FMO DATABASE

FMODB ID: 898ZY

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	OptH
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	-822363.875758
FMO2-HF: Nuclear repulsion	780039.773904
FMO2-HF: Total energy	-42324.101854
FMO2-MP2: Total energy	-42447.502787

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.
-4.848	-2.045	0.495	-1.235	-2.063	0.002

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 : 0.057 / q_NPA : 0.017

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	0.044	0.010	3.789	-1.218	-0.091	0.004	-0.470	-0.661	0.001
4	A	10	VAL	0	0.053	0.041	3.047	0.166	0.813	0.149	-0.214	-0.582	-0.001
5	A	11	ARG	1	0.963	0.970	2.650	-4.132	-3.103	0.342	-0.551	-0.820	0.002
6	A	12	VAL	0	0.011	0.008	6.187	0.418	0.418	0.000	0.000	0.000	0.000
7	A	13	LEU	0	0.073	0.046	8.027	0.172	0.172	0.000	0.000	0.000	0.000
8	A	14	GLN	0	-0.006	-0.004	7.812	0.198	0.198	0.000	0.000	0.000	0.000
9	A	15	GLU	-1	-0.965	-0.974	10.430	-0.032	-0.032	0.000	0.000	0.000	0.000
10	A	16	LEU	0	0.001	0.001	12.241	0.063	0.063	0.000	0.000	0.000	0.000
11	A	17	ASN	0	0.064	0.023	13.386	0.076	0.076	0.000	0.000	0.000	0.000
12	A	18	LYS	1	0.931	0.963	12.358	0.193	0.193	0.000	0.000	0.000	0.000
13	A	19	GLN	0	-0.021	-0.013	15.877	0.025	0.025	0.000	0.000	0.000	0.000
14	A	20	ARG	1	0.877	0.930	18.117	0.209	0.209	0.000	0.000	0.000	0.000
15	A	21	GLU	-1	-0.958	-0.960	18.333	-0.142	-0.142	0.000	0.000	0.000	0.000
16	A	22	LYS	1	0.857	0.932	18.691	0.091	0.091	0.000	0.000	0.000	0.000
17	A	23	GLY	0	0.000	-0.004	22.709	0.011	0.011	0.000	0.000	0.000	0.000
18	A	24	GLN	0	-0.036	-0.027	19.916	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	25	TYR	0	-0.025	-0.022	19.631	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	26	CYS	0	-0.072	-0.010	21.546	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	27	ASP	-1	-0.831	-0.900	23.363	-0.103	-0.103	0.000	0.000	0.000	0.000
22	A	28	ALA	0	0.005	0.009	24.788	0.007	0.007	0.000	0.000	0.000	0.000
23	A	29	THR	0	-0.056	-0.037	25.780	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	30	LEU	0	-0.008	-0.021	24.996	0.003	0.003	0.000	0.000	0.000	0.000
25	A	31	ASP	-1	-0.888	-0.930	29.114	-0.061	-0.061	0.000	0.000	0.000	0.000
26	A	32	VAL	0	0.074	0.046	29.452	0.000	0.000	0.000	0.000	0.000	0.000
27	A	33	GLY	0	0.003	-0.011	32.674	0.001	0.001	0.000	0.000	0.000	0.000
28	A	34	GLY	0	0.010	0.013	35.335	0.002	0.002	0.000	0.000	0.000	0.000
29	A	35	LEU	0	-0.076	-0.033	30.242	0.002	0.002	0.000	0.000	0.000	0.000
30	A	36	VAL	0	0.039	0.028	29.680	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	37	PHE	0	-0.011	-0.015	24.611	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	38	LYS	1	0.932	0.978	24.129	0.077	0.077	0.000	0.000	0.000	0.000
33	A	39	ALA	0	0.025	0.000	21.279	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	40	HIS	0	0.067	0.080	17.775	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	41	TRP	0	0.051	0.016	20.857	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	42	SER	0	-0.012	-0.004	18.329	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	43	VAL	0	0.030	0.019	15.444	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	44	LEU	0	0.000	-0.003	17.794	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	45	ALA	0	0.014	0.000	21.006	0.004	0.004	0.000	0.000	0.000	0.000
40	A	46	CYS	0	-0.103	-0.040	16.499	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	47	CYS	0	0.006	0.012	17.335	-0.016	-0.016	0.000	0.000	0.000	0.000
42	A	48	SER	0	-0.020	-0.005	19.796	0.015	0.015	0.000	0.000	0.000	0.000
43	A	49	HIS	0	0.085	0.022	23.498	0.006	0.006	0.000	0.000	0.000	0.000
44	A	50	PHE	0	-0.057	-0.019	26.381	0.010	0.010	0.000	0.000	0.000	0.000
45	A	51	PHE	0	0.032	-0.011	24.314	0.007	0.007	0.000	0.000	0.000	0.000
46	A	52	GLN	0	-0.064	-0.036	22.647	0.015	0.015	0.000	0.000	0.000	0.000
47	A	53	ARG	1	0.862	0.920	26.520	0.092	0.092	0.000	0.000	0.000	0.000
48	A	54	ILE	0	-0.058	-0.005	29.694	0.006	0.006	0.000	0.000	0.000	0.000
49	A	55	TYR	0	0.005	0.016	26.088	0.002	0.002	0.000	0.000	0.000	0.000
50	A	56	GLY	0	0.041	-0.002	29.634	0.002	0.002	0.000	0.000	0.000	0.000
51	A	57	ASP	-1	-0.923	-0.957	29.734	-0.061	-0.061	0.000	0.000	0.000	0.000
52	A	58	GLY	0	-0.060	-0.025	32.293	0.003	0.003	0.000	0.000	0.000	0.000
53	A	59	THR	0	-0.025	-0.025	35.205	0.003	0.003	0.000	0.000	0.000	0.000
54	A	60	GLY	0	-0.018	0.011	33.204	0.001	0.001	0.000	0.000	0.000	0.000
55	A	61	GLY	0	0.005	0.011	31.951	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	62	SER	0	-0.068	-0.042	31.552	0.003	0.003	0.000	0.000	0.000	0.000
57	A	63	VAL	0	0.011	0.015	30.157	0.002	0.002	0.000	0.000	0.000	0.000
58	A	64	VAL	0	0.007	0.012	31.954	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	65	LEU	0	-0.049	-0.026	29.467	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	66	PRO	0	0.024	0.011	32.762	0.004	0.004	0.000	0.000	0.000	0.000
61	A	67	ALA	0	0.082	0.016	34.069	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	68	GLY	0	-0.045	-0.009	35.586	0.000	0.000	0.000	0.000	0.000	0.000
63	A	69	PHE	0	0.009	-0.012	30.438	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	70	ALA	0	-0.007	-0.018	30.532	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	71	GLU	-1	-0.944	-0.966	30.445	-0.074	-0.074	0.000	0.000	0.000	0.000
66	A	72	ILE	0	0.009	-0.002	27.666	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	73	PHE	0	-0.001	-0.001	25.779	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	74	GLY	0	0.037	0.015	24.235	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	75	LEU	0	0.001	0.015	22.329	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	76	LEU	0	-0.012	-0.001	21.183	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	77	LEU	0	0.014	0.007	20.643	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	78	ASP	-1	-0.832	-0.926	18.266	-0.199	-0.199	0.000	0.000	0.000	0.000
73	A	79	PHE	0	-0.029	-0.025	16.548	-0.039	-0.039	0.000	0.000	0.000	0.000
74	A	80	PHE	0	-0.026	-0.009	15.903	-0.033	-0.033	0.000	0.000	0.000	0.000
75	A	81	TYR	0	-0.025	-0.068	14.076	-0.038	-0.038	0.000	0.000	0.000	0.000
76	A	82	THR	0	-0.104	-0.058	12.083	-0.060	-0.060	0.000	0.000	0.000	0.000
77	A	83	GLY	0	0.010	0.016	12.235	-0.041	-0.041	0.000	0.000	0.000	0.000
78	A	84	HIS	0	-0.050	-0.027	13.987	0.035	0.035	0.000	0.000	0.000	0.000
79	A	85	LEU	0	0.028	0.014	16.557	0.012	0.012	0.000	0.000	0.000	0.000
80	A	86	ALA	0	0.026	0.028	20.254	0.008	0.008	0.000	0.000	0.000	0.000
81	A	87	LEU	0	-0.003	-0.015	22.472	0.014	0.014	0.000	0.000	0.000	0.000
82	A	88	THR	0	-0.008	0.000	25.110	0.006	0.006	0.000	0.000	0.000	0.000
83	A	89	SER	0	-0.023	-0.027	28.406	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	90	GLY	0	0.008	0.005	31.662	0.002	0.002	0.000	0.000	0.000	0.000
85	A	91	ASN	0	0.054	0.035	26.730	0.002	0.002	0.000	0.000	0.000	0.000
86	A	92	ARG	1	0.929	0.982	28.915	0.091	0.091	0.000	0.000	0.000	0.000
87	A	93	ASP	-1	-0.886	-0.959	29.983	-0.080	-0.080	0.000	0.000	0.000	0.000
88	A	94	GLN	0	-0.054	-0.023	31.658	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	95	VAL	0	0.024	0.008	25.269	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	96	LEU	0	0.019	0.002	28.063	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	97	LEU	0	-0.025	-0.013	29.418	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	98	ALA	0	0.032	0.015	28.705	0.001	0.001	0.000	0.000	0.000	0.000
93	A	99	ALA	0	0.021	0.009	25.884	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	100	LYS	1	0.887	0.939	27.231	0.084	0.084	0.000	0.000	0.000	0.000
95	A	101	GLU	-1	-0.899	-0.929	29.947	-0.077	-0.077	0.000	0.000	0.000	0.000
96	A	102	LEU	0	-0.052	-0.026	26.407	0.002	0.002	0.000	0.000	0.000	0.000
97	A	103	ARG	0	-0.026	-0.002	26.789	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	104	VAL	0	0.043	0.026	21.803	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	105	PRO	0	-0.009	-0.021	22.623	0.001	0.001	0.000	0.000	0.000	0.000
100	A	106	GLU	-1	-0.856	-0.940	16.889	-0.272	-0.272	0.000	0.000	0.000	0.000
101	A	107	ALA	0	0.004	0.015	21.113	0.002	0.002	0.000	0.000	0.000	0.000
102	A	108	VAL	0	-0.017	-0.006	22.749	0.011	0.011	0.000	0.000	0.000	0.000
103	A	109	GLU	-1	-0.927	-0.959	22.315	-0.161	-0.161	0.000	0.000	0.000	0.000
104	A	110	LEU	0	0.015	0.013	18.836	0.008	0.008	0.000	0.000	0.000	0.000
105	A	111	CYS	0	-0.062	-0.025	23.303	0.010	0.010	0.000	0.000	0.000	0.000
106	A	112	GLN	0	-0.110	-0.071	26.628	0.006	0.006	0.000	0.000	0.000	0.000
107	A	113	SER	0	0.020	0.014	24.963	0.010	0.010	0.000	0.000	0.000	0.000
108	A	114	PHE	0	-0.038	-0.008	25.108	0.004	0.004	0.000	0.000	0.000	0.000
109	A	115	GLN	0	0.000	0.004	26.758	0.007	0.007	0.000	0.000	0.000	0.000
110	A	116	PRO	0	-0.053	-0.018	27.840	-0.001	-0.001	0.000	0.000	0.000	0.000

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