FMO DATABASE

FMODB ID: VR9M1

Calculation Name: 3KU7-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3KU7

Chain ID: A

ChEMBL ID:
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UniProt ID: O25099

Base Structure: X-ray

Registration Date: 2023-06-19

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	64
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-351997.775649
FMO2-HF: Nuclear repulsion	326273.861097
FMO2-HF: Total energy	-25723.914552
FMO2-MP2: Total energy	-25798.941075

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:13:ALA)

Summations of interaction energy for fragment #1(A:13:ALA)

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.
0.49	4.558	-0.009	-2.003	-2.056	0.006

Interaction energy analysis for fragmet #1(A:13:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.066 / q_NPA : 0.030

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	15	THR	0	-0.022	-0.039	3.600	-1.162	2.382	-0.011	-1.901	-1.632	0.006
4	A	16	ALA	0	0.030	0.040	3.497	0.392	0.817	0.004	-0.078	-0.352	0.000
5	A	17	THR	0	0.020	0.019	4.608	-0.730	-0.716	-0.001	-0.009	-0.003	0.000
6	A	18	ASP	-1	-0.854	-0.906	7.342	-1.541	-1.541	0.000	0.000	0.000	0.000
7	A	19	ARG	1	0.835	0.903	4.261	3.759	3.844	-0.001	-0.015	-0.069	0.000
8	A	20	LEU	0	-0.010	0.006	11.696	0.026	0.026	0.000	0.000	0.000	0.000
9	A	21	LYS	1	0.776	0.881	14.704	0.435	0.435	0.000	0.000	0.000	0.000
10	A	22	LEU	0	0.008	0.008	16.719	0.022	0.022	0.000	0.000	0.000	0.000
11	A	23	ILE	0	-0.002	0.000	19.460	0.008	0.008	0.000	0.000	0.000	0.000
12	A	24	LEU	0	0.003	-0.002	22.496	0.010	0.010	0.000	0.000	0.000	0.000
13	A	25	ALA	0	-0.019	0.003	26.110	0.007	0.007	0.000	0.000	0.000	0.000
14	A	26	LYS	1	0.810	0.892	28.010	0.099	0.099	0.000	0.000	0.000	0.000
15	A	27	GLU	-1	-0.888	-0.942	31.567	-0.085	-0.085	0.000	0.000	0.000	0.000
16	A	28	ARG	1	0.948	0.992	31.589	0.075	0.075	0.000	0.000	0.000	0.000
17	A	29	THR	0	-0.014	-0.017	33.818	0.003	0.003	0.000	0.000	0.000	0.000
18	A	30	LEU	0	0.007	0.001	36.268	0.003	0.003	0.000	0.000	0.000	0.000
19	A	31	ASN	0	0.003	0.005	37.214	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	32	LEU	0	-0.008	0.005	34.895	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	33	PRO	0	0.059	0.020	36.408	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	34	TYR	0	0.023	0.014	35.079	0.003	0.003	0.000	0.000	0.000	0.000
23	A	35	MET	0	0.058	0.035	29.900	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	36	GLU	-1	-0.793	-0.876	30.154	-0.116	-0.116	0.000	0.000	0.000	0.000
25	A	37	GLU	-1	-0.822	-0.909	30.894	-0.099	-0.099	0.000	0.000	0.000	0.000
26	A	38	MET	0	-0.022	-0.012	30.961	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	39	ARG	1	0.826	0.906	25.013	0.124	0.124	0.000	0.000	0.000	0.000
28	A	40	LYS	1	0.834	0.901	27.339	0.088	0.088	0.000	0.000	0.000	0.000
29	A	41	GLU	-1	-0.896	-0.940	28.268	-0.127	-0.127	0.000	0.000	0.000	0.000
30	A	42	ILE	0	-0.008	-0.009	25.325	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	43	ILE	0	-0.012	-0.010	22.221	-0.018	-0.018	0.000	0.000	0.000	0.000
32	A	44	ALA	0	0.004	0.006	24.678	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	45	VAL	0	-0.026	-0.020	26.803	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	46	ILE	0	0.031	0.016	20.613	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	47	GLN	0	-0.013	-0.002	21.800	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	48	LYS	1	0.906	0.984	23.267	0.162	0.162	0.000	0.000	0.000	0.000
37	A	49	TYR	0	-0.042	-0.042	24.404	0.011	0.011	0.000	0.000	0.000	0.000
38	A	50	THR	0	-0.023	-0.036	18.976	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	51	LYS	1	0.859	0.935	19.706	0.205	0.205	0.000	0.000	0.000	0.000
40	A	52	SER	0	-0.015	-0.013	16.420	0.023	0.023	0.000	0.000	0.000	0.000
41	A	53	SER	0	0.019	-0.003	17.854	0.030	0.030	0.000	0.000	0.000	0.000
42	A	54	ASP	-1	-0.958	-0.951	13.258	-0.368	-0.368	0.000	0.000	0.000	0.000
43	A	55	ILE	0	-0.012	-0.025	16.241	-0.048	-0.048	0.000	0.000	0.000	0.000
44	A	56	HIS	0	0.029	0.024	15.183	0.052	0.052	0.000	0.000	0.000	0.000
45	A	57	PHE	0	-0.011	-0.016	17.793	-0.022	-0.022	0.000	0.000	0.000	0.000
46	A	58	LYS	1	0.845	0.935	16.540	0.308	0.308	0.000	0.000	0.000	0.000
47	A	59	THR	0	-0.010	-0.023	21.741	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	60	LEU	0	0.029	0.017	24.185	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	61	ASP	-1	-0.889	-0.934	19.593	-0.155	-0.155	0.000	0.000	0.000	0.000
50	A	62	SER	0	-0.066	-0.046	21.776	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	63	ASN	0	-0.021	-0.024	22.684	0.027	0.027	0.000	0.000	0.000	0.000
52	A	64	GLN	0	0.007	0.013	25.570	0.001	0.001	0.000	0.000	0.000	0.000
53	A	65	SER	0	0.010	0.005	29.414	0.003	0.003	0.000	0.000	0.000	0.000
54	A	66	VAL	0	-0.007	0.001	28.589	0.002	0.002	0.000	0.000	0.000	0.000
55	A	67	GLU	-1	-0.873	-0.951	28.007	-0.096	-0.096	0.000	0.000	0.000	0.000
56	A	68	THR	0	-0.037	-0.043	22.464	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	69	ILE	0	0.023	0.028	23.805	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	70	GLU	-1	-0.829	-0.912	17.821	-0.332	-0.332	0.000	0.000	0.000	0.000
59	A	71	VAL	0	0.005	-0.009	19.198	0.017	0.017	0.000	0.000	0.000	0.000
60	A	72	GLU	-1	-0.820	-0.891	13.358	-0.412	-0.412	0.000	0.000	0.000	0.000
61	A	73	ILE	0	-0.007	-0.012	15.217	0.043	0.043	0.000	0.000	0.000	0.000
62	A	74	ILE	0	0.051	0.032	10.629	-0.124	-0.124	0.000	0.000	0.000	0.000
63	A	75	LEU	0	-0.041	-0.013	12.925	0.129	0.129	0.000	0.000	0.000	0.000
64	A	76	PRO	0	-0.002	0.009	13.102	-0.049	-0.049	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:ALA)