FMO DATABASE

FMODB ID: 89KYY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-505036.213023
FMO2-HF: Nuclear repulsion	469437.67938
FMO2-HF: Total energy	-35598.533643
FMO2-MP2: Total energy	-35702.934374

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.
-12.916	-12.105	12.121	-6.922	-6.01	-0.074

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 : 0.010 / q_NPA : -0.002

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	VAL	0	0.004	0.009	3.793	0.744	1.686	0.003	-0.423	-0.522	0.002
4	A	7	ASN	0	-0.024	-0.031	5.933	0.148	0.148	0.000	0.000	0.000	0.000
5	A	8	VAL	0	0.011	0.004	9.646	-0.067	-0.067	0.000	0.000	0.000	0.000
6	A	9	PRO	0	-0.043	-0.008	11.913	0.077	0.077	0.000	0.000	0.000	0.000
7	A	10	ASN	0	0.037	0.002	14.614	0.043	0.043	0.000	0.000	0.000	0.000
8	A	11	CYS	0	0.008	0.011	15.975	-0.034	-0.034	0.000	0.000	0.000	0.000
9	A	12	ASN	0	0.072	0.029	17.455	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	13	THR	0	0.021	0.020	18.158	0.006	0.006	0.000	0.000	0.000	0.000
11	A	14	THR	0	0.069	0.014	20.939	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.853	0.942	12.097	0.600	0.600	0.000	0.000	0.000	0.000
13	A	16	TYR	0	0.024	-0.025	11.961	0.030	0.030	0.000	0.000	0.000	0.000
14	A	17	GLN	0	0.002	0.006	18.065	0.017	0.017	0.000	0.000	0.000	0.000
15	A	18	GLN	0	0.031	0.024	21.218	0.021	0.021	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.010	0.004	15.214	0.008	0.008	0.000	0.000	0.000	0.000
17	A	20	ALA	0	0.028	0.023	19.434	0.013	0.013	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.900	0.943	20.969	0.134	0.134	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.041	-0.029	21.517	0.010	0.010	0.000	0.000	0.000	0.000
20	A	23	ALA	0	0.014	0.009	19.920	0.008	0.008	0.000	0.000	0.000	0.000
21	A	24	VAL	0	-0.018	-0.007	22.017	0.014	0.014	0.000	0.000	0.000	0.000
22	A	25	ALA	0	-0.007	0.002	25.250	0.010	0.010	0.000	0.000	0.000	0.000
23	A	26	ILE	0	-0.002	-0.005	22.231	0.005	0.005	0.000	0.000	0.000	0.000
24	A	27	TYR	0	0.019	0.009	24.685	0.008	0.008	0.000	0.000	0.000	0.000
25	A	28	ASN	0	-0.009	-0.020	26.367	0.012	0.012	0.000	0.000	0.000	0.000
26	A	29	TYR	0	-0.055	-0.012	29.117	0.005	0.005	0.000	0.000	0.000	0.000
27	A	30	HIS	0	0.002	-0.011	25.280	0.008	0.008	0.000	0.000	0.000	0.000
28	A	31	GLU	-1	-0.934	-0.971	28.310	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	32	GLN	0	-0.104	-0.042	31.204	0.008	0.008	0.000	0.000	0.000	0.000
30	A	33	ALA	0	-0.021	0.014	30.925	0.004	0.004	0.000	0.000	0.000	0.000
31	A	34	HIS	0	-0.015	-0.025	33.087	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	35	LEU	0	-0.023	-0.001	27.523	0.003	0.003	0.000	0.000	0.000	0.000
33	A	36	THR	0	0.002	0.000	30.610	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	37	PHE	0	-0.033	-0.014	22.490	0.003	0.003	0.000	0.000	0.000	0.000
35	A	38	VAL	0	0.002	0.005	26.737	0.000	0.000	0.000	0.000	0.000	0.000
36	A	39	GLU	-1	-0.946	-0.983	24.677	-0.027	-0.027	0.000	0.000	0.000	0.000
37	A	40	ASN	0	-0.079	-0.046	19.064	0.017	0.017	0.000	0.000	0.000	0.000
38	A	41	LEU	0	0.038	0.024	20.109	0.006	0.006	0.000	0.000	0.000	0.000
39	A	42	ASN	0	-0.007	-0.019	15.426	0.019	0.019	0.000	0.000	0.000	0.000
40	A	43	CYS	0	-0.001	-0.004	12.409	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	44	LYS	1	0.938	0.986	8.470	-0.489	-0.489	0.000	0.000	0.000	0.000
42	A	45	GLU	-1	-0.785	-0.877	7.686	-0.701	-0.701	0.000	0.000	0.000	0.000
43	A	46	GLN	0	-0.008	-0.015	1.992	2.274	3.101	1.572	-1.051	-1.348	-0.003
44	A	47	LEU	0	-0.054	-0.025	5.006	0.745	0.745	0.000	0.000	0.000	0.000
45	A	48	GLY	0	0.006	-0.004	5.618	-0.469	-0.469	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.722	-0.826	1.908	-17.359	-18.694	10.519	-5.294	-3.890	-0.073
47	A	50	GLY	0	-0.038	-0.001	6.444	0.264	0.264	0.000	0.000	0.000	0.000
48	A	51	ASP	-1	-0.835	-0.885	9.336	-0.568	-0.568	0.000	0.000	0.000	0.000
49	A	52	TYR	0	-0.080	-0.061	12.296	0.035	0.035	0.000	0.000	0.000	0.000
50	A	53	TYR	0	-0.079	-0.049	14.210	0.038	0.038	0.000	0.000	0.000	0.000
51	A	54	TYR	0	0.005	-0.009	18.752	0.019	0.019	0.000	0.000	0.000	0.000
52	A	55	ILE	0	-0.007	-0.001	21.048	0.003	0.003	0.000	0.000	0.000	0.000
53	A	56	THR	0	0.020	0.015	24.588	0.004	0.004	0.000	0.000	0.000	0.000
54	A	57	LEU	0	-0.042	-0.020	26.228	0.001	0.001	0.000	0.000	0.000	0.000
55	A	58	ALA	0	-0.015	-0.008	29.822	0.002	0.002	0.000	0.000	0.000	0.000
56	A	59	ALA	0	-0.008	-0.004	31.429	0.001	0.001	0.000	0.000	0.000	0.000
57	A	60	THR	0	-0.023	-0.023	33.542	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	61	ASP	-1	-0.853	-0.932	35.624	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	62	ASP	-1	-0.932	-0.971	37.351	0.007	0.007	0.000	0.000	0.000	0.000
60	A	63	ALA	0	-0.025	-0.001	39.453	0.001	0.001	0.000	0.000	0.000	0.000
61	A	64	GLY	0	-0.034	-0.014	40.795	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.759	0.875	40.988	0.011	0.011	0.000	0.000	0.000	0.000
63	A	66	LYS	1	0.971	0.980	37.375	0.025	0.025	0.000	0.000	0.000	0.000
64	A	67	ALA	0	-0.017	-0.008	35.979	0.000	0.000	0.000	0.000	0.000	0.000
65	A	68	ILE	0	0.012	0.000	32.266	0.000	0.000	0.000	0.000	0.000	0.000
66	A	69	TYR	0	0.020	-0.007	29.392	0.003	0.003	0.000	0.000	0.000	0.000
67	A	70	GLU	-1	-0.901	-0.944	27.239	-0.092	-0.092	0.000	0.000	0.000	0.000
68	A	71	ALA	0	-0.010	-0.007	23.269	0.007	0.007	0.000	0.000	0.000	0.000
69	A	72	LYS	1	0.829	0.919	17.450	0.220	0.220	0.000	0.000	0.000	0.000
70	A	73	ILE	0	-0.004	-0.007	16.392	0.020	0.020	0.000	0.000	0.000	0.000
71	A	74	GLY	0	0.032	0.024	14.105	-0.039	-0.039	0.000	0.000	0.000	0.000
72	A	75	VAL	0	0.007	-0.007	11.003	0.077	0.077	0.000	0.000	0.000	0.000
73	A	76	VAL	0	0.002	0.006	5.545	-0.138	-0.138	0.000	0.000	0.000	0.000
74	A	77	GLU	-1	-0.867	-0.940	7.950	-0.030	-0.030	0.000	0.000	0.000	0.000
75	A	78	SER	0	-0.108	-0.076	3.124	1.018	1.395	0.027	-0.154	-0.250	0.000
76	A	79	ALA	0	-0.057	-0.033	5.457	0.777	0.777	0.000	0.000	0.000	0.000
77	A	80	GLY	0	-0.003	0.003	7.122	-0.023	-0.023	0.000	0.000	0.000	0.000
78	A	81	TRP	0	-0.043	-0.007	9.453	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	82	THR	0	0.031	-0.001	11.189	-0.127	-0.127	0.000	0.000	0.000	0.000
80	A	83	GLY	0	-0.021	0.000	14.198	0.049	0.049	0.000	0.000	0.000	0.000
81	A	84	VAL	0	-0.031	-0.019	16.178	-0.037	-0.037	0.000	0.000	0.000	0.000
82	A	85	GLU	-1	-0.859	-0.929	15.693	-0.207	-0.207	0.000	0.000	0.000	0.000
83	A	86	GLU	-1	-0.795	-0.883	19.939	-0.059	-0.059	0.000	0.000	0.000	0.000
84	A	87	PHE	0	-0.006	-0.010	23.448	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	88	LYS	1	0.810	0.892	26.064	0.064	0.064	0.000	0.000	0.000	0.000
86	A	89	LEU	0	-0.006	0.006	29.490	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	90	VAL	0	-0.016	-0.008	31.298	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	91	GLY	0	0.020	0.004	34.132	0.000	0.000	0.000	0.000	0.000	0.000
89	A	92	SER	0	-0.014	0.005	37.178	0.001	0.001	0.000	0.000	0.000	0.000
90	A	93	LEU	0	-0.024	-0.020	36.314	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	94	GLU	-1	-0.823	-0.882	40.553	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	95	HIS	0	-0.035	-0.012	43.903	0.001	0.001	0.000	0.000	0.000	0.000

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