FMO DATABASE

FMODB ID: LZKG9

Calculation Name: 2RK9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-989512.971519
FMO2-HF: Nuclear repulsion	940276.039259
FMO2-HF: Total energy	-49236.932259
FMO2-MP2: Total energy	-49379.35078

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.
-18.544	-23.918	13.514	-3.895	-4.245	0.023

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 : -0.054 / q_NPA : -0.025

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	6	ARG	1	0.860	0.907	1.934	-17.174	-22.548	13.514	-3.895	-4.245	0.023
4	A	7	VAL	0	0.010	0.015	6.497	-0.335	-0.335	0.000	0.000	0.000	0.000
5	A	8	VAL	0	0.003	0.005	9.234	0.160	0.160	0.000	0.000	0.000	0.000
6	A	9	PRO	0	-0.029	-0.020	11.848	-0.082	-0.082	0.000	0.000	0.000	0.000
7	A	10	GLU	-1	-0.763	-0.831	15.658	-0.133	-0.133	0.000	0.000	0.000	0.000
8	A	11	LEU	0	-0.020	-0.014	18.000	0.022	0.022	0.000	0.000	0.000	0.000
9	A	12	TYR	0	0.027	0.021	21.323	-0.013	-0.013	0.000	0.000	0.000	0.000
10	A	13	CYS	0	-0.090	-0.043	23.949	0.023	0.023	0.000	0.000	0.000	0.000
11	A	14	PHE	0	-0.037	-0.037	26.843	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.814	-0.898	29.795	0.012	0.012	0.000	0.000	0.000	0.000
13	A	16	ILE	0	0.072	0.053	23.628	0.016	0.016	0.000	0.000	0.000	0.000
14	A	17	ASN	0	0.002	0.004	26.728	0.001	0.001	0.000	0.000	0.000	0.000
15	A	18	VAL	0	-0.041	-0.008	28.633	0.009	0.009	0.000	0.000	0.000	0.000
16	A	19	SER	0	-0.022	-0.026	25.277	0.016	0.016	0.000	0.000	0.000	0.000
17	A	20	GLN	0	-0.013	-0.016	23.346	0.019	0.019	0.000	0.000	0.000	0.000
18	A	21	SER	0	-0.013	-0.023	24.669	0.008	0.008	0.000	0.000	0.000	0.000
19	A	22	PHE	0	-0.061	-0.027	25.224	0.013	0.013	0.000	0.000	0.000	0.000
20	A	23	PHE	0	0.020	-0.010	19.019	0.018	0.018	0.000	0.000	0.000	0.000
21	A	24	VAL	0	-0.011	0.009	22.133	0.020	0.020	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.925	-0.967	23.649	0.074	0.074	0.000	0.000	0.000	0.000
23	A	26	VAL	0	-0.130	-0.063	26.296	0.003	0.003	0.000	0.000	0.000	0.000
24	A	27	LEU	0	-0.082	-0.035	21.953	0.019	0.019	0.000	0.000	0.000	0.000
25	A	28	GLY	0	0.002	0.013	21.657	0.032	0.032	0.000	0.000	0.000	0.000
26	A	29	PHE	0	-0.051	-0.028	15.891	0.020	0.020	0.000	0.000	0.000	0.000
27	A	30	GLU	-1	-0.940	-0.966	17.045	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	31	VAL	0	-0.002	-0.013	17.248	0.003	0.003	0.000	0.000	0.000	0.000
29	A	32	LYS	1	0.793	0.887	9.658	0.226	0.226	0.000	0.000	0.000	0.000
30	A	33	TYR	0	-0.061	-0.037	13.686	-0.039	-0.039	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.835	-0.917	18.441	-0.048	-0.048	0.000	0.000	0.000	0.000
32	A	35	ARG	1	0.750	0.849	18.819	0.181	0.181	0.000	0.000	0.000	0.000
33	A	36	PRO	0	0.033	0.010	23.409	0.011	0.011	0.000	0.000	0.000	0.000
34	A	37	ASP	-1	-0.967	-0.974	26.526	-0.124	-0.124	0.000	0.000	0.000	0.000
35	A	38	GLU	-1	-0.865	-0.904	23.267	-0.183	-0.183	0.000	0.000	0.000	0.000
36	A	39	GLU	-1	-0.947	-0.974	25.953	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	40	PHE	0	0.029	0.032	16.428	0.001	0.001	0.000	0.000	0.000	0.000
38	A	41	VAL	0	-0.001	-0.017	20.263	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	42	TYR	0	-0.052	-0.040	9.960	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	43	LEU	0	-0.012	-0.015	15.952	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	44	THR	0	-0.023	-0.039	11.306	0.047	0.047	0.000	0.000	0.000	0.000
42	A	45	LEU	0	0.026	0.028	13.822	-0.043	-0.043	0.000	0.000	0.000	0.000
43	A	46	ASP	-1	-0.928	-0.966	13.674	0.526	0.526	0.000	0.000	0.000	0.000
44	A	47	GLY	0	-0.036	-0.015	9.744	0.115	0.115	0.000	0.000	0.000	0.000
45	A	48	VAL	0	-0.096	-0.048	8.905	0.200	0.200	0.000	0.000	0.000	0.000
46	A	49	ASP	-1	-0.759	-0.837	9.371	-0.268	-0.268	0.000	0.000	0.000	0.000
47	A	50	VAL	0	-0.042	-0.019	11.467	0.091	0.091	0.000	0.000	0.000	0.000
48	A	51	MET	0	-0.013	0.000	13.478	-0.091	-0.091	0.000	0.000	0.000	0.000
49	A	52	LEU	0	-0.017	-0.010	16.907	0.038	0.038	0.000	0.000	0.000	0.000
50	A	53	GLU	-1	-0.838	-0.926	20.712	-0.126	-0.126	0.000	0.000	0.000	0.000
51	A	54	GLY	0	0.064	0.032	23.021	0.021	0.021	0.000	0.000	0.000	0.000
52	A	55	ILE	0	-0.100	-0.040	26.836	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	67	LEU	0	-0.018	-0.011	29.921	0.004	0.004	0.000	0.000	0.000	0.000
54	A	68	GLU	-1	-0.982	-0.999	32.834	0.078	0.078	0.000	0.000	0.000	0.000
55	A	69	PHE	0	-0.037	0.006	29.699	0.005	0.005	0.000	0.000	0.000	0.000
56	A	70	PRO	0	-0.046	-0.010	28.237	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	71	LEU	0	0.014	-0.018	27.082	0.002	0.002	0.000	0.000	0.000	0.000
58	A	72	GLY	0	0.008	-0.005	24.325	0.003	0.003	0.000	0.000	0.000	0.000
59	A	73	SER	0	-0.020	-0.012	24.663	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	74	GLY	0	0.028	0.014	25.666	0.006	0.006	0.000	0.000	0.000	0.000
61	A	75	VAL	0	-0.031	-0.002	19.759	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	76	ASN	0	-0.043	-0.032	18.142	0.011	0.011	0.000	0.000	0.000	0.000
63	A	77	PHE	0	-0.018	-0.013	15.128	0.024	0.024	0.000	0.000	0.000	0.000
64	A	78	GLN	0	0.006	0.010	9.584	0.058	0.058	0.000	0.000	0.000	0.000
65	A	79	TRP	0	-0.007	-0.016	10.146	0.151	0.151	0.000	0.000	0.000	0.000
66	A	80	ASP	-1	-0.789	-0.876	6.465	-1.068	-1.068	0.000	0.000	0.000	0.000
67	A	81	VAL	0	-0.073	-0.043	8.402	0.422	0.422	0.000	0.000	0.000	0.000
68	A	82	ILE	0	-0.013	-0.019	6.146	-0.311	-0.311	0.000	0.000	0.000	0.000
69	A	83	ASP	-1	-0.895	-0.950	8.782	-0.138	-0.138	0.000	0.000	0.000	0.000
70	A	84	ILE	0	0.012	0.011	12.468	0.086	0.086	0.000	0.000	0.000	0.000
71	A	85	GLU	-1	-0.833	-0.896	14.281	-0.196	-0.196	0.000	0.000	0.000	0.000
72	A	86	PRO	0	0.008	-0.016	15.704	0.033	0.033	0.000	0.000	0.000	0.000
73	A	87	LEU	0	0.014	0.025	13.956	0.036	0.036	0.000	0.000	0.000	0.000
74	A	88	TYR	0	0.045	0.024	17.283	0.032	0.032	0.000	0.000	0.000	0.000
75	A	89	GLN	0	-0.071	-0.041	19.825	0.033	0.033	0.000	0.000	0.000	0.000
76	A	90	ARG	1	1.009	1.007	18.739	-0.096	-0.096	0.000	0.000	0.000	0.000
77	A	91	VAL	0	-0.001	0.011	20.255	0.021	0.021	0.000	0.000	0.000	0.000
78	A	92	ASN	0	-0.051	-0.049	22.942	0.010	0.010	0.000	0.000	0.000	0.000
79	A	93	GLU	-1	-0.985	-0.992	24.662	-0.022	-0.022	0.000	0.000	0.000	0.000
80	A	94	SER	0	-0.133	-0.076	24.630	0.014	0.014	0.000	0.000	0.000	0.000
81	A	95	ALA	0	-0.021	-0.011	25.584	0.010	0.010	0.000	0.000	0.000	0.000
82	A	96	ALA	0	0.059	0.036	26.828	0.001	0.001	0.000	0.000	0.000	0.000
83	A	97	ASP	-1	-0.937	-0.966	27.713	0.006	0.006	0.000	0.000	0.000	0.000
84	A	98	SER	0	-0.044	-0.021	25.200	0.007	0.007	0.000	0.000	0.000	0.000
85	A	99	ILE	0	-0.068	-0.032	23.347	0.004	0.004	0.000	0.000	0.000	0.000
86	A	100	TYR	0	0.007	0.008	23.619	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	101	LEU	0	-0.026	-0.012	21.264	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	102	ALA	0	0.021	0.009	22.410	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	103	LEU	0	-0.048	-0.022	17.440	-0.018	-0.018	0.000	0.000	0.000	0.000
90	A	104	GLU	-1	-0.823	-0.889	19.126	-0.234	-0.234	0.000	0.000	0.000	0.000
91	A	105	SER	0	-0.007	-0.038	18.140	-0.041	-0.041	0.000	0.000	0.000	0.000
92	A	106	LYS	1	0.846	0.929	17.252	0.257	0.257	0.000	0.000	0.000	0.000
93	A	107	SER	0	-0.003	-0.010	17.050	-0.088	-0.088	0.000	0.000	0.000	0.000
94	A	108	TYR	0	0.031	0.022	16.975	0.046	0.046	0.000	0.000	0.000	0.000
95	A	109	GLN	0	-0.045	-0.028	18.951	-0.037	-0.037	0.000	0.000	0.000	0.000
96	A	110	CYS	0	-0.022	-0.018	16.413	-0.033	-0.033	0.000	0.000	0.000	0.000
97	A	111	GLY	0	0.014	0.025	18.985	-0.026	-0.026	0.000	0.000	0.000	0.000
98	A	112	ASP	-1	-0.908	-0.951	21.831	-0.382	-0.382	0.000	0.000	0.000	0.000
99	A	113	SER	0	-0.047	-0.024	18.495	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	114	ILE	0	-0.020	-0.011	18.808	0.027	0.027	0.000	0.000	0.000	0.000
101	A	115	ALA	0	0.010	0.019	14.201	-0.058	-0.058	0.000	0.000	0.000	0.000
102	A	116	THR	0	-0.002	-0.032	14.407	0.085	0.085	0.000	0.000	0.000	0.000
103	A	117	GLN	0	-0.022	0.005	10.597	0.016	0.016	0.000	0.000	0.000	0.000
104	A	118	LYS	1	0.871	0.946	13.619	0.472	0.472	0.000	0.000	0.000	0.000
105	A	119	GLN	0	0.006	0.000	13.798	0.013	0.013	0.000	0.000	0.000	0.000
106	A	120	PHE	0	0.019	0.012	16.000	0.020	0.020	0.000	0.000	0.000	0.000
107	A	121	MET	0	-0.011	-0.001	17.787	0.008	0.008	0.000	0.000	0.000	0.000
108	A	122	VAL	0	-0.042	-0.016	20.110	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	123	GLN	0	0.009	0.015	21.897	0.009	0.009	0.000	0.000	0.000	0.000
110	A	124	THR	0	-0.051	-0.049	21.853	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	125	PRO	0	-0.001	-0.021	24.662	-0.010	-0.010	0.000	0.000	0.000	0.000
112	A	126	ASP	-1	-0.823	-0.894	25.345	0.177	0.177	0.000	0.000	0.000	0.000
113	A	127	GLY	0	-0.012	-0.014	26.861	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	128	TYR	0	-0.012	0.010	21.752	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	129	LEU	0	0.020	0.014	21.810	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	130	PHE	0	-0.012	-0.002	15.862	0.037	0.037	0.000	0.000	0.000	0.000
117	A	131	ARG	1	0.879	0.901	15.489	0.135	0.135	0.000	0.000	0.000	0.000
118	A	132	PHE	0	0.026	0.027	13.454	-0.022	-0.022	0.000	0.000	0.000	0.000
119	A	133	CYS	0	-0.022	-0.020	10.936	-0.028	-0.028	0.000	0.000	0.000	0.000
120	A	134	GLN	0	0.000	-0.014	8.988	0.138	0.138	0.000	0.000	0.000	0.000
121	A	135	ASP	-1	-0.929	-0.969	8.047	-1.380	-1.380	0.000	0.000	0.000	0.000

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