FMO DATABASE

FMODB ID: 3JVRL

Calculation Name: 2RK5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RK5

Chain ID: A

ChEMBL ID:

UniProt ID: O68574

Base Structure: X-ray

Registration Date: 2023-09-23

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-600617.553874
FMO2-HF: Nuclear repulsion	566742.256658
FMO2-HF: Total energy	-33875.297215
FMO2-MP2: Total energy	-33975.445784

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:3:GLN)

Summations of interaction energy for fragment #1(A:3:GLN)

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.
-16.928	-12.913	11.212	-4.824	-10.4	0.019

Interaction energy analysis for fragmet #1(A:3:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : -0.001

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	5	ARG	1	0.914	0.961	3.823	-1.200	0.180	-0.022	-0.626	-0.733	0.001
4	A	6	GLU	-1	-0.854	-0.917	6.235	0.466	0.466	0.000	0.000	0.000	0.000
5	A	7	ILE	0	-0.150	-0.088	9.881	-0.012	-0.012	0.000	0.000	0.000	0.000
6	A	8	ALA	0	-0.026	-0.015	12.322	-0.058	-0.058	0.000	0.000	0.000	0.000
7	A	9	ASP	-1	-0.822	-0.902	14.653	0.324	0.324	0.000	0.000	0.000	0.000
8	A	10	ASN	0	-0.031	-0.004	15.031	0.009	0.009	0.000	0.000	0.000	0.000
9	A	11	THR	0	-0.029	-0.017	13.889	0.012	0.012	0.000	0.000	0.000	0.000
10	A	12	TYR	0	0.038	0.020	8.379	0.019	0.019	0.000	0.000	0.000	0.000
11	A	13	ILE	0	-0.084	-0.034	7.199	0.046	0.046	0.000	0.000	0.000	0.000
12	A	14	VAL	0	0.047	0.023	4.143	-0.285	-0.174	-0.001	-0.044	-0.066	0.000
13	A	15	LEU	0	-0.060	-0.030	2.344	-4.903	-4.532	6.196	-2.238	-4.328	0.025
14	A	16	GLY	0	0.014	0.000	4.470	-0.580	-0.396	-0.001	-0.015	-0.168	0.000
15	A	17	THR	0	-0.045	-0.047	4.092	0.856	0.994	0.002	-0.054	-0.085	0.000
16	A	18	MET	0	-0.012	0.031	2.113	-2.799	-1.742	5.017	-1.613	-4.461	-0.006
17	A	19	THR	0	0.055	0.029	3.814	-0.404	-0.030	0.020	-0.107	-0.286	0.000
18	A	20	LEU	0	0.057	0.014	6.155	-0.133	-0.133	0.000	0.000	0.000	0.000
19	A	21	ASN	0	-0.007	0.000	8.783	0.126	0.126	0.000	0.000	0.000	0.000
20	A	22	ASP	-1	-0.883	-0.942	4.083	-5.525	-5.125	0.001	-0.127	-0.273	-0.001
21	A	23	PHE	0	-0.047	-0.046	5.828	0.418	0.418	0.000	0.000	0.000	0.000
22	A	24	ASN	0	0.011	0.004	6.587	0.280	0.280	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.950	-0.960	8.149	-1.018	-1.018	0.000	0.000	0.000	0.000
24	A	26	TYR	0	-0.082	-0.040	5.665	0.437	0.437	0.000	0.000	0.000	0.000
25	A	27	PHE	0	-0.034	-0.033	6.553	0.198	0.198	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.929	-0.944	10.338	0.032	0.032	0.000	0.000	0.000	0.000
27	A	29	THR	0	-0.069	-0.038	11.967	0.051	0.051	0.000	0.000	0.000	0.000
28	A	30	ASP	-1	-0.909	-0.911	13.696	-0.064	-0.064	0.000	0.000	0.000	0.000
29	A	31	LEU	0	-0.025	-0.001	11.375	0.031	0.031	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.913	-0.964	14.183	-0.110	-0.110	0.000	0.000	0.000	0.000
31	A	33	SER	0	-0.028	-0.029	16.052	0.033	0.033	0.000	0.000	0.000	0.000
32	A	34	ASP	-1	-0.857	-0.917	17.167	0.005	0.005	0.000	0.000	0.000	0.000
33	A	35	ASN	0	-0.109	-0.065	18.397	0.020	0.020	0.000	0.000	0.000	0.000
34	A	36	VAL	0	-0.036	-0.004	13.076	0.084	0.084	0.000	0.000	0.000	0.000
35	A	37	ASP	-1	-0.858	-0.916	10.963	-0.157	-0.157	0.000	0.000	0.000	0.000
36	A	38	THR	0	-0.086	-0.043	7.722	-0.255	-0.255	0.000	0.000	0.000	0.000
37	A	39	ILE	0	0.060	0.035	5.824	-0.039	-0.039	0.000	0.000	0.000	0.000
38	A	40	ALA	0	-0.036	-0.017	8.530	-0.131	-0.131	0.000	0.000	0.000	0.000
39	A	41	GLY	0	-0.042	-0.013	10.477	-0.192	-0.192	0.000	0.000	0.000	0.000
40	A	42	PHE	0	0.087	0.041	11.870	-0.083	-0.083	0.000	0.000	0.000	0.000
41	A	43	TYR	0	-0.021	-0.036	12.440	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	44	LEU	0	-0.037	-0.034	14.067	-0.053	-0.053	0.000	0.000	0.000	0.000
43	A	45	THR	0	-0.062	-0.037	16.275	-0.083	-0.083	0.000	0.000	0.000	0.000
44	A	46	GLY	0	0.008	0.018	17.174	-0.051	-0.051	0.000	0.000	0.000	0.000
45	A	47	VAL	0	-0.047	-0.020	17.732	-0.028	-0.028	0.000	0.000	0.000	0.000
46	A	48	GLY	0	-0.005	0.007	19.955	-0.033	-0.033	0.000	0.000	0.000	0.000
47	A	49	THR	0	-0.009	-0.015	20.600	-0.034	-0.034	0.000	0.000	0.000	0.000
48	A	50	ILE	0	-0.053	-0.027	17.953	0.056	0.056	0.000	0.000	0.000	0.000
49	A	51	PRO	0	0.016	0.031	17.092	-0.023	-0.023	0.000	0.000	0.000	0.000
50	A	52	SER	0	0.055	0.009	19.285	0.043	0.043	0.000	0.000	0.000	0.000
51	A	53	GLN	0	-0.058	-0.039	19.267	0.047	0.047	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.948	-0.992	20.423	0.418	0.418	0.000	0.000	0.000	0.000
53	A	55	GLU	-1	-0.960	-0.963	23.030	0.302	0.302	0.000	0.000	0.000	0.000
54	A	56	LYS	1	0.887	0.945	18.657	-0.547	-0.547	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.874	-0.925	18.894	0.354	0.354	0.000	0.000	0.000	0.000
56	A	58	HIS	1	0.798	0.886	17.822	-0.365	-0.365	0.000	0.000	0.000	0.000
57	A	59	PHE	0	0.039	0.026	15.984	-0.030	-0.030	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.897	-0.950	16.873	0.338	0.338	0.000	0.000	0.000	0.000
59	A	61	VAL	0	-0.027	-0.012	15.481	-0.025	-0.025	0.000	0.000	0.000	0.000
60	A	62	GLU	-1	-0.915	-0.954	18.221	0.138	0.138	0.000	0.000	0.000	0.000
61	A	63	SER	0	-0.035	-0.074	16.108	-0.021	-0.021	0.000	0.000	0.000	0.000
62	A	64	ASN	0	-0.007	-0.007	16.233	0.015	0.015	0.000	0.000	0.000	0.000
63	A	65	GLY	0	0.025	0.004	19.190	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	66	LYS	1	0.778	0.901	15.389	-0.046	-0.046	0.000	0.000	0.000	0.000
65	A	67	HIS	0	0.008	0.012	18.339	-0.022	-0.022	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.021	-0.014	12.410	0.033	0.033	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.804	-0.883	15.676	0.405	0.405	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.039	-0.026	11.693	0.090	0.090	0.000	0.000	0.000	0.000
69	A	71	ILE	0	0.000	-0.002	13.491	-0.059	-0.059	0.000	0.000	0.000	0.000
70	A	72	ASN	0	-0.011	0.009	13.336	0.123	0.123	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.959	-0.988	11.531	1.137	1.137	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.912	0.951	11.699	-0.991	-0.991	0.000	0.000	0.000	0.000
73	A	75	VAL	0	0.020	0.007	12.678	0.201	0.201	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.857	0.918	10.903	-1.508	-1.508	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.906	-0.942	15.462	0.512	0.512	0.000	0.000	0.000	0.000
76	A	78	GLY	0	0.068	0.047	17.819	-0.021	-0.021	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.936	0.972	10.745	-1.009	-1.009	0.000	0.000	0.000	0.000
78	A	80	VAL	0	0.062	0.033	11.255	0.043	0.043	0.000	0.000	0.000	0.000
79	A	81	THR	0	-0.085	-0.062	8.932	0.221	0.221	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.922	0.965	7.446	-0.958	-0.958	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.071	0.047	8.307	-0.416	-0.416	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.940	0.980	9.148	-0.500	-0.500	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.006	0.007	8.606	-0.029	-0.029	0.000	0.000	0.000	0.000
84	A	86	LEU	0	-0.017	-0.014	11.737	0.005	0.005	0.000	0.000	0.000	0.000
85	A	87	VAL	0	0.037	0.015	12.889	-0.021	-0.021	0.000	0.000	0.000	0.000
86	A	88	SER	0	-0.007	-0.002	15.850	-0.020	-0.020	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLN)