	TYR	0	-0.055	-0.029	26.596	0.001	0.001	0.000	0.000	0.000	0.000
50	A	56	GLY	0	0.047	0.002	29.821	0.001	0.001	0.000	0.000	0.000	0.000
51	A	57	ASP	-1	-0.885	-0.910	29.951	-0.060	-0.060	0.000	0.000	0.000	0.000
52	A	58	GLY	0	-0.024	-0.006	32.450	0.004	0.004	0.000	0.000	0.000	0.000
53	A	59	THR	0	-0.050	-0.039	35.319	0.003	0.003	0.000	0.000	0.000	0.000
54	A	60	GLY	0	0.043	0.041	32.972	0.002	0.002	0.000	0.000	0.000	0.000
55	A	61	GLY	0	-0.013	-0.001	32.194	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	62	SER	0	-0.063	-0.057	32.086	0.005	0.005	0.000	0.000	0.000	0.000
57	A	63	VAL	0	-0.046	-0.003	30.240	0.000	0.000	0.000	0.000	0.000	0.000
58	A	64	VAL	0	-0.003	0.002	32.610	0.001	0.001	0.000	0.000	0.000	0.000
59	A	65	LEU	0	-0.015	-0.006	29.755	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	66	PRO	0	0.016	0.006	33.481	0.005	0.005	0.000	0.000	0.000	0.000
61	A	67	ALA	0	0.070	0.013	34.719	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	68	GLY	0	-0.034	-0.006	35.695	0.000	0.000	0.000	0.000	0.000	0.000
63	A	69	PHE	0	0.031	0.008	30.786	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	70	ALA	0	0.012	-0.004	30.826	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	71	GLU	-1	-0.926	-0.941	30.853	-0.055	-0.055	0.000	0.000	0.000	0.000
66	A	72	ILE	0	-0.010	-0.016	28.102	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	73	PHE	0	-0.015	-0.002	25.964	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	74	GLY	0	0.031	0.019	24.475	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	75	LEU	0	0.038	0.021	22.454	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	76	LEU	0	-0.028	-0.006	21.576	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	77	LEU	0	0.006	0.003	20.824	-0.019	-0.019	0.000	0.000	0.000	0.000
72	A	78	ASP	-1	-0.798	-0.915	18.432	-0.147	-0.147	0.000	0.000	0.000	0.000
73	A	79	PHE	0	-0.029	0.015	16.843	-0.035	-0.035	0.000	0.000	0.000	0.000
74	A	80	PHE	0	-0.001	-0.007	16.310	-0.040	-0.040	0.000	0.000	0.000	0.000
75	A	81	TYR	0	-0.031	-0.036	14.394	-0.037	-0.037	0.000	0.000	0.000	0.000
76	A	82	THR	0	-0.086	-0.071	12.239	-0.040	-0.040	0.000	0.000	0.000	0.000
77	A	83	GLY	0	-0.004	0.013	12.500	-0.052	-0.052	0.000	0.000	0.000	0.000
78	A	84	HIS	0	-0.051	-0.032	14.502	0.038	0.038	0.000	0.000	0.000	0.000
79	A	85	LEU	0	0.040	0.017	16.876	0.012	0.012	0.000	0.000	0.000	0.000
80	A	86	ALA	0	0.019	0.024	20.645	0.005	0.005	0.000	0.000	0.000	0.000
81	A	87	LEU	0	-0.034	-0.017	22.966	0.013	0.013	0.000	0.000	0.000	0.000
82	A	88	THR	0	-0.004	-0.016	25.680	0.005	0.005	0.000	0.000	0.000	0.000
83	A	89	SER	0	-0.006	-0.028	28.728	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	90	GLY	0	-0.003	0.013	31.913	0.003	0.003	0.000	0.000	0.000	0.000
85	A	91	ASN	0	0.058	0.035	27.172	0.001	0.001	0.000	0.000	0.000	0.000
86	A	92	ARG	1	0.828	0.916	28.953	0.089	0.089	0.000	0.000	0.000	0.000
87	A	93	ASP	-1	-0.829	-0.926	29.986	-0.084	-0.084	0.000	0.000	0.000	0.000
88	A	94	GLN	0	-0.040	-0.030	31.669	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	95	VAL	0	0.020	0.010	25.619	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	96	LEU	0	-0.015	-0.011	28.578	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	97	LEU	0	-0.012	-0.004	29.991	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	98	ALA	0	0.028	0.013	29.222	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	99	ALA	0	0.011	0.005	26.177	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	100	LYS	1	0.855	0.925	27.698	0.091	0.091	0.000	0.000	0.000	0.000
95	A	101	GLU	-1	-0.925	-0.949	30.559	-0.076	-0.076	0.000	0.000	0.000	0.000
96	A	102	LEU	0	-0.029	-0.027	26.903	0.001	0.001	0.000	0.000	0.000	0.000
97	A	103	ARG	0	0.002	0.025	27.094	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	104	VAL	0	0.035	0.028	22.228	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	105	PRO	0	-0.016	-0.019	22.887	0.001	0.001	0.000	0.000	0.000	0.000
100	A	106	GLU	-1	-0.867	-0.933	17.350	-0.310	-0.310	0.000	0.000	0.000	0.000
101	A	107	ALA	0	0.036	0.025	21.459	0.005	0.005	0.000	0.000	0.000	0.000
102	A	108	VAL	0	-0.009	-0.004	23.134	0.013	0.013	0.000	0.000	0.000	0.000
103	A	109	GLU	-1	-0.962	-0.967	22.445	-0.178	-0.178	0.000	0.000	0.000	0.000
104	A	110	LEU	0	0.021	0.016	19.161	0.011	0.011	0.000	0.000	0.000	0.000
105	A	111	CYS	0	-0.036	-0.016	23.732	0.012	0.012	0.000	0.000	0.000	0.000
106	A	112	GLN	0	-0.013	-0.008	26.999	0.016	0.016	0.000	0.000	0.000	0.000
107	A	113	SER	0	-0.022	-0.019	25.422	0.009	0.009	0.000	0.000	0.000	0.000
108	A	114	PHE	0	-0.041	-0.008	25.232	0.002	0.002	0.000	0.000	0.000	0.000
109	A	115	GLN	0	-0.006	-0.007	27.466	0.007	0.007	0.000	0.000	0.000	0.000
110	A	116	PRO	0	-0.033	-0.003	28.435	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:GLY)