FMO DATABASE

FMODB ID: 391ZL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-988191.536301
FMO2-HF: Nuclear repulsion	938954.740057
FMO2-HF: Total energy	-49236.796244
FMO2-MP2: Total energy	-49379.225056

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.
-16.487	-17.057	7.095	-2.576	-3.95	0.017

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 : -0.049 / q_NPA : -0.041

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	0.859	0.916	2.119	-13.304	-13.874	7.095	-2.576	-3.950	0.017
4	A	7	VAL	0	0.024	0.022	6.336	-0.351	-0.351	0.000	0.000	0.000	0.000
5	A	8	VAL	0	-0.001	-0.004	9.125	0.108	0.108	0.000	0.000	0.000	0.000
6	A	9	PRO	0	-0.025	-0.019	11.618	-0.042	-0.042	0.000	0.000	0.000	0.000
7	A	10	GLU	-1	-0.770	-0.835	15.330	-0.256	-0.256	0.000	0.000	0.000	0.000
8	A	11	LEU	0	-0.013	-0.024	17.818	0.039	0.039	0.000	0.000	0.000	0.000
9	A	12	TYR	0	0.014	0.012	21.039	-0.018	-0.018	0.000	0.000	0.000	0.000
10	A	13	CYS	0	-0.094	-0.041	23.845	0.025	0.025	0.000	0.000	0.000	0.000
11	A	14	PHE	0	-0.019	-0.026	26.659	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.843	-0.922	29.979	-0.044	-0.044	0.000	0.000	0.000	0.000
13	A	16	ILE	0	0.079	0.035	23.931	0.012	0.012	0.000	0.000	0.000	0.000
14	A	17	ASN	0	0.032	0.021	26.988	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	18	VAL	0	-0.049	-0.005	29.013	0.006	0.006	0.000	0.000	0.000	0.000
16	A	19	SER	0	-0.027	-0.023	25.156	0.015	0.015	0.000	0.000	0.000	0.000
17	A	20	GLN	0	-0.010	-0.012	23.504	0.015	0.015	0.000	0.000	0.000	0.000
18	A	21	SER	0	-0.001	-0.017	24.692	0.002	0.002	0.000	0.000	0.000	0.000
19	A	22	PHE	0	-0.058	-0.014	24.885	0.012	0.012	0.000	0.000	0.000	0.000
20	A	23	PHE	0	0.026	-0.006	19.068	0.016	0.016	0.000	0.000	0.000	0.000
21	A	24	VAL	0	-0.013	0.010	22.084	0.010	0.010	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.925	-0.965	23.673	-0.016	-0.016	0.000	0.000	0.000	0.000
23	A	26	VAL	0	-0.125	-0.059	26.632	0.011	0.011	0.000	0.000	0.000	0.000
24	A	27	LEU	0	-0.103	-0.055	21.611	0.018	0.018	0.000	0.000	0.000	0.000
25	A	28	GLY	0	0.003	0.019	21.827	0.021	0.021	0.000	0.000	0.000	0.000
26	A	29	PHE	0	-0.045	-0.031	15.935	0.010	0.010	0.000	0.000	0.000	0.000
27	A	30	GLU	-1	-0.936	-0.968	17.472	-0.186	-0.186	0.000	0.000	0.000	0.000
28	A	31	VAL	0	-0.019	-0.016	17.533	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	32	LYS	1	0.801	0.897	10.039	0.684	0.684	0.000	0.000	0.000	0.000
30	A	33	TYR	0	-0.064	-0.043	13.789	-0.017	-0.017	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.857	-0.929	18.896	-0.167	-0.167	0.000	0.000	0.000	0.000
32	A	35	ARG	1	0.790	0.875	18.092	0.316	0.316	0.000	0.000	0.000	0.000
33	A	36	PRO	0	0.023	0.001	23.236	0.016	0.016	0.000	0.000	0.000	0.000
34	A	37	ASP	-1	-0.976	-0.974	26.650	-0.197	-0.197	0.000	0.000	0.000	0.000
35	A	38	GLU	-1	-0.847	-0.893	22.669	-0.277	-0.277	0.000	0.000	0.000	0.000
36	A	39	GLU	-1	-0.951	-0.977	25.777	-0.083	-0.083	0.000	0.000	0.000	0.000
37	A	40	PHE	0	0.039	0.032	16.434	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	41	VAL	0	-0.010	-0.023	20.138	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	42	TYR	0	-0.067	-0.048	10.040	-0.022	-0.022	0.000	0.000	0.000	0.000
40	A	43	LEU	0	0.008	-0.006	16.068	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	44	THR	0	-0.024	-0.042	11.488	0.002	0.002	0.000	0.000	0.000	0.000
42	A	45	LEU	0	0.023	0.020	13.620	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	46	ASP	-1	-0.936	-0.972	13.639	0.240	0.240	0.000	0.000	0.000	0.000
44	A	47	GLY	0	-0.052	-0.023	9.683	0.100	0.100	0.000	0.000	0.000	0.000
45	A	48	VAL	0	-0.077	-0.028	8.586	0.033	0.033	0.000	0.000	0.000	0.000
46	A	49	ASP	-1	-0.738	-0.835	9.584	-0.717	-0.717	0.000	0.000	0.000	0.000
47	A	50	VAL	0	-0.028	-0.009	11.658	0.107	0.107	0.000	0.000	0.000	0.000
48	A	51	MET	0	-0.030	-0.004	13.528	-0.091	-0.091	0.000	0.000	0.000	0.000
49	A	52	LEU	0	-0.024	-0.012	16.962	0.056	0.056	0.000	0.000	0.000	0.000
50	A	53	GLU	-1	-0.845	-0.930	20.759	-0.218	-0.218	0.000	0.000	0.000	0.000
51	A	54	GLY	0	0.005	0.012	23.193	0.027	0.027	0.000	0.000	0.000	0.000
52	A	55	ILE	0	-0.061	-0.023	26.907	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	67	LEU	0	-0.032	-0.020	30.062	0.004	0.004	0.000	0.000	0.000	0.000
54	A	68	GLU	-1	-0.971	-0.994	32.720	0.068	0.068	0.000	0.000	0.000	0.000
55	A	69	PHE	0	-0.044	0.015	29.614	0.001	0.001	0.000	0.000	0.000	0.000
56	A	70	PRO	0	-0.028	-0.010	28.446	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	71	LEU	0	0.014	-0.012	26.968	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	72	GLY	0	0.011	-0.010	24.269	0.000	0.000	0.000	0.000	0.000	0.000
59	A	73	SER	0	-0.007	0.003	24.397	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	74	GLY	0	0.015	0.000	25.160	0.007	0.007	0.000	0.000	0.000	0.000
61	A	75	VAL	0	-0.015	0.005	19.356	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	76	ASN	0	-0.026	-0.023	17.703	0.032	0.032	0.000	0.000	0.000	0.000
63	A	77	PHE	0	-0.023	-0.016	15.153	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	78	GLN	0	0.032	0.036	9.919	0.084	0.084	0.000	0.000	0.000	0.000
65	A	79	TRP	0	-0.019	-0.025	10.205	0.052	0.052	0.000	0.000	0.000	0.000
66	A	80	ASP	-1	-0.797	-0.890	6.159	-1.670	-1.670	0.000	0.000	0.000	0.000
67	A	81	VAL	0	-0.068	-0.037	8.570	0.519	0.519	0.000	0.000	0.000	0.000
68	A	82	ILE	0	-0.014	-0.016	6.484	-0.255	-0.255	0.000	0.000	0.000	0.000
69	A	83	ASP	-1	-0.919	-0.964	9.041	0.029	0.029	0.000	0.000	0.000	0.000
70	A	84	ILE	0	0.033	0.015	12.771	0.077	0.077	0.000	0.000	0.000	0.000
71	A	85	GLU	-1	-0.850	-0.916	14.520	-0.144	-0.144	0.000	0.000	0.000	0.000
72	A	86	PRO	0	-0.001	-0.007	15.655	0.024	0.024	0.000	0.000	0.000	0.000
73	A	87	LEU	0	0.041	0.037	14.362	0.031	0.031	0.000	0.000	0.000	0.000
74	A	88	TYR	0	0.044	0.025	17.742	0.018	0.018	0.000	0.000	0.000	0.000
75	A	89	GLN	0	-0.050	-0.038	20.158	0.026	0.026	0.000	0.000	0.000	0.000
76	A	90	ARG	1	0.996	1.009	19.145	-0.216	-0.216	0.000	0.000	0.000	0.000
77	A	91	VAL	0	0.000	0.004	20.239	0.015	0.015	0.000	0.000	0.000	0.000
78	A	92	ASN	0	-0.058	-0.047	22.978	0.000	0.000	0.000	0.000	0.000	0.000
79	A	93	GLU	-1	-0.980	-0.980	25.480	0.039	0.039	0.000	0.000	0.000	0.000
80	A	94	SER	0	-0.134	-0.075	24.496	0.012	0.012	0.000	0.000	0.000	0.000
81	A	95	ALA	0	-0.034	-0.025	25.921	0.005	0.005	0.000	0.000	0.000	0.000
82	A	96	ALA	0	0.070	0.040	26.735	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	97	ASP	-1	-0.954	-0.973	28.130	0.020	0.020	0.000	0.000	0.000	0.000
84	A	98	SER	0	-0.044	-0.019	25.268	0.006	0.006	0.000	0.000	0.000	0.000
85	A	99	ILE	0	-0.063	-0.025	23.559	0.003	0.003	0.000	0.000	0.000	0.000
86	A	100	TYR	0	-0.021	-0.011	23.740	0.000	0.000	0.000	0.000	0.000	0.000
87	A	101	LEU	0	-0.015	-0.007	20.973	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	102	ALA	0	0.003	-0.001	22.561	0.001	0.001	0.000	0.000	0.000	0.000
89	A	103	LEU	0	-0.031	-0.020	17.918	-0.025	-0.025	0.000	0.000	0.000	0.000
90	A	104	GLU	-1	-0.845	-0.897	19.519	-0.269	-0.269	0.000	0.000	0.000	0.000
91	A	105	SER	0	-0.036	-0.041	18.294	-0.043	-0.043	0.000	0.000	0.000	0.000
92	A	106	LYS	1	0.834	0.918	17.425	0.353	0.353	0.000	0.000	0.000	0.000
93	A	107	SER	0	0.000	-0.035	17.126	-0.062	-0.062	0.000	0.000	0.000	0.000
94	A	108	TYR	0	0.044	0.030	16.956	0.044	0.044	0.000	0.000	0.000	0.000
95	A	109	GLN	0	-0.053	-0.039	19.062	-0.028	-0.028	0.000	0.000	0.000	0.000
96	A	110	CYS	0	-0.026	-0.015	16.262	-0.054	-0.054	0.000	0.000	0.000	0.000
97	A	111	GLY	0	0.016	0.025	18.833	-0.026	-0.026	0.000	0.000	0.000	0.000
98	A	112	ASP	-1	-0.908	-0.949	21.554	-0.441	-0.441	0.000	0.000	0.000	0.000
99	A	113	SER	0	-0.047	-0.026	18.394	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	114	ILE	0	-0.029	-0.019	19.011	0.020	0.020	0.000	0.000	0.000	0.000
101	A	115	ALA	0	0.010	0.021	14.169	-0.054	-0.054	0.000	0.000	0.000	0.000
102	A	116	THR	0	0.010	-0.006	14.800	0.101	0.101	0.000	0.000	0.000	0.000
103	A	117	GLN	0	-0.008	0.001	10.797	0.043	0.043	0.000	0.000	0.000	0.000
104	A	118	LYS	1	0.856	0.935	13.861	0.440	0.440	0.000	0.000	0.000	0.000
105	A	119	GLN	0	0.006	-0.005	14.169	0.007	0.007	0.000	0.000	0.000	0.000
106	A	120	PHE	0	0.039	0.019	16.347	0.023	0.023	0.000	0.000	0.000	0.000
107	A	121	MET	0	-0.007	0.003	18.039	0.005	0.005	0.000	0.000	0.000	0.000
108	A	122	VAL	0	-0.016	0.003	20.291	0.005	0.005	0.000	0.000	0.000	0.000
109	A	123	GLN	0	0.004	0.014	21.806	0.002	0.002	0.000	0.000	0.000	0.000
110	A	124	THR	0	-0.049	-0.045	21.545	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	125	PRO	0	0.017	-0.014	24.412	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	126	ASP	-1	-0.871	-0.921	25.095	0.193	0.193	0.000	0.000	0.000	0.000
113	A	127	GLY	0	-0.015	-0.019	26.706	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	128	TYR	0	-0.013	0.011	21.484	-0.013	-0.013	0.000	0.000	0.000	0.000
115	A	129	LEU	0	0.035	0.021	21.713	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	130	PHE	0	-0.029	-0.014	15.720	0.022	0.022	0.000	0.000	0.000	0.000
117	A	131	ARG	1	0.892	0.921	15.651	0.225	0.225	0.000	0.000	0.000	0.000
118	A	132	PHE	0	-0.014	0.004	13.512	-0.024	-0.024	0.000	0.000	0.000	0.000
119	A	133	CYS	0	-0.013	-0.013	11.067	-0.031	-0.031	0.000	0.000	0.000	0.000
120	A	134	GLN	0	0.029	0.003	9.016	0.172	0.172	0.000	0.000	0.000	0.000
121	A	135	ASP	-1	-0.913	-0.943	8.420	-1.605	-1.605	0.000	0.000	0.000	0.000

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