FMO DATABASE

FMODB ID: G5731

Calculation Name: 5KUX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5KUX

Chain ID: A

ChEMBL ID:

UniProt ID:

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	92
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-505065.910978
FMO2-HF: Nuclear repulsion	469467.974378
FMO2-HF: Total energy	-35597.9366
FMO2-MP2: Total energy	-35702.349021

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:GLY)

Summations of interaction energy for fragment #1(A:4:GLY)

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.
-13.943	-12.193	12.757	-7.8	-6.706	-0.086

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.007

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	VAL	0	0.002	0.006	3.793	0.297	1.309	0.003	-0.472	-0.543	0.002
4	A	7	ASN	0	-0.069	-0.051	5.928	0.108	0.108	0.000	0.000	0.000	0.000
5	A	8	VAL	0	0.032	0.016	9.641	-0.084	-0.084	0.000	0.000	0.000	0.000
6	A	9	PRO	0	-0.025	0.004	11.913	0.076	0.076	0.000	0.000	0.000	0.000
7	A	10	ASN	0	0.062	0.007	14.611	0.054	0.054	0.000	0.000	0.000	0.000
8	A	11	CYS	0	-0.003	0.019	15.995	-0.036	-0.036	0.000	0.000	0.000	0.000
9	A	12	ASN	0	0.072	0.050	17.455	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	13	THR	0	0.014	0.011	18.269	0.007	0.007	0.000	0.000	0.000	0.000
11	A	14	THR	0	0.076	0.020	20.940	0.004	0.004	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.958	0.998	12.914	0.524	0.524	0.000	0.000	0.000	0.000
13	A	16	TYR	0	-0.005	-0.035	12.158	0.038	0.038	0.000	0.000	0.000	0.000
14	A	17	GLN	0	-0.024	-0.018	18.070	0.021	0.021	0.000	0.000	0.000	0.000
15	A	18	GLN	0	-0.047	-0.014	21.048	0.021	0.021	0.000	0.000	0.000	0.000
16	A	19	LEU	0	0.018	0.003	15.180	0.007	0.007	0.000	0.000	0.000	0.000
17	A	20	ALA	0	0.028	0.025	19.444	0.016	0.016	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.943	0.963	20.969	0.105	0.105	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.011	0.001	21.731	0.008	0.008	0.000	0.000	0.000	0.000
20	A	23	ALA	0	0.007	0.006	20.086	0.008	0.008	0.000	0.000	0.000	0.000
21	A	24	VAL	0	-0.019	-0.009	22.176	0.013	0.013	0.000	0.000	0.000	0.000
22	A	25	ALA	0	-0.012	0.002	25.417	0.008	0.008	0.000	0.000	0.000	0.000
23	A	26	ILE	0	0.000	-0.006	22.315	0.004	0.004	0.000	0.000	0.000	0.000
24	A	27	TYR	0	0.011	0.009	24.871	0.009	0.009	0.000	0.000	0.000	0.000
25	A	28	ASN	0	0.001	-0.013	26.540	0.011	0.011	0.000	0.000	0.000	0.000
26	A	29	TYR	0	-0.072	-0.025	29.284	0.002	0.002	0.000	0.000	0.000	0.000
27	A	30	HIS	0	-0.020	-0.020	25.781	0.004	0.004	0.000	0.000	0.000	0.000
28	A	31	GLU	-1	-0.928	-0.965	28.555	0.019	0.019	0.000	0.000	0.000	0.000
29	A	32	GLN	0	-0.052	-0.017	31.384	0.004	0.004	0.000	0.000	0.000	0.000
30	A	33	ALA	0	-0.034	0.009	31.130	0.003	0.003	0.000	0.000	0.000	0.000
31	A	34	HIS	0	-0.013	-0.026	33.269	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	35	LEU	0	-0.026	-0.005	27.657	0.002	0.002	0.000	0.000	0.000	0.000
33	A	36	THR	0	-0.001	-0.005	30.624	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	37	PHE	0	-0.042	-0.018	22.508	0.003	0.003	0.000	0.000	0.000	0.000
35	A	38	VAL	0	0.008	0.007	26.732	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	39	GLU	-1	-0.954	-0.988	24.670	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	40	ASN	0	-0.069	-0.042	19.043	0.022	0.022	0.000	0.000	0.000	0.000
38	A	41	LEU	0	0.025	0.014	20.131	0.003	0.003	0.000	0.000	0.000	0.000
39	A	42	ASN	0	0.027	-0.016	15.611	0.003	0.003	0.000	0.000	0.000	0.000
40	A	43	CYS	0	-0.062	-0.020	13.601	-0.015	-0.015	0.000	0.000	0.000	0.000
41	A	44	LYS	1	0.965	0.988	8.513	-0.646	-0.646	0.000	0.000	0.000	0.000
42	A	45	GLU	-1	-0.829	-0.905	7.397	-0.737	-0.737	0.000	0.000	0.000	0.000
43	A	46	GLN	0	0.009	0.000	1.928	2.500	2.791	2.049	-1.022	-1.318	-0.002
44	A	47	LEU	0	-0.067	-0.033	5.023	0.727	0.727	0.000	0.000	0.000	0.000
45	A	48	GLY	0	-0.003	-0.008	5.629	-0.527	-0.527	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.747	-0.878	1.940	-18.071	-18.037	10.660	-6.129	-4.565	-0.086
47	A	50	GLY	0	-0.035	0.002	6.401	0.292	0.292	0.000	0.000	0.000	0.000
48	A	51	ASP	-1	-0.891	-0.928	9.354	-0.611	-0.611	0.000	0.000	0.000	0.000
49	A	52	TYR	0	-0.060	-0.053	12.280	0.049	0.049	0.000	0.000	0.000	0.000
50	A	53	TYR	0	-0.026	-0.005	14.254	0.006	0.006	0.000	0.000	0.000	0.000
51	A	54	TYR	0	-0.005	-0.016	18.749	0.022	0.022	0.000	0.000	0.000	0.000
52	A	55	ILE	0	-0.002	0.002	21.386	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	56	THR	0	0.035	0.023	24.591	0.005	0.005	0.000	0.000	0.000	0.000
54	A	57	LEU	0	-0.044	-0.020	26.429	0.000	0.000	0.000	0.000	0.000	0.000
55	A	58	ALA	0	-0.010	-0.008	29.831	0.002	0.002	0.000	0.000	0.000	0.000
56	A	59	ALA	0	-0.013	-0.008	31.482	0.001	0.001	0.000	0.000	0.000	0.000
57	A	60	THR	0	-0.018	-0.024	33.570	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	61	ASP	-1	-0.845	-0.925	35.667	0.007	0.007	0.000	0.000	0.000	0.000
59	A	62	ASP	-1	-0.924	-0.972	37.405	0.020	0.020	0.000	0.000	0.000	0.000
60	A	63	ALA	0	-0.032	-0.002	39.514	0.000	0.000	0.000	0.000	0.000	0.000
61	A	64	GLY	0	-0.029	-0.018	40.845	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.834	0.937	41.064	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	66	LYS	1	0.967	0.983	37.198	0.014	0.014	0.000	0.000	0.000	0.000
64	A	67	ALA	0	-0.025	-0.010	35.983	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	68	ILE	0	0.010	0.000	32.372	0.000	0.000	0.000	0.000	0.000	0.000
66	A	69	TYR	0	0.026	0.001	29.363	0.003	0.003	0.000	0.000	0.000	0.000
67	A	70	GLU	-1	-0.927	-0.965	27.266	-0.064	-0.064	0.000	0.000	0.000	0.000
68	A	71	ALA	0	-0.005	-0.003	23.235	0.008	0.008	0.000	0.000	0.000	0.000
69	A	72	LYS	1	0.924	0.973	18.005	0.137	0.137	0.000	0.000	0.000	0.000
70	A	73	ILE	0	-0.010	-0.007	16.434	0.021	0.021	0.000	0.000	0.000	0.000
71	A	74	GLY	0	0.048	0.030	14.177	-0.042	-0.042	0.000	0.000	0.000	0.000
72	A	75	VAL	0	-0.003	-0.011	10.914	0.076	0.076	0.000	0.000	0.000	0.000
73	A	76	VAL	0	0.008	0.009	5.577	-0.110	-0.110	0.000	0.000	0.000	0.000
74	A	77	GLU	-1	-0.874	-0.946	7.959	0.044	0.044	0.000	0.000	0.000	0.000
75	A	78	SER	0	-0.093	-0.036	2.875	1.384	1.797	0.045	-0.177	-0.280	0.000
76	A	79	ALA	0	-0.040	-0.023	5.519	0.650	0.650	0.000	0.000	0.000	0.000
77	A	80	GLY	0	-0.009	0.000	7.184	-0.074	-0.074	0.000	0.000	0.000	0.000
78	A	81	TRP	0	-0.043	0.001	9.507	-0.026	-0.026	0.000	0.000	0.000	0.000
79	A	82	THR	0	0.022	-0.006	11.265	-0.127	-0.127	0.000	0.000	0.000	0.000
80	A	83	GLY	0	-0.022	-0.006	14.258	0.040	0.040	0.000	0.000	0.000	0.000
81	A	84	VAL	0	-0.038	-0.021	16.270	-0.038	-0.038	0.000	0.000	0.000	0.000
82	A	85	GLU	-1	-0.941	-0.987	15.671	-0.088	-0.088	0.000	0.000	0.000	0.000
83	A	86	GLU	-1	-0.859	-0.933	20.039	-0.023	-0.023	0.000	0.000	0.000	0.000
84	A	87	PHE	0	-0.008	-0.013	23.536	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	88	LYS	1	0.882	0.954	26.141	0.022	0.022	0.000	0.000	0.000	0.000
86	A	89	LEU	0	-0.010	0.002	29.565	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	90	VAL	0	-0.013	0.002	31.363	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	91	GLY	0	0.011	-0.006	34.184	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	92	SER	0	-0.021	0.001	37.218	0.001	0.001	0.000	0.000	0.000	0.000
90	A	93	LEU	0	-0.025	-0.021	36.571	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	94	GLU	-1	-0.891	-0.936	40.577	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	95	HIS	0	-0.029	-0.011	43.932	0.000	0.000	0.000	0.000	0.000	0.000

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