FMO DATABASE

FMODB ID: 72LRK

Calculation Name: 2O4D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2O4D

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I6M1

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	144
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1310328.18823
FMO2-HF: Nuclear repulsion	1253265.993278
FMO2-HF: Total energy	-57062.194952
FMO2-MP2: Total energy	-57226.460765

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:2:THR)

Summations of interaction energy for fragment #1(A:2: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.
-13.396	-9.598	7.843	-5.597	-6.044	-0.032

Interaction energy analysis for fragmet #1(A:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.004

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	4	ARG	1	0.949	0.984	3.829	0.639	2.832	-0.022	-1.159	-1.012	0.002
4	A	5	LEU	0	0.012	0.007	6.304	0.073	0.073	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.925	-0.959	6.103	1.490	1.490	0.000	0.000	0.000	0.000
6	A	7	TRP	0	0.061	0.000	8.114	-0.076	-0.076	0.000	0.000	0.000	0.000
7	A	8	ALA	0	-0.003	0.005	10.248	-0.066	-0.066	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.931	0.966	9.675	-0.970	-0.970	0.000	0.000	0.000	0.000
9	A	10	ALA	0	-0.004	0.008	12.501	-0.060	-0.060	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.005	-0.002	14.476	-0.054	-0.054	0.000	0.000	0.000	0.000
11	A	12	PRO	0	0.046	0.013	16.080	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.880	-0.931	17.177	0.181	0.181	0.000	0.000	0.000	0.000
13	A	14	ALA	0	-0.017	-0.009	16.524	-0.022	-0.022	0.000	0.000	0.000	0.000
14	A	15	TYR	0	-0.015	-0.012	12.712	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.014	0.003	15.997	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	17	ALA	0	-0.009	-0.001	19.316	-0.020	-0.020	0.000	0.000	0.000	0.000
17	A	18	MET	0	-0.025	-0.007	15.981	-0.031	-0.031	0.000	0.000	0.000	0.000
18	A	19	LEU	0	-0.007	-0.009	15.695	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	20	GLY	0	-0.016	-0.002	18.973	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.011	0.006	20.021	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.777	-0.857	17.493	0.015	0.015	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.912	0.963	20.944	-0.107	-0.107	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.048	-0.033	23.860	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	25	LEU	0	0.042	0.018	21.484	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	26	ALA	0	-0.057	-0.022	23.369	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.849	0.921	25.034	-0.062	-0.062	0.000	0.000	0.000	0.000
27	A	28	ALA	0	-0.023	0.018	27.656	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	29	GLY	0	-0.040	-0.012	29.458	0.002	0.002	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.017	0.001	26.701	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.795	-0.874	27.931	-0.037	-0.037	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.911	0.934	19.741	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	33	PRO	0	0.057	0.013	23.275	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.035	0.034	23.718	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	35	ILE	0	0.013	0.007	20.833	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.813	-0.912	17.740	-0.083	-0.083	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.009	0.010	19.248	-0.040	-0.040	0.000	0.000	0.000	0.000
37	A	38	VAL	0	0.032	0.025	20.960	-0.029	-0.029	0.000	0.000	0.000	0.000
38	A	39	TYR	0	-0.042	-0.073	16.028	-0.035	-0.035	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.003	0.010	15.243	-0.058	-0.058	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.867	0.915	17.067	0.212	0.212	0.000	0.000	0.000	0.000
41	A	42	THR	0	-0.006	-0.015	17.984	-0.019	-0.019	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.016	-0.020	13.224	-0.031	-0.031	0.000	0.000	0.000	0.000
43	A	44	GLN	0	-0.008	0.000	14.648	-0.062	-0.062	0.000	0.000	0.000	0.000
44	A	45	ILE	0	-0.072	-0.015	16.538	-0.031	-0.031	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.062	-0.045	15.974	0.006	0.006	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.015	0.032	14.222	-0.031	-0.031	0.000	0.000	0.000	0.000
47	A	48	CYS	0	-0.063	-0.001	9.809	-0.145	-0.145	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.061	0.014	7.841	0.062	0.062	0.000	0.000	0.000	0.000
49	A	50	TYR	0	0.026	0.011	4.000	0.066	0.243	-0.001	-0.016	-0.161	0.000
50	A	51	CYS	0	-0.011	-0.023	6.869	0.398	0.398	0.000	0.000	0.000	0.000
51	A	52	VAL	0	0.018	0.013	10.410	0.136	0.136	0.000	0.000	0.000	0.000
52	A	53	ASN	0	0.014	0.007	7.656	0.136	0.136	0.000	0.000	0.000	0.000
53	A	54	MET	0	-0.040	-0.006	9.402	0.153	0.153	0.000	0.000	0.000	0.000
54	A	55	HIS	1	0.896	0.936	10.844	0.197	0.197	0.000	0.000	0.000	0.000
55	A	56	ALA	0	0.054	0.048	13.743	0.042	0.042	0.000	0.000	0.000	0.000
56	A	57	ASN	0	-0.030	-0.024	11.170	0.025	0.025	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.878	-0.959	14.736	0.068	0.068	0.000	0.000	0.000	0.000
58	A	59	ALA	0	-0.003	-0.004	16.620	0.021	0.021	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.840	0.909	15.529	0.256	0.256	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.864	0.946	16.537	-0.072	-0.072	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.060	-0.022	20.440	0.015	0.015	0.000	0.000	0.000	0.000
62	A	63	GLY	0	0.002	0.002	22.877	0.000	0.000	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.828	-0.880	21.825	-0.113	-0.113	0.000	0.000	0.000	0.000
64	A	65	THR	0	-0.006	0.002	23.428	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.761	-0.889	20.708	-0.215	-0.215	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.033	-0.003	23.546	-0.025	-0.025	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.768	0.815	25.097	0.099	0.099	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.012	-0.005	18.741	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	70	GLN	0	-0.052	-0.026	20.817	-0.037	-0.037	0.000	0.000	0.000	0.000
70	A	71	ALA	0	0.012	0.008	22.395	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	72	LEU	0	0.000	0.011	20.012	0.003	0.003	0.000	0.000	0.000	0.000
72	A	73	CYS	0	-0.078	-0.045	20.735	0.003	0.003	0.000	0.000	0.000	0.000
73	A	74	VAL	0	-0.005	-0.007	22.669	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	75	TRP	0	0.006	0.004	25.219	0.025	0.025	0.000	0.000	0.000	0.000
75	A	76	GLN	0	-0.003	-0.008	27.565	0.009	0.009	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.903	-0.943	30.664	-0.108	-0.108	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.091	-0.030	29.012	0.001	0.001	0.000	0.000	0.000	0.000
78	A	79	PRO	0	0.004	-0.012	32.129	0.004	0.004	0.000	0.000	0.000	0.000
79	A	80	TYR	0	-0.029	-0.021	28.864	0.011	0.011	0.000	0.000	0.000	0.000
80	A	81	PHE	0	0.000	0.009	25.416	0.001	0.001	0.000	0.000	0.000	0.000
81	A	82	THR	0	0.018	0.009	30.814	0.004	0.004	0.000	0.000	0.000	0.000
82	A	83	PRO	0	0.049	0.014	32.908	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	84	ARG	1	0.839	0.910	32.049	0.039	0.039	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.779	-0.876	28.404	-0.099	-0.099	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.859	0.929	29.295	0.101	0.101	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.056	0.049	31.000	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.027	0.005	27.763	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.013	-0.004	24.436	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.014	0.012	27.080	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	91	TRP	0	-0.002	-0.009	28.141	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	92	THR	0	-0.018	-0.025	22.692	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	93	GLU	-1	-0.795	-0.860	24.576	-0.221	-0.221	0.000	0.000	0.000	0.000
93	A	94	GLN	0	-0.016	-0.018	25.736	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.009	0.004	26.065	0.000	0.000	0.000	0.000	0.000	0.000
95	A	96	ALA	0	-0.047	-0.013	21.682	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	97	ARG	1	0.808	0.884	23.117	0.209	0.209	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.068	0.042	25.490	0.009	0.009	0.000	0.000	0.000	0.000
98	A	99	SER	0	-0.064	-0.038	25.354	0.006	0.006	0.000	0.000	0.000	0.000
99	A	100	GLN	0	-0.049	-0.027	26.337	0.000	0.000	0.000	0.000	0.000	0.000
100	A	101	GLY	0	0.004	0.008	29.072	0.004	0.004	0.000	0.000	0.000	0.000
101	A	102	ALA	0	-0.047	-0.015	32.022	0.000	0.000	0.000	0.000	0.000	0.000
102	A	103	LEU	0	0.042	0.019	30.392	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	104	PRO	0	-0.017	-0.007	33.761	0.006	0.006	0.000	0.000	0.000	0.000
104	A	105	HIS	0	0.026	0.001	37.034	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	106	GLY	0	0.034	0.021	39.886	0.003	0.003	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.010	0.013	31.907	0.000	0.000	0.000	0.000	0.000	0.000
107	A	108	LEU	0	0.009	-0.006	35.150	0.000	0.000	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.923	-0.972	36.738	-0.042	-0.042	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.893	-0.937	36.480	-0.071	-0.071	0.000	0.000	0.000	0.000
110	A	111	LEU	0	-0.054	-0.040	31.703	0.000	0.000	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.863	0.918	35.815	0.036	0.036	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.991	-0.961	38.683	-0.048	-0.048	0.000	0.000	0.000	0.000
113	A	114	HIS	0	-0.091	-0.048	35.564	0.000	0.000	0.000	0.000	0.000	0.000
114	A	115	PHE	0	-0.066	-0.030	30.898	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.818	-0.900	36.097	-0.018	-0.018	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.784	-0.934	36.014	-0.028	-0.028	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.821	0.915	33.663	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.758	-0.876	32.368	-0.030	-0.030	0.000	0.000	0.000	0.000
119	A	120	ILE	0	0.017	0.022	31.191	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	121	ALA	0	-0.022	-0.001	30.873	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	122	GLU	-1	-0.804	-0.919	28.648	-0.006	-0.006	0.000	0.000	0.000	0.000
122	A	123	LEU	0	0.027	0.015	26.316	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	124	THR	0	-0.010	-0.021	26.077	-0.014	-0.014	0.000	0.000	0.000	0.000
124	A	125	LEU	0	-0.016	0.003	24.492	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	126	ALA	0	0.026	0.010	22.532	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	127	VAL	0	0.025	0.012	21.341	-0.014	-0.014	0.000	0.000	0.000	0.000
127	A	128	SER	0	-0.029	-0.019	21.411	-0.021	-0.021	0.000	0.000	0.000	0.000
128	A	129	ALA	0	0.007	0.006	19.562	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	130	ILE	0	-0.046	0.004	14.515	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	131	ASN	0	0.030	0.003	16.377	-0.070	-0.070	0.000	0.000	0.000	0.000
131	A	132	ALA	0	0.007	0.011	17.438	-0.030	-0.030	0.000	0.000	0.000	0.000
132	A	133	TRP	0	-0.027	-0.041	12.719	0.016	0.016	0.000	0.000	0.000	0.000
133	A	134	ASN	0	0.019	-0.019	12.502	-0.051	-0.051	0.000	0.000	0.000	0.000
134	A	135	ARG	1	0.879	0.944	12.966	0.111	0.111	0.000	0.000	0.000	0.000
135	A	136	PHE	0	-0.005	0.003	11.687	-0.023	-0.023	0.000	0.000	0.000	0.000
136	A	137	GLY	0	0.020	-0.003	8.853	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	138	VAL	0	-0.001	-0.005	8.437	-0.323	-0.323	0.000	0.000	0.000	0.000
138	A	139	GLY	0	-0.001	0.012	10.315	-0.064	-0.064	0.000	0.000	0.000	0.000
139	A	140	MET	0	-0.067	-0.026	8.682	0.057	0.057	0.000	0.000	0.000	0.000
140	A	141	GLY	0	-0.016	-0.014	6.796	0.148	0.148	0.000	0.000	0.000	0.000
141	A	142	MET	0	-0.064	-0.027	4.190	-1.169	-0.823	0.000	-0.130	-0.216	0.000
142	A	143	GLN	0	-0.051	-0.028	2.248	-0.053	1.331	1.619	-1.274	-1.729	0.001
143	A	144	PRO	0	-0.026	-0.010	1.883	-11.465	-12.154	6.247	-2.954	-2.603	-0.035
144	A	145	GLU	-1	-0.955	-0.963	3.991	-1.705	-1.318	0.000	-0.064	-0.323	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)