FMO DATABASE

FMODB ID: 5J28Z

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	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	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge	DAS=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1071780.236478
FMO2-HF: Nuclear repulsion	1023107.770334
FMO2-HF: Total energy	-48672.466144
FMO2-MP2: Total energy	-48818.646405

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.
-19.265	-13.185	3	-3.174	-5.904	0.02

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 : 0.005 / q_NPA : -0.012

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	-0.818	-0.917	3.249	-1.274	0.938	0.062	-0.897	-1.377	0.001
4	B	12	GLU	-1	-0.903	-0.919	2.372	-5.708	-3.404	2.846	-1.810	-3.340	0.017
5	B	13	ALA	0	-0.032	-0.031	3.897	-1.912	-1.445	0.015	-0.117	-0.366	0.001
6	B	14	LEU	0	0.061	0.036	5.879	-0.465	-0.465	0.000	0.000	0.000	0.000
7	B	15	LYS	1	0.900	0.937	5.489	-0.553	-0.553	0.000	0.000	0.000	0.000
8	B	16	ARG	1	0.852	0.918	3.636	-3.755	-3.571	0.000	-0.035	-0.148	0.000
9	B	17	LEU	0	0.059	0.049	9.737	-0.161	-0.161	0.000	0.000	0.000	0.000
10	B	18	GLU	-1	-0.925	-0.949	11.685	0.195	0.195	0.000	0.000	0.000	0.000
11	B	19	ALA	0	-0.048	-0.027	12.670	-0.097	-0.097	0.000	0.000	0.000	0.000
12	B	20	SER	0	-0.043	-0.062	13.781	-0.032	-0.032	0.000	0.000	0.000	0.000
13	B	21	ARG	1	0.841	0.920	15.559	-0.455	-0.455	0.000	0.000	0.000	0.000
14	B	22	LYS	1	0.948	0.970	16.980	-0.206	-0.206	0.000	0.000	0.000	0.000
15	B	23	ALA	0	-0.011	-0.011	18.490	-0.033	-0.033	0.000	0.000	0.000	0.000
16	B	24	LEU	0	0.020	0.015	19.669	-0.025	-0.025	0.000	0.000	0.000	0.000
17	B	25	LEU	0	-0.017	-0.023	21.429	-0.026	-0.026	0.000	0.000	0.000	0.000
18	B	26	ALA	0	-0.056	-0.026	23.263	-0.021	-0.021	0.000	0.000	0.000	0.000
19	B	27	LEU	0	-0.026	0.001	24.208	-0.012	-0.012	0.000	0.000	0.000	0.000
20	B	28	LEU	0	-0.002	-0.010	24.997	-0.011	-0.011	0.000	0.000	0.000	0.000
21	B	29	ARG	1	0.951	0.999	25.109	-0.165	-0.165	0.000	0.000	0.000	0.000
22	B	31	ALA	0	-0.023	-0.024	29.920	-0.002	-0.002	0.000	0.000	0.000	0.000
23	B	32	DAS	-1	-0.879	-0.938	31.638	0.099	0.099	0.000	0.000	0.000	0.000
24	B	33	PRO	0	-0.036	-0.039	34.681	0.006	0.006	0.000	0.000	0.000	0.000
25	B	34	DAL	0	-0.001	0.013	36.321	0.001	0.001	0.000	0.000	0.000	0.000
26	B	35	TRP	0	0.022	-0.001	27.811	0.004	0.004	0.000	0.000	0.000	0.000
27	B	36	LEU	0	-0.008	0.002	30.072	0.011	0.011	0.000	0.000	0.000	0.000
28	B	37	SER	0	0.007	-0.012	32.609	0.012	0.012	0.000	0.000	0.000	0.000
29	B	38	DAL	0	0.039	0.018	34.879	-0.005	-0.005	0.000	0.000	0.000	0.000
30	B	39	PRO	0	-0.033	-0.027	33.630	0.008	0.008	0.000	0.000	0.000	0.000
31	B	40	LEU	0	0.020	0.040	31.779	0.009	0.009	0.000	0.000	0.000	0.000
32	B	41	ARG	1	0.810	0.860	34.013	-0.148	-0.148	0.000	0.000	0.000	0.000
33	B	42	GLU	-1	-0.806	-0.879	32.924	0.148	0.148	0.000	0.000	0.000	0.000
34	B	43	GLY	0	-0.023	-0.005	33.712	0.008	0.008	0.000	0.000	0.000	0.000
35	B	44	ALA	0	-0.025	-0.003	31.450	0.008	0.008	0.000	0.000	0.000	0.000
36	B	45	TRP	0	0.037	-0.016	24.837	-0.008	-0.008	0.000	0.000	0.000	0.000
37	B	46	THR	0	0.002	0.005	31.283	0.004	0.004	0.000	0.000	0.000	0.000
38	B	47	PRO	0	0.038	0.013	28.083	0.018	0.018	0.000	0.000	0.000	0.000
39	B	48	LEU	0	0.000	0.011	27.385	0.020	0.020	0.000	0.000	0.000	0.000
40	B	49	MET	0	0.012	0.037	28.340	0.008	0.008	0.000	0.000	0.000	0.000
41	B	50	VAL	0	-0.030	0.007	23.639	0.022	0.022	0.000	0.000	0.000	0.000
42	B	51	ALA	0	-0.006	-0.020	23.551	0.032	0.032	0.000	0.000	0.000	0.000
43	B	52	GLU	-1	-0.895	-0.959	23.883	0.229	0.229	0.000	0.000	0.000	0.000
44	B	53	HIS	0	-0.011	-0.003	22.069	0.043	0.043	0.000	0.000	0.000	0.000
45	B	54	VAL	0	0.000	-0.004	18.429	0.032	0.032	0.000	0.000	0.000	0.000
46	B	55	ALA	0	0.015	0.015	19.898	0.038	0.038	0.000	0.000	0.000	0.000
47	B	56	LEU	0	0.002	-0.001	21.707	0.013	0.013	0.000	0.000	0.000	0.000
48	B	57	VAL	0	0.033	0.024	17.320	0.007	0.007	0.000	0.000	0.000	0.000
49	B	58	GLU	-1	-0.774	-0.855	16.094	0.592	0.592	0.000	0.000	0.000	0.000
50	B	59	ASP	-1	-0.758	-0.850	18.262	0.273	0.273	0.000	0.000	0.000	0.000
51	B	60	SER	0	-0.038	-0.030	20.368	-0.021	-0.021	0.000	0.000	0.000	0.000
52	B	61	THR	0	-0.021	-0.013	13.804	0.026	0.026	0.000	0.000	0.000	0.000
53	B	62	ALA	0	0.023	0.016	16.425	0.011	0.011	0.000	0.000	0.000	0.000
54	B	63	ARG	1	0.798	0.874	17.726	-0.288	-0.288	0.000	0.000	0.000	0.000
55	B	64	VAL	0	-0.014	0.005	15.919	-0.041	-0.041	0.000	0.000	0.000	0.000
56	B	65	LEU	0	0.017	0.014	11.859	-0.021	-0.021	0.000	0.000	0.000	0.000
57	B	66	ARG	1	0.952	0.993	15.706	-0.269	-0.269	0.000	0.000	0.000	0.000
58	B	67	ARG	1	0.884	0.933	19.022	-0.292	-0.292	0.000	0.000	0.000	0.000
59	B	68	LEU	0	0.031	0.018	14.217	-0.031	-0.031	0.000	0.000	0.000	0.000
60	B	69	ARG	1	0.813	0.896	16.712	-0.205	-0.205	0.000	0.000	0.000	0.000
61	B	70	ARG	1	0.875	0.924	17.697	-0.168	-0.168	0.000	0.000	0.000	0.000
62	B	71	LEU	0	-0.029	-0.013	19.636	-0.018	-0.018	0.000	0.000	0.000	0.000
63	B	72	ALA	0	-0.026	0.010	16.911	-0.015	-0.015	0.000	0.000	0.000	0.000
64	B	73	DAL	0	-0.032	-0.003	19.003	-0.031	-0.031	0.000	0.000	0.000	0.000
65	B	104	LEU	0	-0.007	-0.020	31.148	-0.004	-0.004	0.000	0.000	0.000	0.000
66	B	105	SER	0	0.021	0.028	34.811	0.002	0.002	0.000	0.000	0.000	0.000
67	B	106	LEU	0	0.064	0.018	29.383	0.011	0.011	0.000	0.000	0.000	0.000
68	B	107	GLU	-1	-0.898	-0.962	30.544	0.128	0.128	0.000	0.000	0.000	0.000
69	B	108	GLU	-1	-0.921	-0.944	31.159	0.153	0.153	0.000	0.000	0.000	0.000
70	B	109	VAL	0	0.027	0.006	26.805	0.013	0.013	0.000	0.000	0.000	0.000
71	B	110	LEU	0	-0.036	-0.028	26.441	0.019	0.019	0.000	0.000	0.000	0.000
72	B	111	ALA	0	0.022	0.018	26.351	0.010	0.010	0.000	0.000	0.000	0.000
73	B	112	LEU	0	-0.028	-0.022	26.302	0.012	0.012	0.000	0.000	0.000	0.000
74	B	113	LEU	0	-0.035	-0.019	21.520	0.024	0.024	0.000	0.000	0.000	0.000
75	B	114	ASP	-1	-0.964	-0.970	21.916	0.207	0.207	0.000	0.000	0.000	0.000
76	B	115	ARG	1	0.931	0.958	22.617	-0.226	-0.226	0.000	0.000	0.000	0.000
77	B	116	ALA	0	-0.045	-0.025	21.107	0.003	0.003	0.000	0.000	0.000	0.000
78	B	117	ARG	1	0.773	0.855	15.329	-0.485	-0.485	0.000	0.000	0.000	0.000
79	B	118	ALA	0	0.017	0.008	18.106	0.018	0.018	0.000	0.000	0.000	0.000
80	B	119	PHE	0	-0.053	-0.022	19.626	-0.005	-0.005	0.000	0.000	0.000	0.000
81	B	120	LEU	0	0.000	-0.011	13.467	0.006	0.006	0.000	0.000	0.000	0.000
82	B	121	LEU	0	0.016	-0.001	13.754	0.035	0.035	0.000	0.000	0.000	0.000
83	B	122	GLU	-1	-0.913	-0.940	15.541	0.128	0.128	0.000	0.000	0.000	0.000
84	B	123	GLU	-1	-0.781	-0.899	15.992	0.205	0.205	0.000	0.000	0.000	0.000
85	B	124	VAL	0	-0.042	-0.033	10.252	0.004	0.004	0.000	0.000	0.000	0.000
86	B	125	ALA	0	-0.029	-0.009	12.402	-0.053	-0.053	0.000	0.000	0.000	0.000
87	B	126	LYS	1	0.861	0.933	14.394	-0.188	-0.188	0.000	0.000	0.000	0.000
88	B	127	ALA	0	-0.061	-0.010	11.570	-0.015	-0.015	0.000	0.000	0.000	0.000
89	B	128	ASP	-1	-0.819	-0.906	11.212	-0.152	-0.152	0.000	0.000	0.000	0.000
90	B	129	PRO	0	-0.064	-0.042	6.229	0.118	0.118	0.000	0.000	0.000	0.000
91	B	130	GLN	0	-0.028	-0.029	6.632	0.037	0.037	0.000	0.000	0.000	0.000
92	B	131	ASN	0	-0.002	0.002	9.211	0.020	0.020	0.000	0.000	0.000	0.000
93	B	132	PRO	0	0.008	0.001	11.202	0.129	0.129	0.000	0.000	0.000	0.000
94	B	133	ALA	0	-0.027	-0.004	13.117	0.041	0.041	0.000	0.000	0.000	0.000
95	B	134	THR	0	-0.034	-0.045	14.047	0.063	0.063	0.000	0.000	0.000	0.000
96	B	135	PHE	0	-0.036	-0.023	15.878	-0.081	-0.081	0.000	0.000	0.000	0.000
97	B	136	PRO	0	0.067	0.036	16.889	0.076	0.076	0.000	0.000	0.000	0.000
98	B	137	HIS	0	0.038	0.019	15.545	-0.041	-0.041	0.000	0.000	0.000	0.000
99	B	138	PRO	0	-0.046	-0.015	18.215	-0.018	-0.018	0.000	0.000	0.000	0.000
100	B	139	PHE	0	-0.064	-0.051	17.126	-0.027	-0.027	0.000	0.000	0.000	0.000
101	B	140	PHE	0	-0.003	0.000	14.017	0.034	0.034	0.000	0.000	0.000	0.000
102	B	141	GLY	0	0.045	0.034	15.576	0.038	0.038	0.000	0.000	0.000	0.000
103	B	142	GLU	-1	-0.866	-0.923	16.877	0.440	0.440	0.000	0.000	0.000	0.000
104	B	143	LEU	0	-0.042	-0.007	11.470	0.141	0.141	0.000	0.000	0.000	0.000
105	B	144	ASN	0	0.091	0.055	8.713	0.119	0.119	0.000	0.000	0.000	0.000
106	B	145	PRO	0	0.026	-0.002	10.041	0.182	0.182	0.000	0.000	0.000	0.000
107	B	146	LEU	0	0.038	0.029	3.315	-0.342	0.235	0.073	-0.173	-0.476	0.000
108	B	147	GLY	0	-0.008	-0.006	7.084	0.552	0.552	0.000	0.000	0.000	0.000
109	B	148	TRP	0	-0.006	-0.021	9.193	0.036	0.036	0.000	0.000	0.000	0.000
110	B	149	LEU	0	0.020	0.019	7.003	-0.040	-0.040	0.000	0.000	0.000	0.000
111	B	150	ARG	1	0.902	0.939	4.010	-4.839	-4.503	0.004	-0.142	-0.197	0.001
112	B	151	ALA	0	-0.019	0.001	7.989	-0.217	-0.217	0.000	0.000	0.000	0.000
113	B	152	ALA	0	0.044	0.022	11.653	-0.142	-0.142	0.000	0.000	0.000	0.000
114	B	153	ALA	0	-0.003	-0.003	8.715	-0.120	-0.120	0.000	0.000	0.000	0.000
115	B	154	TYR	0	-0.060	-0.035	10.707	-0.148	-0.148	0.000	0.000	0.000	0.000
116	B	155	HIS	0	0.001	0.008	12.035	-0.116	-0.116	0.000	0.000	0.000	0.000
117	B	156	GLU	-1	-0.663	-0.798	14.587	0.435	0.435	0.000	0.000	0.000	0.000
118	B	157	ALA	0	-0.014	-0.012	13.132	-0.091	-0.091	0.000	0.000	0.000	0.000
119	B	158	HIS	0	-0.052	-0.020	15.174	-0.092	-0.092	0.000	0.000	0.000	0.000
120	B	159	HIS	0	0.023	-0.003	17.470	-0.044	-0.044	0.000	0.000	0.000	0.000
121	B	160	LEU	0	-0.020	0.012	17.183	-0.045	-0.045	0.000	0.000	0.000	0.000
122	B	161	LYS	1	0.969	0.977	16.189	-0.464	-0.464	0.000	0.000	0.000	0.000
123	B	162	ALA	0	-0.003	0.017	20.614	-0.034	-0.034	0.000	0.000	0.000	0.000
124	B	163	LEU	0	0.004	-0.002	23.258	-0.030	-0.030	0.000	0.000	0.000	0.000
125	B	164	GLN	0	-0.032	-0.037	20.628	-0.004	-0.004	0.000	0.000	0.000	0.000
126	B	165	ALA	0	-0.042	0.000	24.725	-0.019	-0.019	0.000	0.000	0.000	0.000
127	B	166	SER	0	-0.041	-0.010	26.443	-0.025	-0.025	0.000	0.000	0.000	0.000

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