FMO DATABASE

FMODB ID: YVZM2

Calculation Name: 2YQY-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YQY

Chain ID: B

ChEMBL ID:

UniProt ID: Q5SLJ0

Base Structure: X-ray

Registration Date: 2023-09-21

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	127
LigandCharge	DAS=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1072068.263559
FMO2-HF: Nuclear repulsion	1023395.368661
FMO2-HF: Total energy	-48672.894898
FMO2-MP2: Total energy	-48819.074108

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(B:9:THR)

Summations of interaction energy for fragment #1(B:9: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.
-19.062	-13.016	1.797	-2.714	-5.131	0.012

Interaction energy analysis for fragmet #1(B:9:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.014

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	B	11	ASP	-1	-0.833	-0.925	3.115	-2.844	-0.729	0.031	-0.795	-1.351	0.000
4	B	12	GLU	-1	-0.854	-0.902	2.611	-2.864	-0.466	1.688	-1.450	-2.636	0.011
5	B	13	ALA	0	-0.031	-0.019	4.116	-1.159	-0.722	0.007	-0.124	-0.320	0.001
6	B	14	LEU	0	0.047	0.032	5.931	-0.277	-0.277	0.000	0.000	0.000	0.000
7	B	15	LYS	1	0.895	0.927	5.950	-0.324	-0.324	0.000	0.000	0.000	0.000
8	B	16	ARG	1	0.836	0.907	3.842	-4.283	-4.087	0.000	-0.044	-0.153	0.000
9	B	17	LEU	0	0.067	0.056	9.775	-0.136	-0.136	0.000	0.000	0.000	0.000
10	B	18	GLU	-1	-0.916	-0.936	11.992	0.026	0.026	0.000	0.000	0.000	0.000
11	B	19	ALA	0	-0.056	-0.032	12.902	-0.080	-0.080	0.000	0.000	0.000	0.000
12	B	20	SER	0	-0.036	-0.056	13.820	-0.022	-0.022	0.000	0.000	0.000	0.000
13	B	21	ARG	1	0.808	0.884	15.604	-0.407	-0.407	0.000	0.000	0.000	0.000
14	B	22	LYS	1	0.947	0.969	16.814	-0.178	-0.178	0.000	0.000	0.000	0.000
15	B	23	ALA	0	-0.008	-0.008	18.528	-0.030	-0.030	0.000	0.000	0.000	0.000
16	B	24	LEU	0	0.010	0.012	19.719	-0.021	-0.021	0.000	0.000	0.000	0.000
17	B	25	LEU	0	-0.007	-0.016	21.477	-0.025	-0.025	0.000	0.000	0.000	0.000
18	B	26	ALA	0	-0.057	-0.030	23.304	-0.020	-0.020	0.000	0.000	0.000	0.000
19	B	27	LEU	0	-0.020	0.004	24.132	-0.011	-0.011	0.000	0.000	0.000	0.000
20	B	28	LEU	0	-0.002	-0.011	24.964	-0.010	-0.010	0.000	0.000	0.000	0.000
21	B	29	ARG	1	0.954	1.000	25.640	-0.143	-0.143	0.000	0.000	0.000	0.000
22	B	31	ALA	0	-0.034	-0.025	29.877	-0.002	-0.002	0.000	0.000	0.000	0.000
23	B	32	DAS	-1	-0.842	-0.921	31.684	0.100	0.100	0.000	0.000	0.000	0.000
24	B	33	PRO	0	-0.021	-0.028	34.662	0.007	0.007	0.000	0.000	0.000	0.000
25	B	34	DAL	0	-0.022	-0.005	36.373	0.001	0.001	0.000	0.000	0.000	0.000
26	B	35	TRP	0	-0.019	-0.019	27.710	0.003	0.003	0.000	0.000	0.000	0.000
27	B	36	LEU	0	-0.004	-0.001	29.919	0.011	0.011	0.000	0.000	0.000	0.000
28	B	37	SER	0	0.000	-0.014	32.669	0.008	0.008	0.000	0.000	0.000	0.000
29	B	38	DAL	0	0.032	0.016	34.783	-0.005	-0.005	0.000	0.000	0.000	0.000
30	B	39	PRO	0	-0.022	-0.028	33.713	0.008	0.008	0.000	0.000	0.000	0.000
31	B	40	LEU	0	0.024	0.045	31.798	0.010	0.010	0.000	0.000	0.000	0.000
32	B	41	ARG	1	0.809	0.860	34.182	-0.162	-0.162	0.000	0.000	0.000	0.000
33	B	42	GLU	-1	-0.811	-0.880	32.815	0.163	0.163	0.000	0.000	0.000	0.000
34	B	43	GLY	0	-0.027	-0.009	33.841	0.008	0.008	0.000	0.000	0.000	0.000
35	B	44	ALA	0	-0.025	-0.005	31.560	0.008	0.008	0.000	0.000	0.000	0.000
36	B	45	TRP	0	0.019	-0.003	24.905	-0.009	-0.009	0.000	0.000	0.000	0.000
37	B	46	THR	0	0.034	0.012	31.348	0.006	0.006	0.000	0.000	0.000	0.000
38	B	47	PRO	0	0.043	0.022	28.141	0.017	0.017	0.000	0.000	0.000	0.000
39	B	48	LEU	0	0.001	0.011	27.446	0.018	0.018	0.000	0.000	0.000	0.000
40	B	49	MET	0	0.010	0.019	28.404	0.007	0.007	0.000	0.000	0.000	0.000
41	B	50	VAL	0	-0.036	0.002	23.732	0.022	0.022	0.000	0.000	0.000	0.000
42	B	51	ALA	0	-0.011	-0.024	23.613	0.031	0.031	0.000	0.000	0.000	0.000
43	B	52	GLU	-1	-0.876	-0.946	23.946	0.212	0.212	0.000	0.000	0.000	0.000
44	B	53	HIS	0	-0.002	-0.002	22.391	0.042	0.042	0.000	0.000	0.000	0.000
45	B	54	VAL	0	0.000	-0.006	18.521	0.032	0.032	0.000	0.000	0.000	0.000
46	B	55	ALA	0	0.018	0.019	19.964	0.030	0.030	0.000	0.000	0.000	0.000
47	B	56	LEU	0	-0.003	-0.002	21.772	0.007	0.007	0.000	0.000	0.000	0.000
48	B	57	VAL	0	0.039	0.028	17.345	0.003	0.003	0.000	0.000	0.000	0.000
49	B	58	GLU	-1	-0.770	-0.843	16.183	0.493	0.493	0.000	0.000	0.000	0.000
50	B	59	ASP	-1	-0.756	-0.838	18.287	0.218	0.218	0.000	0.000	0.000	0.000
51	B	60	SER	0	-0.033	-0.031	20.331	-0.024	-0.024	0.000	0.000	0.000	0.000
52	B	61	THR	0	-0.023	-0.022	13.852	0.026	0.026	0.000	0.000	0.000	0.000
53	B	62	ALA	0	0.012	0.015	16.424	0.001	0.001	0.000	0.000	0.000	0.000
54	B	63	ARG	1	0.801	0.870	17.727	-0.254	-0.254	0.000	0.000	0.000	0.000
55	B	64	VAL	0	-0.018	0.004	15.956	-0.040	-0.040	0.000	0.000	0.000	0.000
56	B	65	LEU	0	0.016	0.012	11.881	-0.023	-0.023	0.000	0.000	0.000	0.000
57	B	66	ARG	1	0.950	0.987	15.707	-0.209	-0.209	0.000	0.000	0.000	0.000
58	B	67	ARG	1	0.892	0.941	19.024	-0.260	-0.260	0.000	0.000	0.000	0.000
59	B	68	LEU	0	0.033	0.015	14.261	-0.027	-0.027	0.000	0.000	0.000	0.000
60	B	69	ARG	1	0.853	0.916	16.597	-0.103	-0.103	0.000	0.000	0.000	0.000
61	B	70	ARG	1	0.886	0.935	17.702	-0.113	-0.113	0.000	0.000	0.000	0.000
62	B	71	LEU	0	-0.039	-0.017	19.618	-0.014	-0.014	0.000	0.000	0.000	0.000
63	B	72	ALA	0	-0.022	0.009	16.903	-0.012	-0.012	0.000	0.000	0.000	0.000
64	B	73	DAL	0	-0.030	-0.002	19.008	-0.027	-0.027	0.000	0.000	0.000	0.000
65	B	104	LEU	0	-0.023	-0.021	31.672	-0.005	-0.005	0.000	0.000	0.000	0.000
66	B	105	SER	0	-0.016	-0.024	34.871	0.003	0.003	0.000	0.000	0.000	0.000
67	B	106	LEU	0	0.067	0.021	29.517	0.010	0.010	0.000	0.000	0.000	0.000
68	B	107	GLU	-1	-0.867	-0.922	30.598	0.114	0.114	0.000	0.000	0.000	0.000
69	B	108	GLU	-1	-0.910	-0.941	31.212	0.131	0.131	0.000	0.000	0.000	0.000
70	B	109	VAL	0	0.020	0.007	26.890	0.010	0.010	0.000	0.000	0.000	0.000
71	B	110	LEU	0	-0.040	-0.028	26.295	0.015	0.015	0.000	0.000	0.000	0.000
72	B	111	ALA	0	0.021	0.018	26.403	0.006	0.006	0.000	0.000	0.000	0.000
73	B	112	LEU	0	-0.023	-0.021	26.485	0.007	0.007	0.000	0.000	0.000	0.000
74	B	113	LEU	0	-0.026	-0.016	21.580	0.019	0.019	0.000	0.000	0.000	0.000
75	B	114	ASP	-1	-0.955	-0.970	21.970	0.151	0.151	0.000	0.000	0.000	0.000
76	B	115	ARG	1	0.908	0.946	22.750	-0.191	-0.191	0.000	0.000	0.000	0.000
77	B	116	ALA	0	-0.038	-0.022	21.142	-0.003	-0.003	0.000	0.000	0.000	0.000
78	B	117	ARG	1	0.781	0.856	15.149	-0.420	-0.420	0.000	0.000	0.000	0.000
79	B	118	ALA	0	0.014	0.009	18.106	-0.001	-0.001	0.000	0.000	0.000	0.000
80	B	119	PHE	0	-0.048	-0.019	19.626	-0.012	-0.012	0.000	0.000	0.000	0.000
81	B	120	LEU	0	-0.011	-0.014	13.668	-0.004	-0.004	0.000	0.000	0.000	0.000
82	B	121	LEU	0	0.015	0.000	13.763	0.006	0.006	0.000	0.000	0.000	0.000
83	B	122	GLU	-1	-0.828	-0.879	15.421	0.030	0.030	0.000	0.000	0.000	0.000
84	B	123	GLU	-1	-0.796	-0.899	16.259	0.083	0.083	0.000	0.000	0.000	0.000
85	B	124	VAL	0	-0.037	-0.028	10.325	-0.013	-0.013	0.000	0.000	0.000	0.000
86	B	125	ALA	0	-0.028	-0.011	12.360	-0.082	-0.082	0.000	0.000	0.000	0.000
87	B	126	LYS	1	0.735	0.843	14.325	-0.109	-0.109	0.000	0.000	0.000	0.000
88	B	127	ALA	0	-0.067	-0.014	11.593	0.002	0.002	0.000	0.000	0.000	0.000
89	B	128	ASP	-1	-0.811	-0.906	11.274	-0.340	-0.340	0.000	0.000	0.000	0.000
90	B	129	PRO	0	-0.061	-0.039	6.219	0.134	0.134	0.000	0.000	0.000	0.000
91	B	130	GLN	0	-0.031	-0.029	6.654	-0.006	-0.006	0.000	0.000	0.000	0.000
92	B	131	ASN	0	0.019	0.019	9.217	0.088	0.088	0.000	0.000	0.000	0.000
93	B	132	PRO	0	0.005	0.003	11.202	0.138	0.138	0.000	0.000	0.000	0.000
94	B	133	ALA	0	-0.021	0.002	13.116	0.056	0.056	0.000	0.000	0.000	0.000
95	B	134	THR	0	-0.039	-0.055	13.942	0.054	0.054	0.000	0.000	0.000	0.000
96	B	135	PHE	0	-0.032	-0.024	15.873	-0.085	-0.085	0.000	0.000	0.000	0.000
97	B	136	PRO	0	0.040	0.033	16.881	0.078	0.078	0.000	0.000	0.000	0.000
98	B	137	HIS	0	0.040	0.017	15.563	-0.033	-0.033	0.000	0.000	0.000	0.000
99	B	138	PRO	0	-0.043	-0.015	18.215	-0.013	-0.013	0.000	0.000	0.000	0.000
100	B	139	PHE	0	-0.065	-0.052	16.931	-0.028	-0.028	0.000	0.000	0.000	0.000
101	B	140	PHE	0	-0.006	-0.006	13.999	0.044	0.044	0.000	0.000	0.000	0.000
102	B	141	GLY	0	0.044	0.035	15.576	0.043	0.043	0.000	0.000	0.000	0.000
103	B	142	GLU	-1	-0.824	-0.902	16.757	0.446	0.446	0.000	0.000	0.000	0.000
104	B	143	LEU	0	-0.039	-0.006	11.278	0.158	0.158	0.000	0.000	0.000	0.000
105	B	144	ASN	0	0.083	0.039	8.158	0.184	0.184	0.000	0.000	0.000	0.000
106	B	145	PRO	0	0.009	-0.002	10.094	0.190	0.190	0.000	0.000	0.000	0.000
107	B	146	LEU	0	0.020	0.022	3.267	-0.306	0.201	0.070	-0.126	-0.451	-0.001
108	B	147	GLY	0	0.002	0.001	7.080	0.588	0.588	0.000	0.000	0.000	0.000
109	B	148	TRP	0	-0.013	-0.026	9.183	0.061	0.061	0.000	0.000	0.000	0.000
110	B	149	LEU	0	0.019	0.021	6.886	-0.022	-0.022	0.000	0.000	0.000	0.000
111	B	150	ARG	1	0.921	0.946	4.072	-6.404	-6.011	0.001	-0.175	-0.220	0.001
112	B	151	ALA	0	-0.024	0.000	8.021	-0.188	-0.188	0.000	0.000	0.000	0.000
113	B	152	ALA	0	0.045	0.021	11.667	-0.134	-0.134	0.000	0.000	0.000	0.000
114	B	153	ALA	0	-0.006	-0.004	8.739	-0.119	-0.119	0.000	0.000	0.000	0.000
115	B	154	TYR	0	-0.044	-0.027	10.762	-0.126	-0.126	0.000	0.000	0.000	0.000
116	B	155	HIS	0	-0.001	0.004	12.102	-0.122	-0.122	0.000	0.000	0.000	0.000
117	B	156	GLU	-1	-0.671	-0.801	14.646	0.414	0.414	0.000	0.000	0.000	0.000
118	B	157	ALA	0	-0.009	-0.008	13.184	-0.091	-0.091	0.000	0.000	0.000	0.000
119	B	158	HIS	0	-0.068	-0.027	15.231	-0.095	-0.095	0.000	0.000	0.000	0.000
120	B	159	HIS	0	0.032	0.004	17.531	-0.043	-0.043	0.000	0.000	0.000	0.000
121	B	160	LEU	0	-0.023	0.008	16.974	-0.047	-0.047	0.000	0.000	0.000	0.000
122	B	161	LYS	1	0.970	0.982	16.299	-0.557	-0.557	0.000	0.000	0.000	0.000
123	B	162	ALA	0	-0.002	0.014	20.664	-0.036	-0.036	0.000	0.000	0.000	0.000
124	B	163	LEU	0	0.012	0.005	23.317	-0.032	-0.032	0.000	0.000	0.000	0.000
125	B	164	GLN	0	-0.014	-0.033	20.289	-0.001	-0.001	0.000	0.000	0.000	0.000
126	B	165	ALA	0	-0.050	-0.007	24.772	-0.020	-0.020	0.000	0.000	0.000	0.000
127	B	166	SER	0	-0.053	-0.007	26.490	-0.037	-0.037	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:9:THR)