FMO DATABASE

FMODB ID: JL5Y9

Calculation Name: 2RK9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RK9

Chain ID: A

ChEMBL ID:

UniProt ID: A3UM69

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	121
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-988086.115866
FMO2-HF: Nuclear repulsion	938849.86044
FMO2-HF: Total energy	-49236.255426
FMO2-MP2: Total energy	-49378.689385

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:4:THR)

Summations of interaction energy for fragment #1(A:4: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.
-12.365	-11.072	3.937	-1.997	-3.231	0.01

Interaction energy analysis for fragmet #1(A:4:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.061 / q_NPA : -0.051

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	A	6	ARG	1	0.886	0.941	2.349	-9.418	-8.125	3.937	-1.997	-3.231	0.010
4	A	7	VAL	0	0.021	0.021	6.336	-0.358	-0.358	0.000	0.000	0.000	0.000
5	A	8	VAL	0	0.000	-0.004	9.179	0.100	0.100	0.000	0.000	0.000	0.000
6	A	9	PRO	0	-0.040	-0.029	11.622	-0.048	-0.048	0.000	0.000	0.000	0.000
7	A	10	GLU	-1	-0.842	-0.910	15.336	-0.218	-0.218	0.000	0.000	0.000	0.000
8	A	11	LEU	0	-0.035	-0.035	17.817	0.037	0.037	0.000	0.000	0.000	0.000
9	A	12	TYR	0	0.004	0.009	21.041	-0.022	-0.022	0.000	0.000	0.000	0.000
10	A	13	CYS	0	-0.087	-0.043	23.854	0.024	0.024	0.000	0.000	0.000	0.000
11	A	14	PHE	0	-0.021	-0.022	26.659	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.862	-0.933	29.992	-0.038	-0.038	0.000	0.000	0.000	0.000
13	A	16	ILE	0	0.096	0.037	23.986	0.012	0.012	0.000	0.000	0.000	0.000
14	A	17	ASN	0	0.040	0.018	26.983	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	18	VAL	0	-0.051	-0.001	29.009	0.006	0.006	0.000	0.000	0.000	0.000
16	A	19	SER	0	-0.014	-0.019	25.043	0.014	0.014	0.000	0.000	0.000	0.000
17	A	20	GLN	0	0.031	0.016	23.397	0.008	0.008	0.000	0.000	0.000	0.000
18	A	21	SER	0	0.001	-0.009	24.691	0.002	0.002	0.000	0.000	0.000	0.000
19	A	22	PHE	0	-0.047	-0.009	24.890	0.011	0.011	0.000	0.000	0.000	0.000
20	A	23	PHE	0	0.024	-0.010	19.247	0.015	0.015	0.000	0.000	0.000	0.000
21	A	24	VAL	0	-0.014	0.012	22.178	0.010	0.010	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.932	-0.967	23.674	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	26	VAL	0	-0.127	-0.057	26.633	0.010	0.010	0.000	0.000	0.000	0.000
24	A	27	LEU	0	-0.102	-0.057	21.574	0.017	0.017	0.000	0.000	0.000	0.000
25	A	28	GLY	0	0.001	0.018	21.839	0.021	0.021	0.000	0.000	0.000	0.000
26	A	29	PHE	0	-0.046	-0.031	16.296	0.009	0.009	0.000	0.000	0.000	0.000
27	A	30	GLU	-1	-0.932	-0.968	17.520	-0.181	-0.181	0.000	0.000	0.000	0.000
28	A	31	VAL	0	-0.020	-0.013	17.526	-0.018	-0.018	0.000	0.000	0.000	0.000
29	A	32	LYS	1	0.879	0.945	10.719	0.690	0.690	0.000	0.000	0.000	0.000
30	A	33	TYR	0	-0.067	-0.046	13.441	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.878	-0.947	18.857	-0.163	-0.163	0.000	0.000	0.000	0.000
32	A	35	ARG	1	0.843	0.921	17.388	0.333	0.333	0.000	0.000	0.000	0.000
33	A	36	PRO	0	0.018	-0.002	23.213	0.014	0.014	0.000	0.000	0.000	0.000
34	A	37	ASP	-1	-0.976	-0.989	26.622	-0.182	-0.182	0.000	0.000	0.000	0.000
35	A	38	GLU	-1	-0.887	-0.921	22.760	-0.260	-0.260	0.000	0.000	0.000	0.000
36	A	39	GLU	-1	-0.951	-0.969	25.772	-0.078	-0.078	0.000	0.000	0.000	0.000
37	A	40	PHE	0	0.010	0.017	16.504	-0.013	-0.013	0.000	0.000	0.000	0.000
38	A	41	VAL	0	-0.001	-0.016	20.051	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	42	TYR	0	-0.071	-0.060	9.967	-0.016	-0.016	0.000	0.000	0.000	0.000
40	A	43	LEU	0	0.002	-0.012	16.045	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	44	THR	0	-0.031	-0.044	11.448	0.002	0.002	0.000	0.000	0.000	0.000
42	A	45	LEU	0	0.030	0.024	13.616	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	46	ASP	-1	-0.943	-0.975	13.651	0.245	0.245	0.000	0.000	0.000	0.000
44	A	47	GLY	0	-0.063	-0.029	9.689	0.093	0.093	0.000	0.000	0.000	0.000
45	A	48	VAL	0	-0.084	-0.031	8.593	0.048	0.048	0.000	0.000	0.000	0.000
46	A	49	ASP	-1	-0.791	-0.865	9.429	-0.606	-0.606	0.000	0.000	0.000	0.000
47	A	50	VAL	0	-0.036	-0.012	11.660	0.108	0.108	0.000	0.000	0.000	0.000
48	A	51	MET	0	-0.042	-0.008	13.467	-0.094	-0.094	0.000	0.000	0.000	0.000
49	A	52	LEU	0	-0.031	-0.016	16.942	0.055	0.055	0.000	0.000	0.000	0.000
50	A	53	GLU	-1	-0.843	-0.928	20.754	-0.200	-0.200	0.000	0.000	0.000	0.000
51	A	54	GLY	0	-0.008	0.007	23.184	0.027	0.027	0.000	0.000	0.000	0.000
52	A	55	ILE	0	-0.042	-0.015	26.900	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	67	LEU	0	-0.059	-0.052	30.230	0.000	0.000	0.000	0.000	0.000	0.000
54	A	68	GLU	-1	-0.944	-0.962	32.767	0.069	0.069	0.000	0.000	0.000	0.000
55	A	69	PHE	0	-0.034	0.022	29.732	0.001	0.001	0.000	0.000	0.000	0.000
56	A	70	PRO	0	-0.038	-0.016	28.480	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	71	LEU	0	0.026	-0.008	26.911	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	72	GLY	0	0.004	-0.013	24.269	0.000	0.000	0.000	0.000	0.000	0.000
59	A	73	SER	0	-0.007	0.001	24.407	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	74	GLY	0	0.018	0.003	25.165	0.007	0.007	0.000	0.000	0.000	0.000
61	A	75	VAL	0	0.001	0.014	19.281	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	76	ASN	0	-0.027	-0.010	17.787	0.026	0.026	0.000	0.000	0.000	0.000
63	A	77	PHE	0	-0.024	-0.019	15.135	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	78	GLN	0	0.039	0.035	10.226	0.078	0.078	0.000	0.000	0.000	0.000
65	A	79	TRP	0	-0.018	-0.024	10.520	0.058	0.058	0.000	0.000	0.000	0.000
66	A	80	ASP	-1	-0.810	-0.893	6.132	-1.673	-1.673	0.000	0.000	0.000	0.000
67	A	81	VAL	0	-0.070	-0.040	8.589	0.532	0.532	0.000	0.000	0.000	0.000
68	A	82	ILE	0	-0.016	-0.023	6.267	-0.279	-0.279	0.000	0.000	0.000	0.000
69	A	83	ASP	-1	-0.928	-0.974	8.700	0.011	0.011	0.000	0.000	0.000	0.000
70	A	84	ILE	0	0.029	0.018	12.380	0.075	0.075	0.000	0.000	0.000	0.000
71	A	85	GLU	-1	-0.879	-0.934	14.125	-0.121	-0.121	0.000	0.000	0.000	0.000
72	A	86	PRO	0	-0.016	-0.017	15.306	0.026	0.026	0.000	0.000	0.000	0.000
73	A	87	LEU	0	0.046	0.043	14.535	0.030	0.030	0.000	0.000	0.000	0.000
74	A	88	TYR	0	0.057	0.026	17.440	0.019	0.019	0.000	0.000	0.000	0.000
75	A	89	GLN	0	-0.060	-0.037	19.772	0.029	0.029	0.000	0.000	0.000	0.000
76	A	90	ARG	1	0.987	1.006	19.429	-0.208	-0.208	0.000	0.000	0.000	0.000
77	A	91	VAL	0	-0.007	-0.001	20.282	0.015	0.015	0.000	0.000	0.000	0.000
78	A	92	ASN	0	-0.066	-0.057	22.981	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	93	GLU	-1	-0.976	-0.982	25.279	0.033	0.033	0.000	0.000	0.000	0.000
80	A	94	SER	0	-0.133	-0.070	24.498	0.011	0.011	0.000	0.000	0.000	0.000
81	A	95	ALA	0	-0.031	-0.025	25.906	0.005	0.005	0.000	0.000	0.000	0.000
82	A	96	ALA	0	0.075	0.041	26.741	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	97	ASP	-1	-0.957	-0.975	28.006	0.019	0.019	0.000	0.000	0.000	0.000
84	A	98	SER	0	-0.053	-0.023	25.200	0.007	0.007	0.000	0.000	0.000	0.000
85	A	99	ILE	0	-0.046	-0.020	23.636	0.004	0.004	0.000	0.000	0.000	0.000
86	A	100	TYR	0	-0.033	-0.015	23.807	0.000	0.000	0.000	0.000	0.000	0.000
87	A	101	LEU	0	-0.022	-0.008	20.831	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	102	ALA	0	0.008	-0.001	22.652	0.002	0.002	0.000	0.000	0.000	0.000
89	A	103	LEU	0	-0.032	-0.017	17.665	-0.024	-0.024	0.000	0.000	0.000	0.000
90	A	104	GLU	-1	-0.931	-0.957	19.696	-0.249	-0.249	0.000	0.000	0.000	0.000
91	A	105	SER	0	-0.038	-0.035	18.371	-0.054	-0.054	0.000	0.000	0.000	0.000
92	A	106	LYS	1	0.987	1.008	17.526	0.357	0.357	0.000	0.000	0.000	0.000
93	A	107	SER	0	0.006	0.006	17.184	-0.093	-0.093	0.000	0.000	0.000	0.000
94	A	108	TYR	0	0.045	0.034	16.878	0.049	0.049	0.000	0.000	0.000	0.000
95	A	109	GLN	0	-0.052	-0.035	19.088	-0.029	-0.029	0.000	0.000	0.000	0.000
96	A	110	CYS	0	-0.029	-0.015	16.242	-0.050	-0.050	0.000	0.000	0.000	0.000
97	A	111	GLY	0	0.019	0.023	18.775	-0.020	-0.020	0.000	0.000	0.000	0.000
98	A	112	ASP	-1	-0.913	-0.951	21.472	-0.443	-0.443	0.000	0.000	0.000	0.000
99	A	113	SER	0	-0.042	-0.022	18.329	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	114	ILE	0	-0.018	-0.017	18.889	0.022	0.022	0.000	0.000	0.000	0.000
101	A	115	ALA	0	-0.004	0.015	14.197	-0.055	-0.055	0.000	0.000	0.000	0.000
102	A	116	THR	0	-0.021	-0.056	14.863	0.089	0.089	0.000	0.000	0.000	0.000
103	A	117	GLN	0	-0.019	-0.018	10.621	0.067	0.067	0.000	0.000	0.000	0.000
104	A	118	LYS	1	0.889	0.952	13.849	0.481	0.481	0.000	0.000	0.000	0.000
105	A	119	GLN	0	-0.013	-0.019	14.261	0.023	0.023	0.000	0.000	0.000	0.000
106	A	120	PHE	0	0.045	0.025	16.437	0.020	0.020	0.000	0.000	0.000	0.000
107	A	121	MET	0	-0.006	0.002	18.126	0.014	0.014	0.000	0.000	0.000	0.000
108	A	122	VAL	0	-0.013	0.003	20.326	0.004	0.004	0.000	0.000	0.000	0.000
109	A	123	GLN	0	0.010	0.016	21.806	0.007	0.007	0.000	0.000	0.000	0.000
110	A	124	THR	0	-0.026	-0.018	21.478	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	125	PRO	0	0.024	-0.013	24.418	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	126	ASP	-1	-0.937	-0.962	25.820	0.185	0.185	0.000	0.000	0.000	0.000
113	A	127	GLY	0	-0.006	-0.014	26.742	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	128	TYR	0	-0.010	0.011	21.493	-0.010	-0.010	0.000	0.000	0.000	0.000
115	A	129	LEU	0	0.041	0.023	21.713	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	130	PHE	0	-0.030	-0.012	15.671	0.022	0.022	0.000	0.000	0.000	0.000
117	A	131	ARG	1	0.970	0.988	15.756	0.204	0.204	0.000	0.000	0.000	0.000
118	A	132	PHE	0	-0.019	0.003	13.436	-0.018	-0.018	0.000	0.000	0.000	0.000
119	A	133	CYS	0	-0.009	-0.009	10.963	-0.040	-0.040	0.000	0.000	0.000	0.000
120	A	134	GLN	0	0.048	0.019	8.551	0.209	0.209	0.000	0.000	0.000	0.000
121	A	135	ASP	-1	-0.892	-0.924	8.228	-1.655	-1.655	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:THR)