FMO DATABASE

FMODB ID: NNVMQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-821587.81243
FMO2-HF: Nuclear repulsion	779263.08846
FMO2-HF: Total energy	-42324.72397
FMO2-MP2: Total energy	-42448.06747

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.
-4.682	-1.823	0.401	-1.209	-2.049	0.001

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	0.063	0.022	3.789	-1.120	0.021	0.004	-0.471	-0.674	0.001
4	A	10	VAL	0	0.035	0.028	2.807	0.178	0.843	0.259	-0.278	-0.645	-0.002
5	A	11	ARG	1	0.959	0.977	3.162	-4.153	-3.100	0.138	-0.460	-0.730	0.002
6	A	12	VAL	0	0.004	0.000	6.184	0.446	0.446	0.000	0.000	0.000	0.000
7	A	13	LEU	0	0.063	0.045	8.030	0.181	0.181	0.000	0.000	0.000	0.000
8	A	14	GLN	0	0.017	0.009	7.628	0.243	0.243	0.000	0.000	0.000	0.000
9	A	15	GLU	-1	-0.890	-0.932	10.437	-0.043	-0.043	0.000	0.000	0.000	0.000
10	A	16	LEU	0	-0.001	0.002	12.221	0.068	0.068	0.000	0.000	0.000	0.000
11	A	17	ASN	0	0.037	0.008	13.387	0.050	0.050	0.000	0.000	0.000	0.000
12	A	18	LYS	1	0.863	0.911	12.640	0.206	0.206	0.000	0.000	0.000	0.000
13	A	19	GLN	0	-0.056	-0.036	15.317	0.036	0.036	0.000	0.000	0.000	0.000
14	A	20	ARG	1	0.825	0.883	17.654	0.225	0.225	0.000	0.000	0.000	0.000
15	A	21	GLU	-1	-0.851	-0.893	18.453	-0.156	-0.156	0.000	0.000	0.000	0.000
16	A	22	LYS	1	0.801	0.914	17.473	0.127	0.127	0.000	0.000	0.000	0.000
17	A	23	GLY	0	0.009	0.000	22.711	0.012	0.012	0.000	0.000	0.000	0.000
18	A	24	GLN	0	-0.027	-0.017	20.060	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	25	TYR	0	-0.027	-0.029	19.489	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	26	CYS	0	-0.063	-0.006	21.471	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	27	ASP	-1	-0.833	-0.900	23.367	-0.116	-0.116	0.000	0.000	0.000	0.000
22	A	28	ALA	0	0.018	0.021	24.598	0.008	0.008	0.000	0.000	0.000	0.000
23	A	29	THR	0	-0.027	-0.029	25.783	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	30	LEU	0	-0.004	-0.012	25.214	0.004	0.004	0.000	0.000	0.000	0.000
25	A	31	ASP	-1	-0.889	-0.937	29.115	-0.065	-0.065	0.000	0.000	0.000	0.000
26	A	32	VAL	0	0.055	0.036	29.473	0.000	0.000	0.000	0.000	0.000	0.000
27	A	33	GLY	0	0.015	-0.002	32.673	0.001	0.001	0.000	0.000	0.000	0.000
28	A	34	GLY	0	0.002	0.009	35.348	0.002	0.002	0.000	0.000	0.000	0.000
29	A	35	LEU	0	-0.071	-0.026	30.179	0.002	0.002	0.000	0.000	0.000	0.000
30	A	36	VAL	0	0.032	0.018	29.937	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	37	PHE	0	-0.008	-0.014	24.836	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	38	LYS	1	0.901	0.964	24.180	0.083	0.083	0.000	0.000	0.000	0.000
33	A	39	ALA	0	0.033	0.005	21.278	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	40	HIS	0	0.057	0.045	17.801	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	41	TRP	0	0.040	0.011	20.861	-0.018	-0.018	0.000	0.000	0.000	0.000
36	A	42	SER	0	-0.010	-0.004	18.542	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	43	VAL	0	0.017	0.009	15.414	-0.017	-0.017	0.000	0.000	0.000	0.000
38	A	44	LEU	0	-0.003	-0.001	17.799	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	45	ALA	0	0.005	-0.004	21.011	0.005	0.005	0.000	0.000	0.000	0.000
40	A	46	CYS	0	-0.100	-0.045	16.487	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	47	CYS	0	0.013	0.015	17.193	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	48	SER	0	-0.029	-0.018	19.800	0.017	0.017	0.000	0.000	0.000	0.000
43	A	49	HIS	0	0.056	0.014	23.503	0.003	0.003	0.000	0.000	0.000	0.000
44	A	50	PHE	0	-0.032	-0.009	26.386	0.010	0.010	0.000	0.000	0.000	0.000
45	A	51	PHE	0	0.042	-0.006	24.451	0.007	0.007	0.000	0.000	0.000	0.000
46	A	52	GLN	0	-0.060	-0.023	22.742	0.015	0.015	0.000	0.000	0.000	0.000
47	A	53	ARG	1	0.833	0.888	26.526	0.099	0.099	0.000	0.000	0.000	0.000
48	A	54	ILE	0	-0.064	-0.011	29.779	0.006	0.006	0.000	0.000	0.000	0.000
49	A	55	TYR	0	-0.050	-0.028	26.329	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	56	GLY	0	0.043	-0.004	29.640	0.002	0.002	0.000	0.000	0.000	0.000
51	A	57	ASP	-1	-0.883	-0.921	29.494	-0.072	-0.072	0.000	0.000	0.000	0.000
52	A	58	GLY	0	-0.040	-0.013	32.193	0.003	0.003	0.000	0.000	0.000	0.000
53	A	59	THR	0	-0.055	-0.040	35.198	0.003	0.003	0.000	0.000	0.000	0.000
54	A	60	GLY	0	0.024	0.035	33.225	0.001	0.001	0.000	0.000	0.000	0.000
55	A	61	GLY	0	-0.007	0.000	31.943	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	62	SER	0	-0.065	-0.043	31.556	0.003	0.003	0.000	0.000	0.000	0.000
57	A	63	VAL	0	-0.001	0.012	29.952	0.002	0.002	0.000	0.000	0.000	0.000
58	A	64	VAL	0	0.006	0.012	31.956	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	65	LEU	0	-0.034	-0.018	29.342	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	66	PRO	0	0.032	0.004	32.951	0.004	0.004	0.000	0.000	0.000	0.000
61	A	67	ALA	0	0.065	0.016	34.069	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	68	GLY	0	-0.045	-0.010	35.585	0.000	0.000	0.000	0.000	0.000	0.000
63	A	69	PHE	0	0.015	-0.005	30.435	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	70	ALA	0	-0.003	-0.013	30.530	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	71	GLU	-1	-0.912	-0.941	30.442	-0.074	-0.074	0.000	0.000	0.000	0.000
66	A	72	ILE	0	0.009	-0.003	27.714	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	73	PHE	0	-0.001	0.002	25.514	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	74	GLY	0	0.039	0.019	24.232	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	75	LEU	0	0.000	0.011	22.326	-0.014	-0.014	0.000	0.000	0.000	0.000
70	A	76	LEU	0	-0.013	0.001	21.181	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	77	LEU	0	0.016	0.010	20.471	-0.017	-0.017	0.000	0.000	0.000	0.000
72	A	78	ASP	-1	-0.800	-0.905	18.247	-0.204	-0.204	0.000	0.000	0.000	0.000
73	A	79	PHE	0	-0.029	-0.011	16.546	-0.039	-0.039	0.000	0.000	0.000	0.000
74	A	80	PHE	0	-0.014	0.000	15.903	-0.033	-0.033	0.000	0.000	0.000	0.000
75	A	81	TYR	0	-0.019	-0.039	14.081	-0.040	-0.040	0.000	0.000	0.000	0.000
76	A	82	THR	0	-0.100	-0.066	12.090	-0.060	-0.060	0.000	0.000	0.000	0.000
77	A	83	GLY	0	0.001	0.011	12.232	-0.039	-0.039	0.000	0.000	0.000	0.000
78	A	84	HIS	0	-0.055	-0.033	13.985	0.038	0.038	0.000	0.000	0.000	0.000
79	A	85	LEU	0	0.027	0.015	16.553	0.011	0.011	0.000	0.000	0.000	0.000
80	A	86	ALA	0	0.018	0.028	20.251	0.009	0.009	0.000	0.000	0.000	0.000
81	A	87	LEU	0	0.003	-0.016	22.467	0.013	0.013	0.000	0.000	0.000	0.000
82	A	88	THR	0	-0.001	-0.007	25.105	0.006	0.006	0.000	0.000	0.000	0.000
83	A	89	SER	0	-0.015	-0.021	28.400	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	90	GLY	0	-0.007	0.000	31.657	0.002	0.002	0.000	0.000	0.000	0.000
85	A	91	ASN	0	0.047	0.034	26.820	0.000	0.000	0.000	0.000	0.000	0.000
86	A	92	ARG	1	0.860	0.940	28.913	0.090	0.090	0.000	0.000	0.000	0.000
87	A	93	ASP	-1	-0.872	-0.955	29.979	-0.081	-0.081	0.000	0.000	0.000	0.000
88	A	94	GLN	0	-0.067	-0.040	31.382	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	95	VAL	0	0.026	0.004	25.197	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	96	LEU	0	-0.005	-0.004	28.062	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	97	LEU	0	-0.022	-0.008	29.417	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	98	ALA	0	0.029	0.011	28.748	0.001	0.001	0.000	0.000	0.000	0.000
93	A	99	ALA	0	0.014	0.007	25.849	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	100	LYS	1	0.867	0.929	27.232	0.089	0.089	0.000	0.000	0.000	0.000
95	A	101	GLU	-1	-0.925	-0.942	29.949	-0.080	-0.080	0.000	0.000	0.000	0.000
96	A	102	LEU	0	-0.030	-0.017	26.490	0.001	0.001	0.000	0.000	0.000	0.000
97	A	103	ARG	0	0.004	0.030	26.793	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	104	VAL	0	0.039	0.026	21.746	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	105	PRO	0	0.004	-0.015	22.673	0.001	0.001	0.000	0.000	0.000	0.000
100	A	106	GLU	-1	-0.874	-0.937	17.108	-0.283	-0.283	0.000	0.000	0.000	0.000
101	A	107	ALA	0	0.029	0.020	21.115	0.003	0.003	0.000	0.000	0.000	0.000
102	A	108	VAL	0	-0.017	-0.008	22.749	0.012	0.012	0.000	0.000	0.000	0.000
103	A	109	GLU	-1	-0.947	-0.961	22.045	-0.159	-0.159	0.000	0.000	0.000	0.000
104	A	110	LEU	0	0.028	0.022	18.800	0.010	0.010	0.000	0.000	0.000	0.000
105	A	111	CYS	0	-0.027	-0.007	23.302	0.010	0.010	0.000	0.000	0.000	0.000
106	A	112	GLN	0	-0.032	-0.031	26.625	0.013	0.013	0.000	0.000	0.000	0.000
107	A	113	SER	0	-0.001	0.000	24.916	0.009	0.009	0.000	0.000	0.000	0.000
108	A	114	PHE	0	-0.049	-0.010	24.836	0.004	0.004	0.000	0.000	0.000	0.000
109	A	115	GLN	0	-0.006	-0.003	26.756	0.008	0.008	0.000	0.000	0.000	0.000
110	A	116	PRO	0	-0.029	-0.006	27.834	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)